- C - Static variable in class chemaxon.core.ChemConst
-
- C_CLOSE_STREAM - Static variable in class chemaxon.formats.MolExporter
-
Close the underlying stream.
- C_FLUSH_STREAM - Static variable in class chemaxon.formats.MolExporter
-
Flush the output stream and force any buffered output bytes to be
written out.
- C_SHIFT_PROP_NAME - Static variable in class chemaxon.calculations.nmr.NMRCalculator
-
Name of the 13C chemical shift atom property.
- Ca - Static variable in class chemaxon.core.ChemConst
-
- CACHE_MOLECULES - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter: "cacheMols".
- CACHE_REMOVE_ALL - Static variable in class chemaxon.struc.MoleculeGraph
-
Cache removal option for clearing all cached info.
- CACHE_REMOVE_AROMATAMODULE - Static variable in class chemaxon.struc.MoleculeGraph
-
Cache removal option for remove module used in aromatization.
- CACHE_REMOVE_CACHEMEMORY - Static variable in class chemaxon.struc.MoleculeGraph
-
Cache removal option for cacheMemory.
- CACHE_REMOVE_GRINVMODULE - Static variable in class chemaxon.struc.MoleculeGraph
-
Cache removal option for remove module used in graph invariant
calculation.
- CACHE_REMOVE_PARITYMODULE - Static variable in class chemaxon.struc.MoleculeGraph
-
Cache removal option for remove module used in parity calculation.
- CACHE_REMOVE_SSSRMODULE - Static variable in class chemaxon.struc.MoleculeGraph
-
Deprecated.
As of Marvin 5.12, no replacement.
SSSR module is not cached any more.
- CACHE_REMOVE_TABS - Static variable in class chemaxon.struc.MoleculeGraph
-
Cache remove option to clear ctab and btab.
- cacheMemory - Variable in class chemaxon.struc.MoleculeGraph
-
- calcBadness(MoleculeGraph, MoleculeGraph, MolAtom, MolBond[]) - Static method in class chemaxon.marvin.util.CleanUtil
-
Calculates a "badness" value for the atomic coordinates.
- calcBracketEndPoints(DPoint3[], DPoint3, double) - Static method in class chemaxon.marvin.util.CleanUtil
-
Calculates the bracket endpoints from the base line of the bracket.
- calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MChemicalStruct
-
Calculates the geometrical center.
- calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MPolyline
-
Calculates the geometrical center.
- calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MRectangle
-
Calculates the geometrical center.
- calcCenter() - Method in class chemaxon.struc.MDocument
-
Calculates the geometrical center.
- calcCenter(CTransform3D) - Method in class chemaxon.struc.MDocument
-
Calculates the geometrical center.
- calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.MObject
-
Calculates the geometrical center.
- calcCenter(DPoint3) - Method in class chemaxon.struc.MoleculeGraph
-
Calculates the geometrical center.
- calcCenter() - Method in class chemaxon.struc.MoleculeGraph
-
Calculates the geometrical center.
- calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.MPoint
-
Calculates the geometrical center.
- calcDehydrogenizedGrinv(int[]) - Method in class chemaxon.struc.MoleculeGraph
-
Calculates the graph invariants with the assumption that hydrogens are
removed.
- calcDividingPoint(DPoint3, DPoint3, double) - Static method in class chemaxon.marvin.util.CleanUtil
-
Calculates the division point of a segment with a given ratio.
- calcHeight() - Method in class chemaxon.struc.MoleculeGraph
-
Calculates the molecule height.
- calcHybridization() - Method in class chemaxon.struc.MoleculeGraph
-
Calculates and sets hybridazation state for each atom.
- calclogD(double) - Method in class chemaxon.marvin.calculations.logDPlugin
-
Returns the logD value at fixed pH.
- calcMaxDist() - Method in class chemaxon.marvin.alignment.MinMaxDistance
-
- calcMinDist() - Method in class chemaxon.marvin.alignment.MinMaxDistance
-
Calculates the minimum distance between two atoms in the molecule.
- calcOrderFromLength() - Method in class chemaxon.struc.MolBond
-
Calculate the bond order from the atomic distances.
- calcOrderFromValence() - Method in class chemaxon.struc.MolBond
-
Calculate bond order from the types and charges of the two atoms.
- calcOutRect() - Method in class chemaxon.struc.MoleculeGraph
-
Calculates the outer rectangle.
- calcOutRect(DPoint3) - Method in class chemaxon.struc.MoleculeGraph
-
Calculates the outer rectangle.
- calcOutRectCenter() - Method in class chemaxon.struc.MoleculeGraph
-
Calculates the center of the outer rectangle.
- calcOutRectCenter(DPoint3) - Method in class chemaxon.struc.MoleculeGraph
-
Calculates the center of the outer rectangle.
- CALCRGB_OFF - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
-
Calculator rgb offset.
- calcSimplePolymerBracket(DPoint3, DPoint3, double) - Static method in class chemaxon.marvin.util.CleanUtil
-
Calculates the points of a simple polymer bracket that belongs to a bond.
- calcStereo2() - Method in class chemaxon.struc.MolBond
-
Computes the stereochemistry of the bond based on the atomic coordinates.
- calcStereo2(MolAtom, MolAtom) - Method in class chemaxon.struc.MolBond
-
Computes the stereochemistry of the bond based on the atomic coordinates.
- calcStereo2(MolAtom, MolAtom, MolAtom, MolAtom) - Static method in class chemaxon.struc.MolBond
-
Computes the stereochemistry of the atom sequence (scheme a1-a2=a3-a4)
based on the atomic coordinates.
- calculate(Molecule) - Method in class chemaxon.calculations.dipole.DipoleCalculator
-
- calculate(Molecule) - Method in class chemaxon.calculations.nmr.NMRCalculator
-
Calculates NMR spectrum for the given input molecule.
- calculate(Molecule) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
-
Run the atropisomer calculation.
- calculate() - Method in class chemaxon.marvin.alignment.MMPAlignment
-
Runs the MCS alignment calculation on the two structures of the
constructor.
- calculate(int[]) - Method in class chemaxon.util.MolAligner
-
Calculate best alignment based on the hit map
- calculateAttachmentPoints() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Calculates the attachment points for the crossing atoms and crossing
bonds and sets the calculated values.
- calculateCIPStereoDescriptors(MoleculeGraph) - Static method in class chemaxon.calculations.cip.CIPStereoCalculator
-
- calculateCIPStereoDescriptors(MoleculeGraph, boolean) - Static method in class chemaxon.calculations.cip.CIPStereoCalculator
-
Calculates the stereo descriptors of the given molecule.
- calculateCIPStereoDescriptors(MoleculeGraph) - Static method in class chemaxon.core.calculations.stereo.CIPStereoRecognizer
-
Calculates the Cahn-Ingold-Prelog (CIP) stereo descriptors for a
specified molecule.
- calculateCIPStereoDescriptors(MoleculeGraph, boolean) - Static method in class chemaxon.core.calculations.stereo.CIPStereoRecognizer
-
- calculateCIPStereoDescriptors(MoleculeGraph, EnumSet<CIPStereoDescriptorIface.CIPType>) - Static method in class chemaxon.core.calculations.stereo.CIPStereoRecognizer
-
Calculates the Cahn-Ingold-Prelog (CIP) stereo descriptors for a
specified molecule.
- calculateCoordinates(Molecule, MolBond[], MoleculeGraph, int, boolean, SelectionMolecule, List<Double>) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Calculates the coordinates during expand and contract.
- calculateCosAFromScalarMul(MolBond, MolBond) - Static method in class chemaxon.checkers.StructureCheckerHelper
-
Calculate the cosines value of the angle between the bonds from the
scalar multiplication of the bonds.
- calculateIntrinsicSolubility(Molecule) - Method in class com.chemaxon.calculations.solubility.SolubilityCalculator
-
Calculates intrinsic solubility.
- calculatePhDependentSolubility(Molecule, double) - Method in class com.chemaxon.calculations.solubility.SolubilityCalculator
-
Calculates pH-dependent solubility.
- calculatePhDependentSolubility(Molecule, double[]) - Method in class com.chemaxon.calculations.solubility.SolubilityCalculator
-
Calculates pH-dependent solubilities.
- CALCULATIONS_PACK - Static variable in class chemaxon.license.LicenseManager
-
Identifier of product: Calculations Pack
- CalculatorPlugin - Class in chemaxon.marvin.plugin
-
Common base class for calculator plugins.
- CalculatorPlugin() - Constructor for class chemaxon.marvin.plugin.CalculatorPlugin
-
Constructor.
- CalculatorPlugin.HydrogenData - Class in chemaxon.marvin.plugin
-
- CalculatorPlugin.HydrogenData(MolAtom, int, int, int) - Constructor for class chemaxon.marvin.plugin.CalculatorPlugin.HydrogenData
-
- CalculatorPluginDisplay - Class in chemaxon.marvin.plugin
-
Common base class for calculator plugin displays.
- CalculatorPluginDisplay() - Constructor for class chemaxon.marvin.plugin.CalculatorPluginDisplay
-
- CalculatorPluginOutput - Class in chemaxon.marvin.plugin
-
Class providing plugin output in table form.
- CalculatorPluginOutput() - Constructor for class chemaxon.marvin.plugin.CalculatorPluginOutput
-
Default constructor.
- CalculatorPluginOutput(CalculatorPlugin) - Constructor for class chemaxon.marvin.plugin.CalculatorPluginOutput
-
Constructor that sets plugin.
- calcWidth() - Method in class chemaxon.struc.MoleculeGraph
-
Calculates the molecule width.
- call() - Method in class chemaxon.marvin.plugin.concurrent.PluginWorkUnit
-
- call() - Method in class chemaxon.marvin.plugin.concurrent.ReusablePluginWorkUnit
-
- call() - Method in class chemaxon.util.concurrent.marvin.CompositeWorkUnit
-
Performs the work unit tasks in a linear fashion, one after the other.
- callback(String, Object) - Method in interface chemaxon.jep.ChemContext
-
Implements CallbackIface.
- callback(String, Object) - Method in class chemaxon.jep.ChemJEP
-
Delegates CallbackIface.callback(String, Object)
to the context.
- callback(String, Object) - Method in class chemaxon.jep.context.AtomContext
-
Implements CallbackIface.
- callback(String, Object) - Method in class chemaxon.jep.context.MolContext
-
Implements CallbackIface.
- callback(String, Object) - Method in class chemaxon.jep.context.ReactionContext
-
Implements CallbackIface.
- callback(String, Object) - Method in class chemaxon.marvin.space.GraphicScene
-
- callback(String, Object) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- callback(String, Object) - Method in class chemaxon.marvin.space.MSpaceEasy
-
Callback function to make avoiding direct calls easier.
- callService(DT, AsyncCallback<T>, Object...) - Method in class chemaxon.marvin.services.ServiceHandler
-
Performs an asynchronous service call.
- callService(DT, Object...) - Method in class chemaxon.marvin.services.ServiceHandler
-
Performs a synchronized service call.
- CAN_BE - Static variable in class chemaxon.formats.recognizer.AbbrevGroupRecognizer
-
Deprecated.
Line can be in the given format.
- CAN_BE - Static variable in class chemaxon.formats.recognizer.PDBRecognizer
-
Deprecated.
Line can be in the given format.
- canBe1LetterPeptide(String) - Static method in class chemaxon.formats.recognizer.PeptideRecognizer
-
Deprecated.
Tests whether a string can be one-letter-abbreviated
peptide name.
A valid name contains only uppercase letters.
- canBe3LetterPeptide(String) - Static method in class chemaxon.formats.recognizer.PeptideRecognizer
-
Deprecated.
Tests whether a string can be three-letter-abbreviated
peptide name.
- canBeBase64(String) - Static method in class chemaxon.formats.recognizer.Base64Recognizer
-
Deprecated.
Tests whether a string can be base64 encoded data.
- canBeBase64Line(String) - Static method in class chemaxon.formats.recognizer.Base64Recognizer
-
Deprecated.
Tests whether a string can be base64 encoded data line.
- canBeCT(int, int) - Method in class chemaxon.struc.MoleculeGraph
-
Determines whether the bond between the specified atoms can be a
CIS/TRANS or not.
- canBeCT(int, int, boolean) - Method in class chemaxon.struc.MoleculeGraph
-
Determines whether the bond between the specified atoms can be a
CIS/TRANS or not.
- canBeCT(MolBond) - Method in class chemaxon.struc.MoleculeGraph
-
Determines whether the given bond can be a
CIS/TRANS or not.
- canBeCT(int, int, boolean) - Method in class chemaxon.struc.RgMolecule
-
Determines whether the bond between the specified atoms can be a
CIS/TRANS or not.
- canBeReactionComponent() - Method in class chemaxon.struc.Molecule
-
Tests whether an object of this class can be a reaction component.
- canBeReactionComponent() - Method in class chemaxon.struc.RgMolecule
-
Tests whether an object of this class can be a reaction component.
- canBeReactionComponent() - Method in class chemaxon.struc.RxnMolecule
-
Tests whether an object of this class can be a reaction component.
- canBeSMARTS(String) - Static method in class chemaxon.formats.recognizer.SMILESRecognizer
-
Deprecated.
Tests whether a string can be SMARTS.
- canBeSMILES(String) - Static method in class chemaxon.formats.recognizer.SMILESRecognizer
-
Deprecated.
Tests whether a string can be SMILES.
- cancel() - Method in class chemaxon.checkers.runner.BasicCheckerRunner
-
- cancel() - Method in interface chemaxon.checkers.runner.CheckerRunner
-
Stops the background thread
- cancel() - Method in class chemaxon.marvin.alignment.MMPAlignment
-
Cancel the ongoing calculation
- cancel() - Method in interface chemaxon.util.Cancelable
-
- Cancelable - Interface in chemaxon.util
-
Represents a task/operation that can be cancelled.
- canRepeat() - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
-
- canRepeat() - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
-
- canRepeat() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns true if repeatedly running the same plugin object
while getting the results on the GUI is allowed, false otherwise.
- carboaliphaticRingCount() - Method in class chemaxon.calculations.Ring
-
Calculates the number of carboaliphatic rings in the molecule (aliphatic
rings containing carbon atoms only).
- carboaliphaticRingCount() - Method in class chemaxon.calculations.TopologyAnalyser
-
- carboaromaticRingCount() - Method in class chemaxon.calculations.Ring
-
Calculates the number of carboaromatic rings in the molecule (aromatic
rings containing carbon atoms only).
- carboaromaticRingCount() - Method in class chemaxon.calculations.TopologyAnalyser
-
- CARBON_VIS_INCHAIN - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Carbon-visibility is switched on in chain.
- CARBON_VIS_INCHAIN_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
String constant for switching on carbon-visibility in chain.
- CARBON_VIS_MASK - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Carbon-visibility mask.
- CARBON_VIS_OFF - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Carbon-visibility is switched off.
- CARBON_VIS_OFF_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
String constant for switching off carbon-visibility.
- CARBON_VIS_OFFSET - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Carbon-visibility offset.
- CARBON_VIS_ON - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Carbon-visibility is switched on.
- CARBON_VIS_ON_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
String constant for switching on carbon-visibility.
- CARBON_VIS_STYLES - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Array of carbon-visibility styles.
- carboRingCount() - Method in class chemaxon.calculations.Ring
-
Calculates the number of carbocyclic rings in the molecule (rings
containing carbon atoms only).
- carboRingCount(int) - Method in class chemaxon.calculations.Ring
-
Calculates the number of carbocyclic rings in the molecule (rings
containing at least a non-carbon atom).
- carboRingCount() - Method in class chemaxon.calculations.TopologyAnalyser
-
- carboRingCount(int) - Method in class chemaxon.calculations.TopologyAnalyser
-
- carboRings() - Method in class chemaxon.calculations.Ring
-
Identifies carbocyclic rings in the molecule (rings containing carbon
atoms only).
- carboRings(int) - Method in class chemaxon.calculations.Ring
-
Identifies carbocyclic rings in the molecule (rings containing carbon
atoms only) having the given number of atoms.
- carboRings() - Method in class chemaxon.calculations.TopologyAnalyser
-
- carboRings(int) - Method in class chemaxon.calculations.TopologyAnalyser
-
- CARTRIDGE - Static variable in class chemaxon.license.LicenseManager
-
Identifier of product: JChem Cartridge
- CATIONIC_TYPE - Static variable in class chemaxon.marvin.space.PharmacophorePoint
-
- CCLENGTH - Static variable in class chemaxon.struc.MolBond
-
Default bond length.
- Cd - Static variable in class chemaxon.core.ChemConst
-
- CDX - Static variable in class chemaxon.formats.MFileFormat
-
ChemDraw CDX file.
- CDXML - Static variable in class chemaxon.formats.MFileFormat
-
ChemDraw CDXML file.
- Ce - Static variable in class chemaxon.core.ChemConst
-
- CELL - Static variable in class chemaxon.marvin.view.ViewParameterConstants
-
Identifier of parameter: "cell".
- CELL_RANGE - Static variable in class chemaxon.marvin.space.GraphicScene
-
- CellOrComponentId - Class in chemaxon.marvin.space
-
Class to identify cells and components.
- CellOrComponentId(int) - Constructor for class chemaxon.marvin.space.CellOrComponentId
-
Creates a cell id.
- CellOrComponentId(int, int) - Constructor for class chemaxon.marvin.space.CellOrComponentId
-
Creates an id.
- CELLSIZE - Static variable in class chemaxon.marvin.plugin.CalculatorPluginDisplay
-
The default viewer cell size.
- center - Variable in class chemaxon.marvin.space.monitor.Control
-
- center - Variable in class chemaxon.marvin.space.monitor.DihedralControl
-
- centerx() - Method in class chemaxon.marvin.space.BoundingBox
-
Returns the x coordinate of the center of the box.
- centery() - Method in class chemaxon.marvin.space.BoundingBox
-
Returns the y coordinate of the center of the box.
- centerz() - Method in class chemaxon.marvin.space.BoundingBox
-
Returns the z coordinate of the center of the box.
- centralizeMoleculeDisplay() - Method in class chemaxon.marvin.beans.MSketchPane
-
Puts the molecule into the center of the display.
- Cf - Static variable in class chemaxon.core.ChemConst
-
- CFNS - Static variable in class chemaxon.jep.context.AtomContext
-
The context function names.
- CFNS - Static variable in class chemaxon.jep.context.ReactionContext
-
The context function names.
- chainAtomCount() - Method in class chemaxon.calculations.Ring
-
Calculates the number of chain atoms in the molecule excluding hydrogens.
- chainAtomCount() - Method in class chemaxon.calculations.TopologyAnalyser
-
- chainBondCount() - Method in class chemaxon.calculations.Ring
-
Calculates the number of chain bonds in the molecule excluding bonds of
hydrogen atoms.
- chainBondCount() - Method in class chemaxon.calculations.TopologyAnalyser
-
- changeColorMapperColors(int) - Method in class chemaxon.marvin.space.SurfaceColoring
-
Switches to another built-in color palette and leaves minimum, maximum
and cutoff values unchanged.
- CHARACTER - Static variable in class chemaxon.naming.DocumentToStructure
-
The starting character offset since the beginning of the document,
for text formats (html, xml, txt).
- charAt(int) - Method in class chemaxon.struc.graphics.MTextDocument
-
Gets a character of the document.
- CHARGE_ON_ATOMS - Static variable in class chemaxon.struc.Sgroup
-
Charge is located on atoms and displayed on atoms.
- CHARGE_ON_GROUP - Static variable in class chemaxon.struc.Sgroup
-
Charge is located on atoms but displayed on the whole group (bracket).
- CHARGE_PLUGIN_GROUP - Static variable in class chemaxon.license.LicenseManager
-
Identifier of plugin: Charge Plugin Group
- CHARGE_WITH_CIRCLE - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter: "chargeWithCircle".
- CHARGE_WITH_CIRCLE_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
- CHARGE_WITH_CIRCLE_OFFSET - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
- CHARGED_H - Static variable in class chemaxon.struc.MolAtom
-
Include charged Hydrogen atom(s).
- ChargePlugin - Class in chemaxon.marvin.calculations
-
Plugin class for partial charge calculation.
- ChargePlugin() - Constructor for class chemaxon.marvin.calculations.ChargePlugin
-
Constructor.
- check(Molecule) - Method in class chemaxon.calculations.dipole.DipoleCalculator
-
- check(Molecule) - Method in class chemaxon.calculations.nmr.NMRCalculator
-
- check(Molecule) - Method in class chemaxon.checkers.AbstractStructureChecker
-
- check(Molecule, MolAtom) - Method in class chemaxon.checkers.AliasChecker
-
- check(Molecule, MolAtom) - Method in class chemaxon.checkers.AtomMapChecker
-
Detects atom of the molecule has atom map.
- check(Molecule, MolAtom) - Method in class chemaxon.checkers.AtomQueryPropertyChecker
-
- check(Molecule, MolAtom) - Method in class chemaxon.checkers.AtomTypeChecker
-
- check(Molecule, MolAtom) - Method in class chemaxon.checkers.AtomValueChecker
-
Detects if the current atom of the molecule has atom value.
- check(Molecule, E) - Method in class chemaxon.checkers.ComponentChecker
-
Checks if the component with index i has problem
- check(Molecule, MolBond) - Method in class chemaxon.checkers.CrossedDoubleBondChecker
-
Examines if the bond is a crossed double bond.
- check(Molecule, MolAtom) - Method in class chemaxon.checkers.ExplicitLonePairChecker
-
- check(Molecule) - Method in class chemaxon.checkers.InvalidChecker
-
- check(Molecule, MolAtom) - Method in class chemaxon.checkers.IsotopeChecker
-
- check(Molecule, MolAtom) - Method in class chemaxon.checkers.MissingAtomMapChecker
-
Check the atom of the molecule with index i has no atom map.
- check(Molecule, MolAtom) - Method in class chemaxon.checkers.MultiCenterChecker
-
- check(Molecule, MolAtom) - Method in class chemaxon.checkers.OverlappingAtomsChecker
-
Examines if an atom is closer to another than the given distance limit.
- check(Molecule, MolBond) - Method in class chemaxon.checkers.OverlappingBondsChecker
-
Detects bond of the molecule is crossing another bond or closer than the limit distance.
- check(Molecule, MolAtom) - Method in class chemaxon.checkers.PseudoAtomChecker
-
- check(Molecule, MolAtom) - Method in class chemaxon.checkers.QueryAtomChecker
-
Detects atom of the molecule is a query atom.
- check(Molecule, MolBond) - Method in class chemaxon.checkers.QueryBondChecker
-
- check(Molecule, MolAtom) - Method in class chemaxon.checkers.RacemateChecker
-
- check(Molecule, MolAtom) - Method in class chemaxon.checkers.RadicalChecker
-
Detects if the current atom has free electrons.
- check(Molecule, MolAtom) - Method in class chemaxon.checkers.RareElementChecker
-
- check(Molecule, MolBond) - Method in class chemaxon.checkers.ReactingCenterBondMarkChecker
-
- check() - Method in class chemaxon.checkers.runner.AdvancedCheckerRunner
-
- check() - Method in class chemaxon.checkers.runner.BasicCheckerRunner
-
- check() - Method in interface chemaxon.checkers.runner.CheckerRunner
-
Invoke a background thread which will run all checkers on the given molecule
- check(Molecule, MolAtom) - Method in class chemaxon.checkers.StarAtomChecker
-
- check(Molecule, MolAtom) - Method in class chemaxon.checkers.StereoInversionRetentionMarkChecker
-
- check(Molecule, MolBond) - Method in class chemaxon.checkers.StraightDoubleBondChecker
-
- check(Molecule) - Method in interface chemaxon.checkers.StructureChecker
-
Detects a specific error in the molecule.
- check(Molecule, MolAtom) - Method in class chemaxon.checkers.ThreeDimensionChecker
-
- check(Molecule, MolAtom) - Method in class chemaxon.checkers.ValencePropertyChecker
-
- check(Molecule) - Method in interface chemaxon.jep.MolCondition
-
Deprecated.
Returns true if molecule should be processed,
false otherwise.
- check(Molecule) - Method in class com.chemaxon.calculations.solubility.SolubilityCalculator
-
- check1(Molecule) - Method in class chemaxon.checkers.AbbreviatedGroupChecker
-
- check1(Molecule) - Method in class chemaxon.checkers.AbsentChiralFlagChecker
-
Determines if a non chiral molecule contains a chiral flag.
- check1(Molecule) - Method in class chemaxon.checkers.AbsoluteStereoConfigurationChecker
-
Determines if all asymmetric centers have absolute stereo configuration
- check1(Molecule) - Method in class chemaxon.checkers.AbstractStructureChecker
-
This method contains the current checking mechanism.
- check1(Molecule) - Method in class chemaxon.checkers.AromaticityErrorChecker
-
- check1(Molecule) - Method in class chemaxon.checkers.AtropisomerChecker
-
- check1(Molecule) - Method in class chemaxon.checkers.AttachedDataChecker
-
Detects attached data in the molecule
- check1(Molecule) - Method in class chemaxon.checkers.BondAngleChecker
-
- check1(Molecule) - Method in class chemaxon.checkers.BondLengthChecker
-
- check1(Molecule) - Method in class chemaxon.checkers.ChiralFlagChecker
-
- check1(Molecule) - Method in class chemaxon.checkers.ChiralFlagErrorChecker
-
Determines if a non chiral molecule contains a chiral flag.
- check1(Molecule) - Method in class chemaxon.checkers.CircularRGroupReferenceChecker
-
- check1(Molecule) - Method in class chemaxon.checkers.ComponentChecker
-
Iterates through the components and checks every component.
- check1(Molecule) - Method in class chemaxon.checkers.CoordinationSystemErrorChecker
-
- check1(Molecule) - Method in class chemaxon.checkers.CovalentCounterionChecker
-
- check1(Molecule) - Method in class chemaxon.checkers.EmptyStructureChecker
-
- check1(Molecule) - Method in class chemaxon.checkers.ExplicitHydrogenChecker
-
Detects implicitizable hydrogen atoms.
- check1(Molecule) - Method in class chemaxon.checkers.EZDoubleBondChecker
-
- check1(Molecule) - Method in class chemaxon.checkers.MetalloceneErrorChecker
-
- check1(Molecule) - Method in class chemaxon.checkers.MissingRGroupChecker
-
- check1(Molecule) - Method in class chemaxon.checkers.MoleculeChargeChecker
-
Detects if molecule has charge
- check1(Molecule) - Method in class chemaxon.checkers.MultiComponentChecker
-
- check1(Molecule) - Method in class chemaxon.checkers.MultipleStereocenterChecker
-
- check1(Molecule) - Method in class chemaxon.checkers.OCRErrorChecker
-
- check1(Molecule) - Method in class chemaxon.checkers.OverlappingAtomsChecker
-
- check1(Molecule) - Method in class chemaxon.checkers.OverlappingBondsChecker
-
- check1(Molecule) - Method in class chemaxon.checkers.RacemateChecker
-
- check1(Molecule) - Method in class chemaxon.checkers.RatomChecker
-
- check1(Molecule) - Method in class chemaxon.checkers.ReactionChecker
-
- check1(Molecule) - Method in class chemaxon.checkers.RelativeStereoChecker
-
- check1(Molecule) - Method in class chemaxon.checkers.RgroupAttachmentCountErrorChecker
-
- check1(Molecule) - Method in class chemaxon.checkers.RgroupAttachmentErrorChecker
-
- check1(Molecule) - Method in class chemaxon.checkers.RgroupOrphanAttachmentErrorChecker
-
- check1(Molecule) - Method in class chemaxon.checkers.RgroupReferenceErrorChecker
-
Deprecated.
- check1(Molecule) - Method in class chemaxon.checkers.RingStrainErrorChecker
-
- check1(Molecule) - Method in class chemaxon.checkers.SolventChecker
-
- check1(Molecule) - Method in class chemaxon.checkers.StereoCareBoxChecker
-
- check1(Molecule) - Method in class chemaxon.checkers.SubstructureChecker
-
- check1(Molecule) - Method in class chemaxon.checkers.UnbalancedReactionChecker
-
- check1(Molecule) - Method in class chemaxon.checkers.UnusedRGroupChecker
-
- check1(Molecule) - Method in class chemaxon.checkers.ValenceErrorChecker
-
- check1(Molecule) - Method in class chemaxon.checkers.WedgeErrorChecker
-
- check1(Molecule) - Method in class chemaxon.checkers.WigglyBondChecker
-
- check1(Molecule) - Method in class chemaxon.checkers.WigglyDoubleBondChecker
-
- checkAndWait() - Method in class chemaxon.checkers.runner.AdvancedCheckerRunner
-
- checkAndWait() - Method in class chemaxon.checkers.runner.BasicCheckerRunner
-
- checkAndWait() - Method in interface chemaxon.checkers.runner.CheckerRunner
-
Execute all the checker instances on the given molecule and return a
List of
StructureCheckerResult
which contains all the identified problems
- checkAtno(int) - Static method in class chemaxon.struc.MolAtom
-
Check if the given atomic number is positive and less then
atomic type maximum value.
- checkBondConsistency() - Method in class chemaxon.struc.MoleculeGraph
-
- checkBondConsistency() - Method in class chemaxon.struc.SelectionMolecule
-
Empty implementation, bond consistency is not checked in case of
selections.
- checkBondConsistency() - Method in class chemaxon.struc.Sgroup
-
- checkBonds(MolAtom) - Method in class chemaxon.struc.Sgroup
-
Add the bonds of the given atom to the sgroup if the given atom and the
other atom of the selected bond is in the sgroup.
- checkBonds(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Add the bonds of the given atom to the sgroup if the given atom and the
other atom of the selected bond is in the sgroup.
- checkConsistency() - Method in class chemaxon.struc.Molecule
-
Deprecated.
As of Marvin 5.7, no replacement.
Not intended for public use, it was intended only for internal debugging.
- checkConsistency() - Method in class chemaxon.struc.MoleculeGraph
-
Deprecated.
As of Marvin 5.7, no replacement.
Not intended for public use, it was intended only for internal debugging.
- checkConsistency() - Method in class chemaxon.struc.RgMolecule
-
Deprecated.
As of Marvin 5.7, no replacement.
Not intended for public use, it was intended only for internal debugging.
- checkConsistencyInEmbeddings() - Method in class chemaxon.struc.Sgroup
-
Checks if the sgroup contains all of the child sgroup's atoms and checks
consistency between atom and bond references.
- CHECKERCONFIG_XML - Static variable in class chemaxon.checkers.StructureCheckerFactory
-
Deprecated.
ChemAxon's default checker configuration file name
- CheckerInfo - Annotation Type in chemaxon.checkers
-
This annotation is responsible for adding GUI based meta data for
StructureChecker
implementations
- CheckerRunner - Interface in chemaxon.checkers.runner
-
The descendant of CheckerRunner interface has to provide the functionality to run
StructureChecker instances automatically
on the given molecule and fix the problems with the associated
StructureFixer instances.
Example:
CheckerRunner can be used directly with the
checkAndWait method.
- CheckerSeverity - Enum in chemaxon.checkers
-
This enum defines the constants which represent the severity of the
StructureChecker
implementations
- checkLicense() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ConformerPlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.HBDAPlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.IonChargePlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
-
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.logDPlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.logPPlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MSAPlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.RefractivityPlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ResonancePlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.TPSAPlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Checks the input molecule.
- checkRlogicRange(int, String) - Method in class chemaxon.struc.RgMolecule
-
Checks an R-logic occurrence range string for syntax errors
and returns a "normalized" string.
- checkSgroupConsistency() - Method in class chemaxon.struc.Molecule
-
Checks the internal consisitency of S-groups.
- checkSgroupConsistency() - Method in class chemaxon.struc.RgMolecule
-
Checks the consistency of S-groups.
- checkSgroupConsistency() - Method in class chemaxon.struc.RxnMolecule
-
Checks the consistency of S-groups.
- checkSgroupGraphConsistency(Sgroup) - Method in class chemaxon.struc.Sgroup
-
Checks whether the parameter s-group contains the atoms of this s-group.
- checkSgroupGraphConsistency(Sgroup) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Checks whether the parameter s-group contain the proper atoms of this
SuperatomSgroup.
- checkType(String, String[]) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Checks result types.
- checkValence(MoleculeGraph) - Method in enum chemaxon.struc.MoleculeGraph.ValenceCheckState
-
Deprecated.
- checkValence(MolAtom) - Method in enum chemaxon.struc.MoleculeGraph.ValenceCheckState
-
Deprecated.
- checkValidity(MDocument, Collection<MolAtom>) - Method in class chemaxon.struc.graphics.MAtomSetPoint
-
Is it a valid object in the document?
- checkValidity(MDocument, Collection<MolAtom>) - Method in class chemaxon.struc.graphics.MEFlowBasePoint
-
Is it a valid object in the document?
- checkValidity(MDocument, Collection<MolAtom>) - Method in class chemaxon.struc.graphics.MPolyline
-
Is it a valid object in the document?
- checkValidity(MDocument, Collection<MolAtom>) - Method in class chemaxon.struc.MObject
-
Is it a valid object in the document?
- CHEM_CURATOR_COMPOUND - Static variable in class chemaxon.license.LicenseManager
-
Identifier of product: ChemCurator Compound
- CHEM_CURATOR_FULL - Static variable in class chemaxon.license.LicenseManager
-
Identifier of product: ChemCurator Markush
- CHEM_CURATOR_VIEWER - Static variable in class chemaxon.license.LicenseManager
-
Identifier of product: ChemCurator Viewer
- chemaxon.calculations - package chemaxon.calculations
-
Contains chemical computation modules.
- chemaxon.calculations.cip - package chemaxon.calculations.cip
-
- chemaxon.calculations.clean - package chemaxon.calculations.clean
-
- chemaxon.calculations.dipole - package chemaxon.calculations.dipole
-
- chemaxon.calculations.hydrogenize - package chemaxon.calculations.hydrogenize
-
- chemaxon.calculations.nmr - package chemaxon.calculations.nmr
-
- chemaxon.calculations.stereo - package chemaxon.calculations.stereo
-
- chemaxon.checkers - package chemaxon.checkers
-
Structure checkers can be used to filter drawing mistakes or special structural elements.
- chemaxon.checkers.result - package chemaxon.checkers.result
-
This package is used to identify problems found in molecules.
- chemaxon.checkers.runner - package chemaxon.checkers.runner
-
This package supports the automatic running of structure checkers.
- chemaxon.checkers.runner.configuration.reader - package chemaxon.checkers.runner.configuration.reader
-
Extension package of the automatic runner functionality.
- chemaxon.common.util - package chemaxon.common.util
-
- chemaxon.core - package chemaxon.core
-
- chemaxon.core.calculations.stereo - package chemaxon.core.calculations.stereo
-
- chemaxon.core.calculations.valencecheck - package chemaxon.core.calculations.valencecheck
-
- chemaxon.fixers - package chemaxon.fixers
-
Structure fixers can be used to fix problems identified by structure checker instances.
- chemaxon.formats - package chemaxon.formats
-
Provides miscellaneous utility classes for converting between various
molecule file formats, importing structures, and compressing Molfiles.
- chemaxon.formats.documents.jchemexcel - package chemaxon.formats.documents.jchemexcel
-
- chemaxon.formats.recognizer - package chemaxon.formats.recognizer
-
Provides classes to recognize files of various file formats.
- chemaxon.jep - package chemaxon.jep
-
Chemical Terms Evaluator classes.
- chemaxon.jep.context - package chemaxon.jep.context
-
Specific chemical terms evaluation contexts.
- chemaxon.license - package chemaxon.license
-
Classes related licenses, license handling, validating, GUI and documentation.
- chemaxon.marvin - package chemaxon.marvin
-
Contains utility classes for rendering molecules.
- chemaxon.marvin.alignment - package chemaxon.marvin.alignment
-
The 3D molecular alignment package that can be used to align two or more 3D molecules onto each other.
- chemaxon.marvin.beans - package chemaxon.marvin.beans
-
Provides bean classes for creating Marvin based user interface.
- chemaxon.marvin.calculations - package chemaxon.marvin.calculations
-
Provides specific plugin, plugin loader and table form output implementations.
- chemaxon.marvin.common - package chemaxon.marvin.common
-
Contains a class for handling user settings.
- chemaxon.marvin.io - package chemaxon.marvin.io
-
Provides classes for molecule import and export through data streams.
- chemaxon.marvin.io.formats - package chemaxon.marvin.io.formats
-
Core package of any import/export module.
- chemaxon.marvin.io.formats.mdl - package chemaxon.marvin.io.formats.mdl
-
Import and export modules for MDL Molfile, SDfile, RDfile, Rxnfile and (ChemAxon) compressed molfile.
- chemaxon.marvin.io.formats.smiles - package chemaxon.marvin.io.formats.smiles
-
- chemaxon.marvin.modules.datatransfer - package chemaxon.marvin.modules.datatransfer
-
Since Marvin 5.3 this package contains the clipboard handler
infrastructure in Marvin.
- chemaxon.marvin.paint - package chemaxon.marvin.paint
-
Defines display options constants.
- chemaxon.marvin.plugin - package chemaxon.marvin.plugin
-
Contains the classes responsible for calculator plugin loading, parameter setting,
running and displaying mechanism.
- chemaxon.marvin.plugin.concurrent - package chemaxon.marvin.plugin.concurrent
-
Classes to achieve concurrent processing of calculator plugins.
- chemaxon.marvin.plugin.gui - package chemaxon.marvin.plugin.gui
-
Calculator plugin common GUI classes.
- chemaxon.marvin.services - package chemaxon.marvin.services
-
Marvin Services provides API and support for accessing remote
services from Marvin Sketch and other tools.
- chemaxon.marvin.services.httpservice - package chemaxon.marvin.services.httpservice
-
- chemaxon.marvin.services.json - package chemaxon.marvin.services.json
-
- chemaxon.marvin.services.localservice - package chemaxon.marvin.services.localservice
-
- chemaxon.marvin.services.soap - package chemaxon.marvin.services.soap
-
- chemaxon.marvin.services.xmlrpcservice - package chemaxon.marvin.services.xmlrpcservice
-
- chemaxon.marvin.sketch - package chemaxon.marvin.sketch
-
Contains the sketcher's core classes and various sketching modes.
- chemaxon.marvin.space - package chemaxon.marvin.space
-
Contains the core classes of MarvinSpace including the graphic canvas and the
basic visualizer classes.
- chemaxon.marvin.space.monitor - package chemaxon.marvin.space.monitor
-
Classes that represent measurement and changing of coordinates according to measurements in MarvinSpace.
- chemaxon.marvin.util - package chemaxon.marvin.util
-
Contains some utilities for example for molecule cleaning and Swing.
- chemaxon.marvin.util.codeassist - package chemaxon.marvin.util.codeassist
-
- chemaxon.marvin.view - package chemaxon.marvin.view
-
Control records in MarvinView.
- chemaxon.marvin.view.swing - package chemaxon.marvin.view.swing
-
Swing support for MarvinView tables.
- chemaxon.naming - package chemaxon.naming
-
Document to Structure and Name to Structure conversion.
- chemaxon.struc - package chemaxon.struc
-
Provides classes for implementing and manipulating chemical structures.
Serialization of these classes is `standardized' in Marvin 5.3.
- chemaxon.struc.graphics - package chemaxon.struc.graphics
-
Contains graphics MDocument elements.
- chemaxon.struc.prop - package chemaxon.struc.prop
-
Utility classes that represent molecular properties and convert molecular property Strings to values and vice versa.
- chemaxon.struc.sgroup - package chemaxon.struc.sgroup
-
S-group related classes and interfaces.
Serialization of the classes is `standardized' in Marvin 3.1.4.
- chemaxon.util - package chemaxon.util
-
Provides general utility classes.
- chemaxon.util.concurrent - package chemaxon.util.concurrent
-
Provides utility classes for concurrent processing.
- chemaxon.util.concurrent.marvin - package chemaxon.util.concurrent.marvin
-
Provides utility classes for concurrent processing in Marvin.
- chemaxon.util.concurrent.processors - package chemaxon.util.concurrent.processors
-
Provides utility classes for concurrent processing.
- chemaxon.util.iterator - package chemaxon.util.iterator
-
Provides iterator classes for molecules and their components.
- ChemConst - Class in chemaxon.core
-
- ChemConst() - Constructor for class chemaxon.core.ChemConst
-
- ChemContext - Interface in chemaxon.jep
-
Interface of expression evaluation contexts.
- ChemJEP - Class in chemaxon.jep
-
Expression parser and evaluator for chemical expressions.
- ChemJEP() - Constructor for class chemaxon.jep.ChemJEP
-
Constructor.
- ChemJEP(Class) - Constructor for class chemaxon.jep.ChemJEP
-
Constructor.
- CHINESE_NAME_TO_STRUCTURE - Static variable in class chemaxon.license.LicenseManager
-
Identifier of product: Chinese Name to Structure
- chiralCenterCount() - Method in class chemaxon.calculations.stereo.Stereochemistry
-
Calculates the number of chiral centers.
- chiralCenterCount() - Method in class chemaxon.calculations.TopologyAnalyser
-
- chiralCenterCount() - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
-
Calculates the number of tetrahedral stereogenic centers.
- chiralCenters() - Method in class chemaxon.calculations.stereo.Stereochemistry
-
Determines the chiral center atoms.
- chiralCenters() - Method in class chemaxon.calculations.TopologyAnalyser
-
- ChiralFlagChecker - Class in chemaxon.checkers
-
- ChiralFlagChecker() - Constructor for class chemaxon.checkers.ChiralFlagChecker
-
Constructs ChiralFlagChecker instance
- ChiralFlagErrorChecker - Class in chemaxon.checkers
-
- ChiralFlagErrorChecker() - Constructor for class chemaxon.checkers.ChiralFlagErrorChecker
-
Default constructor
- CHIRALITY_M - Static variable in interface chemaxon.struc.StereoConstants
-
Axially chiral atom with M configuration.
- CHIRALITY_MASK - Static variable in interface chemaxon.struc.StereoConstants
-
Chirality mask in flags.
- CHIRALITY_P - Static variable in interface chemaxon.struc.StereoConstants
-
Axially chiral atom with P configuration.
- CHIRALITY_R - Static variable in interface chemaxon.struc.StereoConstants
-
Chiral atom of R configuration.
- CHIRALITY_r - Static variable in interface chemaxon.struc.StereoConstants
-
Pseudo-asymmetric chiral atom of r configuration.
- CHIRALITY_S - Static variable in interface chemaxon.struc.StereoConstants
-
Chiral atom of S configuration.
- CHIRALITY_s - Static variable in interface chemaxon.struc.StereoConstants
-
Pseudo-asymmetric chiral atom of s configuration.
- CHIRALITY_SUPPORT - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter: "chiralitySupport".
- CHIRALITYSUPPORT_ALL - Static variable in interface chemaxon.struc.StereoConstants
-
R/S shown always.
- CHIRALITYSUPPORT_NONE - Static variable in interface chemaxon.struc.StereoConstants
-
R/S not shown for any molecule.
- CHIRALITYSUPPORT_SELECTED - Static variable in interface chemaxon.struc.StereoConstants
-
R/S shown only if chiral flag is set in molecule or
the atom's enhanced stereo type is absolute.
- CIPStereoCalculator - Class in chemaxon.calculations.cip
-
Stereo calculator with the Cahn, Ingold, Prelog priority rules.
- CIPStereoCalculator() - Constructor for class chemaxon.calculations.cip.CIPStereoCalculator
-
- CIPStereoDescriptorIface - Interface in chemaxon.struc
-
Cahn-Ingold-Prelog (CIP) stereodescriptor interface.
- CIPStereoDescriptorIface.CIPType - Enum in chemaxon.struc
-
- CIPStereoDescriptorIface.CIPValue - Interface in chemaxon.struc
-
- CIPStereoDescriptorIface.CIPValue.AtropStereoIUPACValue - Enum in chemaxon.struc
-
- CIPStereoDescriptorIface.CIPValue.AtropStereoValue - Enum in chemaxon.struc
-
- CIPStereoDescriptorIface.CIPValue.AxialStereoIUPACValue - Enum in chemaxon.struc
-
- CIPStereoDescriptorIface.CIPValue.AxialStereoValue - Enum in chemaxon.struc
-
- CIPStereoDescriptorIface.CIPValue.CisTransStereoIUPACValue - Enum in chemaxon.struc
-
- CIPStereoDescriptorIface.CIPValue.CisTransStereoValue - Enum in chemaxon.struc
-
- CIPStereoDescriptorIface.CIPValue.TetrahedralStereoIUPACValue - Enum in chemaxon.struc
-
- CIPStereoDescriptorIface.CIPValue.TetrahedralStereoValue - Enum in chemaxon.struc
-
- CIPStereoRecognizer - Class in chemaxon.core.calculations.stereo
-
Detection of Cahn-Ingold-Prelog (CIP) stereo descriptors: tetrahedral, axial,
cis/trans and atrop stereo features.
- CIPStereoRecognizer() - Constructor for class chemaxon.core.calculations.stereo.CIPStereoRecognizer
-
- CIRCLED_CHARGE_FONT - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter: "circledChargeFont".
- CIRCLED_CHARGE_SIZE - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter: "circledChargeSize".
- CircularRGroupReferenceChecker - Class in chemaxon.checkers
-
- CircularRGroupReferenceChecker() - Constructor for class chemaxon.checkers.CircularRGroupReferenceChecker
-
Initializes the checker
- CIS - Static variable in interface chemaxon.struc.StereoConstants
-
Cis double bond.
- CisDoubleBondFilter - Class in com.chemaxon.calculations.stereoanal.filters.cistrans
-
Filter for CIS double bonds.
- CisDoubleBondFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.cistrans.CisDoubleBondFilter
-
- cisDoubleBonds() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
-
Calculates the CIS double bonds.
- CisTransDoubleBondFilter - Class in com.chemaxon.calculations.stereoanal.filters.cistrans
-
Filter for cis-trans stereo centers.
- CisTransDoubleBondFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.cistrans.CisTransDoubleBondFilter
-
- cisTransDoubleBonds() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
-
Calculates the CIS-TRANS double bonds.
- cisTransDoubleBondsWithAttachedData() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
-
Calculates the CIS-TRANS double bonds with attached data.
- CisTransStereoCenter - Class in com.chemaxon.calculations.stereoanal.stereocenters
-
Cis-trans stereo center implementation.
- CisTransStereoCenter(AtomSelection, CIPStereoDescriptorIface.CIPValue.CisTransStereoIUPACValue, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter
-
Constructs a new instance of cis-trans stereo center with attached data.
- CisTransStereoCenter(AtomSelection, CIPStereoDescriptorIface.CIPValue.CisTransStereoIUPACValue) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter
-
Constructs a new instance of cis-trans stereo center.
- CisTransStereoCenter(AtomSelection, StereoConstants.StereoValue.CisTransStereo, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter
-
Deprecated.
- CisTransStereoCenter(AtomSelection, StereoConstants.StereoValue.CisTransStereo) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter
-
Deprecated.
- CisTransStereoDescriptor - Class in chemaxon.struc
-
- CisTransStereoDescriptor(CIPStereoDescriptorIface.CIPValue.CisTransStereoValue, StereoActivePart, StereoActivePart) - Constructor for class chemaxon.struc.CisTransStereoDescriptor
-
- Cl - Static variable in class chemaxon.core.ChemConst
-
- CLASS - Static variable in class chemaxon.marvin.services.localservice.LocalServiceDescriptor
-
Property key for Service class name as
String
- clean(MoleculeGraph, int, String, MProgressMonitor) - Static method in class chemaxon.calculations.clean.Cleaner
-
Calculates atom coordinates.
- clean(MoleculeGraph, int, String) - Static method in class chemaxon.calculations.clean.Cleaner
-
Calculates atom coordinates.
- clean(MoleculeGraph, int) - Static method in class chemaxon.calculations.clean.Cleaner
-
Calculates atom coordinates.
- clean(int) - Method in class chemaxon.formats.MolConverter.Builder
-
Enables cleaning.
- clean(int, String) - Method in class chemaxon.formats.MolConverter.Builder
-
Enables cleaning.
- clean(int, String) - Method in class chemaxon.formats.MolConverter.Options
-
Deprecated.
- clean(int) - Method in class chemaxon.formats.MolConverter.Options
-
Deprecated.
- clean(int, String, int, String, MProgressMonitor, String[]) - Method in class chemaxon.marvin.view.MDocStorage
-
Clean the specified cell.
- clean(int, String) - Method in class chemaxon.struc.MoleculeGraph
-
- clean(int, String, MProgressMonitor) - Method in class chemaxon.struc.MoleculeGraph
-
- clean3d(Molecule) - Static method in class chemaxon.marvin.alignment.MMPAlignment
-
Utility for preprocessing structure for alignment.
- clean3d(Molecule, int) - Static method in class chemaxon.marvin.alignment.MMPAlignment
-
Utility for preprocessing structure for alignment.
- cleanAll(int, String, MProgressMonitor, String[]) - Method in class chemaxon.marvin.view.MDocStorage
-
Clean all cells.
- Cleaner - Class in chemaxon.calculations.clean
-
Class to clean MoleculeGraphs, Molecules, SelectionMolecules and Sgroups.
- Cleaner() - Constructor for class chemaxon.calculations.clean.Cleaner
-
- CleanFixer - Class in chemaxon.fixers
-
- CleanFixer() - Constructor for class chemaxon.fixers.CleanFixer
-
- CLEANING_2D_OPTIONS - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter: "clean2dOpts".
- CLEANING_3D_OPTIONS - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter: "clean3dOpts".
- CLEANING_DIMENSION - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter: "cleanDim".
- CLEANING_OPTIONS - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter: "cleanOpts".
- cleanup() - Method in class chemaxon.marvin.space.GraphicComponent
-
- cleanup() - Method in class chemaxon.marvin.space.PharmacophoreArrow
-
- cleanup() - Method in class chemaxon.marvin.space.PharmacophorePoint
-
- cleanup(long) - Method in interface chemaxon.util.concurrent.ConcurrentProcessor
-
Cancels work currently executed under the control of this
ConcurrentProcessor instance, awaits termination of associated
worker threads and releases any resource this processor has reserved.
- cleanup() - Method in interface chemaxon.util.concurrent.ConcurrentProcessor
-
- cleanupRemovedRgroupMember(MoleculeGraph, int) - Method in class chemaxon.struc.RgMolecule
-
Clean-up after R-group removal.
- CleanUtil - Class in chemaxon.marvin.util
-
Utility methods for cleaning.
- CleanUtil() - Constructor for class chemaxon.marvin.util.CleanUtil
-
- clear() - Method in class chemaxon.formats.MolConverter.Builder
-
Clears all settings.
- clear() - Method in class chemaxon.formats.MolConverter.Options
-
Deprecated.
- clear() - Method in interface chemaxon.jep.ChemContext
-
Clears the context.
- clear() - Method in class chemaxon.jep.context.AtomContext
-
Clears the context.
- clear() - Method in class chemaxon.jep.context.MolContext
-
Clears the context.
- clear() - Method in class chemaxon.jep.context.ReactionContext
-
Clears the context.
- clear() - Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
-
Clears the display.
- clear() - Method in class chemaxon.marvin.space.BoundingBox
-
Clears all previously set coordinate from the box.
- clear() - Method in class chemaxon.marvin.space.monitor.Monitor
-
Deletes all items from selectedItems.
- clear() - Method in class chemaxon.struc.MDocument
-
Clears the document.
- clear() - Method in class chemaxon.struc.MolAtom
-
Clear query properties, charge, and hcount.
- clear() - Method in class chemaxon.struc.Molecule
-
Clears the molecule.
- clear() - Method in class chemaxon.struc.MoleculeGraph
-
Clears the molecule.
- clear() - Method in class chemaxon.struc.MPropertyContainer
-
Clears properties.
- clear() - Method in class chemaxon.struc.MSelectionDocument
-
Clears the document.
- clearAllCellStyle() - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
Clears all the previously set cell style of the property columns
- clearAllColumnWidth() - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
Clears all the previously set width of the property columns
- clearAssigned() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
-
- clearCachedInfo(int) - Method in class chemaxon.struc.MoleculeGraph
-
Deletes the cached information depending on the given options.
- clearCheckerMarks() - Method in class chemaxon.struc.MDocument
-
Clears the checker marks
- clearClipboard() - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
-
Clears the clipboard by creating an empty Transferable and placing it on the clipboard.
- clearExtraLabel() - Method in class chemaxon.struc.MolAtom
-
Clears the extra label.
- clearExtraLabels() - Method in class chemaxon.struc.Molecule
-
Clears extra atom labels.
- clearForImport(String) - Method in class chemaxon.struc.Molecule
-
Initializes molecule for import.
- clearForImport(String) - Method in class chemaxon.struc.MoleculeGraph
-
Clears the bonds vector, the properties, the flags, and sets the
origin coordinates to 0.
- clearForImport(String) - Method in class chemaxon.struc.RgMolecule
-
Clear the edges vector and the properties.
- clearForImport(String) - Method in class chemaxon.struc.RxnMolecule
-
Clear the edges vector and the properties.
- clearHistory() - Method in class chemaxon.marvin.beans.MSketchPane
-
Reset undo queue.
- clearHits() - Method in class chemaxon.naming.DocumentExtractor
-
Deprecated.
Clears the list of hits.
- clearLines() - Method in class chemaxon.struc.graphics.MTextBox
-
Clears all lines.
- clearObjects() - Method in class chemaxon.struc.Molecule
-
- clearObjects() - Method in class chemaxon.struc.RgMolecule
-
- clearObjects() - Method in class chemaxon.struc.RxnMolecule
-
Deletes the graphical objects from this.
- clearObjects() - Method in class chemaxon.struc.Sgroup
-
Clears all MObject-s that belong to this S-groups.
- clearProperties() - Method in class chemaxon.struc.MolAtom
-
Removes all properties from this atom.
- clearProperties() - Method in class chemaxon.struc.MolBond
-
Removes all properties from this bond.
- clearProperties() - Method in class chemaxon.struc.Molecule
-
Clears RDfile/SDfile properties.
- clearPropertyColumnNames() - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
Clears the display name list of properties
- clearQProps() - Method in class chemaxon.struc.MolAtom
-
Clears query props.
- clearSelection(int) - Method in class chemaxon.marvin.space.GraphicScene
-
Sets all components and parts of components to be unselected in the given cell.
- clearSelections() - Method in class chemaxon.marvin.space.GraphicCell
-
Sets all components and parts of components to be unselected.
- clearSets() - Method in class chemaxon.struc.MDocument
-
Clears the atomSets and the bondSets.
- CLIPBOARD_OPERATION_GET - Static variable in interface chemaxon.marvin.modules.datatransfer.MTransferable
-
Flag that indicates an import operation
- CLIPBOARD_OPERATION_PUT - Static variable in interface chemaxon.marvin.modules.datatransfer.MTransferable
-
Flag that indicates an export operation
- CLIPBOARD_OPERATION_UNDEFINED - Static variable in interface chemaxon.marvin.modules.datatransfer.MTransferable
-
Undefined clipboard operation state identifier
- CLIPBOARD_ORIGIN_IS_FILE - Static variable in interface chemaxon.marvin.modules.datatransfer.MTransferable
-
Temporary property name to mark the molecule if it comes from a file via the clipboard
- ClipboardHandler - Class in chemaxon.marvin.modules.datatransfer
-
Facade of the Clipboard handling in Marvin.
- clipboardOperation - Variable in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
-
Clipboard operation type.
- clipSurface(BoundingBox) - Method in class chemaxon.marvin.space.SurfaceComponent
-
The bounding box of the surface can be used to determine 6 clipping planes
and clip (do not draw) parts lying outside of the box.
- clone() - Method in class chemaxon.checkers.AbstractStructureChecker
-
- clone() - Method in class chemaxon.checkers.StructureCheckerDescriptor
-
- clone() - Method in class chemaxon.checkers.SubstructureChecker
-
- clone() - Method in class chemaxon.fixers.StructureFixerDescriptor
-
- clone() - Method in class chemaxon.formats.MolConverter.Builder
-
Clones the object.
- clone() - Method in class chemaxon.formats.MolConverter.Options
-
Deprecated.
- clone() - Method in class chemaxon.marvin.util.MolImageSize
-
Deprecated.
- clone() - Method in class chemaxon.struc.DPoint3
-
Make an identical copy.
- clone() - Method in class chemaxon.struc.graphics.MAtomSetPoint
-
- clone() - Method in class chemaxon.struc.graphics.MBracket
-
- clone() - Method in class chemaxon.struc.graphics.MChemicalStruct
-
Creates a clone.
- clone() - Method in class chemaxon.struc.graphics.MEFlow
-
- clone() - Method in class chemaxon.struc.graphics.MEFlowBasePoint
-
- clone() - Method in class chemaxon.struc.graphics.MEllipse
-
- clone() - Method in class chemaxon.struc.graphics.MFont
-
Creates a clone.
- clone() - Method in class chemaxon.struc.graphics.MMidPoint
-
- clone() - Method in class chemaxon.struc.graphics.MMidPoint.Sticky
-
- clone() - Method in class chemaxon.struc.graphics.MPolyline
-
- clone() - Method in class chemaxon.struc.graphics.MRectangle
-
- clone() - Method in class chemaxon.struc.graphics.MRectanglePoint
-
- clone() - Method in class chemaxon.struc.graphics.MRectanglePoint.Sticky
-
- clone() - Method in class chemaxon.struc.graphics.MRoundedRectangle
-
- clone() - Method in class chemaxon.struc.graphics.MTextBox
-
- clone() - Method in class chemaxon.struc.MDocument
-
Creates a clone.
- clone() - Method in class chemaxon.struc.MObject
-
Creates a clone.
- clone() - Method in class chemaxon.struc.MolAtom
-
Clones the atom.
- clone() - Method in class chemaxon.struc.MolBond
-
Make a copy of this object.
- clone() - Method in class chemaxon.struc.Molecule
-
Makes an identical copy of the molecule.
- clone() - Method in class chemaxon.struc.MoleculeGraph
-
Make an identical copy of the molecule.
- clone() - Method in class chemaxon.struc.MPoint
-
- clone() - Method in class chemaxon.struc.MPropertyContainer
-
Clones this object.
- clone() - Method in class chemaxon.struc.prop.MBooleanProp
-
Clones the object.
- clone() - Method in class chemaxon.struc.prop.MCollectionProp
-
Clones the object.
- clone() - Method in class chemaxon.struc.prop.MDoubleArrayProp
-
Clones the object.
- clone() - Method in class chemaxon.struc.prop.MDoubleProp
-
Clones the object.
- clone() - Method in class chemaxon.struc.prop.MHCoords3DProp
-
Clones the object.
- clone() - Method in class chemaxon.struc.prop.MIntegerArrayProp
-
Clones the object.
- clone() - Method in class chemaxon.struc.prop.MIntegerProp
-
Clones the object.
- clone() - Method in class chemaxon.struc.prop.MMoleculeProp
-
Clones the object.
- clone() - Method in class chemaxon.struc.prop.MObjectProp
-
Clones the object.
- clone() - Method in class chemaxon.struc.prop.MStringProp
-
Clones the object.
- clone() - Method in class chemaxon.struc.QueryBond
-
Make a copy of this object.
- clone() - Method in class chemaxon.struc.RgMolecule
-
Clone the markush structure.
- clone() - Method in class chemaxon.struc.RxnMolecule
-
Make an identical copy of the reaction structure.
- clone() - Method in class chemaxon.struc.SelectionMolecule
-
Create a clone of this SelectionMolecule.
- clone() - Method in class chemaxon.struc.sgroup.SgroupAtom
-
- clone() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Clones the SuperatomSgroup (and not the
Molecule).
- clone() - Method in class chemaxon.util.HitColoringAndAlignmentOptions
-
Makes an identical copy of the Options
- cloneAtoms(int[], MoleculeGraph) - Method in class chemaxon.struc.Molecule
-
Copies the specified atoms.
- cloneAtoms(int[], MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
-
Copies the specified atoms.
- cloneBond(MolAtom, MolAtom) - Method in class chemaxon.struc.MolBond
-
Clones this bond.
- cloneBond(MolAtom, MolAtom) - Method in class chemaxon.struc.QueryBond
-
Clones this bond.
- cloneCollectionProp(Set) - Method in class chemaxon.struc.prop.MCollectionProp
-
Clones the object.
- cloneCollectionProp(Set) - Method in class chemaxon.struc.prop.MHashProp
-
Clones the object.
- cloneCollectionProp(Set) - Method in class chemaxon.struc.prop.MListProp
-
Clones the object.
- clonecopy(MoleculeGraph) - Method in class chemaxon.struc.Molecule
-
Makes another molecule identical to this one.
- clonecopy(int[], MoleculeGraph) - Method in class chemaxon.struc.Molecule
-
Copies the specified atoms and bonds of this molecule to another one.
- clonecopy(MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
-
Make another molecule identical to this one.
- clonecopy(int[], MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
-
Copies the specified atoms of this molecule graph to another one.
- clonecopy(MoleculeGraph) - Method in class chemaxon.struc.RgMolecule
-
Make another molecule identical to this one.
- clonecopy(int[], MoleculeGraph) - Method in class chemaxon.struc.RgMolecule
-
Copies the specified atoms of this graph to another one.
- clonecopy(MoleculeGraph) - Method in class chemaxon.struc.RxnMolecule
-
Make another molecule identical to this one.
- clonecopy(int[], MoleculeGraph) - Method in class chemaxon.struc.RxnMolecule
-
Copies the specified nodes and edges of this graph to another one.
- clonecopy(MoleculeGraph) - Method in class chemaxon.struc.SelectionMolecule
-
Copies the clones of atoms and bonds of this graph to another one.
- clonecopyMoleculeGraphWithoutSgroups(int[], MolBond[], int, MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
-
Copies the specified atoms and bonds of this molecule graph to another one.
- clonecopyMoleculeGraphWithoutSgroups(int[], MolBond[], int, MoleculeGraph) - Method in class chemaxon.struc.SelectionMolecule
-
Copies the specified atoms and bonds of this graph to another one.
- clonecopyWithoutSgroups(Molecule) - Method in class chemaxon.struc.Molecule
-
Copies the all the contents except the S-groups into another molecule
object.
- cloneDocument() - Method in class chemaxon.struc.MDocument
-
Creates a clone.
- cloneDocument() - Method in class chemaxon.struc.MSelectionDocument
-
Creates a clone.
- cloneFromSgroupCopy() - Method in class chemaxon.struc.sgroup.SgroupAtom
-
Clones the S-group superatom partially.
- cloneItem() - Method in class chemaxon.checkers.AbstractStructureChecker
-
- cloneItem() - Method in class chemaxon.checkers.InvalidChecker
-
- cloneItem() - Method in interface chemaxon.checkers.StructureChecker
-
Returns a clone of this StructureChecker instance
- cloneLeavingGroups(SuperatomSgroup) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Deprecated.
As of Marvin 6.2, no replacement.
Not supported feature.
- clonelesscopy(MoleculeGraph) - Method in class chemaxon.struc.Molecule
-
Deprecated.
as of Marvin 6.3.
Not supported feature.
- clonelesscopy(MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
-
Deprecated.
as of Marvin 6.3.
Not supported feature.
- clonelesscopy(MoleculeGraph) - Method in class chemaxon.struc.RgMolecule
-
Deprecated.
as of Marvin 6.3.
Not supported feature.
- clonelesscopy(MoleculeGraph) - Method in class chemaxon.struc.RxnMolecule
-
Deprecated.
as of Marvin 6.3.
Not supported feature.
- cloneMainMolecule() - Method in class chemaxon.struc.MDocument
-
Creates a clone.
- cloneMainMoleculeGraph() - Method in class chemaxon.struc.MDocument
-
Creates a clone.
- cloneMFont() - Method in class chemaxon.struc.graphics.MFont
-
Creates a clone.
- cloneMolecule() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
-
- cloneMolecule() - Method in class chemaxon.struc.Molecule
-
- cloneMoleculeWithDocument() - Method in class chemaxon.struc.Molecule
-
Makes an identical copy of the molecule and its document.
- cloneMoleculeWithDocument() - Method in class chemaxon.struc.RgMolecule
-
- cloneMoleculeWithDocument() - Method in class chemaxon.struc.RxnMolecule
-
- cloneProp() - Method in class chemaxon.struc.MDocument.Prop
-
Creates a clone.
- cloneProp() - Method in class chemaxon.struc.MProp
-
Clones the object.
- cloneProp() - Method in class chemaxon.struc.prop.MBooleanProp
-
Clones the object.
- cloneProp() - Method in class chemaxon.struc.prop.MCollectionProp
-
Clones the object.
- cloneProp() - Method in class chemaxon.struc.prop.MDoubleArrayProp
-
Clones the object.
- cloneProp() - Method in class chemaxon.struc.prop.MDoubleProp
-
Clones the object.
- cloneProp() - Method in class chemaxon.struc.prop.MHCoords3DProp
-
Clones the object.
- cloneProp() - Method in class chemaxon.struc.prop.MIntegerArrayProp
-
Clones the object.
- cloneProp() - Method in class chemaxon.struc.prop.MIntegerProp
-
Clones the object.
- cloneProp() - Method in class chemaxon.struc.prop.MMoleculeProp
-
Clones the object.
- cloneProp() - Method in class chemaxon.struc.prop.MObjectProp
-
Clones the object.
- cloneProp() - Method in class chemaxon.struc.prop.MStringProp
-
Clones the object.
- cloneSets(MDocument) - Method in class chemaxon.struc.MDocument
-
Clones the atom/bond sets from doc.
- cloneSgroup(Molecule, Sgroup) - Method in class chemaxon.struc.Sgroup
-
Gets a new Sgroup instance.
- cloneSgroup(Molecule, Sgroup, int[]) - Method in class chemaxon.struc.Sgroup
-
Gets a new Sgroup instance.
- cloneSgroup(Molecule, Sgroup, int[]) - Method in class chemaxon.struc.sgroup.DataSgroup
-
Gets a new DataSgroup instance.
- cloneSgroup(Molecule, Sgroup, int[]) - Method in class chemaxon.struc.sgroup.MulticenterSgroup
-
Gets a new Sgroup instance.
- cloneSgroup(Molecule, Sgroup, int[]) - Method in class chemaxon.struc.sgroup.MultipleSgroup
-
Gets a new Sgroup instance.
- cloneSgroup(Molecule, Sgroup, int[]) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
-
Gets a new Sgroup instance.
- cloneSgroup(Molecule, Sgroup, int[]) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Gets a new Sgroup instance.
- cloneStructure() - Method in class chemaxon.struc.Sgroup
-
Gets the clone of the structure stored.
- cloneTemporraryObjects(MDocument) - Method in class chemaxon.struc.MDocument
-
- close() - Method in class chemaxon.formats.MolConverter
-
Closes the exporter and the output stream.
- close(int) - Method in class chemaxon.formats.MolConverter
-
Closes the exporter.
- close() - Method in class chemaxon.formats.MolExporter
-
- close(int) - Method in class chemaxon.formats.MolExporter
-
- close() - Method in class chemaxon.formats.MolImporter
-
Close the underlying input stream.
- close() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
-
Interrupts parsing.
- close() - Method in class chemaxon.marvin.io.formats.MoleculeImporter
-
- close() - Method in class chemaxon.marvin.io.MDocSource
-
Closes the underlying input stream(s).
- close() - Method in class chemaxon.marvin.io.MolExportModule
-
Close the stream.
- close() - Method in class chemaxon.marvin.io.MRecordImporter
-
Closes the input stream.
- close() - Method in interface chemaxon.marvin.io.MRecordReader
-
Closes the input stream.
- close() - Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
-
Closes the output.
- close(int) - Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
-
Closes the output.
- close() - Method in class chemaxon.util.concurrent.marvin.MolInputProducer
-
Closes the importers.
- CLOSED_FLAG - Static variable in class chemaxon.struc.graphics.MPolyline
-
Closed flag.
- closeSketcher(int) - Method in class chemaxon.marvin.beans.MViewPane
-
Closes the sketcher window that belongs the the specified cell.
- closeWindow(int) - Method in class chemaxon.marvin.beans.MViewPane
-
Closes the detached viewer window of the specified cell.
- closeWindows() - Method in class chemaxon.marvin.beans.MarvinPane
-
Closes all windows opened by this MarvinPane.
- Cm - Static variable in class chemaxon.core.ChemConst
-
- CML - Static variable in class chemaxon.formats.MFileFormat
-
Chemical Markup Language.
- Co - Static variable in class chemaxon.core.ChemConst
-
- CodeAssistFactory - Class in chemaxon.marvin.util.codeassist
-
Manages the creation of Chemical Terms related components, such as the Code Assist text field,
toolbars, favorite and macro handling components, and validation response component.
- CodeAssistFactory.CodeAssistConfiguration - Class in chemaxon.marvin.util.codeassist
-
- CodeAssistFactory.CodeAssistConfiguration() - Constructor for class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
-
- codeHIsotopeMass(int, int) - Static method in class chemaxon.marvin.io.formats.mdl.MolfileUtil
-
Add mass number information to the given code.
- color - Variable in class chemaxon.marvin.space.GraphicComponent
-
- color - Variable in class chemaxon.marvin.space.MoleculeComponent
-
- color - Variable in class chemaxon.marvin.space.SurfaceComponent
-
- color(Molecule, Molecule, HitColoringAndAlignmentOptions) - Static method in class chemaxon.util.HitDisplayUtil
-
Only for internal use!
- color3 - Variable in class chemaxon.marvin.space.SurfaceComponent
-
- COLOR_MAPPER_BLUE_TO_GREEN - Static variable in class chemaxon.marvin.space.SurfaceColoring
-
Built-in blue-cyan-green palette will be used.
- COLOR_MAPPER_BLUE_TO_RED - Static variable in class chemaxon.marvin.space.SurfaceColoring
-
Built-in blue-lightgray-red palette will be used.
- COLOR_MAPPER_FIRE - Static variable in class chemaxon.marvin.space.SurfaceColoring
-
Built-in "fire" palette will be used.
- COLOR_MAPPER_GREEN_TO_BLUE - Static variable in class chemaxon.marvin.space.SurfaceColoring
-
Built-in green-cyan-blue palette will be used.
- COLOR_MAPPER_RAINBOW - Static variable in class chemaxon.marvin.space.SurfaceColoring
-
Built-in rainbow palette will be used.
- COLOR_MAPPER_RED_TO_BLUE - Static variable in class chemaxon.marvin.space.SurfaceColoring
-
Built-in red-lightgray-blue palette will be used.
- COLOR_MAPPER_REVERSE_RAINBOW - Static variable in class chemaxon.marvin.space.SurfaceColoring
-
Built-in reverse rainbow palette will be used.
- COLOR_SCHEME - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter: "colorScheme".
- COLOR_SCHEMES - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Array of color schemes strings.
- ColorGenerator - Class in chemaxon.marvin.util
-
A final class which provides a static access to a color distant color creator class.
- ColorGenerator() - Constructor for class chemaxon.marvin.util.ColorGenerator
-
- colorHit(Molecule, Molecule, int[], HitColoringAndAlignmentOptions) - Static method in class chemaxon.util.HitDisplayUtil
-
Returns the colored copy of the specified target structure,
the original target is kept unchanged.
- coloring(boolean) - Method in class chemaxon.marvin.space.SurfaceComponent
-
- coloring - Variable in class chemaxon.util.HitColoringAndAlignmentOptions
-
- COLORING_ALL - Static variable in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Constant for setting all coloring options, currently scaffold and R-groups.
- COLORING_NONE - Static variable in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Constant for no hit coloring.
- COLORING_RGROUPS - Static variable in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Constant for R-group coloring.
- COLORING_SCAFFOLD - Static variable in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Constant for scaffold coloring.
- COLORS_MASK - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Color scheme mask in display option flags.
- COLORS_OFFSET - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Color scheme offset in display option flags.
- colorType - Variable in class chemaxon.marvin.space.MoleculeComponent
-
- COLS - Static variable in class chemaxon.marvin.view.ViewParameterConstants
-
Identifier of parameter: "cols".
- com.chemaxon.calculations.solubility - package com.chemaxon.calculations.solubility
-
- com.chemaxon.calculations.stereoanal - package com.chemaxon.calculations.stereoanal
-
API of the Stereo Analysis Plugin.
- com.chemaxon.calculations.stereoanal.filters - package com.chemaxon.calculations.stereoanal.filters
-
Core filter classes.
- com.chemaxon.calculations.stereoanal.filters.atrop - package com.chemaxon.calculations.stereoanal.filters.atrop
-
Atrop stereo filter implementations.
- com.chemaxon.calculations.stereoanal.filters.axial - package com.chemaxon.calculations.stereoanal.filters.axial
-
Axial stereo filter implementations.
- com.chemaxon.calculations.stereoanal.filters.cistrans - package com.chemaxon.calculations.stereoanal.filters.cistrans
-
Cis-trans stereo filter implementations.
- com.chemaxon.calculations.stereoanal.filters.tetrahedral - package com.chemaxon.calculations.stereoanal.filters.tetrahedral
-
Tetrahedral stereo filter implementations.
- com.chemaxon.calculations.stereoanal.stereocenters - package com.chemaxon.calculations.stereoanal.stereocenters
-
Stereocenter implementations of Stereo Analysis API.
- com.chemaxon.common.annotations - package com.chemaxon.common.annotations
-
- com.chemaxon.mapper - package com.chemaxon.mapper
-
- com.chemaxon.version - package com.chemaxon.version
-
- compare(StructureFixer, StructureFixer) - Method in class chemaxon.fixers.FixerPriorityComparator
-
- compareTo(TransferableDescriptor) - Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor
-
Comparison method which uses the priority field for ordering.
- compareTo(Object) - Method in class chemaxon.marvin.plugin.PluginFactory.PluginRecord
-
- compile(String) - Method in class chemaxon.jep.ChemJEP
-
Compiles the expression string to an inner structure.
- compile(String) - Method in class chemaxon.jep.Evaluator
-
Compiles the expression, creates
ChemJEP object.
- compile(String, Class) - Method in class chemaxon.jep.Evaluator
-
Compiles the expression, creates
ChemJEP object.
- compile(String, Class, SymbolTable) - Method in class chemaxon.jep.Evaluator
-
Compiles the expression, creates
ChemJEP object.
- component - Variable in class chemaxon.marvin.space.monitor.Control
-
- COMPONENT_RANGE - Static variable in class chemaxon.marvin.space.GraphicScene
-
- COMPONENT_TYPE_ATOM - Static variable in class chemaxon.marvin.space.MacroMoleculeComponent
-
- COMPONENT_TYPE_ATOM - Static variable in class chemaxon.marvin.space.MoleculeComponent
-
- COMPONENT_TYPE_BOND - Static variable in class chemaxon.marvin.space.MacroMoleculeComponent
-
- COMPONENT_TYPE_BOND - Static variable in class chemaxon.marvin.space.MoleculeComponent
-
- COMPONENT_TYPE_ENTIRE - Static variable in class chemaxon.marvin.space.GraphicComponent
-
Indicates if the entire component is selected by picking.
- COMPONENT_TYPE_MOLECULE - Static variable in class chemaxon.marvin.space.MacroMoleculeComponent
-
- COMPONENT_TYPE_MOLECULE - Static variable in class chemaxon.marvin.space.MoleculeComponent
-
- COMPONENT_TYPE_RESIDUE - Static variable in class chemaxon.marvin.space.MacroMoleculeComponent
-
- componentBecameSelected() - Method in class chemaxon.marvin.space.GraphicCell
-
Returns true if a component became selected previously.
- componentBecameSelected(int) - Method in class chemaxon.marvin.space.GraphicScene
-
Returns true if a component became selected previously in the given cell.
- componentBecameUnselected() - Method in class chemaxon.marvin.space.GraphicCell
-
Returns true if a component became unselected previously.
- componentBecameUnselected(int) - Method in class chemaxon.marvin.space.GraphicScene
-
Returns true if a component became unselected previously in the given cell.
- ComponentChecker<E> - Class in chemaxon.checkers
-
Descendants of the abstract ComponentChecker class implement detect problems related to
disconnected components (fragments).
- ComponentChecker(StructureCheckerErrorType) - Constructor for class chemaxon.checkers.ComponentChecker
-
Constructor to create a Structure checker instance with the given errorType.
- ComponentElement - Class in chemaxon.marvin.space
-
Class to identify parts of GraphicComponents mainly during selection.
- ComponentElement(GraphicComponent, int, int) - Constructor for class chemaxon.marvin.space.ComponentElement
-
Creates a new instance of ComponentElement of a simple
(not structured) GraphicComponent.
- ComponentElement(GraphicComponent, int, Integer) - Constructor for class chemaxon.marvin.space.ComponentElement
-
Creates a new instance of ComponentElement.
- ComponentElement(GraphicComponent, int, int, int) - Constructor for class chemaxon.marvin.space.ComponentElement
-
Creates a new instance of ComponentElement of a complex (structured) GraphicComponent.
- ComponentElement(GraphicComponent, int, int, Integer) - Constructor for class chemaxon.marvin.space.ComponentElement
-
Creates a new instance of ComponentElement.
- ComponentElement(ComponentElement) - Constructor for class chemaxon.marvin.space.ComponentElement
-
Copies the given ComponentElement.
- componentHidden(ComponentEvent) - Method in class chemaxon.marvin.beans.MarvinPane
-
Hides windows if the parent frame is hidden.
- componentMoved(ComponentEvent) - Method in class chemaxon.marvin.beans.MarvinPane
-
Does nothing.
- componentResized(ComponentEvent) - Method in class chemaxon.marvin.beans.MarvinPane
-
Does nothing.
- componentShown(ComponentEvent) - Method in class chemaxon.marvin.beans.MarvinPane
-
Shows windows if the parent frame is hidden.
- CompositeInputProducer - Class in chemaxon.util.concurrent.marvin
-
Input producer composed of an array of input producers.
- CompositeInputProducer() - Constructor for class chemaxon.util.concurrent.marvin.CompositeInputProducer
-
Constructor.
- CompositeInputProducer(InputProducer[]) - Constructor for class chemaxon.util.concurrent.marvin.CompositeInputProducer
-
Constructor.
- CompositeWorkUnit - Class in chemaxon.util.concurrent.marvin
-
Work unit composed of an array of work units, to be called in a linear fashion
in a single thread, one after the other in the specified order.
- CompositeWorkUnit() - Constructor for class chemaxon.util.concurrent.marvin.CompositeWorkUnit
-
Constructor.
- CompositeWorkUnit(WorkUnit[]) - Constructor for class chemaxon.util.concurrent.marvin.CompositeWorkUnit
-
Constructor.
- CompositeWorkUnitFactory - Class in chemaxon.util.concurrent.marvin
-
Work unit factory composed of an aray of work unit factories.
- CompositeWorkUnitFactory(WorkUnitFactory[]) - Constructor for class chemaxon.util.concurrent.marvin.CompositeWorkUnitFactory
-
Constructor.
- composition(int) - Method in class chemaxon.calculations.ElementalAnalyser
-
Gets the elemental analysis, the relative percent composition of a pure
chemical substance by element (w/w%).
- COMPRESS - Static variable in class chemaxon.formats.MdlCompressor
-
Compression flag.
- computeFunctionScale() - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
Computes the scaling factor for the unscaled NMR spectrum function.
- computeFunctionScale(double, double[]) - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
- computeSurface(MacroMoleculeComponent.MoleculeVisualizer) - Method in class chemaxon.marvin.space.MSpaceEasy
-
Activates the container cell of the MoleculeVisualizer, and
computes its Connolly surface.
- computeSurface(String) - Method in class chemaxon.marvin.space.MSpaceEasy
-
Computes the given type of surface in the active cell of the viewer.
- ConcurrentProcessor - Interface in chemaxon.util.concurrent
-
Executes jobs in parallel and returns their results iterator-style.
- ConcurrentProcessors - Class in chemaxon.util.concurrent.processors
-
- CONFIDENCE - Static variable in class chemaxon.naming.DocumentToStructure
-
The confidence that the structure is correct.
- config - Variable in class chemaxon.checkers.StructureCheckOptions
-
The configuration of the structure check.
- CONFIG_DIR - Static variable in class chemaxon.jep.Evaluator
-
Default directory for storing configuration files.
- ConfigurationReader - Interface in chemaxon.checkers.runner.configuration.reader
-
This interface is provided for classes which can read the configuration of
CheckerRunner.
- CONFIRM_TRANSFER - Static variable in class chemaxon.marvin.view.ViewParameterConstants
-
Identifier of parameter: "confirmTransfer".
- CONFORMATION_PLUGIN_GROUP - Static variable in class chemaxon.license.LicenseManager
-
Identifier of plugin: Conformation Plugin Group
- ConformerPlugin - Class in chemaxon.marvin.calculations
-
Plugin class for conformer calculation.
- ConformerPlugin() - Constructor for class chemaxon.marvin.calculations.ConformerPlugin
-
Constructor.
- CONJUGATED - Static variable in class chemaxon.struc.MolBond
-
Conjugation state of the bond.
- connectOriginalBondsToNewAtom(MolAtom, MolAtom, MolBond[]) - Method in class chemaxon.struc.Molecule
-
- connectOriginalBondsToNewAtom(MolAtom, MolAtom, MolBond[]) - Method in class chemaxon.struc.MoleculeGraph
-
Sets the original connections to the new atom.
- connectToSgroupOfAtom(SuperatomSgroup, MolAtom) - Method in class chemaxon.struc.graphics.MAtomSetPoint
-
- connectToSgroupOfAtom(SuperatomSgroup, MolAtom) - Method in class chemaxon.struc.graphics.MEFlowBasePoint
-
- connectToSgroupOfAtom(SuperatomSgroup, MolAtom) - Method in class chemaxon.struc.MObject
-
- constant - Variable in class chemaxon.marvin.services.ServiceArgument
-
field indicates constant argument
- containerFrame - Variable in class chemaxon.marvin.space.MSpaceEasy
-
- contains(String) - Method in class chemaxon.checkers.AbbreviatedGroupChecker.Abbreviations
-
Gets whether the abbreviations contain the specified abbreviation
- contains(float, float, float) - Method in class chemaxon.marvin.space.BoundingBox
-
Tells whether the given location is inside the box.
- contains(MObject) - Method in class chemaxon.struc.MDocument
-
Searches an object in the document.
- contains(MDocument) - Method in class chemaxon.struc.MDocument
-
Tests whether the document contains all objects of another document.
- contains(MolAtom) - Method in class chemaxon.struc.Molecule
-
Checks if the molecule graph contains the specified atom.
- contains(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
-
Checks if the molecule graph contains the specified atom.
- contains(MolBond) - Method in class chemaxon.struc.MoleculeGraph
-
Checks if the molecule graph contains the specified bond, or a bond which
is equals with the given bond.
- contains(MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
-
Does the molecule graph contain the specified fragment?
- contains(MProp) - Method in class chemaxon.struc.MPropertyContainer
-
Tests whether the container contains the specified property object.
- contains(MProp) - Method in class chemaxon.struc.prop.MCollectionProp
-
Tests whether the collection contains the specified property.
- contains(MolAtom) - Method in class chemaxon.struc.RgMolecule
-
Checks if the root structure or an R-group contains the specified node.
- contains(MolBond) - Method in class chemaxon.struc.RgMolecule
-
Checks if the root structure or an R-group contains the specified edge.
- contains(MolAtom) - Method in class chemaxon.struc.RxnMolecule
-
Checks if a reactant, agent or product structure contains the specified
node.
- contains(MolBond) - Method in class chemaxon.struc.RxnMolecule
-
Checks if a reactant, agent or product structure contains the specified
edge.
- contains(MolAtom) - Method in class chemaxon.struc.Sgroup
-
Is this atom contained by the s-group?
- containsAllAtomsOf(Sgroup) - Method in class chemaxon.struc.Sgroup
-
Checks if the S-group contains the atoms of another S-group.
- containsAtom(MolAtom) - Method in class chemaxon.struc.graphics.MAtomSetPoint
-
Checks if the atom set contains the specified atom object.
- containsAtom(MolAtom) - Method in class chemaxon.struc.graphics.MChemicalStruct
-
Checks if the atom set contains the specified atom object.
- containsAtom(MolAtom) - Method in class chemaxon.struc.graphics.MEFlowBasePoint
-
Checks if the atom set contains the specified atom object.
- containsAtom(MolAtom) - Method in class chemaxon.struc.graphics.MPolyline
-
Checks if the atom set contains the specified atom object.
- containsAtom(MolAtom) - Method in class chemaxon.struc.MObject
-
Checks if the object contains the specified atom reference.
- containsComponent(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicCell
-
Tells whether the component is in the cell.
- containsComponent(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicScene
-
Returns true if the component exists in the scene.
- containsCoordinateBond(MoleculeGraph) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Decides whether a molecule graph contains coordinate bonds.
- containsLadderTypePolymer() - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
-
Decides whether the structure of this sgroup contains a
ladder-type repeating unit.
- containsMulticenterSgroup(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Decides whether a molecule contains Multicenter S-groups.
- containsOnlyOne(Class) - Method in class chemaxon.struc.MDocument
-
Tests whether the document contains only one object of the specified
class.
- containsPoint(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MRoundedRectangle
-
- containsPoint(DPoint3, CTransform3D) - Method in class chemaxon.struc.MObject
-
- containsPropertyKey(String) - Method in class chemaxon.struc.MolAtom
-
Returns true if this atom has a mapping for the specified property key.
- containsPropertyKey(String) - Method in class chemaxon.struc.MolBond
-
Returns true if this bond has a mapping for the specified property key.
- containsPseudoAtom(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns true if molecule contains pseudo atom.
- containsSRUSgroup(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Decides whether a molecule contains SRU S-groups.
- CONTEXT - Static variable in class chemaxon.naming.DocumentToStructure
-
The context of the structure recognized in the text.
- CONTEXT_INDEX - Static variable in class chemaxon.naming.DocumentToStructure
-
Index of the hit inside the context.
- contract(int) - Method in class chemaxon.struc.Sgroup
-
- contract(int) - Method in interface chemaxon.struc.sgroup.Expandable
-
Contracts the S-group.
- contract(int) - Method in class chemaxon.struc.sgroup.MultipleSgroup
-
Contracts this S-group.
- contract(int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Contracts this S-group.
- ContractGroupFixer - Class in chemaxon.fixers
-
- ContractGroupFixer() - Constructor for class chemaxon.fixers.ContractGroupFixer
-
- contractOrExpandSgroups(int, String, boolean) - Method in class chemaxon.marvin.view.MDocStorage
-
Contract or expand S-groups in the specified cell.
- contractOrExpandSgroupsAll(boolean) - Method in class chemaxon.marvin.view.MDocStorage
-
Contract or expand S-groups in all molecules.
- contractSgroups() - Method in class chemaxon.struc.Molecule
-
Contracts all S-groups.
- contractSgroups(int) - Method in class chemaxon.struc.Molecule
-
Contracts all S-groups.
- Control - Class in chemaxon.marvin.space.monitor
-
Transformation on a GraphicComponent that changes the coordinates, and not just the view.
- Control() - Constructor for class chemaxon.marvin.space.monitor.Control
-
Creates a new instance of Control
- control(int, int) - Method in class chemaxon.marvin.space.monitor.Control
-
Does control on x-y events.
- control(int) - Method in class chemaxon.marvin.space.monitor.Control
-
Does control on z event.
- control(int) - Method in class chemaxon.marvin.space.monitor.DihedralControl
-
One part of the molecule being in one of the end of the torsion bond
will be rotated around the bond.
- control(int, int) - Method in class chemaxon.marvin.space.monitor.DihedralControl
-
Does nothing.
- control - Variable in class chemaxon.marvin.space.monitor.DihedralMonitor
-
- control(int) - Method in class chemaxon.marvin.space.monitor.DihedralMonitor
-
Passes the control event to the control.
- control(int, int) - Method in class chemaxon.marvin.space.monitor.GlobalLocationControl
-
Changes the location say translates the component of the control
in the global coordinate system.
- control(int) - Method in class chemaxon.marvin.space.monitor.GlobalLocationControl
-
Changes the location say translates the component of the control
in the global coordinate system.
- control(int, int) - Method in class chemaxon.marvin.space.monitor.GlobalOrientationControl
-
Changes the orientation say rotates the component of the control
in the global coordinate system.
- control(int) - Method in class chemaxon.marvin.space.monitor.GlobalOrientationControl
-
Changes the orientation that is rotates the component of the control
in the global coordinate system.
- control(int, int) - Method in class chemaxon.marvin.space.monitor.LocalLocationControl
-
Changes the location say translates the component of the control
in its local coordinate system.
- control(int) - Method in class chemaxon.marvin.space.monitor.LocalLocationControl
-
Changes the location say translates the component of the control
in its local coordinate system.
- control(int, int) - Method in class chemaxon.marvin.space.monitor.LocalOrientationControl
-
Changes the orientation say rotates the component of the control
in its local coordinate system.
- control(int) - Method in class chemaxon.marvin.space.monitor.LocalOrientationControl
-
Changes the orientation say rotates the component of the control
in its local coordinate system.
- control - Variable in class chemaxon.marvin.space.monitor.Monitor
-
- control(int, int) - Method in class chemaxon.marvin.space.monitor.PositionMonitor
-
Causes the monitor's controll to take action with 2 parameters.
- control(int) - Method in class chemaxon.marvin.space.monitor.PositionMonitor
-
Causes the monitor's controll to take action with 1 parameter.
- control(int) - Method in class chemaxon.marvin.space.monitor.ResizeControl
-
Resizes the component in z direction uniformly which means that it will
either increase or decrease its size with one unit or do nothing
if the given value was positive, negative or zero.
- control(int, int) - Method in class chemaxon.marvin.space.monitor.ResizeControl
-
Resizes the component in x, y direction uniformly which means that it will
either increase or decrease its size with one unit or do nothing
if the given value was positive, negative or zero.
- convert(Molecule, Map<String, Map<? extends Object, ? extends Object>>) - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
-
- convert(Molecule, Map<String, Map<? extends Object, ? extends Object>>) - Method in class chemaxon.checkers.result.MetalloceneCheckerResult
-
- convert(Molecule, Map<String, Map<? extends Object, ? extends Object>>) - Method in class chemaxon.checkers.result.RgroupCheckerResult
-
- convert(Molecule, Map<String, Map<? extends Object, ? extends Object>>) - Method in class chemaxon.checkers.result.SgroupCheckerResult
-
- convert(Molecule, Map<String, Map<? extends Object, ? extends Object>>) - Method in interface chemaxon.checkers.result.StructureCheckerResult
-
This method converts the entities contained in this result according to the convertData.
- convert(String) - Method in class chemaxon.checkers.StructureCheckOptions.ModeConverter
-
- convert(String) - Method in class chemaxon.checkers.StructureCheckOptions.TypeConverter
-
- convert() - Method in class chemaxon.formats.MdlCompressor
-
Compression/decompression
- convert(byte[], int) - Static method in class chemaxon.formats.MdlCompressor
-
(Un)compress the specified molfile or SDfile.
- convert(String, int) - Static method in class chemaxon.formats.MdlCompressor
-
(Un)compress the specified molfile or SDfile.
- convert() - Method in class chemaxon.formats.MolConverter
-
Convert the next molecule.
- convert(double[][]) - Static method in class chemaxon.marvin.alignment.AlignRigidEasy
-
- convert(Molecule) - Method in class chemaxon.marvin.io.formats.mdl.MolExport
-
Creates an MDL mol or compressed mol representation of the molecule.
- convert(Molecule) - Method in class chemaxon.marvin.io.MolExportModule
-
Convert a molecule to a string or byte array.
- convert(String) - Method in interface chemaxon.naming.NameConverter
-
Convert a name into the corresponding structure.
- ConvertAliasToGroupFixer - Class in chemaxon.fixers
-
A descendant of
AbstractStructureFixer which converts the aliases to
contracted abbreviated groups in the molecule
- ConvertAliasToGroupFixer() - Constructor for class chemaxon.fixers.ConvertAliasToGroupFixer
-
- ConvertConstants - Class in chemaxon.checkers.result
-
This class contains convert relevant constants
- ConvertConstants() - Constructor for class chemaxon.checkers.result.ConvertConstants
-
- convertCoordinateBondsToData(Molecule) - Method in class chemaxon.marvin.io.formats.mdl.MolExport
-
Converts coordinate bonds to data sgroups (attached data)
with field name MRV_COORDINATE_BOND.
- convertExplicitHToImplicit(MoleculeGraph, int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
-
Convert explicit Hydrogen atoms of the molecule to implicit.
- convertExplicitHToImplicit(MoleculeGraph) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
-
Convert explicit Hydrogen atoms of the molecule to implicit.
- convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
-
Convert explicit Hydrogen atoms attached to the specified atoms of the
molecule to implicit.
- convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
-
Convert explicit Hydrogen atoms attached to the specified atoms of a
molecule to implicit.
- convertExplicitLonePairsToImplicit(MoleculeGraph) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
-
Converts explicit lone pairs from a molecule to implicit.
- convertImplicitHToExplicit(MoleculeGraph, MolAtom[]) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
-
Convert implicit Hydrogen atoms of the specified atoms in a molecule
to explicit.
- convertImplicitHToExplicit(MoleculeGraph) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
-
Convert implicit Hydrogen atoms of the molecule to explicit.
- convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
-
Convert implicit Hydrogen atoms of the specified atoms in a molecule to explicit.
- convertImplicitLonePairsToExplicit(MoleculeGraph, MolAtom[]) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
-
Convert implicit lone pairs of the atoms of a molecule to explicit.
- convertMultiCenterSgroupsToData(Molecule) - Method in class chemaxon.marvin.io.formats.mdl.MolExport
-
Deprecated.
as of Marvin 6.1. we only export Multicenter s-groups in MOL
V3000 format
- convertPageSettingsToData(Molecule) - Method in class chemaxon.marvin.io.formats.mdl.MolExport
-
Converts page setting of multipage molecular document to data sgroups (attached data)
with field name MRV_PAGE_XXX.
- ConvertPseudoToGroupFixer - Class in chemaxon.fixers
-
A descendant of
AbstractStructureFixer which converts the pseudo
informations to contracted abbreviated groups in the molecule
- ConvertPseudoToGroupFixer() - Constructor for class chemaxon.fixers.ConvertPseudoToGroupFixer
-
- convertResult(Molecule, Molecule, StructureCheckerResult, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.AbbreviatedGroupChecker
-
This implementation does nothing.
- convertResult(Molecule, Molecule, StructureCheckerResult, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.AbstractStructureChecker
-
Handles the mapping of a cloned and expanded molecule result to the original molecule.
- convertResult(Molecule, Molecule, StructureCheckerResult, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.CircularRGroupReferenceChecker
-
This implementation does nothing.
- convertResult(Molecule, Molecule, StructureCheckerResult, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.MissingRGroupChecker
-
This implementation does nothing.
- convertResult(Molecule, Molecule, StructureCheckerResult, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.RgroupReferenceErrorChecker
-
Deprecated.
This implementation does nothing.
- convertResult(StructureCheckerResult) - Method in class chemaxon.checkers.runner.BasicCheckerRunner
-
This method provides the possibility to convert back the affected
properties of the result if there was any convert in the molecule
structure before check.
- convertResult(StructureCheckerResult) - Method in class chemaxon.checkers.runner.SketchCheckerRunner
-
This method converts the result by changing the atoms and bonds back to the original instead
of the cloned ones
- convertResult(Molecule, Molecule, StructureCheckerResult, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.UnusedRGroupChecker
-
This implementation does nothing.
- ConvertToAtomFixer - Class in chemaxon.fixers
-
A descendant of
AbstractStructureFixer which converts the aliases to
atom with atom number contained in the alias information
- ConvertToAtomFixer() - Constructor for class chemaxon.fixers.ConvertToAtomFixer
-
- ConvertToCarbonFixer - Class in chemaxon.fixers
-
- ConvertToCarbonFixer() - Constructor for class chemaxon.fixers.ConvertToCarbonFixer
-
- ConvertToCrossedDoubleBondFixer - Class in chemaxon.fixers
-
- ConvertToCrossedDoubleBondFixer() - Constructor for class chemaxon.fixers.ConvertToCrossedDoubleBondFixer
-
- ConvertToElementalFormFixer - Class in chemaxon.fixers
-
- ConvertToElementalFormFixer() - Constructor for class chemaxon.fixers.ConvertToElementalFormFixer
-
- convertToFrags() - Method in class chemaxon.struc.Molecule
-
Converts this molecule to its disconnected fragments, expanding all
S-groups and keeping disconnected Multicenter S-groups in the same fragment,
but ungroupping and separating fragments in all other types of S-groups.
- ConvertToIonicFormFixer - Class in chemaxon.fixers
-
A descendant of
AbstractStructureFixer which converts the incorrectly
drawn (connected to bond, no charge) covalent counter ion representation into
ionic form.
- ConvertToIonicFormFixer() - Constructor for class chemaxon.fixers.ConvertToIonicFormFixer
-
- ConvertToPlainDoubleBondFixer - Class in chemaxon.fixers
-
Converts non-stereo double bonds with invalid stereo mark (crossed, wiggly) to plain double bonds.
- ConvertToPlainDoubleBondFixer() - Constructor for class chemaxon.fixers.ConvertToPlainDoubleBondFixer
-
- ConvertToSingleBondFixer - Class in chemaxon.fixers
-
- ConvertToSingleBondFixer() - Constructor for class chemaxon.fixers.ConvertToSingleBondFixer
-
- convertToSmilingFormat(Molecule) - Static method in class chemaxon.formats.MFileFormatUtil
-
Tries to convert a molecule to a SMILES related format.
- convertToSmilingFormat(MProp) - Static method in class chemaxon.formats.MFileFormatUtil
-
Try to convert a property to text with a SMILES related format argument.
- convertToString(MDocument, String, int) - Static method in class chemaxon.formats.MolExporter
-
Converts the document to text format.
- convertToString(MProp, String) - Static method in class chemaxon.marvin.io.MPropHandler
-
Converts the property to text format.
- convertToString(MPropertyContainer, String) - Static method in class chemaxon.marvin.io.MPropHandler
-
Convert key of MPropertyContainer to string.
- convertToString(String, int) - Method in class chemaxon.struc.MDocument.Prop
-
- convertToString(String, int) - Method in class chemaxon.struc.MProp
-
- convertToString(String) - Method in class chemaxon.struc.MProp
-
- convertToString(String, int) - Method in class chemaxon.struc.prop.MBooleanProp
-
- convertToString(String, int) - Method in class chemaxon.struc.prop.MDoubleArrayProp
-
- convertToString(String, int) - Method in class chemaxon.struc.prop.MDoubleProp
-
- convertToString(String, int) - Method in class chemaxon.struc.prop.MHashProp
-
- convertToString(String, int) - Method in class chemaxon.struc.prop.MHCoords3DProp
-
- convertToString(String, int) - Method in class chemaxon.struc.prop.MIntegerArrayProp
-
- convertToString(String, int) - Method in class chemaxon.struc.prop.MIntegerProp
-
- convertToString(String, int) - Method in class chemaxon.struc.prop.MListProp
-
- convertToString(String, int) - Method in class chemaxon.struc.prop.MMoleculeProp
-
- convertToString(String, int) - Method in class chemaxon.struc.prop.MObjectProp
-
- convertToString(String, int) - Method in class chemaxon.struc.prop.MStringProp
-
- ConvertToWigglyDoubleBondFixer - Class in chemaxon.fixers
-
- ConvertToWigglyDoubleBondFixer() - Constructor for class chemaxon.fixers.ConvertToWigglyDoubleBondFixer
-
- convertTransform(CTransform3D, boolean) - Method in class chemaxon.struc.graphics.MRectangle
-
- COORDDEP - Static variable in class chemaxon.struc.MProp
-
Coordinate dependent property.
- COORDINATE - Static variable in class chemaxon.struc.MolBond
-
Coordinate bond flag.
- COORDINATE_BOND_ARROW_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
- COORDINATE_BOND_AT_MULTICENTER_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
- COORDINATE_BOND_AT_MULTICENTER_OFFSET - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
- COORDINATE_BOND_AT_MULTICENTER_STYLES - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
- COORDINATE_BOND_HASHED_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
- COORDINATE_BOND_SOLID_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
- COORDINATE_BOND_STYLE - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter: "coordinateBondStyle".
- COORDINATE_BOND_STYLE_AT_MULTICENTER - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter: "coordinateBondStyleAtMulticenter".
- COORDINATE_BOND_STYLE_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
- COORDINATE_BOND_STYLE_OFFSET - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
- COORDINATE_BOND_STYLES - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
- CoordinationSystemErrorChecker - Class in chemaxon.checkers
-
Detects errors of multicenter coordination systems.
- CoordinationSystemErrorChecker() - Constructor for class chemaxon.checkers.CoordinationSystemErrorChecker
-
Default constructor
- COORDS_UPDATE - Static variable in interface chemaxon.struc.sgroup.Expandable
-
Deprecated.
As of Marvin 6.2, no replacement.
Not supported feature.
- COPY_AS_FORMAT - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Default format to be selected on Copy as dialog.
- COPY_AS_IMAGE_BITMAP - Static variable in interface chemaxon.marvin.util.CopyOptConstants
-
Deprecated.
- COPY_AS_IMAGE_EMF - Static variable in interface chemaxon.marvin.util.CopyOptConstants
-
Deprecated.
- COPY_AS_OLE - Static variable in interface chemaxon.marvin.util.CopyOptConstants
-
Deprecated.
- COPY_AS_TEXT - Static variable in interface chemaxon.marvin.util.CopyOptConstants
-
Deprecated.
- COPY_OPTIONS - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Deprecated.
since 5.3.3 has no sense
- CopyOptConstants - Interface in chemaxon.marvin.util
-
Deprecated.
since 5.2.1 the whole copy-paste engine was refactored. The constants defined in this
interface either non exists in the new implementation or its value has changed. See
the constants own description for details.
- copyProperties(MBracket) - Method in class chemaxon.struc.graphics.MBracket
-
Copies line properties to another line object.
- copyProperties(MPolyline) - Method in class chemaxon.struc.graphics.MEFlow
-
- copyProperties(MPolyline) - Method in class chemaxon.struc.graphics.MPolyline
-
Copies line properties to another line object.
- correctCornersRadius(double, double) - Method in class chemaxon.struc.graphics.MRoundedRectangle
-
- countAllAtoms() - Method in class chemaxon.struc.MolAtom
-
Counts all atoms represented by this atom.
- countAllAtoms() - Method in class chemaxon.struc.Sgroup
-
Counts the total number of atoms recursively.
- countAllAtoms() - Method in class chemaxon.struc.sgroup.SgroupAtom
-
Counts all atoms represented by this atom.
- countEnumerations() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Returns the number of all enumerated structures,
no arithmetic overflow because counts in
BigInteger.
- countEnumerationsMagnitude() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Returns the magnitude (the number of decimal "digits")
of the number of all enumerated structures.
- countExpandableContractableSgroups() - Method in class chemaxon.struc.Molecule
-
Counts the expandable and contractable S-groups.
- countOrderedComponentSgroups() - Method in class chemaxon.struc.Molecule
-
Counts the ordered component S-groups.
- countRecords(MProgressMonitor, int, Runnable, int) - Method in class chemaxon.marvin.view.MDocStorage
-
Counts the total number of records and sets the size of the document storage.
- countRecordsInFraction(double, int, MProgressMonitor) - Method in class chemaxon.marvin.view.MDocStorage
-
Deprecated.
- COVALENT_HYDRATION_ERROR_REMARK - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
-
Covalent hydration error remark.
- CovalentCounterionChecker - Class in chemaxon.checkers
-
A descendant of
AbstractStructureChecker detecting covalently bonded counterions
(alkaline alcoholates, carboxylates an thio analogs).
- CovalentCounterionChecker() - Constructor for class chemaxon.checkers.CovalentCounterionChecker
-
Default constructor
- CovalentCounterionFixer - Class in chemaxon.fixers
-
- CovalentCounterionFixer() - Constructor for class chemaxon.fixers.CovalentCounterionFixer
-
Deprecated.
- covalentRadiusOf(int, int) - Static method in class chemaxon.struc.MolAtom
-
Gets the covalent radius in C-C bond length units.
- CPK_SCHEME - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
CPK color scheme in display option flags.
- CPK_SCHEME_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
CPK color scheme.
- Cr - Static variable in class chemaxon.core.ChemConst
-
- crdMolRefresh() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
-
- crdSafeRefresh() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
-
- create(byte[]) - Static method in class chemaxon.marvin.alignment.AlignmentMolecule
-
Deprecated.
- create(ShapeData, AlignmentProperties.DegreeOfFreedomType) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
-
- create(Molecule, AlignmentProperties.DegreeOfFreedomType) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
-
- create(Molecule) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D
-
- create(String, String) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Loads a plugin, first tries to load it from CLASSPATH, then from JAR.
- create(int, InputProducer) - Static method in class chemaxon.util.concurrent.processors.ConcurrentProcessors
-
- create(int, InputProducer, WorkUnitFactory) - Static method in class chemaxon.util.concurrent.processors.ConcurrentProcessors
-
- create(String) - Static method in class chemaxon.util.DotfileUtil
-
Opens a dotfile for writing.
- createArgument(T) - Static method in class chemaxon.marvin.services.ServiceArgument
-
Returns a service argument based on value
- createArgument(String, T) - Static method in class chemaxon.marvin.services.ServiceArgument
-
Returns a service argument based on value
- createArgumentAs(T, Class<T>) - Static method in class chemaxon.marvin.services.ServiceArgument
-
Returns a service argument based on value and type
- createArgumentAs(String, T, Class<T>) - Static method in class chemaxon.marvin.services.ServiceArgument
-
Returns a service argument based on value and type
- createArray(String, String, int, int) - Static method in class chemaxon.marvin.io.MPropHandler
-
Creates an array property.
- createArrayXSD(String, String, int, int) - Static method in class chemaxon.marvin.io.MPropHandler
-
Creates an array property from the XSD type.
- createAtomIterator() - Method in class chemaxon.util.iterator.IteratorFactory
-
Constructs an atom iterator for the specified molecule of the factory
according to the atom related behavior set in the factory.
- createAtomNeighbourIterator(MolAtom) - Method in class chemaxon.util.iterator.IteratorFactory
-
Constructs an iterator to get the atom neighbours of the specified atom.
- createBHtab() - Method in class chemaxon.struc.MoleculeGraph
-
Deprecated.
As of Marvin 6.2, no replacement.
No replacement.
- createBHtab() - Method in class chemaxon.struc.RxnMolecule
-
Creates the graph union's bond table extended with implicit hydrogen
atoms.
- createBondIterator() - Method in class chemaxon.util.iterator.IteratorFactory
-
Constructs a bond iterator for the specified molecule of the factory
according to bond related behavior set in the factory.
- createBondNeighbourIterator(MolAtom) - Method in class chemaxon.util.iterator.IteratorFactory
-
Constructs an iterator to get the bonds connecting to the specified atom.
- createBracket(Sgroup, DPoint3[], int) - Static method in class chemaxon.marvin.util.CleanUtil
-
- createChemicalTermsTextPane() - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Creates a
JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
Default help text will be shown in empty textpane.
- createChemicalTermsTextPane(CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
- createChemicalTermsTextPane(boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Creates a
JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
- createChemicalTermsTextPane(boolean, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
- createChemicalTermsTextPane(boolean, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
- createChemicalTermsTextPane(boolean, boolean, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
- createChemicalTermsTextPane(boolean, boolean, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
- createChemicalTermsTextPane(String) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
- createChemicalTermsTextPane(String, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
- createChemicalTermsTextPane(String, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
- createChemicalTermsTextPane(String, boolean, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
- createChemicalTermsTextPane(String, boolean, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
- createChemicalTermsTextPane(String, boolean, boolean, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
- createChemicalTermsTextPane(String, boolean, boolean, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
- createChemicalTermsTextPane(String, String) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
- createChemicalTermsTextPane(String, String, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
- createChemicalTermsTextPane(String, String, boolean, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
- createChemicalTermsTextPane(String, String, boolean, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
- createChemicalTermsTextPane(String, String, boolean, String) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
- createChemicalTermsTextPane(String, String, boolean, String, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
- createChemicalTermsTextPane(String, String, boolean, String, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
- createChemicalTermsTextPane(String, String, boolean, String, boolean, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
- createChemicalTermsTextPane(CodeAssistFactory.CodeAssistConfiguration) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Creates a
JTextPane instance with code assist capabilities.
- createChemicalTermsTextPane(String, String, boolean, String, boolean, CodeAssistDataProvider.Context, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Creates a
JTextPane instance with code assist capabilities.
- createCHtab() - Method in class chemaxon.struc.MoleculeGraph
-
Creates the connection table extended with implicit hydrogen atoms.
- createCHtab() - Method in class chemaxon.struc.RxnMolecule
-
Creates the graph union's connection table extended with implicit
hydrogen atoms.
- createCompatible(MTextAttributes, MTextAttributes, MFont, MTextAttributes.MFontCreator) - Method in class chemaxon.struc.graphics.MTextAttributes
-
- createConstantFromString(String, Class<?>) - Static method in class chemaxon.marvin.services.ServiceArgument
-
- createDefaultParameterPanel(String, Component) - Static method in class chemaxon.marvin.plugin.PluginFactory
-
Creates default parameter panel based on XML config.
- createDefaultParameterPanel(Class, String, Component) - Static method in class chemaxon.marvin.plugin.PluginFactory
-
- createDehydrogenizedReadOnlyGraph() - Method in class chemaxon.struc.MoleculeGraph
-
Creates a dehydrogenized version of the molecule.
- createEMF(String, String) - Static method in class chemaxon.util.ImageExportUtil
-
Creates a .NET based EMF picture.
- createExportModule() - Method in class chemaxon.formats.MFileFormat
-
Creates the export module.
- createExportModule(String) - Method in class chemaxon.formats.MFileFormat
-
Creates the export module.
- createExportModule(String) - Static method in class chemaxon.formats.MFileFormatUtil
-
Creates an export module for the specified format.
- createExportModule(String, String) - Static method in class chemaxon.formats.MFileFormatUtil
-
Creates an export module for the specified format with the specified encoding.
- createGData() - Method in class chemaxon.marvin.space.SurfaceComponent
-
- createGearch() - Method in class chemaxon.struc.Molecule
-
- createGearch() - Method in class chemaxon.struc.MoleculeGraph
-
- createGearch() - Method in class chemaxon.struc.RgMolecule
-
- createGearch() - Method in class chemaxon.struc.RxnMolecule
-
- createGearch() - Method in class chemaxon.struc.SelectionMolecule
-
- createGroup() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
- createImage(Buffer, int, int) - Method in class chemaxon.marvin.space.GraphicScene
-
- createImageExporterParameter(Properties, String, MDocument) - Static method in class chemaxon.util.ImageExportUtil
-
Creates the Image Exporter parameter String based on the values in the Properties object.
- createImportMod(MolInputStream) - Static method in class chemaxon.marvin.io.MRecordImporter
-
Creates an importer for the specified molecule input stream.
- createImportMod(String) - Static method in class chemaxon.marvin.io.MRecordImporter
-
Creates an importer for the specified molecule format.
- createImportModule() - Method in class chemaxon.formats.MFileFormat
-
Creates the molecule import module.
- createInput() - Method in class chemaxon.util.concurrent.marvin.ReusableInputProducer
-
- createLicenseManagerPanel() - Static method in class chemaxon.license.LicenseManager
-
Creates the main panel which is used for end-user license managing.
- createMenu(ResourceBundle, String) - Static method in class chemaxon.marvin.beans.MarvinPane
-
Deprecated.
as of Marvin 3.3.1, replaced by SwingUtil.createMenu
- createMenu(ResourceBundle, String) - Static method in class chemaxon.marvin.util.SwingUtil
-
Utility method to create a menu with a label specified as a resource.
- createMenu(ResourceBundle, String, boolean) - Static method in class chemaxon.marvin.util.SwingUtil
-
Creates a menu with a label specified as a resource.
- createMenuItem(ResourceBundle, String, Class<?>, boolean) - Static method in class chemaxon.marvin.util.SwingUtil
-
Creates a menu item with a label specified as a resource.
- createMenuItem(ResourceBundle, String, boolean) - Static method in class chemaxon.marvin.util.SwingUtil
-
Creates a menu with a label specified as a resource.
- createMenuItem(ResourceBundle, String) - Static method in class chemaxon.marvin.util.SwingUtil
-
Creates a menu with a label specified as a resource.
- createMessagePane(String) - Static method in class chemaxon.marvin.util.SwingUtil
-
Creates a message pane with HTML text content.
- createMMoleculeProp(String) - Static method in class chemaxon.marvin.io.MPropHandler
-
- createModifiedInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.logPPlugin
-
Returns the major tautomeric form of the molecule.
- createModifiedInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
-
Returns the molecule form with largest distribution.
- createModifiedInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
-
Returns the major tautomeric form of the molecule.
- createModifiedInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Returns the canonical tautomeric form of the molecule.
- createModifiedInputMolecule(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns the modified input molecule (e.g.
- createMol() - Method in class chemaxon.formats.MolImporter
-
Creates a target molecule object for import.
- createMol() - Method in class chemaxon.marvin.io.formats.mdl.MolImport
-
Creates a new target molecule object.
- createMol() - Method in class chemaxon.marvin.io.MolImportModule
-
Creates a new target molecule object for the import.
- createMol() - Method in class chemaxon.marvin.io.MRecordImporter
-
Creates an empty target molecule for import.
- createMolConverter(InputStream, OutputStream, String[], int[]) - Static method in class chemaxon.formats.MolConverter
-
Creates a MolConverter instance with the attributes specified in the
parameters.
- createMolecule() - Method in class chemaxon.struc.Sgroup
-
Creates a molecule object that contains only this group.
- createMolecule(Molecule) - Method in class chemaxon.struc.Sgroup
-
Creates a cloned sgroup instance and a molecule object that contains only
this sgroup.
- createMolecule() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Creates a molecule object that contains only one
SuperatomSgroup
identical to this one.
- createMoleculeFromInputStream(InputStream) - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
-
Helper function to get Molecule or MacroMolecule from the given InputStream with MolImporter.
- createMoleculeIterator(Collection<Molecule>) - Static method in class chemaxon.util.iterator.MoleculeIteratorFactory
-
- createMoleculeIterator(Molecule[]) - Static method in class chemaxon.util.iterator.MoleculeIteratorFactory
-
- createMolIfNeeded() - Method in class chemaxon.marvin.io.MRecordImporter
-
Creates an empty target molecule for import if non-concurrent mode,
returns null if concurrent mode.
- createNeighbourBonds(Molecule, MolBond, boolean) - Static method in class chemaxon.checkers.StructureCheckerHelper
-
This method returns a
List of
MolBond which contains all
bonds which are in isNeighbour relation with the
MolBond instance
represented by parameter bond
- createNewCell() - Method in class chemaxon.marvin.space.GraphicScene
-
Sets an empty cell to be the active cell.
- createNext() - Method in class chemaxon.struc.graphics.MTextAttributes
-
Creates identical attributes for the next section.
- createParameterPanel() - Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
-
Creates the parameter panel.
- createPooledWu(int, InputProducer, WorkUnitFactory) - Static method in class chemaxon.util.concurrent.processors.ConcurrentProcessors
-
For test only
- createReaction(Molecule, DPoint3[], int) - Static method in class chemaxon.struc.RxnMolecule
-
Creates a reaction.
- createReaction(MoleculeGraph, DPoint3[]) - Static method in class chemaxon.struc.RxnMolecule
-
Creates a reaction.
- createRecognizer() - Method in class chemaxon.formats.MFileFormat
-
Creates a recognizer module.
- createRecognizer(String) - Method in class chemaxon.formats.MFileFormat
-
- createRecordReader(MolInputStream, String) - Method in class chemaxon.formats.MFileFormat
-
Creates the record reader.
- createRecordReader(InputStream, String) - Static method in class chemaxon.formats.MFileFormatUtil
-
Creates a record reader for an input stream.
- createRecordReader(InputStream, String, String, String) - Static method in class chemaxon.formats.MFileFormatUtil
-
Creates a record reader for an input stream.
- createResult(Molecule, List<MolAtom>) - Method in class chemaxon.checkers.AliasChecker
-
- createResult(Molecule, List<MolAtom>) - Method in class chemaxon.checkers.AtomChecker
-
- createResult(Molecule, List<MolAtom>) - Method in class chemaxon.checkers.AtomQueryPropertyChecker
-
- createResult(Molecule, List<MolBond>) - Method in class chemaxon.checkers.BondChecker
-
- createResult(Molecule, List<E>) - Method in class chemaxon.checkers.ComponentChecker
-
- createResult(Molecule, List<MolAtom>) - Method in class chemaxon.checkers.PseudoAtomChecker
-
- createResult(Molecule, List<StructureCheckerResult>) - Method in class chemaxon.checkers.ReactionChecker
-
This method a merged StructureCheckerResult from the
List
of
StructureCheckerResult which contains the problems of the components in
the reaction
- createResultView(String, MolPanel) - Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
-
- createRgComponentIterator() - Method in class chemaxon.util.iterator.IteratorFactory
-
Constructs an rgroup definition component iterator for the specified
molecule of the factory if the molecule is an RgMolecule, an empty
iterator otherwise.
- createRotationAboutBond(MolBond, double) - Static method in class chemaxon.marvin.util.CleanUtil
-
Creates a rotation transformation about a bond.
- createRxnComponentIterator() - Method in class chemaxon.util.iterator.IteratorFactory
-
Constructs a reaction component iterator for the specified molecule of
the factory if the molecule is an RxnMolecule, an empty iterator
otherwise.
- createSavedCoordsArray(MoleculeGraph) - Static method in class chemaxon.marvin.util.CleanUtil
-
Creates an empty array for the atomic coordinates of a structure.
- createScalar(String, String) - Static method in class chemaxon.marvin.io.MPropHandler
-
Creates a scalar property.
- createScalar(String, String, MProgressMonitor) - Static method in class chemaxon.marvin.io.MPropHandler
-
Creates a scalar property.
- createScalarXSD(String, String) - Static method in class chemaxon.marvin.io.MPropHandler
-
Creates a scalar property from the XSD type.
- createSelectionPanel(int) - Method in class chemaxon.marvin.space.MSpaceEasy
-
Adds the basic MarvinSpace selection panel to the container.
- createSelectionPanelAndProgressBar() - Method in class chemaxon.marvin.space.MSpaceEasy
-
Adds the basic MarvinSpace selection panel to the container.
- createSgroupIterator() - Method in class chemaxon.util.iterator.IteratorFactory
-
Constructs an s-group iterator for the specified molecule of the factory.
- createSmolecule() - Method in class chemaxon.struc.MoleculeGraph
-
Creates a
Smolecule represenation of this molecule.
- createSpacePanel(Molecule[]) - Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
-
Creates space panel with given molecules,
creates colored surface to each molecule.
- createStandardizedMolecule(Molecule, boolean) - Method in class chemaxon.marvin.calculations.ResonancePlugin
-
- createStandardizedMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ResonancePlugin
-
Creates standardized molecule, the original input molecule is cloned
only if the original molecule should not be modified.
- createStandardizedMolecule(Molecule, boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Deprecated.
- createStandardizedMolecule(Molecule) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Creates standardized molecule, the original input molecule is cloned
only if the original molecule should not be modified.
- createStandardizedMolecule(Molecule, boolean) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
- createStandardizedMolecule(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Creates standardized molecule, the original input molecule is cloned.
- createSubPanel(String) - Static method in class chemaxon.marvin.util.SwingUtil
-
Creates a sub-panel with a title.
- createTopLeftConstraints() - Static method in class chemaxon.marvin.util.SwingUtil
-
Creates GridBagConstraints for the top left component.
- createViewPanel(Molecule[]) - Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
-
Creates view panel with given molecules,
places molecule properties in formatted texts.
- createViewPanel(Molecule[], int, int, int, int) - Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
-
Creates view panel with given molecules,
places molecule properties in formatted texts.
- createVisitor(ImmutableList.Builder<T>) - Method in class com.chemaxon.calculations.stereoanal.filters.AbstractStereoFilter
-
Constructs the specified visitor implementation.
- createVisitor(ImmutableList.Builder<AtropStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.atrop.AtropFilter
-
Constructs the specified visitor implementation.
- createVisitor(ImmutableList.Builder<AtropStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.atrop.KnownAtropFilter
-
Constructs the specified visitor implementation.
- createVisitor(ImmutableList.Builder<AtropStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.atrop.UnknownAtropFilter
-
Constructs the specified visitor implementation.
- createVisitor(ImmutableList.Builder<AxialStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.axial.AxialFilter
-
Constructs the specified visitor implementation.
- createVisitor(ImmutableList.Builder<AxialStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.axial.KnownAxialFilter
-
Constructs the specified visitor implementation.
- createVisitor(ImmutableList.Builder<AxialStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.axial.UnknownAxialFilter
-
Constructs the specified visitor implementation.
- createVisitor(ImmutableList.Builder<CisTransStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.cistrans.CisDoubleBondFilter
-
Constructs the specified visitor implementation.
- createVisitor(ImmutableList.Builder<CisTransStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.cistrans.CisTransDoubleBondFilter
-
Constructs the specified visitor implementation.
- createVisitor(ImmutableList.Builder<CisTransStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.cistrans.TransDoubleBondFilter
-
Constructs the specified visitor implementation.
- createVisitor(ImmutableList.Builder<StereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.HasAttachedDataFilter
-
Constructs the specified visitor implementation.
- createVisitor(ImmutableList.Builder<TetrahedralStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.tetrahedral.KnownResolvedTetrahedralFilter
-
Constructs the specified visitor implementation.
- createVisitor(ImmutableList.Builder<TetrahedralStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.tetrahedral.RacemicTetrahedralFilter
-
Constructs the specified visitor implementation.
- createVisitor(ImmutableList.Builder<TetrahedralStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.tetrahedral.TetrahedralFilter
-
Constructs the specified visitor implementation.
- createVisitor(ImmutableList.Builder<TetrahedralStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.tetrahedral.UnknownResolvedTetrahedralFilter
-
Constructs the specified visitor implementation.
- createVisitor(ImmutableList.Builder<TetrahedralStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.tetrahedral.UnresolvedTetrahedralFilter
-
Constructs the specified visitor implementation.
- createWorkUnit() - Method in class chemaxon.util.concurrent.marvin.CompositeWorkUnitFactory
-
- createWorkUnit() - Method in interface chemaxon.util.concurrent.WorkUnitFactory
-
- CRITICAL_ERROR_MSG - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
-
Critical error message.
- cross(DPoint3, DPoint3) - Static method in class chemaxon.struc.DPoint3
-
Calculates the cross product of the two vectors
- CrossedDoubleBondChecker - Class in chemaxon.checkers
-
A descendant of
BondChecker for the detection of unspecified double bonds
represented by crossed bond type.
- CrossedDoubleBondChecker() - Constructor for class chemaxon.checkers.CrossedDoubleBondChecker
-
Default constructor
- CrossedDoubleBondFixer - Class in chemaxon.fixers
-
- CrossedDoubleBondFixer() - Constructor for class chemaxon.fixers.CrossedDoubleBondFixer
-
Deprecated.
- Cs - Static variable in class chemaxon.core.ChemConst
-
- CSMDL_IN - Static variable in class chemaxon.formats.MFileFormat
-
ChemAxon Compressed Molfiles, RGfiles, Rgfiles, SDfiles or RDfiles.
- CSMOL_OUT - Static variable in class chemaxon.formats.MFileFormat
-
ChemAxon Compressed Molfiles and Rgfiles.
- CSRDF - Static variable in class chemaxon.formats.MFileFormat
-
ChemAxon Compressed RDfiles.
- CSRXN_OUT - Static variable in class chemaxon.formats.MFileFormat
-
ChemAxon Compressed Rxnfiles.
- CSSDF_OUT - Static variable in class chemaxon.formats.MFileFormat
-
ChemAxon Compressed SDfiles.
- ctab - Variable in class chemaxon.struc.MoleculeGraph
-
Connection table.
- CTransform3D - Class in chemaxon.struc
-
3D transformation matrix.
- CTransform3D(CTransform3D) - Constructor for class chemaxon.struc.CTransform3D
-
Copy constructor.
- CTransform3D() - Constructor for class chemaxon.struc.CTransform3D
-
Constructs an identity transformation.
- CTSPECIFIC_H - Static variable in class chemaxon.struc.MolAtom
-
Deprecated.
As of Marvin 5.11
Graph invariants are checked by default
when calculating CIS/TRANS stereo, so this option is out of
use.
- CTUMASK - Static variable in interface chemaxon.struc.StereoConstants
-
Double bond stereo mask.
- CTUNKNOWN - Static variable in interface chemaxon.struc.StereoConstants
-
Deprecated.
As of Marvin 6.1,
Usage:
In the specified methods the CIS|TRANS or
CIS|TRANS|CTUNSPEC values are used instead.
- CTUNSPEC - Static variable in interface chemaxon.struc.StereoConstants
-
Unspecified double bond.
- Cu - Static variable in class chemaxon.core.ChemConst
-
- CubeRecognizer - Class in chemaxon.formats.recognizer
-
Deprecated.
as of Marvin 2014.07.21.0 intended for internal use only
- CubeRecognizer() - Constructor for class chemaxon.formats.recognizer.CubeRecognizer
-
Deprecated.
- currentBond - Variable in class chemaxon.util.iterator.IteratorFactory.NeighbourIterator
-
Current bond pointer of the iterator.
- cursorDown(boolean) - Method in class chemaxon.struc.graphics.MTextBox
-
Move the cursor down.
- cursorToRowEnd(boolean) - Method in class chemaxon.struc.graphics.MTextBox
-
- cursorToRowStart(boolean) - Method in class chemaxon.struc.graphics.MTextBox
-
- cursorUp(boolean) - Method in class chemaxon.struc.graphics.MTextBox
-
Moves the cursor up.
- CUSTOM_NAME - Static variable in class chemaxon.checkers.StructureCheckerDescriptor
-
custom name property
- CUSTOMIZATION_ENABLED - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter: "customizationEnabled".
- customPaletteColors - Variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- CXSMARTS - Static variable in class chemaxon.formats.MFileFormat
-
ChemAxon Extended SMARTS.
- CXSMILES - Static variable in class chemaxon.formats.MFileFormat
-
ChemAxon Extended SMILES.
- cyclomaticNumber() - Method in class chemaxon.calculations.TopologyAnalyser
-
Calculates the smallest number of graph edges which must be removed such
that no circuit remains.
- Ga - Static variable in class chemaxon.core.ChemConst
-
- gatherBaseColors() - Static method in class chemaxon.marvin.util.ColorGenerator
-
Creates a
Collection of the base colors.
These colors are:
- black
- white
- red
- green
- blue
- cyan
- magenta
- yellow.
- gatherBaseColorsAndBaseMoleculeColors(boolean) - Static method in class chemaxon.marvin.util.ColorGenerator
-
Creates a
Collection of the base Molecule RGB colors and base colors.
These colors are the atom label RGB colors of:
- H
- C
- N
- O
- S
- F
- P
- Cl
- Br
- I.
- gatherBaseMoleculeColors(boolean) - Static method in class chemaxon.marvin.util.ColorGenerator
-
Creates a
Collection of the base Molecule RGB colors.
These colors are the atom label RGB colors of:
- H
- C
- N
- O
- S
- F
- P
- Cl
- Br
- I.
and
- black
- white
- gatherBlackAndWhite() - Static method in class chemaxon.marvin.util.ColorGenerator
-
- GAUSSIAN_CUBE - Static variable in class chemaxon.formats.MFileFormat
-
Gaussian Cube files.
- GAUSSIAN_INPUT - Static variable in class chemaxon.formats.MFileFormat
-
Gaussian Input Format.
- GAUSSIAN_INPUTZ - Static variable in class chemaxon.formats.MFileFormat
-
Gaussian Input Format: Z-matrix.
- GAUSSIAN_OUTPUT - Static variable in class chemaxon.formats.MFileFormat
-
Gaussian output format.
- Gd - Static variable in class chemaxon.core.ChemConst
-
- Ge - Static variable in class chemaxon.core.ChemConst
-
- gearch - Variable in class chemaxon.struc.MoleculeGraph
-
- gearch() - Method in interface chemaxon.struc.Smolecule
-
Gets graph search algorithms.
- generate(int, Molecule, boolean, boolean) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
-
- generate(int, int, Molecule, boolean, boolean) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
-
- generateBracketCoords(Sgroup, int) - Static method in class chemaxon.marvin.util.CleanUtil
-
Generates brackets with coordinates for a specified S-group.
- generateBracketCoords(Sgroup, int, boolean) - Static method in class chemaxon.marvin.util.CleanUtil
-
Generates brackets with coordinates for a specified S-group.
- generateColors(int, Collection<Color>) - Static method in class chemaxon.marvin.util.ColorGenerator
-
Generates the specified number of different
Colors, which are different enough from
the specified forbidden colors.
- generateColors(int) - Static method in class chemaxon.marvin.util.ColorGenerator
-
Generates the specified number of different
Colors, with no forbidden colors.
- generateData(int, Molecule, boolean, boolean) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
-
Deprecated.
- generateEMFToFile(String, String, String) - Static method in class chemaxon.util.ImageExportUtil
-
Creates a new .NET based EMF picture and saves it to the given file.
- generateRawDisplayList() - Method in class chemaxon.marvin.space.SurfaceComponent
-
- GEOMETRY_PLUGIN_GROUP - Static variable in class chemaxon.license.LicenseManager
-
Identifier of plugin: Geometry Plugin Group
- GeometryPlugin - Class in chemaxon.marvin.calculations
-
Plugin class for geometric properties calculations.
- GeometryPlugin() - Constructor for class chemaxon.marvin.calculations.GeometryPlugin
-
Constructor.
- get(String) - Method in class chemaxon.struc.MPropertyContainer
-
Gets a property object.
- get(int) - Method in class chemaxon.struc.prop.MHashProp
-
Gets a value.
- get(String) - Method in class chemaxon.struc.prop.MHashProp
-
Gets a value.
- get(int) - Method in class chemaxon.struc.prop.MListProp
-
Gets the specified element.
- get3DMolecule() - Method in class chemaxon.marvin.calculations.MSAPlugin
-
Returns the 3D molecule used in 3D surface area calculation.
- getAbsoluteCellIndex(int) - Method in class chemaxon.marvin.beans.MViewPane
-
Determines the absolute cell index of a visible cell
- getAbsoluteCellIndex(JComponent) - Method in class chemaxon.marvin.beans.MViewPane
-
Determines in which cell the specified component is located.
- getAbsoluteLabelVisible() - Method in class chemaxon.marvin.common.UserSettings
-
Are Absolute labels visible?
- getAbsoluteXY() - Method in class chemaxon.struc.sgroup.DataSgroup
-
Gets the X and Y coordinates of the data label in the molecule's
coordinate system, considering absolute/relative placement.
- getAbundance(int, int) - Static method in class chemaxon.struc.PeriodicSystem
-
Natural abundance of the isotope
- getAcceptorAtomCount() - Method in class chemaxon.marvin.calculations.HBDAPlugin
-
Returns the overall acceptor atom count (without multiplicity) in the molecule.
- getAcceptorCount(int) - Method in class chemaxon.marvin.calculations.HBDAPlugin
-
Returns the atomic acceptor count corresponding to the specified atom index.
- getAcceptorCount() - Method in class chemaxon.marvin.calculations.HBDAPlugin
-
Returns the overall acceptor count (with multiplicity) in the molecule.
- getAccuracyMode() - Method in class chemaxon.marvin.alignment.MMPAlignmentProperties
-
- getActionMap() - Method in class chemaxon.struc.graphics.MTextBox
-
Returns the ActionMap used to determine what Action to fire for
particular KeyStroke binding.
- getActionStringTokens() - Method in class chemaxon.checkers.StructureCheckerDescriptor
-
Gets the action string token of the checker
- getActionStringTokens() - Method in class chemaxon.fixers.StructureFixerDescriptor
-
Gets the action string token of the fixer
- getActiveCell() - Method in class chemaxon.marvin.space.GraphicScene
-
Returns the active cell of the scene.
- getActiveCellIndex() - Method in class chemaxon.marvin.space.GraphicScene
-
Returns the index of the active cell.
- getAgent(int) - Method in class chemaxon.struc.RxnMolecule
-
Gets an agent.
- getAgentCount() - Method in class chemaxon.struc.RxnMolecule
-
Gets the number of agents.
- getAgents() - Method in class chemaxon.struc.RxnMolecule
-
Gets all agents in an array.
- getAlias() - Method in class chemaxon.marvin.services.ServiceArgument
-
Returns the argument alias.
- getAliasstr() - Method in class chemaxon.struc.MolAtom
-
Gets the alias string or pseudo atom type string for pseudo atoms.
- getAlignedMoleculesAsFragments() - Method in class chemaxon.marvin.alignment.Alignment
-
- getAlignedMoleculesAsFragments() - Method in class chemaxon.marvin.alignment.PairwiseAlignment
-
- getAlignedMoleculesAsFragments() - Method in interface chemaxon.marvin.alignment.PairwiseComparison
-
After the similarity calculation the final orientations and conformations
can be retrieved as a single molecule.
- getAlignedMoleculesAsFragments() - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D
-
- getAlignedQuery() - Method in class chemaxon.marvin.alignment.PairwiseAlignment
-
- getAlignedQuery() - Method in interface chemaxon.marvin.alignment.PairwiseComparison
-
- getAlignedQuery() - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D
-
- getAlignedTarget() - Method in class chemaxon.marvin.alignment.PairwiseAlignment
-
- getAlignedTarget() - Method in interface chemaxon.marvin.alignment.PairwiseComparison
-
- getAlignedTarget() - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D
-
- getAlignedWithNewCoordinates() - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
-
- getAlignmentMode() - Method in class chemaxon.util.HitColoringAndAlignmentOptions
-
Returns the alignment mode.
- getAlignScaffold() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Gets the scaffold aligning mode
- getAliphaticAtomCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns the aliphatic atom count.
- getAliphaticBondCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns the aliphatic bond count.
- getAliphaticRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns the aliphatic ring count.
- getAliphaticRingCount(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns the number of aliphatic rings (SSSR smallest set of smallest
rings) of a given size in the molecule.
- getAliphaticRingCountOfSize(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
- getAliphaticRings() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Identifies the aliphatic rings in the molecule.
- getAliphaticRings(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Indentifies aliphatic rings in the molecule having a given size (number
of atoms).
- getAllAtomCount() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
-
Returns the atom count (including implicit hydrogens).
- getAllAtomCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns the atom count.
- getAllAttachAtoms() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Gets the attachment atoms (atoms having attachment point).
- getAllComponents(Class) - Method in class chemaxon.marvin.space.GraphicScene
-
- getAllFragments() - Method in class chemaxon.struc.RxnMolecule
-
Gets the list of reaction fragments (product, reactant, agent components)
that build up this reaction.
- getAllMolecules() - Method in class chemaxon.struc.MDocument
-
Gets an array containing all molecule objects.
- getAllNonEmptyMolecules() - Method in class chemaxon.struc.MDocument
-
Gets an array containing all non-empty molecule objects.
- getAllObjects() - Method in class chemaxon.struc.MDocument
-
Gets all objects stored in this document and from the chemical structure of the document.
- getAllObjects() - Method in class chemaxon.struc.Molecule
-
- getAllObjects() - Method in class chemaxon.struc.RgMolecule
-
- getAllObjects() - Method in class chemaxon.struc.RxnMolecule
-
- getAllPositions() - Method in class chemaxon.naming.DocumentExtractor.Hit
-
Deprecated.
- getAngle(int, int, int) - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
Returns the angle of 3 atoms.
- getAngle(int[]) - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
Returns the angle of 3 atoms.
- getAngleCheckerResult() - Method in class chemaxon.checkers.result.BondAngleCheckerResult
-
Returns the internal representation of the angle checker result, which contains all information required
to fix bond angle errors.
- getAnimated() - Method in class chemaxon.marvin.beans.MViewPane
-
Gets index of animated cells of the table (or simple viewer).
- getAnimDelay() - Method in class chemaxon.marvin.beans.MViewPane
-
Gets the repeat delay for animations.
- getAnimFPS() - Method in class chemaxon.marvin.beans.MViewPane
-
Gets the frames per second for animations.
- getAnyBondStyles() - Method in class chemaxon.marvin.MolPrinter
-
Gets the any bond style.
- getArcAngle() - Method in class chemaxon.struc.graphics.MPolyline
-
Gets the central angle of the arc.
- getArcCenter(DPoint3, DPoint3, double) - Static method in class chemaxon.struc.graphics.MPolyline
-
Returns the arc center.
- getArcHeight() - Method in class chemaxon.struc.graphics.MRoundedRectangle
-
- getArcRadius(CTransform3D) - Method in class chemaxon.struc.graphics.MPolyline
-
Gets the arc radius.
- getArcRadius(DPoint3, DPoint3, double) - Static method in class chemaxon.struc.graphics.MPolyline
-
- getArcWidth() - Method in class chemaxon.struc.graphics.MRoundedRectangle
-
- getAromataType() - Method in class chemaxon.checkers.result.AromaticityCheckerResult
-
Returns the type of the aromatization
- getAromaticAndAliphaticRings(int, boolean, boolean, int, int) - Method in class chemaxon.struc.MoleculeGraph
-
Returns the aromatic and or aliphatic ring atom indexes.
Note: This method does not aromatize the already aromatized rings.
- getAromaticAtomCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns the aromatic atom count.
- getAromaticBondCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns the aromatic bond count.
- getAromaticRingCharge(int) - Method in class chemaxon.marvin.calculations.ChargePlugin
-
Returns the total partial charge of the smallest aromatic ring
containing the specified atom.
- getAromaticRingCharge(int, int) - Method in class chemaxon.marvin.calculations.ChargePlugin
-
Returns the partial charge of the smallest aromatic ring
containing the specified atom.
- getAromaticRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns the aromatic ring count.
- getAromaticRingCount(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns the number of aromatic rings (SSSR smallest set of smallest
rings) of a given size in the molecule.
- getAromaticRingCountOfSize(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
- getAromaticRings() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Identifies the aromatic rings in the molecule.
- getAromaticRings(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Indentifies aromatic rings in the molecule having a given size (number
of rings).
- getAromaticSystemCharge(int) - Method in class chemaxon.marvin.calculations.ChargePlugin
-
Returns the total partial charge of the aromatic system
containing the specified atom.
- getAromaticSystemCharge(int, int) - Method in class chemaxon.marvin.calculations.ChargePlugin
-
Returns the partial charge of the aromatic system
containing the specified atom.
- getAromatizedStructures() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Returns the enumerated structures in aromatized form.
- getAromatizeMethod() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the aromatize method.
- getAromType() - Method in class chemaxon.checkers.AromaticityErrorChecker
-
Returns the aromType
- getArrayFlags() - Method in interface chemaxon.struc.Smolecule
-
Gets info about the used arrays.
- getArrowAsProperty() - Method in class chemaxon.struc.RxnMolecule
-
Gets the properties (type, endpoint coordinates) of the reaction arrow in
this reaction.
- getArrowFlags(int) - Method in class chemaxon.struc.graphics.MPolyline
-
Gets the arrow flags.
- getArrowLength(int) - Method in class chemaxon.struc.graphics.MPolyline
-
Gets the arrow head length.
- getArrowWidth(int) - Method in class chemaxon.struc.graphics.MPolyline
-
Gets the arrow head width.
- getASA() - Method in class chemaxon.marvin.calculations.MSAPlugin
-
Returns water accessible surface area calculated using a radius of 1.4 A for the water molecule.
- getASAHydrophobic() - Method in class chemaxon.marvin.calculations.MSAPlugin
-
Returns water accessible surface area of all hydrophobic (|qi|<0.125) atoms.
- getASANegative() - Method in class chemaxon.marvin.calculations.MSAPlugin
-
Returns water accessible surface area of all atoms with negative partial charge (strictly less than 0).
- getASAPlus() - Method in class chemaxon.marvin.calculations.MSAPlugin
-
Returns water accessible surface area of all atoms with positive partial charge (strictly greater than 0).
- getASAPolar() - Method in class chemaxon.marvin.calculations.MSAPlugin
-
Returns water accessible surface area of all polar (|qi|>=0.125) atoms.
- getAscent(Graphics, FontMetrics) - Method in class chemaxon.struc.graphics.MTextDocument.Portion
-
Gets the ascent of this portion.
- getAssociatedComponents() - Method in class chemaxon.marvin.space.GraphicComponent
-
Returns an Iterator that can enumerate the components
associated to (depending on) this component.
- getAssociatedNonQueryFormat() - Method in class chemaxon.formats.MFileFormat
-
Gets the associated non-query format.
- getAssociatedQueryFormat() - Method in class chemaxon.formats.MFileFormat
-
Gets the associated query format.
- getAsymmetricAtomCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns the number of asymmetric atoms.
- getAsymmetricAtoms() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Determines the asymmetric atoms.
- getAtno() - Method in class chemaxon.struc.MolAtom
-
Gets the atomic number.
- getAtom() - Method in class chemaxon.jep.context.AtomContext
-
Returns the input atom index.
- getAtom(Object) - Static method in class chemaxon.struc.graphics.MEFlow
-
Gets the atom at the terminus of an arrow.
- getAtom() - Method in class chemaxon.struc.graphics.MEFlowBasePoint
-
Gets the atom.
- getAtom(int) - Method in class chemaxon.struc.MoleculeGraph
-
Gets the nth atom.
- getAtom(int) - Method in class chemaxon.struc.RgMolecule
-
Gets a node in the graph union.
- getAtom(int) - Method in class chemaxon.struc.RxnMolecule
-
Gets a node.
- getAtom(int) - Method in class chemaxon.struc.Sgroup
-
Gets an atom in the S-group.
- getAtom1() - Method in class chemaxon.struc.MolBond
-
Gets the first endpoint.
- getAtom1(int) - Method in interface chemaxon.struc.Smolecule
-
Gets the index of the first atom of the specified bond.
- getAtom2() - Method in class chemaxon.struc.MolBond
-
Gets the second endpoint.
- getAtom2(int) - Method in interface chemaxon.struc.Smolecule
-
Gets the index of the second atom of the specified bond.
- getAtomArray() - Method in class chemaxon.struc.graphics.MAtomSetPoint
-
- getAtomArray() - Method in class chemaxon.struc.MoleculeGraph
-
Creates an array of atoms.
- getAtomArray() - Method in class chemaxon.struc.Sgroup
-
Gets the array of atoms in the S-group.
- getAtomCount() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
-
- getAtomCount(int) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
-
Returns the number of atoms with given atomic number
(including its isotopes).
- getAtomCount(int, int) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
-
Returns the number of atoms with given atomic number
in the molecule isotope with the specified mass number.
- getAtomCount() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns the number of atoms in the input molecule.
- getAtomCount(boolean) - Method in class chemaxon.marvin.space.MoleculeComponent
-
Returns the number of atoms in the molecule with arbitrarily enumerating hydrogens.
- getAtomCount() - Method in interface chemaxon.struc.Incomplecule
-
Gets the number of atoms.
- getAtomCount() - Method in class chemaxon.struc.MoleculeGraph
-
Gets the number of atoms.
- getAtomCount(int) - Method in class chemaxon.struc.MoleculeGraph
-
Gets the number of atoms with the given atomic number.
- getAtomCount() - Method in class chemaxon.struc.RgMolecule
-
Gets the number of nodes in the root structure.
- getAtomCount(int) - Method in class chemaxon.struc.RgMolecule
-
Gets the number of atoms with the given atomic number in the root
structure.
- getAtomCount() - Method in class chemaxon.struc.RxnMolecule
-
Returns the number of nodes in the graph union.
- getAtomCount(int) - Method in class chemaxon.struc.RxnMolecule
-
Gets the number of atoms with the given atomic number in the unified
molecule graph of the reaction.
- getAtomCount() - Method in class chemaxon.struc.Sgroup
-
Gets the number of atoms in the S-group.
- getAtomFont() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the atom symbol font name.
- getAtomicNumber(String) - Static method in class chemaxon.struc.MolAtom
-
Deprecated.
As of Marvin 5.9, replaced by a similar method
PeriodicSystem.findAtomicNumber(String).
The recommended method does not work for symbol
not representing a chemical element (e.g. R-atom, any atom),
as this method should not have worked on them either.
- getAtomicNumber(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
- getAtomicNumber(String) - Static method in class chemaxon.struc.PeriodicSystem
-
- getAtomicRadius(int) - Static method in class chemaxon.struc.PeriodicSystem
-
Atomic radius of the element Angstroms.
- getAtomicSurfaceAreaIncrement(int) - Method in class chemaxon.marvin.calculations.MSAPlugin
-
Returns the 3D surface area increments.
- getAtomIndex(int) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns the atom index in the standardized molecule,
or the atom index itself if the input molecule has not been standardized.
- getAtomIndex() - Method in class chemaxon.marvin.plugin.CalculatorPlugin.HydrogenData
-
- getAtomIndexes() - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
Returns the atom indices of the NMR active nuclei.
- getAtomIndexMap() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
- getAtomIterator(boolean) - Method in class chemaxon.marvin.space.MoleculeComponent
-
Returns the iterator of the atoms of the molecule.
- getAtomIterator() - Method in class chemaxon.struc.MoleculeGraph
-
Returns an iterator over the atoms in this molecule in proper sequence.
- getAtomIterator() - Method in class chemaxon.struc.RgMolecule
-
Returns an iterator over the atoms in this molecule in proper sequence.
- getAtomIterator() - Method in class chemaxon.struc.RxnMolecule
-
Returns an iterator over the atoms in this molecule in proper sequence.
- getAtomlogPHIncrement(int) - Method in class chemaxon.marvin.calculations.logPPlugin
-
- getAtomlogPIncrement(int) - Method in class chemaxon.marvin.calculations.logPPlugin
-
Returns the logP increment for the specified atom.
- getAtomMap() - Method in class chemaxon.struc.MolAtom
-
Gets the atom-atom mapping number.
- getAtomMap(int) - Method in interface chemaxon.struc.Smolecule
-
Gets the atom-atom mapping number.
- getAtomMappingMethod() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the atom mapping method.
- getAtomNumberingType() - Method in class chemaxon.marvin.beans.MarvinPane
-
Determines the atom numbering.
- getAtomNumberingType() - Method in class chemaxon.marvin.MolPrinter
-
Returns atom numbering type.
- getAtomOf(MElectronContainer) - Method in class chemaxon.struc.graphics.MChemicalStruct
-
- getAtomProperty() - Method in class chemaxon.marvin.space.AtomProperty
-
- getAtomProperty() - Method in class chemaxon.marvin.space.MoleculeComponent
-
See MoleculeIterators.AtomPropertyInterface for details.
- getAtomReferenceList() - Method in class chemaxon.struc.MoleculeGraph
- getAtoms() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
-
- getAtoms() - Method in interface chemaxon.checkers.result.StructureCheckerResult
-
- getAtoms() - Method in class chemaxon.struc.graphics.MAtomSetPoint
-
Gets the atoms.
- getAtoms(Object) - Static method in class chemaxon.struc.graphics.MEFlow
-
Gets the atom or atoms at the terminus of an arrow.
- getAtoms() - Method in class chemaxon.struc.MDocument.CheckerMark
-
- getAtomSelections() - Method in class chemaxon.marvin.space.MoleculeComponent
-
- getAtomSetColor(int) - Method in class chemaxon.marvin.beans.MarvinPane
-
Gets the color of an atom set.
- getAtomSetColor(int) - Method in class chemaxon.struc.MDocument
-
Gets an atom set color.
- getAtomSetColorMode(int) - Method in class chemaxon.struc.MDocument
-
Gets the atom set coloring mode.
- getAtomSetFont(int) - Method in class chemaxon.struc.MDocument
-
Gets an atom set font.
- getAtomSetRGB(int) - Method in class chemaxon.struc.MDocument
-
Gets an atom set color.
- getAtomSetSize() - Method in class chemaxon.struc.MDocument
-
Gets the size of the atom set.
- getAtomsize() - Method in class chemaxon.marvin.beans.MarvinPane
-
Gets the atom size.
- getAtomSize() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the atom size in C-C bond length units.
- getAtomsize() - Method in class chemaxon.marvin.MolPrinter
-
- getAtomSize() - Method in class chemaxon.marvin.MolPrinter
-
Returns the atom size in units of regular bond length.
- getAtomStereo(int) - Method in interface chemaxon.struc.Smolecule
-
Gets atom stereo properties as an integer.
- getAtomSymbol(int, int, int[], CTransform3D) - Method in class chemaxon.struc.MolAtom
-
Gets the string representation of the atom symbol.
- getAtomSymbol(int, int, int[], CTransform3D) - Method in class chemaxon.struc.sgroup.SgroupAtom
-
Gets the string representation of the atom symbol.
- getAtomSymbolListAsString(MolAtom[]) - Static method in class chemaxon.struc.Sgroup
-
- getAtomType(int) - Method in interface chemaxon.struc.Smolecule
-
Gets the type of an atom.
- getAtropBonds() - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
-
After the calculate method finished.
- getAttach() - Method in class chemaxon.struc.MolAtom
-
- getAttach(MolAtom) - Static method in class chemaxon.struc.Sgroup
-
Gets the attachment point information from the ExtraAtomProperties
- getAttachAtoms() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
- getAttachedData() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AtropStereoCenter
-
- getAttachedData() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter
-
- getAttachedData() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter
-
- getAttachedData() - Method in interface com.chemaxon.calculations.stereoanal.stereocenters.StereoCenter
-
Gets the attached data.
- getAttachedData() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter
-
- getAttachFromExtraAtomProp() - Method in class chemaxon.struc.MolAtom
-
Gets the attachment information stored in the extra atom properties
- getAttachmentPoint(int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Gets the attachment point that's order is given as parameter
- getAttachmentPointCount() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Gets the number of the attachment points.
- getAttachmentPointOrders(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Gets the attachment orders of the given attachment atom.
- getAttachmentPointOrders() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Gets the orders with which attachment point exists
- getAttachmentPoints() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Gets the sorted copy of the attachment point list.
- getAttachParentSgroup() - Method in class chemaxon.struc.MolAtom
-
Gets the smallest containing sgroup which can have
the attachment point information of this atom.
- getAttrFont(MTextAttributes) - Method in class chemaxon.struc.graphics.MTextDocument
-
Gets the font for the specified attribute object.
- getAttribute(String) - Method in class chemaxon.struc.graphics.MBracket
-
Gets the value of an attribute.
- getAttribute(String) - Method in class chemaxon.struc.graphics.MEFlow
-
- getAttribute(String) - Method in class chemaxon.struc.graphics.MPolyline
-
Gets the value of an attribute.
- getAttribute(String) - Method in class chemaxon.struc.graphics.MRectangle
-
Gets the value of an attribute.
- getAttribute(String) - Method in class chemaxon.struc.graphics.MRoundedRectangle
-
Gets the value of an attribute.
- getAttribute(String) - Method in class chemaxon.struc.graphics.MTextBox
-
Gets the value of an attribute.
- getAttribute(String) - Method in class chemaxon.struc.MObject
-
Gets the value of an attribute.
- getAttributes(int, int, int) - Method in class chemaxon.struc.graphics.MTextDocument
-
Gets the common attributes of the selected text.
- getAttributes() - Method in class chemaxon.struc.graphics.MTextDocument.Section
-
Gets the attributes.
- getAutoScale() - Method in class chemaxon.marvin.beans.MSketchPane
-
Returns autoscale property.
- getAutoTabScale() - Method in class chemaxon.marvin.beans.MViewPane
-
Is tab scale automatically changed?
- getAvailableCheckers() - Method in class chemaxon.checkers.StructureCheckerFactory
-
Deprecated.
Returns a list of checkers available
- getAveragePolarizabilityComponent() - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
-
- getAWTFont() - Method in class chemaxon.struc.graphics.MFont
-
Gets an AWT font instance.
- getBackground() - Method in class chemaxon.struc.MObject
-
Gets the background color of the object.
- getBackgroundColor() - Method in class chemaxon.marvin.MolPrinter
-
Returns the current background color.
- getBackgroundColor() - Method in class chemaxon.marvin.space.GraphicScene
-
Returns the background color of the scene.
- getBackgroundColor() - Method in class chemaxon.marvin.space.monitor.Label
-
Returns the background color of the label.
- getBackgroundColorF() - Method in class chemaxon.marvin.space.GraphicScene
-
- getBalabanIndex() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Calculates the Balaban distance connectivity of the molecule, which is
the average distance sum connectivity.
- getBallRadius() - Method in class chemaxon.marvin.beans.MarvinPane
-
Gets the ball radius in units of covalent radius.
- getBallRadius() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the ball radius for ball and stick mode.
- getBallRadius() - Method in class chemaxon.marvin.MolPrinter
-
Gets the ball radius for "ball and stick" mode.
- getBaseElectronContainerIndex() - Method in class chemaxon.struc.graphics.MEFlow
-
- getBaseElectronIndexInContainer() - Method in class chemaxon.struc.graphics.MEFlow
-
- getBaseFont() - Method in class chemaxon.struc.graphics.MTextAttributes
-
Gets the base font.
- getBaseFont() - Method in class chemaxon.struc.graphics.MTextBox
-
Gets the base font.
- getBaseFontFamily() - Method in class chemaxon.struc.graphics.MTextBox
-
Gets the base font family.
- getBaseFontStyle() - Method in class chemaxon.struc.graphics.MTextBox
-
Gets the base font style.
- getBestTabScale(int) - Method in class chemaxon.marvin.beans.MViewPane
-
Gets the best scale value for a molecule cell.
- getBestTabScale() - Method in class chemaxon.marvin.beans.MViewPane
-
Gets the smallest best scale value in the molecule table.
- getBFactor(int) - Method in class chemaxon.marvin.space.AtomProperty.MoleculeAtomProperty
-
- getBFactor(int) - Method in class chemaxon.marvin.space.AtomProperty.SmoleculeAtomProperty
-
- getBFactorPalette() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
-
Returns the palette that is used when the coloring mode of the component
is b-factor coloring.
- getBicycloStereo() - Method in class chemaxon.struc.MolAtom
-
Gets the previously stored bicyclo stereo information of this atom.
- getBond(Object) - Static method in class chemaxon.struc.graphics.MEFlow
-
Gets the bond at the terminus of an arrow.
- getBond(int) - Method in class chemaxon.struc.MolAtom
-
Gets the i-th bond.
- getBond(int) - Method in class chemaxon.struc.MoleculeGraph
-
Gets the nth bond.
- getBond(int) - Method in class chemaxon.struc.RgMolecule
-
Gets an edge in the graph union.
- getBond(int) - Method in class chemaxon.struc.RxnMolecule
-
Gets an edge.
- getBond(int) - Method in class chemaxon.util.iterator.IteratorFactory.BondIterator
-
Returns a bond of a specified index.
- getBond(int) - Method in class chemaxon.util.iterator.IteratorFactory.NeighbourIterator
-
Returns a bond of a specified index.
- getBondArray() - Method in class chemaxon.struc.MolAtom
-
Gets the bonds connected to this atom.
- getBondArray() - Method in class chemaxon.struc.MoleculeGraph
-
Creates an array of bonds.
- getBondArray() - Method in class chemaxon.struc.Sgroup
-
Gets all bonds connecting two atoms that are both in the Sgroup
- getBondConnectionInfo() - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
-
Gets a bond triplet which stores the crossing bond and flip
information.
- getBondCorrespondence() - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
-
Gets four bonds that store the crossing bond and flip
information.
- getBondCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns the bond count.
- getBondCount(boolean) - Method in class chemaxon.marvin.space.MoleculeComponent
-
Returns the number of bonds in the molecule with arbitrarily enumerating hydrogens.
- getBondCount() - Method in interface chemaxon.struc.Incomplecule
-
Gets the number of bonds
- getBondCount() - Method in class chemaxon.struc.MolAtom
-
Gets the number of bonds/ligands.
- getBondCount() - Method in class chemaxon.struc.MoleculeGraph
-
Gets the number of bonds.
- getBondCount() - Method in class chemaxon.struc.RgMolecule
-
Gets the number of edges in the root structure.
- getBondCount() - Method in class chemaxon.struc.RxnMolecule
-
Gets the number of edges in the graph union.
- getBondFlags() - Method in class chemaxon.marvin.plugin.CalculatorPlugin.HydrogenData
-
- getBondFlags(int) - Method in interface chemaxon.struc.Smolecule
-
Gets the bond descriptor flags.
- getBondIndex(int, int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns the index of the bond connecting two atoms,
-1 if the two atoms are not connected by bond.
- getBondIndex(int, int) - Method in interface chemaxon.struc.Smolecule
-
Gets the index of the bond between the specified atoms.
- getBondIterator(boolean) - Method in class chemaxon.marvin.space.MoleculeComponent
-
Returns the iterator of the atoms of the molecule.
- getBondIterator() - Method in class chemaxon.struc.MoleculeGraph
-
Returns an iterator over the bonds in this molecule in proper sequence.
- getBondIterator() - Method in class chemaxon.struc.RgMolecule
-
Returns an iterator over the bonds in this molecule in proper sequence.
- getBondIterator() - Method in class chemaxon.struc.RxnMolecule
-
Returns an iterator over the bonds in this molecule in proper sequence.
- getBonds() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
-
- getBonds() - Method in interface chemaxon.checkers.result.StructureCheckerResult
-
- getBonds() - Method in class chemaxon.struc.MDocument.CheckerMark
-
- getBonds(MolAtom) - Method in class chemaxon.struc.Molecule
-
Returns the bonds attached to the given atom.
- getBonds(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
-
Returns the bonds attached to the given atom in this molecule graph.
- getBondSetColor(int) - Method in class chemaxon.struc.MDocument
-
Gets a bond set color.
- getBondSetColorMode(int) - Method in class chemaxon.struc.MDocument
-
Gets the bond set coloring mode.
- getBondSetRGB(int) - Method in class chemaxon.struc.MDocument
-
Gets a bond set color.
- getBondSetSize() - Method in class chemaxon.struc.MDocument
-
Gets the bond set size.
- getBondSetThickness(int) - Method in class chemaxon.struc.MDocument
-
Gets a bond set thickness.
- getBondSpacing() - Method in class chemaxon.marvin.beans.MarvinPane
-
Gets the double bond spacing.
- getBondSpacing() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the double bond spacing.
- getBondSpacing() - Method in class chemaxon.marvin.MolPrinter
-
Returns the double bond spacing that is the distance of the two lines representing a double
bond.
- getBondTable() - Method in class chemaxon.struc.MoleculeGraph
-
Gets the bond (edge) table.
- getBondTable() - Method in class chemaxon.struc.RgMolecule
-
Gets the bond table of the root structre.
- getBondTable() - Method in class chemaxon.struc.RxnMolecule
-
Gets the bond table for the graph union.
- getBondTo(MolAtom) - Method in class chemaxon.struc.MolAtom
-
Finds the bond that connects this atom to another atom.
- getBondType(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Determines the type of a bond (aromatic bonds are automatically recognized)
- getBondType() - Method in class chemaxon.struc.MolBond
-
Gets the type of the bond.
- getBondType(int) - Method in interface chemaxon.struc.Smolecule
-
Gets the type of a bond.
- getBondType(int, int) - Method in interface chemaxon.struc.Smolecule
-
Gets the type of a bond between the two specified atoms.
- getBondWidth() - Method in class chemaxon.marvin.beans.MarvinPane
-
- getBondWidth() - Method in class chemaxon.marvin.MolPrinter
-
- getBorderColor() - Method in class chemaxon.marvin.space.monitor.Label
-
Returns the border color of the label.
- getBorderWidth() - Method in class chemaxon.marvin.beans.MViewPane
-
Gets the width of the border between cells.
- getBottom() - Method in class chemaxon.marvin.space.GraphicCell
-
Returns the y coordinate of the bottom of the cell in pixels.
- getBoundAttachAtoms() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Gets atoms with attachment point having crossing bond and the related
leaving group is not visible.
- getBoundingBox() - Method in class chemaxon.marvin.space.GraphicComponent
-
Returns the smallest box containing the graphic component.
- getBoundingBox() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- getBoundingBox() - Method in class chemaxon.marvin.space.MoleculeComponent
-
Returns the
BoundingBox that is the smallest container box of the component.
- getBoundingBoxAndSetSphereRadius() - Method in class chemaxon.marvin.space.GraphicCell
-
Computes the radius of the bounding sphere in order to set the z coordinate
of the camera properly.
- getBoundingCenter() - Method in class chemaxon.marvin.space.BoundingBox
-
Returns the center of the box as a vector.
- getBoundingRadius() - Method in class chemaxon.marvin.space.BoundingBox
-
Returns the radius of the bounding sphere of the box, which is
the distance between the lower-left-front corner and the center.
- getBoundingRectangle(MoleculeGraph[]) - Method in class chemaxon.marvin.MolPrinter
-
Returns the bounding rectangle of the specified molecules using the current scale factor.
- getBoundingSphereRadius() - Method in class chemaxon.marvin.space.GraphicComponent
-
Returns the radius of the bounding sphere of the component.
- getBoundRectSize() - Method in class chemaxon.marvin.beans.MSketchPane
-
Gets the size of the bounding rectangle.
- getBracketCount() - Method in class chemaxon.struc.Sgroup
-
Gets the number of brackets in this S-group.
- getBracketOrientation() - Method in class chemaxon.struc.graphics.MBracket
-
Gets the orientation of the bracket.
- getBrackets() - Method in class chemaxon.struc.Sgroup
-
Gets all graphic brackets from this Sgroup
- getBreakingChars() - Method in class chemaxon.struc.graphics.MTextBox
-
Gets the breaking characters after that the text in the text
box can be broken if it doesn't fit into the text box.
- getBtab() - Method in class chemaxon.struc.MoleculeGraph
-
- getBufferedImage() - Method in class chemaxon.marvin.space.GraphicScene
-
Returns the Canvas as a BufferedImage with the same size in pixels.
- getBuildDate() - Static method in class com.chemaxon.version.VersionInfo
-
Returns the build date as string (in local time zone).
- getBuildTime() - Static method in class com.chemaxon.version.VersionInfo
-
Returns the build time as string (in local time zone).
- getBuildTimestamp() - Static method in class com.chemaxon.version.VersionInfo
-
Returns the build date and time.
- getBuildTimestampStr() - Static method in class com.chemaxon.version.VersionInfo
-
Returns the build date and time as string in UTC time zone.
- getBuiltInPalette(int) - Static method in class chemaxon.marvin.space.SurfaceColoring
-
Returns the colors of a built-in palette.
- getBuiltInPalette(Object) - Static method in class chemaxon.marvin.space.SurfaceColoring
-
Returns the colors of a built-in palette.
- getBuiltInPalettes() - Static method in class chemaxon.marvin.space.SurfaceColoring
-
Returns the string identifiers of the built-in palettes.
- getC(int) - Method in class chemaxon.marvin.beans.MViewPane
-
Gets the state of a checkbox in a GridBagView table.
- getCacheCapacity() - Method in class chemaxon.marvin.view.MDocStorage
-
Gets the maximum number of cached documents.
- getCachedDoc(int, String) - Method in class chemaxon.marvin.view.MDocStorage
-
Gets the specified document if it is present in the memory.
- getCachedDocIndices() - Method in class chemaxon.marvin.view.MDocStorage
-
Gets the indices of cached records.
- getCachedResults(Molecule, boolean) - Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
-
Returns cached results, separated from the plugin object,
so that no further enqueries needed to the plugin to get the result.
- getCacheLock() - Method in class chemaxon.marvin.view.MDocStorage
-
Gets the synchronization lock for caching operations.
- getCalcMolecule() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns the molecule used in the calculation.
- getCameraZ() - Method in class chemaxon.marvin.space.GraphicCell
-
Returns the z coordinate of the camera.
- getCanvasComponent() - Method in class chemaxon.marvin.beans.MSketchPane
-
Determines canvas component of MarvinSketch.
- getCanvasComponent(int) - Method in class chemaxon.marvin.beans.MViewPane
-
Deprecated.
as of Marvin 3.0, replaced by getVisibleCellComponent
- getCapacity() - Method in class chemaxon.marvin.view.MDocStorage
-
Gets the total capacity.
- getCarboaliphaticRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Calculates the number of carboaliphatic rings in the molecule (aliphatic
rings containing carbon atoms only).
- getCarboaromaticRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Calculates the number of carboaromatic rings in the molecule (aromatic
rings containing carbon atoms only).
- getCarbonVisibility() - Method in class chemaxon.marvin.MolPrinter
-
Returns the visibility style of the C labels on Carbon atoms.
- getCarboRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns the carbo ring count.
- getCarboRingCount(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Calculates the number of carbocyclic rings in the molecule (rings
containing at least a non-carbon atom).
- getCarboRings() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Identifies carbocyclic rings in the molecule (rings containing carbon
atoms only).
- getCarboRings(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Identifies carbocyclic rings in the molecule (rings containing carbon
atoms only) having the given number of atoms.
- getCategory(Molecule, double) - Method in class com.chemaxon.calculations.solubility.SolubilityCategories
-
Calculates the solubility category of molecule.
- getCell() - Method in class chemaxon.marvin.space.GraphicComponent
-
Returns the container cell of the component.
- getCell(int) - Method in class chemaxon.marvin.space.GraphicScene
-
Returns the GraphicCell which has the given index.
- getCellButtom() - Method in class chemaxon.marvin.space.GraphicScene
-
Returns the y coordinate of the buttom of the active cell in pixels.
- getCellCount() - Method in class chemaxon.marvin.beans.MViewPane
-
Gets the number of molecule cells in the table.
- getCellCount() - Method in class chemaxon.marvin.space.GraphicScene
-
Returns the number of cells in the scene.
- getCellDrawProperty(String) - Method in class chemaxon.marvin.space.GraphicCell
-
Returns the value of the cell-range drawing property with the given name.
- getCellDrawProperty(String) - Method in class chemaxon.marvin.space.GraphicScene
-
Returns the draw property from the active cell or null if there is no active cell
or the property is not defined in the active cell.
- getCellDrawProperty(int, String) - Method in class chemaxon.marvin.space.GraphicScene
-
Returns the draw property from the given cell or null if not defined.
- getCellEditorValue() - Method in class chemaxon.marvin.beans.MViewEditor
-
Returns the edited molecule that is a
Molecule instance.
- getCellHeight() - Method in class chemaxon.marvin.space.GraphicScene
-
Returns the height of the cells.
- getCellIndex() - Method in class chemaxon.marvin.space.CellOrComponentId
-
Returns the internal index of the cell either this is a cell id or a component id.
- getCellLeft() - Method in class chemaxon.marvin.space.GraphicScene
-
Returns the x coordinate of the left edge of the active cell.
- getCellRight() - Method in class chemaxon.marvin.space.GraphicScene
-
Returns the x coordinate of the right edge of the active cell.
- getCellTop() - Method in class chemaxon.marvin.space.GraphicScene
-
Returns the y coordinate of the top of the active cell.
- getCellWidth() - Method in class chemaxon.marvin.space.GraphicScene
-
Returns the width of the cells.
- getCenter() - Method in class chemaxon.marvin.space.monitor.Control
-
Returns the center of the transformation.
- getCenter(int, int) - Method in class chemaxon.struc.RxnMolecule
-
Gets the geometrical center of a reaction component.
- getCentralAtom() - Method in class chemaxon.struc.sgroup.MulticenterSgroup
-
Gets the central atom of this sgroup.
- getChainAtomCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns the chain atom count.
- getChainBondCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns the chain bond count.
- getChangedAtomIndexes() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Returns the indexes of the atoms changed during tautomerization.
- getChangeSupport() - Method in class chemaxon.checkers.runner.BasicCheckerRunner
-
Returns the changeSupport
- getCharactersRead() - Method in class chemaxon.naming.DocumentExtractor.ProgressInfo
-
Deprecated.
- getCharge(int) - Method in class chemaxon.marvin.space.AtomProperty.MoleculeAtomProperty
-
- getCharge(int) - Method in class chemaxon.marvin.space.AtomProperty.SmoleculeAtomProperty
-
- getCharge() - Method in class chemaxon.struc.MolAtom
-
Gets the charge.
- getCharge(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
- getCharge() - Method in class chemaxon.struc.sgroup.SgroupAtom
-
Returns the sum of the charges in the corresponding superatom s-group.
- getCharge(int) - Method in interface chemaxon.struc.Smolecule
-
Gets the charge of an ion.
- getChargeDensity(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
-
Returns the total charge density of an atom
calculated with HMO,
Double.NaN for no value.
- getChargeDistribution() - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
-
Returns the charge distribution array over pH values.
- getChargeFont() - Method in class chemaxon.marvin.MolPrinter
-
Gets the circled charge's font.
- getChargeFontSize() - Method in class chemaxon.marvin.MolPrinter
-
Gets the circled charge's font's size.
- getChargeLocation() - Method in class chemaxon.struc.Sgroup
-
Returns the charge location attribute of the S-group.
- getChecker(String, Map<String, String>) - Method in class chemaxon.checkers.StructureCheckerFactory
-
Deprecated.
This method creates a requested (type represented in checkerId)
StructureChecker instance with the give parameters
- getCheckerConfigFileName() - Method in class chemaxon.marvin.common.UserSettings
-
- getCheckerConfiguration() - Method in class chemaxon.checkers.runner.BasicCheckerRunner
-
- getCheckerConfiguration() - Method in interface chemaxon.checkers.runner.CheckerRunner
-
Gets the list of available checkers
- getCheckerConfigURL() - Method in class chemaxon.marvin.common.UserSettings
-
Returns the URL of configuration for Checkers in marvin sketch.
- getCheckerList() - Method in class chemaxon.checkers.runner.BasicCheckerRunner
-
Returns the checkerList
- getCheckerList() - Method in class chemaxon.checkers.runner.configuration.reader.ActionStringBasedConfigurationReader
-
- getCheckerList() - Method in interface chemaxon.checkers.runner.configuration.reader.ConfigurationReader
-
- getCheckerList() - Method in class chemaxon.checkers.runner.configuration.reader.XMLBasedConfigurationReader
-
- getCheckerMarks() - Method in class chemaxon.struc.MDocument
-
Returns the array of checker marks
NOTE: checker marks will be reset on any molecule change
- getChild() - Method in interface chemaxon.common.util.MProgressMonitor
-
Gets the child of this progress monitor.
- getChildSgroup(int) - Method in class chemaxon.struc.Sgroup
-
Gets a child S-group.
- getChildSgroupCount() - Method in class chemaxon.struc.Sgroup
-
Gets the number of child S-groups.
- getChildSgroups() - Method in class chemaxon.struc.Sgroup
-
Gets the children of this S-group.
- getChiralCenterCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Calculates the number of tetrahedral stereogenic centers.
- getChiralCenters() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Determines the chiral center atoms.
- getChirality(int) - Method in class chemaxon.struc.MoleculeGraph
-
Computes the chirality of an atom of the Molecule instance based on both
the coordinates of the neighboring atoms and the stereo information of
the bonds to those.
- getChirality(int) - Method in interface chemaxon.struc.Smolecule
-
Gets the chirality of an atom.
- getChiralityOfOriginalLigand() - Method in class chemaxon.marvin.plugin.CalculatorPlugin.HydrogenData
-
- getChiralitySupport() - Method in class chemaxon.marvin.beans.MarvinPane
-
Gets chirality support level.
- getChiralitySupport() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the chirality support parameter.
- getChiralitySupport() - Method in class chemaxon.marvin.MolPrinter
-
Returns the current chirality display mode.
- getCIPValue() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AtropStereoCenter
-
- getCIPValue() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter
-
- getCIPValue() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter
-
- getCIPValue() - Method in interface com.chemaxon.calculations.stereoanal.stereocenters.StereoCenter
-
Returns the stereo center value.
- getCIPValue() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter
-
- getCircledChargeFont() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the circled charge symbol font name.
- getCircledChargeSize() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the circled charge font size in C-C bond length units.
- getClassName() - Method in class chemaxon.marvin.services.localservice.LocalServiceDescriptor
-
Returns the full class name of the service
- getClean2dOpts() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the 2D cleaning options.
- getClean3dOpts() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the 3D cleaning options.
- getCleanDim() - Method in class chemaxon.marvin.beans.MarvinPane
-
Gets the number of space dimensions for cleaning.
- getClip(CTransform3D) - Method in class chemaxon.struc.graphics.MRectangle
-
Gets the clipping rectangle.
- getClipboard() - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
-
Returns the default Toolkit's system clipboard if available, otherwise returns a new
singleton clipboard instance.
- getClipboardContents() - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
-
Inits and return the transferable of the Clipboard for later import.
- getColor() - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
-
- getColor() - Method in enum chemaxon.marvin.alignment.AlignmentProperties
-
- getColor() - Method in class chemaxon.marvin.space.ComponentElement
-
Returns the color that is assigned to the ComponentElement.
- getColor() - Method in class chemaxon.marvin.space.GraphicComponent
-
Returns the constant color of the component.
- getColor() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- getColor() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
Returns the constant color of the surface.
- getColor() - Method in class chemaxon.marvin.space.MoleculeComponent
-
- getColor() - Method in class chemaxon.marvin.space.monitor.Control
-
Returns the color of the control.
- getColor() - Method in class chemaxon.marvin.space.monitor.DihedralControl
-
Returns the color of the control.
- getColor() - Method in class chemaxon.marvin.space.monitor.GlobalLocationControl
-
Returns the color of the control.
- getColor() - Method in class chemaxon.marvin.space.monitor.GlobalOrientationControl
-
Returns the color of the control.
- getColor() - Method in class chemaxon.marvin.space.monitor.LocalLocationControl
-
Returns the color of the control.
- getColor() - Method in class chemaxon.marvin.space.monitor.LocalOrientationControl
-
Returns the color of the control.
- getColor() - Method in class chemaxon.marvin.space.monitor.ResizeControl
-
Returns the color of the control.
- getColor() - Method in class chemaxon.marvin.space.PharmacophoreArrow
-
Returns the color of the component.
- getColor() - Method in class chemaxon.marvin.space.PharmacophorePoint
-
Returns the color of the PharmacophorePoint.
- getColor() - Method in class chemaxon.marvin.space.SurfaceComponent
-
Returns the constant color of the surface.
- getColor() - Method in class chemaxon.struc.MDocument.CheckerMark
-
- getColor() - Method in class chemaxon.struc.MObject
-
Gets the color of the object.
- getColor3() - Method in class chemaxon.marvin.space.SurfaceComponent
-
Returns the constant color of the surface.
- getColor3F() - Method in class chemaxon.marvin.space.SurfaceComponent
-
Returns the constant color of the surface.
- getColorF() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- getColorF() - Method in class chemaxon.marvin.space.MoleculeComponent
-
- getColorF() - Method in class chemaxon.marvin.space.SurfaceComponent
-
Returns the constant color of the surface.
- getColoring() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Returns the hit coloring options.
- getColoringScheme() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
-
- getColors() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
-
- getColors() - Method in class chemaxon.marvin.alignment.Pharmacophore3D
-
- getColorScheme() - Method in class chemaxon.marvin.beans.MarvinPane
-
Gets the color scheme.
- getColorScheme() - Method in class chemaxon.marvin.MolPrinter
-
Returns the current color scheme.
- getColorType() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- getColorType() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
Returns the color type of the surface.
- getColorType() - Method in class chemaxon.marvin.space.MoleculeComponent
-
Returns the color type of the visualizer.
- getColumn(int) - Static method in class chemaxon.core.ChemConst
-
The column or group of an element in the periodic system.
- getColumn(int) - Static method in class chemaxon.struc.MolAtom
-
The column or group of an element in the periodic system.
- getColumnCount() - Method in class chemaxon.marvin.space.GraphicScene
-
Returns the number of columns in the scene.
- getColumnWidth() - Method in class chemaxon.marvin.view.swing.TableOptions
-
Gets the default column width.
- getColumnWidth(int) - Method in class chemaxon.marvin.view.swing.TableOptions
-
Gets the default width of a specified column.
- getColumnWidthsString() - Method in class chemaxon.marvin.view.swing.TableOptions
-
Gets a parameter string containing column widths.
- getCommandKeyStroke(int) - Static method in class chemaxon.marvin.util.SwingUtil
-
Gets the command keystroke preferred on the current platform.
- getComment() - Method in class chemaxon.struc.Molecule
-
Gets the comment.
- getComment() - Method in class chemaxon.struc.RgMolecule
-
Gets the comment of the root molecule.
- getCommonActions() - Method in class chemaxon.marvin.beans.MarvinPane
-
Deprecated.
- getCommonActions() - Method in class chemaxon.marvin.beans.MSketchPane
-
Deprecated.
- getCommonActions() - Method in class chemaxon.marvin.beans.MViewPane
-
Gets the common actions.
- getCompatibleAttributes(MTextAttributes, MFont, MTextAttributes.MFontCreator, int) - Method in class chemaxon.struc.graphics.MTextAttributes
-
Gets the compatible attributes.
- getComponent(Molecule, int) - Method in class chemaxon.checkers.AtomChecker
-
- getComponent(Molecule, int) - Method in class chemaxon.checkers.BondChecker
-
- getComponent(Molecule, int) - Method in class chemaxon.checkers.ComponentChecker
-
Gets the component from the molecule with index i.
- getComponent() - Method in class chemaxon.marvin.plugin.gui.ParameterPanel
-
Returns the parameter panel component.
- getComponent() - Method in interface chemaxon.marvin.plugin.ParameterPanelHandler
-
Returns the parameter panel component.
- getComponent() - Method in class chemaxon.marvin.space.ComponentElement
-
Returns the component which contains this ComponentElement.
- getComponent(int) - Method in class chemaxon.marvin.space.GraphicCell
-
Returns the component having the given index.
- getComponent(int) - Method in class chemaxon.marvin.space.MacroMoleculeComponent
-
Returns its visualizer with the given index.
- getComponent() - Method in class chemaxon.marvin.space.monitor.DihedralMonitor
-
Returns the molecule whose atoms are monitored.
- getComponent() - Method in class chemaxon.marvin.space.monitor.Label
-
Returns the GraphicComponent of the only selected item.
- getComponent() - Method in class chemaxon.marvin.space.monitor.PositionMonitor
-
Returns the GraphicComponent of the only selected item.
- getComponent(long) - Method in class chemaxon.struc.RxnMolecule
-
Gets a reactant, product or agent.
- getComponent(int, int) - Method in class chemaxon.struc.RxnMolecule
-
Gets a reactant, product or agent.
- getComponentCount(Molecule) - Method in class chemaxon.checkers.AtomChecker
-
- getComponentCount(Molecule) - Method in class chemaxon.checkers.BondChecker
-
- getComponentCount(Molecule) - Method in class chemaxon.checkers.ComponentChecker
-
Gets the number of the components in the molecule
- getComponentCount() - Method in class chemaxon.marvin.space.GraphicCell
-
Returns the number of components of the cell including monitors, surfaces and so on.
- getComponentCount(int) - Method in class chemaxon.struc.RxnMolecule
-
Gets the number of reactants, products or agents.
- getComponentElement() - Method in class chemaxon.marvin.space.GraphicComponent
-
Returns the previously picked but unprocessed ComponentElement or the whole
component as a ComponentElement, if no picking happened.
- getComponentElement() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
-
Returns the previously picked but unprocessed ComponentElement or the whole
component as a ComponentElement, if no picking happened.
- getComponentElement(MacroMoleculeComponent.MoleculeVisualizer) - Method in class chemaxon.marvin.space.MacroMoleculeComponent
-
Returns the visualizer as a ComponentElement.
- getComponentElement() - Method in class chemaxon.marvin.space.MoleculeComponent
-
Returns the previously picked but unprocessed ComponentElement or the whole
component as a ComponentElement, if no picking happened.
- getComponentFlags(long) - Method in class chemaxon.struc.RxnMolecule
-
Gets the reaction component type flags from the ID.
- getComponentID(Molecule) - Method in class chemaxon.struc.RxnMolecule
-
Gets the ID of a reaction component.
- getComponentID(MolAtom) - Method in class chemaxon.struc.RxnMolecule
-
Gets the reaction component ID of an atom.
- getComponentID(MolBond) - Method in class chemaxon.struc.RxnMolecule
-
Gets the reaction component ID of a bond.
- getComponentIds() - Method in class chemaxon.checkers.result.ReactionCheckerResult
-
Deprecated.
Returns the
List of the ids of the components affected by the problem
- getComponentIndex() - Method in class chemaxon.marvin.space.CellOrComponentId
-
Returns the internal index of the component or -1 if this is a cell id.
- getComponentIndex(long) - Method in class chemaxon.struc.RxnMolecule
-
Gets the reactant, product or agent index from the ID.
- getComponentIterator() - Method in class chemaxon.marvin.space.GraphicCell
-
Returns the iterator of the GraphicComponents of the cell.
- getComponentIterator() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
-
Returns the Iterator of its visualizers.
- getComponentPartId() - Method in class chemaxon.marvin.space.ComponentElement
-
In case of complex components the componentPartId identifies
a part of the component.
- getComponents(Molecule) - Static method in class chemaxon.checkers.StructureCheckerUtility
-
A recursive algorithm collecting all components (reactants, agents and
products of reaction molecules, R-group definitions of Rg-Molecules) of
the molecule.
- getComponents() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
-
Returns its visualizers.
- getComponentType(long) - Method in class chemaxon.struc.RxnMolecule
-
Gets the reaction component type from the ID.
- getComposition() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
-
Calculates the elemental analysis, the relative percent composition of a pure
chemical substance by element (w/w%).
- getConformer(int) - Method in class chemaxon.marvin.calculations.ConformerPlugin
-
Returns a conformer.
- getConformerCount() - Method in class chemaxon.marvin.calculations.ConformerPlugin
-
Returns the number of different conformers.
- getConformers() - Method in class chemaxon.marvin.calculations.ConformerPlugin
-
Returns all conformers in a Molecule[] array.
- getConfTryCountLimit() - Method in class chemaxon.marvin.alignment.MMPAlignmentProperties
-
- getConnectedObject(int) - Method in class chemaxon.struc.MDocument
-
Gets an object from the document or from the chemical structure of the document.
- getConnectedObjectCount() - Method in class chemaxon.struc.MDocument
-
Gets the number of objects in this document and in the chemical structure of this document.
- getConnectivity() - Method in class chemaxon.struc.Sgroup
-
Gets S-group connectivity.
- getContext() - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
-
Returns the evaluation context
- getContext() - Method in class chemaxon.struc.sgroup.DataSgroup
-
Gets the context of the data sgroup.
- getContextFunctionNames() - Method in interface chemaxon.jep.ChemContext
-
Returns context element accessor function names.
- getContextFunctionNames() - Method in class chemaxon.jep.context.AtomContext
-
Returns {"mol", "fingerprint", "atom"}.
- getContextFunctionNames() - Method in class chemaxon.jep.context.MolContext
-
Returns {"mol", "fingerprint"}.
- getContextFunctionNames() - Method in class chemaxon.jep.context.ReactionContext
-
Returns {"reactant", "product", "ratom", "patom"}.
- getContextId() - Method in class chemaxon.struc.sgroup.DataSgroup
-
Gets the id of the context of the data sgroup.
- getControl() - Method in class chemaxon.marvin.space.monitor.PositionMonitor
-
Returns the control of this monitor.
- getControllableObject(String) - Method in class chemaxon.marvin.space.GraphicCell
-
Returns a component if there is any which allows itself to be controlled.
- getControllableObject(String) - Method in class chemaxon.marvin.space.GraphicScene
-
Returns a selected component from the active cell what can be controlled
by the given tye controller.
- getCoordinateBondStyle() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the "coordinative" bond line style when both atoms are single.
- getCoordinateBondStyle() - Method in class chemaxon.marvin.MolPrinter
-
Gets the coordinate bond line style when both atoms are single.
- getCoordinateBondStyleAtMulticenter() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the "coordinative" bond line style when one of the atoms is multicenter.
- getCoordinateBondStyleAtMulticenter() - Method in class chemaxon.marvin.MolPrinter
-
Gets the coordinate bond line style.
- getCoordinates(float[]) - Method in class chemaxon.marvin.space.ComponentElement
-
Returns the world coordinates of the ComponentElement.
- getCoordinates(float[]) - Method in class chemaxon.marvin.space.GraphicComponent
-
Gets the coordinates of the previously picked but not yet processed part
if there is any in the given preallocated array.
- getCoordinates(ComponentElement, float[]) - Method in class chemaxon.marvin.space.GraphicComponent
-
Gets the coordinates of the given ComponentElement in the given preallocated array.
- getCoordinates(ComponentElement, float[]) - Method in class chemaxon.marvin.space.MacroMoleculeComponent
-
Sets the coordinates of the given ComponentElement in the given array.
- getCoordinates(ComponentElement, float[]) - Method in class chemaxon.marvin.space.MoleculeComponent
-
Sets the coordinates of the given element in the given preallocated array.
- getCoordinates(float[]) - Method in class chemaxon.marvin.space.monitor.AngleMonitor
-
Returns the centroid of the selected elements.
- getCoordinates(float[]) - Method in class chemaxon.marvin.space.monitor.DihedralMonitor
-
Returns the centroid of the second and third selected elements.
- getCoordinates(float[]) - Method in class chemaxon.marvin.space.monitor.Label
-
Returns the coordinates of the selected item as a GeomCalc vector.
- getCoordinates(ComponentElement, float[]) - Method in class chemaxon.marvin.space.monitor.Label
-
Returns the coordinates of the selected item as a GeomCalc vector.
- getCoordinates(float[]) - Method in class chemaxon.marvin.space.monitor.MeasurementMonitor
-
Returns the centroid of the selected elements.
- getCoordinates(ComponentElement, float[]) - Method in class chemaxon.marvin.space.monitor.MeasurementMonitor
-
Returns the centroid of the selected elements.
- getCoordinates(float[]) - Method in class chemaxon.marvin.space.monitor.PositionMonitor
-
Returns the coordinates of the selected item.
- getCoordinates(ComponentElement, float[]) - Method in class chemaxon.marvin.space.monitor.PositionMonitor
-
Returns the coordinates of the selected item.
- getCoordinates(ComponentElement, float[]) - Method in class chemaxon.marvin.space.PharmacophoreArrow
-
Gets the position of the component.
- getCoordinates(ComponentElement, float[]) - Method in class chemaxon.marvin.space.PharmacophorePoint
-
Gets the position of the pharmacophore point.
- getCoordinatesOfAligned() - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
-
- getCoordinatesOfReference() - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
-
- getCopyAsFormat() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the selected format from the Copy As dialog.
- getCopyAsTransferableNames() - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
-
Returns the format's names that are available in the current environment as transfer types
for the Copy As dialog.
- getCorrectionLibraryIds() - Static method in class chemaxon.marvin.calculations.pKaPlugin
-
Returns the id's of available pKa correction libraries.
- getCount() - Method in class chemaxon.marvin.plugin.PluginFactory
-
Returns the number of plugin records.
- getCouplingConstants() - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
Returns coupling constants.
- getCouplingConstants(NMRSpectrum.Unit) - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
Returns coupling constants in the given unit.
- getCovalentRadius(int) - Static method in class chemaxon.struc.PeriodicSystem
-
Covalent radius of the element in Angstroms.
- getCovalentRadius(int, int) - Static method in class chemaxon.struc.PeriodicSystem
-
Covalent radius of the element in specific bond type in Angstroms.
- getCrossingAtoms(MolBond[]) - Method in class chemaxon.struc.Sgroup
-
Gets the atoms that have crossing bonds.
- getCrossingAtoms(MolBond[]) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Gets the atoms from the S-group that have crossing bonds.
- getCrossingBonds(MolBond[], DPoint3, DPoint3) - Static method in class chemaxon.marvin.util.MoleculeUtil
-
Deprecated.
as of Marvin 5.11.1
- getCSSR() - Method in class chemaxon.struc.MoleculeGraph
-
Gets the Complete Set of Smallest Ring atom indexes array.
- getCtab() - Method in class chemaxon.struc.MoleculeGraph
-
Gets the connection table.
- getCtab() - Method in class chemaxon.struc.RgMolecule
-
Gets the connection table of the root structure.
- getCtab() - Method in class chemaxon.struc.RxnMolecule
-
Gets the connection table for the graph union.
- getCTAtom1() - Method in class chemaxon.struc.MolBond
-
Gets the first atom for cis/trans stereo calculation.
- getCTAtom4() - Method in class chemaxon.struc.MolBond
-
Gets the fourth atom for cis/trans stereo calculation.
- getCurrent() - Method in class chemaxon.checkers.runner.BasicCheckerRunner
-
- getCurrent() - Method in interface chemaxon.checkers.runner.CheckerRunner
-
- getCurrentCheckerName() - Method in class chemaxon.checkers.runner.BasicCheckerRunner
-
- getCurrentCheckerName() - Method in interface chemaxon.checkers.runner.CheckerRunner
-
- getCurrentDefaultFontMetrics() - Method in class chemaxon.struc.graphics.MTextBox
-
Gets the current default FontMetrics.
- getCurrentForeground() - Method in class chemaxon.struc.graphics.MTextBox
-
Gets the current color.
- getCurrentHeight() - Method in class chemaxon.struc.graphics.MTextBox
-
Gets the current height of the text.
- getCurrentScriptCount(int) - Method in class chemaxon.struc.graphics.MTextBox
-
Gets the number of subscripts or superscripts on the last normal
character.
- getCurrentSubLevel() - Method in class chemaxon.struc.graphics.MTextBox
-
Gets the current subscript/superscript level.
- getCurrentTextAttributes(int) - Method in class chemaxon.struc.graphics.MTextBox
-
Gets the common attributes of the selected text or attributes for the
next character to be typed.
- getCurrentWidth() - Method in class chemaxon.struc.graphics.MTextBox
-
Gets the current width of the text.
- getCursorColumn() - Method in class chemaxon.struc.graphics.MTextBox
-
Gets the cursor's column number.
- getCursorPos() - Method in class chemaxon.struc.graphics.MTextBox
-
Gets the cursor position.
- getCursorRow() - Method in class chemaxon.struc.graphics.MTextBox
-
Gets the cursor's row number.
- getCusromToolBar(JTextPane, String) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Returns a custom toolbar for textPane instance
NOTE: textPane have to be created with this factory
- getCustomName() - Method in class chemaxon.checkers.StructureCheckerDescriptor
-
Returns the customName
- getCyclomaticNumber() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Calculates the smallest number of graph edges which must be removed such
that no circuit remains.
- getData() - Method in class chemaxon.struc.sgroup.DataSgroup
-
Gets the data value to be set.
- getData() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AttachedData
-
Gets the data field.
- getDataFromClipboard(DataFlavor) - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
-
- getDataLine(int) - Method in class chemaxon.struc.sgroup.DataSgroup
-
Gets a line of data.
- getDataLineCount() - Method in class chemaxon.struc.sgroup.DataSgroup
-
Gets the number of data lines.
- getDataToClipboard(DataFlavor) - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
-
Returns the clipboard representation of the given
Molecule.
- getDebug() - Method in class chemaxon.marvin.beans.MarvinPane
-
Gets the debugging level.
- getDefaultAbbrevgroups() - Static method in class chemaxon.checkers.StructureCheckerHelper
-
Imports default and user abbreviations and returns them in a
AbbrevGroupStorage.
- getDefaultFont() - Method in class chemaxon.struc.graphics.MTextDocument
-
Gets the default font.
- getDefaultProperty(String) - Method in class chemaxon.marvin.common.UserSettings
-
Gets the value of the given key in the default configuration or null if the key does not
exist.
- getDefaultSaveFormat() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the default molecule format in the "Save As" dialog.
- getDefaultScale() - Static method in class chemaxon.marvin.beans.MSketchPane
-
Returns the default scale factor which is equivalent to 100% magnification.
- getDefaultServiceDescriptorEditorProvider() - Static method in class chemaxon.marvin.services.ServiceDescriptorTools
-
- getDefaultServiceDescriptorReader() - Static method in class chemaxon.marvin.services.ServiceDescriptorTools
-
- getDefaultServiceDescriptorWriter() - Static method in class chemaxon.marvin.services.ServiceDescriptorTools
-
- getDefaultServiceDialogProvider() - Static method in class chemaxon.marvin.services.ServiceDescriptorTools
-
- getDefaultSize() - Method in class chemaxon.marvin.view.swing.TableSupport
-
Gets the default size of an MViewPane containing the generated table.
- getDefaultStyle() - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
Returns the style applied for the value cells of the columns
having no explicit formatting.
- getDefaultValue() - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
- getDependentRgroupDefinition(int) - Method in class chemaxon.struc.RgMolecule
-
Gets the R-group definition's index which depends on the referenced
R-group definition.
- getDescent(Graphics, FontMetrics) - Method in class chemaxon.struc.graphics.MTextDocument.Portion
-
Gets the descent of this portion.
- getDescription() - Method in class chemaxon.checkers.AbstractStructureChecker
-
- getDescription() - Method in class chemaxon.checkers.InvalidChecker
-
- getDescription() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
-
- getDescription() - Method in interface chemaxon.checkers.result.StructureCheckerResult
-
- getDescription() - Method in interface chemaxon.checkers.StructureChecker
-
Deprecated.
This method isn't needed anymore and will be removed in 6.0
- getDescription() - Method in class chemaxon.checkers.StructureCheckerDescriptor
-
Returns the description
- getDescription() - Method in class chemaxon.fixers.AbstractStructureFixer
-
- getDescription() - Method in interface chemaxon.fixers.StructureFixer
-
Deprecated.
- getDescription() - Method in class chemaxon.fixers.StructureFixerDescriptor
-
Returns the description
- getDescription() - Method in class chemaxon.formats.MFileFormat
-
Gets the format description.
- getDescription(String, String) - Static method in class chemaxon.marvin.common.UserSettings
-
Gets the human readable description of a property.
- getDescription() - Method in class chemaxon.marvin.space.ComponentElement
-
Returns the brief description of the ComponentElement,
for example type of the atom.
- getDescription() - Method in class chemaxon.marvin.space.GraphicComponent
-
Returs the short description of the component or of the previously picked
but not yet processed part if there is any or the description of the whole component.
- getDescription(ComponentElement) - Method in class chemaxon.marvin.space.GraphicComponent
-
Returs the short description of the given part of the component.
- getDescription(ComponentElement) - Method in class chemaxon.marvin.space.MacroMoleculeComponent
-
Returns the short description of the given element.
- getDescription(ComponentElement) - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- getDescription(ComponentElement) - Method in class chemaxon.marvin.space.MoleculeComponent
-
Returs the short description of the given part of the component.
- getDescription() - Method in class chemaxon.marvin.space.monitor.MeasurementMonitor
-
Returns the measurement as a description.
- getDescription(ComponentElement) - Method in class chemaxon.marvin.space.monitor.MeasurementMonitor
-
Returns the measurement as a description.
- getDescription() - Method in class chemaxon.marvin.space.PharmacophoreArrow
-
Returns a descriptive text.
- getDescription() - Method in class chemaxon.marvin.space.PharmacophorePoint
-
Returns textual description.
- getDescription() - Method in class chemaxon.marvin.util.OptionDescriptor
-
Gets the description.
- getDescriptor() - Method in class chemaxon.checkers.AbstractStructureChecker
-
- getDescriptor() - Method in class chemaxon.checkers.InvalidChecker
-
- getDescriptor() - Method in interface chemaxon.checkers.StructureChecker
-
- getDescriptor() - Method in class chemaxon.fixers.AbstractStructureFixer
-
- getDescriptor() - Method in interface chemaxon.fixers.StructureFixer
-
Gets the descriptor object of the fixer.
- getDescriptor() - Method in interface chemaxon.marvin.services.ServiceDescriptorEditor
-
Returns the ServiceDescriptor represented by editor state or null
if the editor is in not valid state
- getDescriptorURI() - Method in class chemaxon.marvin.services.json.JsonServiceDescriptor
-
Gets the URI of the JSON RPC descriptor file
- getDesiredLength() - Method in class chemaxon.struc.MolBond
-
- getDesiredLength(boolean) - Method in class chemaxon.struc.MolBond
-
- getDesiredLength(int, int, int) - Method in class chemaxon.struc.MoleculeGraph
-
- getDesiredLength(MolBond) - Method in class chemaxon.struc.MoleculeGraph
-
- getDf1() - Method in enum chemaxon.marvin.alignment.AlignmentProperties.FlexibilityMode
-
- getDf2() - Method in enum chemaxon.marvin.alignment.AlignmentProperties.FlexibilityMode
-
- getDialog(Component, ServiceDescriptor) - Method in interface chemaxon.marvin.services.ServiceDialogProvider
-
Returns dialog with argument editor and result view
- getDihedral(int, int, int, int) - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
Returns the dihedral of 4 atoms.
- getDihedral(int[]) - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
Returns the dihedral of 4 atoms.
- getDim() - Method in class chemaxon.struc.MoleculeGraph
-
Gets the dimension.
- getDipole() - Method in class chemaxon.calculations.dipole.DipoleResult
-
Returns the length of the dipole moment vector.
- getDipoleVector() - Method in class chemaxon.calculations.dipole.DipoleResult
-
Returns the dipole moment vector.
- getDipoleX() - Method in class chemaxon.calculations.dipole.DipoleResult
-
Returns the x component of the dipole moment vector.
- getDipoleY() - Method in class chemaxon.calculations.dipole.DipoleResult
-
Returns the y component of the dipole moment vector.
- getDipoleZ() - Method in class chemaxon.calculations.dipole.DipoleResult
-
Returns the z component of the dipole moment vector.
- getDirectory() - Method in class chemaxon.marvin.beans.MarvinPane
-
Sets the working directory.
- getDisabledGroupTypes() - Method in class chemaxon.marvin.beans.MSketchPane
-
- getDisplay(int) - Method in class chemaxon.marvin.plugin.PluginFactory
-
Gets a display object, loads it if needed.
- getDisplay() - Method in class chemaxon.marvin.plugin.PluginFactory.PluginRecord
-
- getDisplayedChars() - Method in class chemaxon.struc.sgroup.DataSgroup
-
Gets the number of characters to be displayed(1...999 or 0 for all)
- getDisplayedLines() - Method in class chemaxon.struc.sgroup.DataSgroup
-
Gets the number of lines to be displayed (0: show all)
- getDisplayMolecule() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
-
Returns the molecule object to be used for GUI display.
- getDisplayMolecule() - Method in class chemaxon.marvin.calculations.MSAPlugin
-
Returns the molecule object to be used for GUI display.
- getDisplayMolecule() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns the molecule object to be used for GUI display.
- getDisplayQuality() - Method in class chemaxon.marvin.MolPrinter
-
Deprecated.
since Marvin 6.4 only high quality exists
- getDispopts() - Method in class chemaxon.marvin.beans.MarvinPane
-
Gets display options.
- getDispopts() - Method in class chemaxon.marvin.MolPrinter
-
Returns the actual display options.
- getDispoptsExt() - Method in class chemaxon.marvin.MolPrinter
-
Returns the actual extended display options.
- getDispQuality() - Method in class chemaxon.marvin.beans.MarvinPane
-
Deprecated.
always return 1. Deprecated Since Marvin 6.4.
- getDistance(int, int) - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
Returns the distance of 2 atoms.
- getDistance(int[]) - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
Returns the distance of 2 atoms.
- getDistanceCount(int, int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Counts the given value in a row of the distance matrix.
- getDistanceDegree(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Calculates the distance degree of an atom, which is the sum of the
corresponding row values in the distance matrix.
- getDoc(int, String) - Method in class chemaxon.marvin.view.MDocStorage
-
Gets the specified document.
- getDoc(int, String, MProgressMonitor) - Method in class chemaxon.marvin.view.MDocStorage
-
Gets the specified document.
- getDocLabel(int, MDocument) - Method in class chemaxon.marvin.io.MDocSource
-
Returns the display label for the given document and document index.
- getDocLabel(int, MDocument) - Method in class chemaxon.marvin.view.MDocStorage
-
Returns the display label for the given document and document index.
- getDocSource() - Method in class chemaxon.marvin.view.MDocStorage
-
Gets the document source.
- getDocSourcePosition() - Method in class chemaxon.marvin.view.MDocStorage
-
Gets the current position in the input.
- getDocStorage() - Method in class chemaxon.marvin.beans.MViewPane
-
Gets the sparse dynamic document storage.
- getDocStorage() - Method in class chemaxon.marvin.view.swing.TableSupport
-
Gets the sparse dynamic document storage.
- getDocument() - Method in class chemaxon.marvin.beans.MSketchPane
-
Gets the document.
- getDocument(int) - Method in class chemaxon.marvin.beans.MViewPane
-
Gets the nth document.
- getDocument(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns encapsulating document, creates it if needed.
- getDocument() - Method in class chemaxon.struc.MoleculeGraph
-
Gets the document object.
- getDocumentForChild(MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
-
Gets the parent document for a child molecule graph.
- getDocuments() - Method in class chemaxon.marvin.beans.MViewPane
-
Gets the array of documents.
- getDomainMax() - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
Returns the upper end of the spectrum.
- getDomainMin() - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
Returns the lower end of the spectrum.
- getDominantTautomerDistribution(int) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Returns the distribution of the dominant tautomer.
- getDonorAtomCount() - Method in class chemaxon.marvin.calculations.HBDAPlugin
-
Returns the overall donor atom count (without multiplicity) in the molecule.
- getDonorCount(int) - Method in class chemaxon.marvin.calculations.HBDAPlugin
-
Returns the atomic donor count corresponding to the specified atom index.
- getDonorCount() - Method in class chemaxon.marvin.calculations.HBDAPlugin
-
Returns the overall donor count (with multiplicity) in the molecule.
- getDotDir() - Static method in class chemaxon.util.DotfileUtil
-
Gets the directory of the configuration files.
- getDotDirName() - Static method in class chemaxon.util.DotfileUtil
-
Gets the subdirectory name of the configuration files.
- getDotDisconnectedFormula() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
-
Calculates the dot-disconnected molecular formula of a multifragment
molecule.
- getDotDisconnectedIsotopeFormula() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
-
Calculates the dot-disconnected isotope formula of a multifragment
molecule.
- getDotDisconnectedIsotopeFormula(boolean) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
-
Calculates the dot-disconnected isotope formula of a multifragment
molecule.
- getDotFile(String) - Static method in class chemaxon.util.DotfileUtil
-
Gets a configuration file with the specified relative path.
- getDotFileWithEnsuredPath(String) - Static method in class chemaxon.util.DotfileUtil
-
- getDoubleArray() - Method in class chemaxon.struc.prop.MDoubleArrayProp
-
Gets the integer value.
- getDoublePrecision() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns the precision.
- getDownWedge() - Method in class chemaxon.marvin.beans.MarvinPane
-
Gets the wedge bond display convention.
- getDownWedge() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the wedge bond display convention.
- getDownWedge() - Method in class chemaxon.marvin.MolPrinter
-
Gets the down wedge orientation.
- getDraggedObject() - Method in class chemaxon.struc.MDocument
-
Gets the dragged object
- getDrawProperties() - Method in class chemaxon.marvin.space.GraphicComponent
-
Returns the set draw properties of the component.
- getDrawProperty(String) - Method in class chemaxon.marvin.space.GraphicComponent
-
Returns the value of a draw property.
- getDrawProperty(String) - Method in class chemaxon.marvin.space.GraphicScene
-
Returns the draw property of the scene or null if the property is not defined.
- getDrawProperty(String) - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- getDrawType() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
Returns the drawing type of the molecular surface.
- getDrawType() - Method in class chemaxon.marvin.space.PharmacophoreArrow
-
Returns the name of the drawing type.
- getDrawType() - Method in class chemaxon.marvin.space.PharmacophorePoint
-
Returns the name of the drawing type.
- getDrawType() - Method in class chemaxon.marvin.space.SurfaceComponent
-
Returns the actual drawing type.
- getDreidingEnergy() - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
Returns the energy of the conformer.
- getDx() - Method in class chemaxon.struc.graphics.MTextAttributes
-
Gets the x shift.
- getDy() - Method in class chemaxon.struc.graphics.MTextAttributes
-
Gets the y shift.
- getEccentricity(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Calculates the eccentricity of an atom, which is the greatest value in
the corresponding row of the distance matrix.
- getEditable() - Method in class chemaxon.marvin.beans.MViewEditor
-
Returns the mode that determines if the structure is editable.
- getEditable() - Method in class chemaxon.marvin.beans.MViewPane
-
Returns the mode that determines if the structure is editable.
- getEditor() - Method in interface chemaxon.marvin.services.ServiceDescriptorEditor
-
Returns the editor component for the ServiceDescriptor
- getEditor(Class<T>) - Method in interface chemaxon.marvin.services.ServiceDescriptorEditorProvider
-
- getEditorClassName() - Method in class chemaxon.checkers.AbstractStructureChecker
-
- getEditorClassName() - Method in class chemaxon.checkers.InvalidChecker
-
- getEditorClassName() - Method in interface chemaxon.checkers.StructureChecker
-
Deprecated.
This method isn't needed anymore and will be removed in 6.0
- getEditorClassName() - Method in class chemaxon.checkers.StructureCheckerDescriptor
-
Returns the editorClassName
- getEditorComponent() - Method in class chemaxon.marvin.beans.MViewEditor
-
Returns the editor component.
- getEFlowsFromAtom(MolAtom) - Static method in class chemaxon.struc.graphics.MEFlow
-
Returns all the EFlow from this atom.
- getEFlowsOfAtom(MolAtom) - Static method in class chemaxon.struc.graphics.MEFlow
-
Returns all the EFlows that are started from this atom or pointing to this atom.
- getEFlowsToAtom(MolAtom) - Static method in class chemaxon.struc.graphics.MEFlow
-
Returns all the EFlows to this atom.
- getEigenVector() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
-
- getElectronContainersOf(MolAtom) - Method in class chemaxon.struc.graphics.MChemicalStruct
-
- getElectronDensity(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
-
Returns the electron density of an atom
calculated with HMO,
Double.NaN for no value.
- getElectronProp() - Method in class chemaxon.struc.MolAtom
-
Returns the number of lone pairs on this atom.
- getElectrophilicEnergy(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
-
Returns the electrophilic energy (localization energy L+) of an atom,
Double.NaN for no value.
- getElectrophilicOrder(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
-
- getElementCount() - Static method in class chemaxon.struc.PeriodicSystem
-
Number of elements in the periodic system
- getElementIndex() - Method in class chemaxon.marvin.space.ComponentElement
-
Returns the internal index of the ComponentElement
in the GraphicComponent.
- getElementType() - Method in class chemaxon.marvin.space.ComponentElement
-
Returns the type of the ComponentElement.
- getEnantiomer(T) - Static method in class chemaxon.calculations.stereo.Stereochemistry
-
Get the enantiomer pair of the given molecule
- getEncapsulatedReader() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
-
Gets the encapsulated record reader if it exists.
- getEncapsulatedReader() - Method in interface chemaxon.marvin.io.MRecordReader
-
Gets the encapsulated record reader if it exists.
- getEnclosingCube() - Method in class chemaxon.struc.MoleculeGraph
-
Gets the cube that encloses the atoms of molecule graph.
- getEncoding() - Method in class chemaxon.marvin.io.MolExportModule
-
Gets the output encoding.
- getEncoding() - Method in class chemaxon.marvin.io.MRecord
-
Gets the encoding.
- getEncoding() - Method in class chemaxon.marvin.io.PositionedInputStream
-
Gets the encoding.
- getEncodingFromOptions(String) - Static method in class chemaxon.formats.MFileFormatUtil
-
Gets the encoding that was explicitly given as an import option.
- getEndDx() - Method in class chemaxon.struc.graphics.MTextDocument.Portion
-
Gets the x shift at the end.
- getEndLineCount() - Method in class chemaxon.marvin.io.MRecord
-
Gets the line number at the ending point.
- getEndPos() - Method in class chemaxon.struc.graphics.MTextDocument.Portion
-
Gets the position of the last character + 1.
- getEndPosition() - Method in class chemaxon.marvin.io.MRecord
-
Gets the end position in the input file.
- getEndPosition() - Method in class chemaxon.struc.MDocument
-
Gets the end position of this document in the input file.
- getEndPosition() - Method in class chemaxon.struc.Molecule
-
Gets the end position of this molecule in the input file.
- getEnergy() - Method in class chemaxon.marvin.calculations.ConformerPlugin
-
Returns the energy of the lowest energy conformer in kcal/mol.
- getEnergy(int) - Method in class chemaxon.marvin.calculations.ConformerPlugin
-
Returns the energy of the i-th conformer in kcal/mol.
- getEnhancedStereo() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.EnhancedStereoGroup
-
- getEnhancedStereo() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter
-
Returns the enhanced stereo group (optional).
- getEnhancedStereoFlags() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
-
Returns the enhanced stereo flags of the molecule.
- getEnhancedStereoGroup(String) - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
-
Gets the EnhancedStereoGroup to which the specified flag is mapped.
- getEnumCodeNeeded() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Tests whether unique Markush enumeration code
should be generated
- getEnumerateMarkush() - Method in class chemaxon.util.HitColoringAndAlignmentOptions
-
Returns true if markush structures should be hit enumerated according
to the query structure.
- getError() - Method in class chemaxon.util.MolAligner
-
Get the error for the best alignment
- getErrorCode() - Method in class chemaxon.checkers.AbstractStructureChecker
-
- getErrorCode() - Method in class chemaxon.checkers.ExternalStructureChecker
-
- getErrorCode() - Method in class chemaxon.checkers.InvalidChecker
-
- getErrorCode() - Method in class chemaxon.checkers.result.DefaultExternalStructureCheckerResult
-
- getErrorCode() - Method in interface chemaxon.checkers.result.ExternalStructureCheckerResult
-
This function returns a
String which identifies the problems thus this
must be unique for each class that implements this interface
- getErrorCode() - Method in interface chemaxon.checkers.StructureChecker
-
- getErrorComponent() - Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
-
Returns a component with the appropriate error message.
- getErrorCount() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
-
Return the error count.
- getErrorDescription(int) - Method in class chemaxon.checkers.AbstractStructureChecker
-
Generate the error description depends on erroCount
- getErrorDescription(StructureCheckerDescriptor, int) - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
-
- getErrorLevel() - Method in exception chemaxon.marvin.plugin.PluginException
-
Returns the error level.
- getErrorMessage() - Method in class chemaxon.checkers.InvalidChecker
-
Gets the error message of the checker instance
- getErrorMessage() - Method in class chemaxon.marvin.calculations.ChargePlugin
-
Returns the calculation error information message if
ChargePlugin.run()
returned false (calculation error): hydrogen valence error.
- getErrorMessage() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
-
- getErrorMessage() - Method in class chemaxon.marvin.calculations.HBDAPlugin
-
Returns the calculation error information message if
HBDAPlugin.run() returned false
(calculation error): hydrogen valence error.
- getErrorMessage() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
-
Returns the calculation error information message if
HuckelAnalysisPlugin.run()
returned false (calculation error): hydrogen valence error.
- getErrorMessage() - Method in class chemaxon.marvin.calculations.IonChargePlugin
-
Returns the calculation error information message if
IonChargePlugin.run()
returned false (calculation error): the number of ionizable atoms
exceeds the specified limit (given in the "ions" parameter) or
hydrogen valence error.
- getErrorMessage() - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
-
Returns the calculation error information message if
IsoelectricPointPlugin.run()
returned false (calculation error): hydrogen valence error.
- getErrorMessage() - Method in class chemaxon.marvin.calculations.logDPlugin
-
Returns the calculation error information message if
logDPlugin.run()
returned false (calculation error): hydrogen valence error.
- getErrorMessage() - Method in class chemaxon.marvin.calculations.logPPlugin
-
Returns the calculation error information message if
logPPlugin.run()
returned false (calculation error): hydrogen valence error.
- getErrorMessage() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
-
Returns the calculation error information message
or the empty string if there is no error.
- getErrorMessage() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
-
Returns the calculation error information message
or the empty string if there is no error.
- getErrorMessage() - Method in class chemaxon.marvin.calculations.MSAPlugin
-
Returns the calculation error information message if
MSAPlugin.run()
returned
false (calculation error).
- getErrorMessage() - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
-
- getErrorMessage() - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Returns the calculation error information message if
pKaPlugin.run()
returned false (calculation error): the number of ionizable atoms
exceeds the specified limit (given in the "ions" parameter) or
hydrogen valence error.
- getErrorMessage() - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
-
Returns the calculation error information message if
PolarizabilityPlugin.run()
returned false (calculation error): hydrogen valence error.
- getErrorMessage() - Method in class chemaxon.marvin.calculations.RefractivityPlugin
-
Returns the calculation error information message if
RefractivityPlugin.run()
returned false (calculation error): hydrogen valence error.
- getErrorMessage() - Method in class chemaxon.marvin.calculations.ResonancePlugin
-
Returns the calculation error information message
or the empty string if there is no error.
- getErrorMessage() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Returns the calculation error information message
or the empty string if there is no error.
- getErrorMessage() - Method in class chemaxon.marvin.calculations.TPSAPlugin
-
Returns the calculation error information message if
run()
returned false (calculation error): hydrogen valence error.
- getErrorMessage() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns the calculation error information message if
CalculatorPlugin.run()
returned
false (calculation error).
- getErrorType() - Method in class chemaxon.checkers.AbstractStructureChecker
-
- getErrorType() - Method in class chemaxon.checkers.InvalidChecker
-
- getErrorType() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
-
- getErrorType() - Method in interface chemaxon.checkers.result.StructureCheckerResult
-
- getErrorType() - Method in interface chemaxon.checkers.StructureChecker
-
- getErrorType() - Method in class chemaxon.checkers.SubstructureChecker
-
- getErrorTypeDefaultFixerMap() - Method in class chemaxon.checkers.runner.configuration.reader.ActionStringBasedConfigurationReader
-
- getErrorTypeDefaultFixerMap() - Method in interface chemaxon.checkers.runner.configuration.reader.ConfigurationReader
-
- getErrorTypeDefaultFixerMap() - Method in class chemaxon.checkers.runner.configuration.reader.XMLBasedConfigurationReader
-
- getEstimatedTotalCharacters() - Method in class chemaxon.naming.DocumentExtractor.ProgressInfo
-
Deprecated.
Return an estimation of the total number of characters in the document.
- getEuler() - Method in class chemaxon.struc.CTransform3D
-
Gets the Euler angles from the rotation transformation.
- getEventHandler() - Method in class chemaxon.marvin.space.GraphicScene
-
Returns the event handler of the scene.
- getEventHandler() - Method in class chemaxon.marvin.space.MSpaceEasy
-
Returns the actual event handler of MarvinSpace.
- getExactMass() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
-
Calculates the weight of the MS molecule ion using the mass of the most
frequent natural isotope for element atoms.
- getExactMass() - Method in class chemaxon.struc.MoleculeGraph
-
Calculates the molecular weight of the molecule using the mass of the most
frequent natural isotope of the atoms.
- getException() - Method in exception chemaxon.marvin.plugin.PluginException
-
Returns the wrapped exception.
- getExcluded() - Method in class chemaxon.checkers.AbbreviatedGroupChecker
-
Gets the excluded abbreviations
- getExplicitHcount() - Method in class chemaxon.struc.MolAtom
-
Gets number of hydrogen connections.
- getExplicitHcount() - Method in class chemaxon.struc.MoleculeGraph
-
Gets the total number of explicit hydrogens attached to the molecule.
- getExplicitHcount(int) - Method in interface chemaxon.struc.Smolecule
-
Gets the number of explicit hydrogen atom neighbors of the given atom.
- getExplicitHydrogenData(Molecule, int) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
- getExplicitHydrogenData(Molecule, int) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
- getExplicitLonePairCount(int) - Method in class chemaxon.struc.MoleculeGraph
-
Gets the explicit lone pair count of the submitted atom.
- getExpression() - Method in class chemaxon.marvin.services.DynamicArgument
-
Returns the expression used for evaluations
- getExtensions() - Method in class chemaxon.formats.MFileFormat
-
Gets the extension list.
- getExternalCheckerConfigURL() - Method in class chemaxon.marvin.common.UserSettings
-
Returns the URL of the configuration file containing the list of external Checkers in marvin
sketch.
- getExternalConnections(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Gets the number of bonds of a specified atom where the neighbor atom
doesn't belong to the S-group.
- getExtraLabel() - Method in class chemaxon.struc.MolAtom
-
Gets the label string (also called atom value):
"result" or "result1|result2".
- getExtraLabelColor() - Method in class chemaxon.struc.MolAtom
-
Gets the extra label color(s):
lower 32 bits and upper 32 bits as
(alpha<<24 + red<<16 + green<<8 + blue).
- getExtraLabelColor(int) - Method in class chemaxon.struc.MolAtom
-
Gets the extra label color:
(alpha<<24 + red<<16 + green<<8 + blue).
- getExtraLabelColor(long, int) - Static method in class chemaxon.struc.MolAtom
-
Gets extra label color from composed color value.
- getExtraLabelSetColorMode(int) - Method in class chemaxon.struc.MDocument
-
Gets the coloring mode of extra label set sequences.
- getExtraLabelSetFont(int) - Method in class chemaxon.struc.MDocument
-
- getExtraLabelSetRGBs(int) - Method in class chemaxon.struc.MDocument
-
- getExtraLabelSetSeq() - Method in class chemaxon.struc.MolAtom
-
- getExtraLabelSetSize() - Method in class chemaxon.struc.MDocument
-
- getEZStereo(MolBond) - Method in class chemaxon.struc.MoleculeGraph
-
Gets E/Z stereo information for the given double bond.
- getFamily() - Method in class chemaxon.struc.graphics.MFont
-
Gets the font family name.
- getFarClip() - Method in class chemaxon.marvin.space.GraphicCell
-
Returns the z coordinate of the farther clipping plane
which is computed considering all components.
- getFavoritesComboBox() - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Creates and returns the favorites combo instance
- getFieldAccessor() - Method in class chemaxon.marvin.view.MDocStorage
-
Gets the field accessor.
- getFieldFont(String) - Method in class chemaxon.marvin.beans.MViewPane
-
Gets the font of a named field in a table.
- getFieldFontSize() - Method in class chemaxon.marvin.view.swing.TableOptions
-
Gets the field font size.
- getFieldName() - Method in class chemaxon.struc.sgroup.DataSgroup
-
Gets the data field name.
- getFields(int, Molecule, String[], MProp[]) - Method in class chemaxon.marvin.io.MFieldAccessor
-
Extracts properties.
- getFieldsShown() - Method in class chemaxon.marvin.view.swing.TableOptions
-
Are SDfile fields shown in table?
- getFieldType() - Method in class chemaxon.struc.sgroup.DataSgroup
-
Gets the field type.
- getFile() - Method in class chemaxon.formats.MolImporter
-
Gets the file object for the input.
- getFile() - Method in class chemaxon.marvin.beans.MarvinPane
-
Gets the current molecule file.
- getFileExtensionLC(File) - Static method in class chemaxon.formats.MFileFormatUtil
-
Gets the file extension in lower case.
- getFileExtensionLC(String) - Static method in class chemaxon.formats.MFileFormatUtil
-
Gets the file extension in lower case.
- getFileName() - Method in class chemaxon.formats.MolImporter
-
Gets the name of the input file
- getFilePointer() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
-
Get the file pointer.
- getFilePointer() - Method in class chemaxon.marvin.io.MRecordImporter
-
Gets the current position in the input file.
- getFilePointer() - Method in interface chemaxon.marvin.io.MRecordReader
-
Gets the current position in the input file.
- getFilePointer() - Method in class chemaxon.marvin.io.PositionedInputStream
-
Get the file pointer.
- getFinalCause() - Method in exception chemaxon.formats.MolFormatException
-
Gets the final cause of the exception.
- getFingerprint() - Method in class chemaxon.jep.context.MolContext
-
Returns the input molecule fingerprint.
- getFingerprint(Object) - Method in class chemaxon.jep.context.MolContext
-
Returns the input molecule fingerprint if argument is the input molecule,
null otherwise.
- getFingerprint(Molecule) - Method in interface chemaxon.jep.FingerprintGenerator
-
Returns the fingerprint of the structure.
- getFiveLongRings() - Method in class chemaxon.checkers.result.MetalloceneCheckerResult
-
This method returns the five long rings in the molecule represented by a
List
of
List of
MolAtom
- getFixedLocation(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MMidPoint
-
Gets the fixed location in the polyline.
- getFixer(String) - Method in class chemaxon.fixers.StructureFixerFactory
-
Deprecated.
This method returns a
StructureFixer instance identified by fixerId parameters
- getFixerClassName() - Method in class chemaxon.checkers.StructureCheckerDescriptor
-
Returns the fixerClassName
- getFixers(StructureCheckerResult) - Method in class chemaxon.checkers.runner.BasicCheckerRunner
-
- getFixers(StructureCheckerResult) - Method in interface chemaxon.checkers.runner.CheckerRunner
-
- getFixers(StructureCheckerResult) - Method in class chemaxon.checkers.runner.SketchCheckerRunner
-
- getFixers() - Method in class chemaxon.fixers.StructureFixerFactory
-
Deprecated.
This method returns all
StructureFixer instances available by the current configuration
- getFixMode() - Method in class chemaxon.checkers.StructureCheckerDescriptor
-
Returns the fixMode
- getFlags() - Method in class chemaxon.formats.MFileFormat
-
Gets the format descriptor flags.
- getFlags() - Method in class chemaxon.marvin.io.MRecord
-
Gets the record descriptor flags.
- getFlags() - Method in class chemaxon.struc.graphics.MPolyline
-
Gets the flags.
- getFlags() - Method in class chemaxon.struc.MolAtom
-
Gets flags.
- getFlags() - Method in class chemaxon.struc.MolBond
-
Gets bond type (4 bits), stereo (2+2+1 bits), topology (2 bits),
bond set (5 bits) and reacting center (7 bits) information.
- getFlags() - Method in class chemaxon.struc.MoleculeGraph
-
Gets the dimension and chiral flags.
- getFlags() - Method in class chemaxon.struc.RgMolecule
-
Gets the dimension and chiral flags.
- getFlexibilityMode() - Method in class chemaxon.marvin.alignment.MMPAlignmentProperties
-
- getFlexibleRingRotatableBondCount() - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
-
- getFlexibleRingSize() - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
-
- getFocus() - Method in class chemaxon.struc.MDocument
-
Gets the focused object
- getFogFactor() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the fog factor.
- getFontFamily() - Method in class chemaxon.struc.graphics.MTextAttributes
-
Gets the font family name.
- getFontMetrics(Graphics, MFont) - Method in class chemaxon.struc.graphics.MTextDocument.Section
-
Gets and updates the font metrics of a document section.
- getFontScale() - Method in class chemaxon.struc.graphics.MTextBox
-
Gets the font scaling factor.
- getFooterAsString() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
-
Gets the footer of the file as a string.
- getFooterAsString() - Method in interface chemaxon.marvin.io.MRecordReader
-
Gets the footer of the file as a string.
- getForefather() - Method in class chemaxon.struc.MoleculeGraph
-
Gets the first parent.
- getForeground() - Method in class chemaxon.struc.graphics.MTextAttributes
-
Gets the foreground color.
- getForegroundColor() - Method in class chemaxon.marvin.space.monitor.Label
-
Returns the foreground color of the label.
- getFormalCharge() - Method in class chemaxon.marvin.calculations.ChargePlugin
-
Returns the formal charge of the molecule.
- getFormalCharge(int) - Method in class chemaxon.marvin.calculations.ChargePlugin
-
Returns the formal charge of a specified atom.
- getFormalCharge() - Method in class chemaxon.struc.MoleculeGraph
-
Gets the (total) formal charge of the molecule.
- getFormat() - Method in class chemaxon.calculations.dipole.DipoleCalculator.Builder
-
Dipole export format.
- getFormat() - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder
-
Spectrum export format.
- getFormat(String) - Static method in class chemaxon.formats.MFileFormatUtil
-
Gets the file format descriptor for the specified codename.
- getFormat() - Method in class chemaxon.formats.MolExporter
-
Gets the output file format.
- getFormat() - Method in class chemaxon.formats.MolImporter
-
Get the file format.
- getFormat() - Method in class chemaxon.formats.MolInputStream
-
Get the molecule file format.
- getFormat() - Method in class chemaxon.marvin.beans.MarvinPane
-
Gets the default molecule file format.
- getFormat() - Method in class chemaxon.marvin.io.MolExportModule
-
Returns the output format.
- getFormat() - Method in class chemaxon.marvin.io.MRecord
-
Gets the full format string of the record.
- getFormat() - Method in class chemaxon.marvin.io.MRecordImporter
-
Gets the file format.
- getFormatNamesWithExtension(String) - Static method in class chemaxon.formats.MFileFormatUtil
-
- getFormatter() - Method in class chemaxon.calculations.dipole.DipoleCalculator
-
- getFormatter() - Method in class chemaxon.calculations.nmr.NMRCalculator
-
- getFormula() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
-
Calculates the molecular formula which is a string listing all atom types
an their occurence in the molecule.
- getFormula(int) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
-
Calculates a fixed digit sortable molecular formula.
- getFormula() - Method in class chemaxon.struc.MoleculeGraph
-
Gets the molecular formula.
- getFormula() - Method in class chemaxon.struc.RgMolecule
-
Gets the molecular formula in Hill order.
- getFormula() - Method in class chemaxon.struc.RxnMolecule
-
Gets the molecular formula in Hill order.
- getFovY() - Method in class chemaxon.marvin.space.GraphicCell
-
Returns the field of view.
- getFragCount() - Method in class chemaxon.struc.MoleculeGraph
-
- getFragCount(int) - Method in class chemaxon.struc.MoleculeGraph
-
Returns the number of fragments for the given fragmentation type.
- getFragIds(int) - Method in class chemaxon.struc.MoleculeGraph
-
Gets an array containing the fragment id for each atom for the given
fragmentation type.
- getFragmentCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns the number of fragments (disconnected parts) of the molecule.
- getFreeAtomSetIndex() - Method in class chemaxon.struc.MDocument
-
Returns the first unused atomset index.
- getFreeAttachAtoms() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Gets the atoms with free attachment points.
- getFreeAttachmentPointCount() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Gets the number of free attachment points.
- getFreeAttachmentPointOrders(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Gets the sorted free attachment orders of the given attachment atom.
- getFreeAttachmentPointOrders() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Gets the increasingly sorted orders of the free attachment points.
- getFreeAttachmentPoints(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
- getFreeBondSetIndex() - Method in class chemaxon.struc.MDocument
-
Returns the first unused bondset index.
- getFreeLegalAttachAtoms() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
- getFrequency() - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder
-
Gets the NMR frequency.
- getFrequency() - Method in class chemaxon.calculations.nmr.NMRCalculator
-
Returns NMR measurement frequency.
- getFrequency() - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
Returns the NMR measurement frequency in MHz unit.
- getFsp3() - Method in class chemaxon.calculations.TopologyAnalyser
-
Calculates the Fsp3 value of the given molecule.
Fsp3 = number of sp3 carbons / number of carbons
- getFsp3() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Calculates the Fsp3 value of the given molecule.
Fsp3 = number of sp3 carbons / number of carbons
- getFunctionalGroupDisplayMolTable() - Method in class chemaxon.jep.Evaluator
-
Returns a hashtable containing |functional group name| -> |displayable molecule representation|.
- getFunctionData() - Method in class chemaxon.jep.Evaluator
-
Returns information about Chemical Terms functions wrapped in chemaxon.jep.CTFunctionData objects.
- getFunctionData(boolean) - Method in class chemaxon.jep.Evaluator
-
Returns information about Chemical Terms functions wrapped in chemaxon.jep.CTFunctionData objects.
- getFunctionParameterData() - Method in class chemaxon.jep.Evaluator
-
- getFunctionScale() - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
- getFusedAliphaticRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Calculates the number of fused aliphatic rings (SSSR smallest set of
smallest aliphatic rings) in the molecule.
- getFusedAliphaticRingCount(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Calculates the number of fused aliphatic rings in the molecule (rings
s).
- getFusedAliphaticRings() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Identifies fused aliphatic rings (SSSR smallest set of smallest aliphatic
rings) in the molecule.
- getFusedAliphaticRings(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Identifies fused aliphatic rings (SSSR smallest set of smallest aliphatic
rings) in the molecule having the given size (number of atoms).
- getFusedAromaticRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Calculates the number of fused aromatic rings (SSSR smallest set of
smallest aromatic rings) in the molecule.
- getFusedAromaticRingCount(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Calculates the number of fused aromatic rings in the molecule (rings
s).
- getFusedAromaticRings() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Identifies fused aromatic rings (SSSR smallest set of smallest aromatic
rings) in the molecule.
- getFusedAromaticRings(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Identifies fused aromatic rings (SSSR smallest set of smallest aromatic
rings) in the molecule having the given size (number of atoms).
- getFusedRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Calculates the number of fused rings (SSSR smallest set of smallest rings)
in the molecule.
- getGenNameFontSize() - Method in class chemaxon.marvin.view.swing.TableOptions
-
Gets the IUPAC name font size.
- getGL() - Method in class chemaxon.marvin.space.GraphicScene
-
Returns the OpenGL2 interface.
- getGLAutoDrawable() - Method in class chemaxon.marvin.space.GraphicScene
-
Returns the GLAutoDrawable object.
- getGLCanvas() - Method in class chemaxon.marvin.space.GraphicScene
-
Returns the GL2 canvas.
- getGLInfo(boolean) - Method in class chemaxon.marvin.space.GraphicScene
-
Returns the OpenGL2 Renderer, Version, and Vendor
and Extensions in VERBOSE_LEVEL_DEVEL mode.
- getGlobalGUIProperties() - Method in class chemaxon.marvin.view.MDocStorage
-
Gets the Global GUI properties.
- getGlobalProperties() - Method in class chemaxon.formats.MolImporter
-
Gets the global properties in a container that was retrieved from
the input stream, earlier.
- getGlobalProperties() - Method in class chemaxon.marvin.io.MRecordImporter
-
Gets the global properties.
- getGrabbedLines() - Method in class chemaxon.marvin.io.PositionedInputStream
-
Gets the grabbed lines.
- getGrabbedMoleculeString() - Method in class chemaxon.formats.MolImporter
-
Gets the last grabbed molecule string with LF style line endings by default.
- getGraphicComponent() - Method in class chemaxon.marvin.space.GraphicComponent
-
- getGraphicComponent(int) - Method in class chemaxon.marvin.space.GraphicScene
-
Returns the GraphicComponent having the given index in the active cell.
- getGraphicComponent(int, int) - Method in class chemaxon.marvin.space.GraphicScene
-
Returns the GraphicComponent of the given cell.
- getGraphicComponent(UOID) - Method in class chemaxon.marvin.space.GraphicScene
-
Returns the GraphicComponent with the given id.
- getGraphicComponent() - Method in class chemaxon.marvin.space.MoleculeComponent
-
- getGraphicComponentCount() - Method in class chemaxon.marvin.space.GraphicScene
-
Returns the total number of GraphicComponents in the cells.
- getGraphicScene() - Method in class chemaxon.marvin.space.MSpaceEasy
-
Returns the GraphicScene of MarvinSpace to be able to explicitly
set more advanced features.
- getGraphUnion() - Method in class chemaxon.struc.MoleculeGraph
-
Gets a molecule graph containing all the atoms and bonds.
- getGraphUnion() - Method in class chemaxon.struc.RgMolecule
-
Gets a graph containing all the atoms and bonds.
- getGraphUnion() - Method in class chemaxon.struc.RxnMolecule
-
Gets a graph containing all the atoms and bonds.
- getGraphUnionAsSelection() - Method in class chemaxon.struc.Molecule
-
Gets a selection molecule containing all the atoms and bonds.
- getGrinv(int[]) - Method in class chemaxon.struc.MoleculeGraph
-
Gets the graph invariants (canonical labels).
- getGrinv(int[], boolean) - Method in class chemaxon.struc.MoleculeGraph
-
- getGrinv(int[], int) - Method in class chemaxon.struc.MoleculeGraph
-
Gets the graph invariants (canonical labels).
- getGrinv() - Method in class chemaxon.struc.MoleculeGraph
-
Gets the graph invariants array.
- getGrinvCC() - Method in class chemaxon.struc.MoleculeGraph
-
Gets the graph invariant change count.
- getGrinvCC() - Method in class chemaxon.struc.MProp
-
Gets the graph invariant change count at the moment of creation.
- getGrinvOptions() - Method in class chemaxon.struc.MoleculeGraph
-
Gets graph invariant calculation options passed to the module.
- getGroup(int) - Method in class chemaxon.marvin.plugin.PluginFactory
-
Gets the menu group for a plugin.
- getGroupedDotDisconnectedFormula() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
-
Calculates the grouped dot-disconnected molecular formula of a multifragment
molecule.
- getGroupMnemonic(int) - Method in class chemaxon.marvin.plugin.PluginFactory
-
Gets the group mnemonic for a plugin.
- getGUIPropertyContainer() - Method in class chemaxon.struc.MDocument
-
- getHalfWidth() - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
Returns NMR half-width.
- getHararyIndex() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Calculates the Harary index which is the half-sum of the off-diagonal
elements of the reciprocal molecular distance matrix of the molecule.
- getHcount(int) - Method in interface chemaxon.struc.Smolecule
-
Gets the total number of hydrogens of an atom.
- getHeadCrossingBonds() - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
-
Gets the head crossing bonds.
- getHeader() - Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
-
Returns the table header.
- getHeader() - Method in class chemaxon.marvin.plugin.concurrent.DefaultPluginWorkUnit
-
Returns the table header.
- getHeader() - Method in class chemaxon.marvin.plugin.concurrent.PluginWorkUnit
-
Returns the table header.
- getHeaderAsString() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
-
Gets the header of the file as a string.
- getHeaderAsString() - Method in interface chemaxon.marvin.io.MRecordReader
-
Gets the header of the file as a string.
- getHeaderNewLineCount() - Method in class chemaxon.marvin.io.MRecord
-
Gets the number of new lines in the molecule header part.
- getHeaderStyle() - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
returns the cell style applied to the header row
- getHeight() - Method in class chemaxon.marvin.space.GraphicCell
-
Returns the height of the cell.
- getHelpText() - Method in class chemaxon.checkers.AbstractStructureChecker
-
- getHelpText() - Method in class chemaxon.checkers.InvalidChecker
-
- getHelpText() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
-
- getHelpText() - Method in interface chemaxon.checkers.result.StructureCheckerResult
-
- getHelpText() - Method in interface chemaxon.checkers.StructureChecker
-
Deprecated.
This method isn't needed anymore and will be removed in 6.0
- getHelpText() - Method in class chemaxon.checkers.StructureCheckerDescriptor
-
Returns the help text
- getHelpText() - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
-
Returns the help text displayed on empty component
- getHeteroaliphaticRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Calculates the number of aliphatic heterocyclic rings in the molecule
(aliphatic rings containing at least a non-carbon atom).
- getHeteroaliphaticRingCount(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Calculates the number of aliphatic heterocyclic rings in the molecule
(aliphatic rings containing at least a non-carbon atom) having a given
size (number of atoms).
- getHeteroaliphaticRings() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Identifies heteroaliphatic rings in the molecule (aliphatic rings
containing at least a non-carbon atom).
- getHeteroaliphaticRings(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Identifies heteroaliphatic rings in the molecule (aliphatic rings
containing at least a non-carbon atom) having a given size (number of atoms).
- getHeteroaromaticRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns the heteroaromatic ring count.
- getHeteroaromaticRingCount(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Calculates the number of aromatic heterocyclic rings in the molecule
(aromatic rings containing at least a non-carbon atom) having a given size
(number of atoms).
- getHeteroaromaticRings() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Identifies heteroaromatic rings in the molecule (aromatic rings containing
at least a non-carbon atom).
- getHeteroaromaticRings(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Identifies heteroaromatic rings in the molecule (aromatic rings containing
at least a non-carbon atom) having a given size (number of atoms).
- getHeteroRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns the hetero ring count.
- getHeteroRingCount(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Calculates the number of heterocyclic rings in the molecule (rings
containing at least a non-carbon atom).
- getHeteroRings() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Identifies heterocyclic rings in the molecule (rings
containing at least a non-carbon atom).
- getHeteroRings(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Indentifies hetero rings in the molecule having a given size (number
of atoms).
- getHitColor() - Method in class chemaxon.util.HitColoringAndAlignmentOptions
-
Returns the color to be used when coloring the substructure hit.
- getHitHomologyColor() - Method in class chemaxon.util.HitColoringAndAlignmentOptions
-
Returns the color used for highlighting user defined homologies in a
substructure hit.
- getHits() - Method in class chemaxon.naming.DocumentExtractor
-
Deprecated.
Returns the hits found in the documents processed so far.
- getHitsFound() - Method in class chemaxon.naming.DocumentExtractor.ProgressInfo
-
Deprecated.
- getHMOChargeDensity(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
-
Returns the total charge density of an atom
calculated with HMO,
Double.NaN for no value.
- getHMOEigenVector() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
-
Returns the eigenvector.
- getHMOElectronDensity(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
-
Returns the electron density of an atom
calculated with HMO,
Double.NaN for no value.
- getHMOElectrophilicEnergy(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
-
Returns the electrophilic energy (localization energy L+) of an atom,
Double.NaN for no value.
- getHMOElectrophilicOrder(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
-
Returns the electrophilic order of an atom,
-1 for no value.
- getHMOHuckelOrbitalCoefficients() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
-
Returns the huckel orbital coefficients.
- getHMONucleophilicEnergy(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
-
Returns the nucleophilic energy (localization energy L-) of an atom,
Double.NaN for no value.
- getHMONucleophilicOrder(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
-
Returns the nucleophilic order of an atom,
-1 for no value.
- getHMORealEigenValue() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
-
Returns the real part of the eigenvalue.
- getHMOTotalPiEnergy() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
-
Returns the total pi energy of the input molecule.
- getHorizontalAlignment() - Method in class chemaxon.struc.graphics.MTextBox
-
Gets the horizontal alignment.
- getHPolarizability(int) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
-
Returns the sum of the implicit H atom polarizability values
around the given heavy atom.
- getHResult(int) - Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
-
Returns the sum result of the H neighbours of the given atom.
- getHuckelOrbitalCoefficients() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
-
- getHybridizationState() - Method in class chemaxon.struc.MolAtom
-
Gets the hybridization state.
- getHybridizationState(int) - Method in interface chemaxon.struc.Smolecule
-
Gets the hybridization state of an atom.
- getHydrogen() - Method in class chemaxon.marvin.plugin.CalculatorPlugin.HydrogenData
-
- getHyperWienerIndex() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Calculates the hyper Wiener index of the molecule.
- getIcon() - Method in class chemaxon.checkers.AbstractStructureChecker
-
- getIcon() - Method in class chemaxon.checkers.InvalidChecker
-
- getIcon() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
-
- getIcon() - Method in interface chemaxon.checkers.result.StructureCheckerResult
-
- getIcon() - Method in interface chemaxon.checkers.StructureChecker
-
Deprecated.
This method isn't needed anymore and will be removed in 6.0
- getIcon() - Method in class chemaxon.checkers.StructureCheckerDescriptor
-
Returns the
Icon related to iconPath property
- getIcon(int) - Method in class chemaxon.marvin.beans.MSketchPaneBeanInfo
-
Returns a MarvinSketch icon in 16x16 or 32x32 size.
- getIcon(int) - Method in class chemaxon.marvin.beans.MViewPaneBeanInfo
-
Returns a MarvinView icon in 16x16 or 32x32 size.
- getIcon() - Method in class chemaxon.marvin.services.localservice.LocalServiceDescriptor
-
- getIcon() - Method in class chemaxon.marvin.services.xmlrpcservice.XMLRPCServiceDescriptor
-
- getIconPath() - Method in class chemaxon.checkers.StructureCheckerDescriptor
-
Returns the icon path
- getId(String) - Static method in class chemaxon.marvin.services.json.JsonServiceDescriptor
-
Gets an ID for a method name, to make sure the client can identify the
answer for the request.
- getId() - Method in class chemaxon.marvin.space.GraphicCell
-
Returns the cell id as a UOID.
- getId() - Method in class chemaxon.marvin.space.GraphicComponent
-
Returns the id of the component.
- getId() - Method in class chemaxon.marvin.space.MoleculeComponent
-
- getIDBackgroundRGBA(int) - Method in class chemaxon.marvin.view.MDocStorage
-
Gets the background color's RGBA value in a record.
- getIDForegroundRGBA(int) - Method in class chemaxon.marvin.view.MDocStorage
-
Gets the foreground color's RGBA value in a record.
- getImage(double) - Method in class chemaxon.marvin.beans.MSketchPane
-
Gets the canvas contents as an image using a scale factor.
Examples:
To get an image with a scale factor equivalent to 100% magnification:
getImage(getDefaultScale());
To get an image with the actual scale factor: getImage(getScale());
- getImage(Dimension) - Method in class chemaxon.marvin.beans.MSketchPane
-
Gets the canvas contents as an image scaled to fit in the specified rectangle.
- getImageImportServiceURL() - Method in class chemaxon.marvin.common.UserSettings
-
- getImageMolecule() - Method in class chemaxon.marvin.calculations.logDPlugin
-
Returns the molecule to be used for legend image.
- getImplicitH() - Method in class chemaxon.marvin.beans.MarvinPane
-
Query the display method of implicit hydrogens.
- getImplicitH() - Method in class chemaxon.marvin.MolPrinter
-
Returns the display method of implicit hydrogens.
- getImplicitHCount(boolean) - Method in class chemaxon.struc.MolAtom
-
Gets the implicit Hydrogen count of the atom.
- getImplicitHcount() - Method in class chemaxon.struc.MolAtom
-
Gets the number of implicit hydrogens attached.
- getImplicitHcount() - Method in class chemaxon.struc.MoleculeGraph
-
Gets the total number of implicit hydrogens attached to the molecule.
- getImplicitHCount(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
- getImplicitHcount(int) - Method in interface chemaxon.struc.Smolecule
-
Gets the number of implicit Hydrogens of an atom.
- getImplicitHcount() - Method in interface chemaxon.struc.Smolecule
-
Gets the total number of implicit Hydrogens.
- getImplicitizableHList(Molecule, int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
-
Gets which atom is an implicitizable hydrogen.
- getImplicitizeFlag() - Method in class chemaxon.checkers.result.ExplicitHydrogenResult
-
Returns the flag which can used to identify which hydrogens should be implicitize.
- getIndex() - Method in class chemaxon.checkers.runner.BasicCheckerRunner
-
Returns the index
- getIndex() - Method in class chemaxon.marvin.space.GraphicCell
-
Returns the internal index of the cell.
- getIndexOfOriginalLigand() - Method in class chemaxon.marvin.plugin.CalculatorPlugin.HydrogenData
-
- getInnerPointRef(int, CTransform3D) - Method in class chemaxon.struc.graphics.MRoundedRectangle
-
- getInputCount() - Method in class chemaxon.formats.MolConverter.Builder
-
Gets the number of input files/streams.
- getInputCount() - Method in class chemaxon.formats.MolConverter.Options
-
Deprecated.
- getInputFormat() - Method in class chemaxon.marvin.io.MRecord
-
Gets the input format.
- getInputFormat() - Method in class chemaxon.struc.MDocument
-
Gets the input file format.
- getInputFormat() - Method in class chemaxon.struc.Molecule
-
Gets the input file format.
- getInputMolDim() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns the input molecule dimension.
- getInputMolecule() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
-
Gets the input molecule.
- getInputPriority() - Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor
-
Priority of the
MTransferable object when importing from clipboard.
- getInputStream(String) - Static method in class chemaxon.marvin.space.MSpaceEasy
-
Creates an InputStream from the given String.
- getInputStreamFromClipboard() - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
-
Gets an InputStream from the clipboard data if the format is supported by this MTransferable
- getInstance() - Static method in class chemaxon.checkers.StructureCheckerFactory
-
Deprecated.
Returns the default factory instance.
- getInstance(String, String) - Static method in class chemaxon.checkers.StructureCheckerFactory
-
Deprecated.
Returns the factory instance for specified paths.
- getIntArray() - Method in class chemaxon.struc.prop.MIntegerArrayProp
-
Gets the integer value.
- getIntegralValueAt(double) - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
Returns the value of the NMR integral function at a given x point.
- getInternalVersionId() - Static method in class com.chemaxon.version.VersionInfo
-
Returns the internal version identifier.
- getIntValue() - Method in enum chemaxon.struc.AtomProperty.Radical
-
Gets the integer representation of the radical.
- getInverseName() - Method in class chemaxon.marvin.util.OptionDescriptor
-
Gets the inverse option name.
- getInvisibleSets() - Method in class chemaxon.marvin.beans.MarvinPane
-
Gets the visibility of the specified atom sets.
- getIonizerErrorMessage() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
-
Returns the calculation error information message
or the empty string if there is no error.
- getIonizerErrorMessage() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
-
Returns the calculation error information message
or the empty string if there is no error.
- getIsotope(int, int) - Static method in class chemaxon.struc.PeriodicSystem
-
Retrieves an isotope of the element
- getIsotopeComposition() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
-
Returns the molecular composition (w/w%).
- getIsotopeComposition(boolean) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
-
Returns the molecular composition (w/w%).
- getIsotopeCount() - Static method in class chemaxon.struc.PeriodicSystem
-
Number of isotopes in the periodic system
- getIsotopeCount(int) - Static method in class chemaxon.struc.PeriodicSystem
-
Number of isotopes of the element
- getIsotopeDistribution() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
-
Calculates the isotopic distributions for the molecule.
- getIsotopeFormula() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
-
Calculates the molecular formula (isotopes are separated).
- getIsotopeFormula(boolean) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
-
Calculates the molecular formula (isotopes are separated).
- getIterator() - Method in class chemaxon.marvin.io.formats.MoleculeImporter
-
Returns an iterator that iterates through all molecules in the file/stream.
- getItsArrow() - Method in class chemaxon.struc.RxnMolecule
-
Gets the reaction arrow of this reaction.
- getJavaVersionStr() - Static method in class com.chemaxon.version.VersionInfo
-
Returns the Java VM version information as string.
- getKey() - Method in class chemaxon.marvin.plugin.gui.OptionsPane
-
Returns the plugin key.
- getKey(int) - Method in class chemaxon.marvin.plugin.PluginFactory
-
Gets the menu key for a plugin.
- getKey(int) - Method in class chemaxon.struc.MPropertyContainer
-
Gets a property key.
- getKey(int) - Method in class chemaxon.struc.prop.MHashProp
-
Gets a key.
- getKeys(int, Molecule) - Method in class chemaxon.marvin.io.MFieldAccessor
-
Gets the keys in a record.
- getKeys() - Method in class chemaxon.struc.MPropertyContainer
-
Returns the property keys.
- getKnownExtension(String) - Static method in class chemaxon.formats.MFileFormatUtil
-
Returns the file extension if it is a known extension.
- getL(int) - Method in class chemaxon.marvin.beans.MViewPane
-
Gets a label.
- getL(int, int) - Method in class chemaxon.marvin.view.MDocStorage
-
Gets a text label in a record.
- getLabel(int) - Method in class chemaxon.marvin.space.AtomProperty.MoleculeAtomProperty
-
- getLabel(int) - Method in class chemaxon.marvin.space.AtomProperty.SmoleculeAtomProperty
-
- getLabelCenter() - Method in class chemaxon.struc.sgroup.SgroupAtom
-
Gets the index of the character in the label the bonds should point to.
- getLabelInformation(String, boolean) - Method in class chemaxon.marvin.space.GraphicComponent
-
Labels will be created associated to this GraphicComponent if the component
supports the given labeltype, and returns arbitrary numbers of ComponentElements
with correct coordinates and description to create a label.
- getLabelInformation(String) - Method in class chemaxon.marvin.space.GraphicComponent
-
- getLabelInformation(String) - Method in class chemaxon.marvin.space.MacroMoleculeComponent
-
Collects the label information of the visualizers.
- getLabelInformation(String) - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- getLabelInformation(String, boolean) - Method in class chemaxon.marvin.space.MoleculeComponent
-
Labels will be created associated to this MoleculeComponent if the labeltype
is "atom", "extraatomlabel" or "molecule".
- getLabelInformation(String) - Method in class chemaxon.marvin.space.MoleculeComponent
-
- getLabels() - Method in class chemaxon.marvin.beans.MarvinPane
-
Deprecated.
use isAtomSymbolsVisible() instead
- getLabels(double[]) - Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
-
Returns formatted array.
- getLargestRing() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Identifies the atoms of the largest ring (number of atoms) in the molecule.
- getLargestRingSize() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns the largest ring size.
- getLargestRingSizeOfAtom(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns the size of largest ring containing the specified atom.
- getLargestRingSystem() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Identifies the atoms of the largest ring system (number of rings) in the
molecule.
- getLargestRingSystemSize() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns the size of the largest ring system (number of rings) in the molecule.
- getLastEOL() - Method in class chemaxon.marvin.io.PositionedInputStream
-
- getLastProcessedLineNum() - Method in class chemaxon.formats.recognizer.Recognizer
-
Deprecated.
as of Marvin 2014.07.21.0 not used
- getLastSketchFrameSize() - Method in class chemaxon.marvin.common.UserSettings
-
- getLeft() - Method in class chemaxon.marvin.space.GraphicCell
-
Returns the x coordinate of the left edge of the active cell.
- getLeftBracket(CTransform3D) - Method in class chemaxon.struc.graphics.MBracket
-
- getLeftName() - Method in class chemaxon.struc.sgroup.SgroupAtom
-
Gets the string that will be shown at the left side of the molecule.
- getLegalAttachAtoms() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
- getLength() - Method in class chemaxon.struc.MolBond
-
Gets the actual length of the bond.
- getLevel() - Method in interface chemaxon.common.util.MProgressMonitor
-
Gets the level of this progress monitor.
- getLevelCount() - Method in class chemaxon.formats.recognizer.RecognizerList
-
Deprecated.
Gets the number of levels.
- getLibrarySizeString() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Returns the string representation of the Markush library size.
- getLicenseExceptionMessage() - Static method in class chemaxon.license.LicenseManager
-
Returns the common message used at license problems.
- getLicenseExceptionPanel(String) - Static method in class chemaxon.license.LicenseManager
-
Returns the common swing component used to indicate missing license.
- getLicenseExceptionPanel(LicenseException) - Static method in class chemaxon.license.LicenseManager
-
Returns the common swing component used to indicate missing license.
- getLigand(int) - Method in class chemaxon.struc.MolAtom
-
Gets the i-th ligand of this atom.
- getLigand(MolAtom, int) - Method in class chemaxon.struc.MoleculeGraph
- getLigandAtno(MolAtom, int) - Method in class chemaxon.struc.MoleculeGraph
- getLigandBondType(MolAtom, int) - Method in class chemaxon.struc.MoleculeGraph
- getLigandCount(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
- getLigandIndex(MolAtom) - Method in class chemaxon.struc.MolAtom
-
Returns the index of the specified ligand in this atom.
- getLigandOrder(MolAtom) - Method in class chemaxon.struc.MolAtom
-
Gets the order of a specified ligand.
- getLigandOrderVisibility() - Method in class chemaxon.marvin.MolPrinter
-
Gets the ligand order visibility setting.
- getLigands() - Method in class chemaxon.struc.MolAtom
-
Returns the atoms connected to this atom by a bond.
- getLigands(Integer) - Method in class chemaxon.struc.SelectionMolecule
-
- getLimitedStructureCount() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Returns the number of structures to be generated.
- getLine(int) - Method in class chemaxon.struc.graphics.MTextBox
-
Gets a line.
- getLineColor() - Method in class chemaxon.struc.MObject
-
Gets the line color of the object.
- getLineCount() - Method in class chemaxon.formats.MolImporter
-
Gets the current line number.
- getLineCount() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
-
Get the current line number.
- getLineCount() - Method in class chemaxon.marvin.io.MolImportModule
-
Returns the line count in the molecule input stream.
- getLineCount() - Method in class chemaxon.marvin.io.MRecordImporter
-
Gets the current line number in the input file.
- getLineCount() - Method in interface chemaxon.marvin.io.MRecordReader
-
Get the current line number.
- getLineCount() - Method in class chemaxon.marvin.io.PositionedInputStream
-
Gets the current line number.
- getLineCount() - Method in class chemaxon.struc.graphics.MTextBox
-
Gets the number of lines.
- getLineMiddlePoint(DPoint3, DPoint3) - Static method in class chemaxon.struc.graphics.MPolyline
-
- getLineNumber() - Method in class chemaxon.marvin.io.MRecordReader.Position
-
Gets the line number.
- getLineNumberInFile() - Method in exception chemaxon.formats.MolFormatException
-
Gets the line number relative to the first line of the file.
- getLineNumberInRecord() - Method in exception chemaxon.formats.MolFormatException
-
Gets the line number relative to the first line of the record.
- getLineNumberMap() - Method in class chemaxon.marvin.io.MRecord
-
Gets the line number to original line number mapping.
- getLineOnScreen(int) - Method in class chemaxon.struc.sgroup.DataSgroup
-
Returns the i-th row of the data sgroup label, as displayed on the screen
(with tag, query operator, units etc.)
- getLinkNodeOuterAtom(int) - Method in class chemaxon.struc.MolAtom
-
Gets the index of one of the link node's outer neighbor atoms.
- getList() - Method in class chemaxon.checkers.AbbreviatedGroupChecker.Abbreviations
-
Gets the list of abbreviations
- getList() - Method in class chemaxon.struc.MolAtom
-
Gets the atom list.
- getList() - Method in class chemaxon.struc.prop.MListProp
-
Gets the array.
- getListeners() - Method in class chemaxon.marvin.view.MDocStorage
-
- getLoadSaveLocation() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the load/save filechooser working directory selection method names, based on the
preferences dialog.
- getLoadWorkingDir() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the filechooser's default working directory, if it is set, and the filechooser working
directory selection method is saveCustomLocation.
- getLocalMaximumPlaces() - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
- getLocalMenuName() - Method in class chemaxon.checkers.AbstractStructureChecker
-
- getLocalMenuName() - Method in class chemaxon.checkers.InvalidChecker
-
- getLocalMenuName() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
-
- getLocalMenuName() - Method in interface chemaxon.checkers.result.StructureCheckerResult
-
- getLocalMenuName() - Method in interface chemaxon.checkers.StructureChecker
-
Deprecated.
This method isn't needed anymore and will be removed in 6.0
- getLocalMenuName() - Method in class chemaxon.checkers.StructureCheckerDescriptor
-
Returns the local menu name
- getLocalParity(int) - Method in class chemaxon.struc.MoleculeGraph
-
Computes the local parity of an atom of the Molecule instance
based on both the coordinates of the neighboring atoms
and the stereo information of the bonds to those.
- getLocalParity(int) - Method in class chemaxon.struc.RgMolecule
-
Computes the local parity of an atom of the RgMolecule instance
based on both the coordinates of the neighboring atoms
and the stereo information of the bonds to those.
- getLocalParity(int) - Method in class chemaxon.struc.RxnMolecule
-
Computes the local parity of an atom of the RxnMolecule instance
based on both the coordinates of the neighboring atoms
and the stereo information of the bonds to those.
- getLocation(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MAtomSetPoint
-
Gets the location.
- getLocation(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MEFlowBasePoint
-
Gets the location.
- getLocation(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MMidPoint
-
Gets the location.
- getLocation(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MMidPoint.Sticky
-
Gets the location.
- getLocation(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MRectanglePoint.Sticky
-
Gets the location.
- getLocation() - Method in class chemaxon.struc.MolAtom
-
Gets the coordinates.
- getLocation(DPoint3) - Method in class chemaxon.struc.MolAtom
-
Gets the coordinates.
- getLocation() - Method in class chemaxon.struc.MoleculeGraph
-
Gets the origin of the molecule.
- getLocation(DPoint3, CTransform3D) - Method in class chemaxon.struc.MPoint
-
Gets the point's location.
- getLocation(CTransform3D) - Method in class chemaxon.struc.MPoint
-
Gets the point's location.
- getLocation() - Method in class chemaxon.struc.MPoint
-
Gets the point's location.
- getLock() - Method in class chemaxon.struc.MolAtom
-
Get lock object for synchronization.
- getLock() - Method in class chemaxon.struc.MolBond
-
Gets lock object for synchronization.
- getLock() - Method in class chemaxon.struc.MoleculeGraph
-
Gets the lock object for synchronization.
- getLog() - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
-
Returns the Logger of the Clipboard handler subsystem.
- getlogD() - Method in class chemaxon.marvin.calculations.logDPlugin
-
- getlogDpI() - Method in class chemaxon.marvin.calculations.logPPlugin
-
Returns the logD value at pI.
- getlogDs() - Method in class chemaxon.marvin.calculations.logDPlugin
-
Returns the logD array.
- getLogger() - Method in class chemaxon.calculations.dipole.DipoleCalculator.Builder
-
Returns the dipole calculator logger.
- getLogger() - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder
-
Gets the calculator logger.
- getLogger() - Method in class chemaxon.checkers.runner.AdvancedCheckerRunner
-
Returns the current logger.
- getLogicalValue(Object) - Static method in class chemaxon.jep.ChemJEP
-
- getLogPercentageLimit() - Method in class chemaxon.marvin.calculations.pKaPlugin
-
- getlogPMicro() - Method in class chemaxon.marvin.calculations.logPPlugin
-
Returns the micro logP value.
- getlogPNonionic() - Method in class chemaxon.marvin.calculations.logPPlugin
-
Returns the logP value for the non-ionic form.
- getLogPTrainingIds() - Static method in class chemaxon.marvin.calculations.logDPlugin
-
Returns the id's of available logP trainings.
- getlogPTrue() - Method in class chemaxon.marvin.calculations.logPPlugin
-
Returns the most typical logP among logD at pI, micro logP and nonionic logP.
- getLonePairCount() - Method in class chemaxon.struc.MolAtom
-
Returns the automatically calculated lone pair count of this atom.
- getLonePairCount(int) - Method in class chemaxon.struc.MoleculeGraph
-
Gets the number of lone pairs.
- getLonePairCount(int) - Method in class chemaxon.struc.RgMolecule
-
Gets the number of lone pairs.
- getLonePairsVisible() - Method in class chemaxon.marvin.beans.MarvinPane
-
Tests whether lone pairs are visible.
- getLowestEnergyConformer() - Method in class chemaxon.marvin.calculations.ConformerPlugin
-
Returns the calculated lowest energy conformer.
- getLowestEnergyConformer() - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
Returns the lowest energy conformer of the molecule.
- getM(int) - Method in class chemaxon.marvin.beans.MViewPane
-
Gets the nth molecule in memory.
- getM(int, String) - Method in class chemaxon.marvin.beans.MViewPane
-
Gets the nth molecule in a text format.
- getMacroMolecule() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
-
Returns the MacroMolecule this component visualizes.
- getMacroMoleculeComponent() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- getMacroMoleculeComponent() - Method in class chemaxon.marvin.space.MoleculeComponent
-
Returns the macromolecule visualizer if this MoleculeComponent visualizes
a ligand in a complex.
- getMacropKaValues(int, double[], int[]) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Calculates the least acidic pKa values in ascending order
or the biggest basic pKa values in descending order.
- getMacropKaValues(int) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Calculates the acidic pKa values in ascending order or the basic pKa values in descending order.
- getMacroSpeciesCharge(int) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Returns the formal charges of a given macrospecies.
- getMag() - Method in class chemaxon.marvin.beans.MSketchPane
-
Deprecated.
As of Marvin 2.8.1, replaced by getScale()
- getMainDoc(int) - Method in class chemaxon.marvin.view.MDocStorage
-
Gets the document at the specified position.
- getMainDoc(int, MProgressMonitor) - Method in class chemaxon.marvin.view.MDocStorage
-
Gets the document at the specified position.
- getMainMolecule(int, Molecule) - Method in class chemaxon.marvin.io.MFieldAccessor
-
Gets the main molecule object in a record.
- getMainMolecule(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
- getMainMoleculeGraph() - Method in class chemaxon.struc.MDocument
-
Gets the main molecule graph.
- getMainMolFieldness() - Method in class chemaxon.marvin.view.swing.TableOptions
-
Tests whether the main molecule is a field.
- getMajorMicrospecies() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
-
- getMajorVersion() - Static method in class com.chemaxon.version.VersionInfo
-
Returns the major version.
- getMap() - Method in class chemaxon.struc.prop.MHashProp
-
Gets the map.
- getMap(MoleculeGraph) - Method in class chemaxon.struc.prop.MHCoords3DProp
-
Gets a map containing MolAtom objects as keys and DPoint3 arrays as
values.
- getMappingStyle() - Method in class com.chemaxon.mapper.AutoMapper
-
Returns the mapping style of the mapper.
- getMappingStyle() - Method in class com.chemaxon.mapper.AutoMapper.Options
-
- getMarkushDisplayMode() - Method in class chemaxon.util.HitColoringAndAlignmentOptions
-
Returns the Markush display mode.
- getMass() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
-
Calculates the molecular weight of the molecule.
- getMass() - Method in class chemaxon.struc.MolAtom
-
Gets the atomic weight.
- getMass() - Method in class chemaxon.struc.MoleculeGraph
-
Calculates the molecular weight of the molecule.
- getMass(int) - Static method in class chemaxon.struc.PeriodicSystem
-
Atomic weight of the element based on the natural abundance of its
isotopes
- getMass(int, int) - Static method in class chemaxon.struc.PeriodicSystem
-
Atomic weight of an isotope
- getMass() - Method in class chemaxon.struc.RgMolecule
-
Calculates the molecular weight of the molecule.
- getMass() - Method in class chemaxon.struc.RxnMolecule
-
Calculates the molecular weight of the molecule.
- getMassno() - Method in class chemaxon.struc.MolAtom
-
Gets the mass number.
- getMassno(int) - Method in interface chemaxon.struc.Smolecule
-
Gets the mass number of an atom.
- getMassPrecision(int) - Static method in class chemaxon.struc.PeriodicSystem
-
The precision of an elemental mass is the number of measured digits after
the decimal separator.
- getMassPrecision(int, int) - Static method in class chemaxon.struc.PeriodicSystem
-
The precision of an isotopic mass is the number of measured digits after
the decimal separator.
- getMaxAttachmentPointOrder(int) - Method in class chemaxon.struc.RgMolecule
-
Gets the maximal attachment point order of R-group definition molecules specified by an R-group ID.
- getMaxCols() - Method in class chemaxon.marvin.view.swing.TableOptions
-
Get maximum value of columns in the table.
- getMaxDimCached() - Method in class chemaxon.marvin.view.MDocStorage
-
Gets the maximum molecule dimension.
- getMaximalProjectionArea() - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
Returns the maximal projection area in Angstrom^2.
- getMaximalProjectionRadius() - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
Returns the radius of the circle surrounding the maximal projection in Angstrom.
- getMaximum() - Method in interface chemaxon.common.util.MProgressMonitor
-
Gets the maximum value.
- getMaximumMappedValue() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
Returns the maximum value of the mapped property on this surface.
- getMaximumValue() - Method in class chemaxon.marvin.space.SurfaceColoring
-
Returns the greatest property value of the surface vertices.
- getMaxRepetitions() - Method in class chemaxon.struc.MolAtom
-
Gets the maximum number of repetitions for a link atom.
- getMaxRgroupAttachmentPointOrder() - Method in class chemaxon.struc.MoleculeGraph
-
Returns the maximal attachment point order of R-group attachment point atoms in
this molecule graph.
- getMaxRows() - Method in class chemaxon.marvin.view.swing.TableOptions
-
Get maximum value of rows in the table
- getMaxSize() - Method in class chemaxon.marvin.view.swing.TableOptions
-
Get the maximum number of molecules displayed in the table.
- getMaxThreadCount() - Method in class com.chemaxon.mapper.AutoMapper.Options
-
- getMaxX() - Method in class chemaxon.marvin.space.BoundingBox
-
Returns the maximum x coordinate of the box.
- getMaxY() - Method in class chemaxon.marvin.space.BoundingBox
-
Returns the maximum y coordinate of the box.
- getMaxZ() - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
- getMaxZ() - Method in class chemaxon.marvin.space.BoundingBox
-
Returns the maximum z coordinate of the box.
- getMChemicalStruct() - Method in class chemaxon.struc.MDocument
-
- getMcsSimilarityLimit() - Method in class chemaxon.marvin.alignment.MMPAlignmentProperties
-
- getMeaningfulFrequencies() - Static method in class chemaxon.calculations.nmr.NMRSpectrum
-
Returns the array of meaningful NMR measurement frequencies in MHz.
- getMElectron() - Method in class chemaxon.struc.graphics.MEFlow
-
- getMElectronContainer() - Method in class chemaxon.struc.graphics.MEFlow
-
- getMElectronContainerIndexInAtom(MolAtom, MElectronContainer) - Method in class chemaxon.struc.graphics.MChemicalStruct
-
- getMElectronContainerOf(MElectron) - Method in class chemaxon.struc.graphics.MChemicalStruct
-
- getMElectronRef() - Method in class chemaxon.struc.graphics.MEFlow
-
- getMenu(int) - Method in class chemaxon.marvin.plugin.PluginFactory
-
Gets the menu string for a plugin.
- getMergedst() - Method in class chemaxon.marvin.beans.MSketchPane
-
Gets the merge distance.
- getMessage() - Method in class com.chemaxon.calculations.stereoanal.ErrorReport
-
Returns an error message.
- getMetalAtoms() - Method in class chemaxon.checkers.result.MetalloceneCheckerResult
-
This method returns the metallocene relevant metal atoms represented
by a
List of
MolAtom.
- getMicrospecies(int) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
-
Returns the microspecies molecule.
- getMicrospeciesCount() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
-
Returns the number of microspecies
- getMidPointLocation(int, CTransform3D) - Method in class chemaxon.struc.graphics.MPolyline
-
Gets the middle point of the arc.
- getMIMEType() - Method in class chemaxon.formats.MFileFormat
-
Deprecated.
as of Marvin 2014.07.21.0 not used
- getMinimalProjectionArea() - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
Returns the minimal projection area in Angstrom^2.
- getMinimalProjectionRadius() - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
Returns the radius of the circle surrounding the minimal projection in Angstrom.
- getMinimumHeight() - Method in class chemaxon.struc.graphics.MTextBox
-
Gets the minimum height of the text.
- getMinimumMappedValue() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
Returns the minimum value of the mapped property on this surface.
- getMinimumValue() - Method in class chemaxon.marvin.space.SurfaceColoring
-
Returns the lowest property value of the surface vertices.
- getMinRepetitions() - Method in class chemaxon.struc.MolAtom
-
Gets the minimum number of repetitions for a link node.
- getMinX() - Method in class chemaxon.marvin.space.BoundingBox
-
Returns the minimum x coordinate of the box.
- getMinY() - Method in class chemaxon.marvin.space.BoundingBox
-
Returns the minimum y coordinate of the box.
- getMinZ() - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
- getMinZ() - Method in class chemaxon.marvin.space.BoundingBox
-
Returns the minimum z coordinate of the box.
- getMirroredArrowFlags(int) - Method in class chemaxon.struc.graphics.MPolyline
-
Mirror transformation for arrow heads.
- getMMFF94Energy() - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
Returns the MMFF94 energy of the structure (default: kcal/mol).
- getMnemonic(int) - Method in class chemaxon.marvin.plugin.PluginFactory
-
Gets the menu mnemonic for a plugin.
- getMode() - Method in enum chemaxon.marvin.alignment.AlignmentAccuracyMode
-
- getMol() - Method in class chemaxon.marvin.beans.MSketchPane
-
Returns the clone of the current molecule being on the canvas.
- getMol(String) - Method in class chemaxon.marvin.beans.MSketchPane
-
Gets the molecule in a text format.
- getMolbg() - Method in class chemaxon.marvin.beans.MarvinPane
-
Gets the molecule background color.
- getMolBytes() - Method in class chemaxon.marvin.io.MRecord
-
Gets the molecule bytes, with preprended header and appended footer
if appropriate.
- getMolCenter(int, String) - Method in class chemaxon.marvin.view.MDocStorage
-
Gets a molecule center.
- getMolCrd() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
-
- getMolecule() - Method in class chemaxon.calculations.dipole.DipoleResult
-
Returns the input molecule of the dipole moment computation.
- getMolecule() - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
Returns the molecule under examination.
- getMolecule() - Method in class chemaxon.calculations.Ring
-
Retrieves the input molecule
- getMolecule() - Method in class chemaxon.calculations.stereo.Stereochemistry
-
Retrieves the input molecule
- getMolecule() - Method in class chemaxon.calculations.TopologyAnalyser
-
Retrieves the input molecule
- getMolecule() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
-
- getMolecule() - Method in interface chemaxon.checkers.result.StructureCheckerResult
-
- getMolecule() - Method in class chemaxon.checkers.runner.BasicCheckerRunner
-
Returns the molecule
- getMolecule() - Method in class chemaxon.checkers.runner.SketchCheckerRunner
-
- getMolecule() - Method in class chemaxon.jep.context.MolContext
-
Returns the input molecule.
- getMolecule() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
-
Returns the Molecule representation of the MacroMolecule.
- getMolecule() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- getMolecule() - Method in class chemaxon.marvin.space.MoleculeComponent
-
Returns the Molecule of the MoleculeComponent.
- getMolecule() - Method in class chemaxon.struc.prop.MMoleculeProp
-
Gets the molecule.
- getMolecule() - Method in interface com.chemaxon.calculations.solubility.SolubilityResult
-
Returns the input molecule.
- getMolecule1Aligned() - Method in class chemaxon.marvin.alignment.MMPAlignmentResult
-
- getMolecule2Aligned() - Method in class chemaxon.marvin.alignment.MMPAlignmentResult
-
- getMoleculeGraph() - Method in class chemaxon.struc.graphics.MChemicalStruct
-
Gets the stored molecule graph.
- getMoleculeIterator() - Method in class chemaxon.marvin.io.MDocSource
-
Gets a molecule iterator for this document source.
- getMoleculeIterator(MolImporter) - Static method in class chemaxon.util.iterator.MoleculeIteratorFactory
-
Gets a molecule iterator from the importer.
- getMoleculeIterators(MolImporter[]) - Static method in class chemaxon.util.iterator.MoleculeIteratorFactory
-
Gets molecule iterators from the importers in an array.
- getMoleculeMovie() - Method in class chemaxon.struc.MDocument
-
Gets the molecule movie.
- getMoleculeName() - Method in class chemaxon.marvin.io.MRecord
-
Returns the name of the molecule in the record.
- getMoleculeOrig() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
-
Gets back a clone of the unmodified input structure.
- getMoleculeString() - Method in class chemaxon.marvin.io.MRecordImporter
-
Gets the last molecule as a string.
- getMoleculeWithAlignedCoordinates(int) - Method in class chemaxon.marvin.alignment.Alignment
-
After the alignment result molecule can be obtained.
- getMolfileExtensions() - Static method in class chemaxon.formats.MFileFormatUtil
-
Gets the array of known molecule file extensions.
- getMolfileFormats() - Static method in class chemaxon.formats.MFileFormatUtil
-
Gets the array of known molecule file formats.
- getMolfileVersion() - Method in class chemaxon.marvin.io.formats.mdl.MolExport
-
Gets the molfile version.
- getMolfileVersion() - Method in class chemaxon.marvin.io.formats.mdl.MolImport
-
Gets the molfile version.
- getMolID() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
-
- getMolImportModule() - Method in class chemaxon.formats.MolImporter
-
- getMolImportModule() - Method in class chemaxon.marvin.io.MRecordImporter
-
- getMolIndex() - Method in exception chemaxon.marvin.io.MolExportException
-
Returns the molecule index.
- getMolInputStream() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
-
Gets the molecule input stream.
- getMolInputStream() - Method in interface chemaxon.marvin.io.MRecordReader
-
Gets the molecule input stream.
- getMolInputStream(String) - Static method in class chemaxon.marvin.space.MSpaceEasy
-
Creates a MolInputStream from the given String to
be able to manually add molecules to the event handler.
- getMolNameFontSize() - Method in class chemaxon.marvin.view.swing.TableOptions
-
Gets the molecule name font size.
- getMolObject(int) - Method in class chemaxon.struc.graphics.MEFlow
-
Gets the electron source or sink.
- getMolPainter(int, String) - Method in class chemaxon.marvin.view.MDocStorage
-
Gets a molecule painter.
- getMolPanel() - Method in class chemaxon.marvin.beans.MarvinPane
-
Returns the underlying panel.
- getMolPolarizability() - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
-
Returns the molecular polarizability value.
- getMolString() - Method in class chemaxon.marvin.io.MRecord
-
Gets the molecule string, with preprended header and appended footer
if appropriate.
- getMonitorColor() - Method in class chemaxon.marvin.space.monitor.DihedralMonitor
-
Returns the color of the control if it exists.
- getMonitorColor() - Method in class chemaxon.marvin.space.monitor.MeasurementMonitor
-
- getMoreErrorMessage() - Method in class chemaxon.checkers.StructureCheckerDescriptor
-
Returns the more error message
- getMostFrequentNaturalIsotope(int) - Static method in class chemaxon.struc.PeriodicSystem
-
Returns the mass number of the most frequent natural isotope of the
element
- getMostLikelyMolFormat(String) - Static method in class chemaxon.formats.MFileFormatUtil
-
Gets the most likey molecule file format from the file name extension.
- getMostSimplifiedMolecule() - Method in class chemaxon.struc.Molecule
-
Gets the simplified molecule object even if there is a parent document
with other objects.
- getMostSimplifiedMolecule() - Method in class chemaxon.struc.RgMolecule
-
Gets the simplified molecule object even if there is a parent document
with other objects.
- getMProp() - Method in class chemaxon.struc.MDocument
-
Gets the document as a property.
- getMrvWithSettings() - Method in class chemaxon.marvin.beans.MSketchPane
-
Gets the molecule in the sketcher with its current settings in MRV format.
- getMsAcceptorCounts() - Method in class chemaxon.marvin.calculations.HBDAPlugin
-
Returns the average acceptor counts over the microspecies distribution for different pH-s.
- getMsCount() - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Returns the number of microspecies and/or distributions.
- getMsDistribution(int) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Returns the microspecies distribution array.
- getMsDistributions() - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Returns the microspecies distribution arrays for all microspecies:
the i-th element is the disrtibution array of the i-th microspecies.
- getMsDonorCounts() - Method in class chemaxon.marvin.calculations.HBDAPlugin
-
Returns the average donor counts over the microspecies distribution for different pH-s.
- getMSketchPane() - Method in class chemaxon.marvin.beans.MSketch
-
- getMSLogic() - Method in class chemaxon.struc.RxnMolecule
-
Gets the hash that stores arrow - reaction mapping.
- getMsMolecule(int) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Returns the microspecies molecule.
- getMultiplets() - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
- getMultiplier() - Method in class chemaxon.struc.sgroup.MultipleSgroup
-
Gets the multiplier.
- getMViewPane() - Method in class chemaxon.marvin.beans.MView
-
- getMViewParam() - Method in class chemaxon.marvin.beans.MViewParams
-
Generates the parameter string that can be set to MViewPane.
- getName() - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
Returns the name of the NMR spectrum.
- getName() - Method in class chemaxon.checkers.AbstractStructureChecker
-
- getName() - Method in class chemaxon.checkers.InvalidChecker
-
- getName() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
-
- getName() - Method in interface chemaxon.checkers.result.StructureCheckerResult
-
- getName() - Method in interface chemaxon.checkers.StructureChecker
-
Deprecated.
This method isn't needed anymore and will be removed in 6.0
- getName() - Method in class chemaxon.checkers.StructureCheckerDescriptor
-
Returns the checker name
- getName() - Method in class chemaxon.fixers.AbstractStructureFixer
-
- getName() - Method in interface chemaxon.fixers.StructureFixer
-
Deprecated.
- getName() - Method in class chemaxon.fixers.StructureFixerDescriptor
-
Returns the fixer name
- getName() - Method in class chemaxon.formats.MFileFormat
-
Gets the codename of the format.
- getName() - Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor
-
- getName() - Method in class chemaxon.marvin.services.ServiceArgument
-
Returns the name of the argument
- getName() - Method in class chemaxon.marvin.space.GraphicComponent
-
Returns the name of the component.
- getName() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- getName() - Method in class chemaxon.marvin.space.PharmacophoreArrow
-
- getName() - Method in class chemaxon.marvin.space.PharmacophorePoint
-
- getName() - Method in class chemaxon.marvin.util.OptionDescriptor
-
Gets the option name.
- getName() - Method in interface chemaxon.struc.Incomplecule
-
Gets the molecule name.
- getName() - Method in class chemaxon.struc.Molecule
-
- getName() - Method in class chemaxon.struc.MoleculeGraph
-
Gets the molecule name.
- getName(int) - Static method in class chemaxon.struc.PeriodicSystem
-
Name of the element
- getName() - Method in class chemaxon.struc.RgMolecule
-
Gets the name of the root molecule.
- getName() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AttachedData
-
Gets the name.
- getNameIOServiceURL() - Method in class chemaxon.marvin.common.UserSettings
-
- getNames() - Method in class chemaxon.formats.MFileFormat
-
Gets all the codenames of the format.
- getNameSpace() - Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor
-
Returns the namespace
- getNavmode() - Method in class chemaxon.marvin.beans.MViewPane
-
Gets the mouse drag action.
- getNearClip() - Method in class chemaxon.marvin.space.GraphicCell
-
Returns the z coordinate of the nearer clipping plane
which is computed considering all components.
- getNeighbor(int, int) - Method in interface chemaxon.struc.Smolecule
-
Gets the index of a neighbor of an atom.
- getNeighborCount(int) - Method in interface chemaxon.struc.Smolecule
-
Gets the number of neighbors of an atom.
- getNewOldIndexMap() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
- getNewToOld() - Method in interface chemaxon.jep.Standardizer
-
- getNext() - Method in class chemaxon.util.concurrent.marvin.CompositeInputProducer
-
Returns the next input object array (one input from each input producer).
- getNext() - Method in class chemaxon.util.concurrent.marvin.MolInputProducer
-
Returns the next input molecule.
- getNext() - Method in class chemaxon.util.concurrent.marvin.ReusableInputProducer
-
Returns the next input object.
- getNextAromatizedStructure() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Returns the next enumerated structure.
- getNextStructure() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Returns the next enumerated structure, or null if no more structures.
- getNodeCount() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
-
- getNodes() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
-
- getNoErrorMessage() - Method in class chemaxon.checkers.StructureCheckerDescriptor
-
Returns the no error message of the concerning checker
- getNonHitBonds(Molecule, Molecule, int[]) - Static method in class chemaxon.util.HitDisplayUtil
-
Returns the bonds of the target molecule that should not be colored
in hit highlighting.
- getNonHitColor() - Method in class chemaxon.util.HitColoringAndAlignmentOptions
-
Returns the color to be used when coloring the part of the
target which is not matching to the query.
- getNonHitColor3D() - Method in class chemaxon.util.HitColoringAndAlignmentOptions
-
Returns the color to be used when coloring the part of the
3D target which is not matching to the query.
- getNonQueryImplicitHcount() - Method in class chemaxon.struc.MolAtom
-
Gets the number of implicit hydrogens attached.
- getNormal(int) - Method in class chemaxon.marvin.space.SurfaceComponent
-
Warning: for internal use only.
- getNotAbsoluteRSChiralCenters(Molecule) - Static method in class chemaxon.checkers.StereoCheckUtility
-
Gets the not absolute (contains non-"and" enhanced) (R) or (S) chiral
centers
- getNotAbsoluteRSChiralCenters(List<MolAtom>) - Static method in class chemaxon.checkers.StereoCheckUtility
-
Gets the not absolute (contains non-"and" enhanced) (R) or (S) chiral
centers
- getNotSpec() - Method in enum chemaxon.marvin.alignment.AlignmentProperties
-
- getNucleophilicEnergy(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
-
Returns the nucleophilic energy (localization energy L-) of an atom,
Double.NaN for no value.
- getNucleophilicOrder(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
-
- getNucleus() - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder
-
Gets the nucleus type.
- getNucleus() - Method in class chemaxon.calculations.nmr.NMRCalculator
-
Returns the NMR active nucleus.
- getNucleusString() - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
Returns the nucleus type string.
- getNucleusType() - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
Returns the type of the nucleus under examination.
- getNumber() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.EnhancedStereo
-
Number of type.
- getNumberOfNMRActiveNuclei() - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
Returns number of the NMR active nuclei.
- getNumElectrons() - Method in class chemaxon.struc.graphics.MEFlow
-
Gets the number of electrons the arrow represents.
- getObject(int) - Method in class chemaxon.struc.MDocument
-
Gets an object from the document.
- getObject(String) - Method in class chemaxon.struc.MPropertyContainer
-
Gets a property object.
- getObjectAtPointer() - Method in class chemaxon.marvin.beans.MSketchPane
-
Get the object at the mouse pointer.
- getObjectContainingSelection() - Method in class chemaxon.struc.MDocument
-
Gets the object that contains the selection.
- getObjectCount() - Method in class chemaxon.struc.MDocument
-
Gets the number of objects in this document.
- getObjectCount() - Method in class chemaxon.struc.Molecule
-
- getObjectCount() - Method in class chemaxon.struc.RgMolecule
-
- getObjectCount() - Method in class chemaxon.struc.RxnMolecule
-
- getObjectFromClipboard() - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
-
Returns the current content of the clipboard if the data can be imported in any of data
formats supported by MolImporter.
- getObjectFromClipboard(String) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
-
Returns the current content of the clipboard if the data can be imported in any of data
formats supported by MolImporter.
- getObjectFromTransferable(Transferable) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
-
Returns the content of Transferable if the data can be imported in any of data formats
supported by MolImporter.
- getObjectFromTransferable(Transferable, String) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
-
Returns the content of Transferable if the data can be imported in any of data formats
supported by MolImporter.
- getObjectsMiddle(DPoint3) - Method in class chemaxon.struc.sgroup.DataSgroup
-
Calculates the middle point of the coordinates of objects this sgroup is
associated to.
- getOffset() - Method in class chemaxon.marvin.view.MDocStorage
-
Gets the offset in the document source.
- getOldNewIndexMap() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
- getOldToNew() - Method in interface chemaxon.jep.Standardizer
-
- getOneErrorMessage() - Method in class chemaxon.checkers.StructureCheckerDescriptor
-
Returns the one error message
- getOperatorToolBar(JTextPane) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Returns the operator toolbar for textPane instance
NOTE: textPane have to be created with this factory
- getOptionDescriptors(String, String, List<OptionDescriptor>) - Method in class chemaxon.marvin.io.formats.mdl.MolExport
-
Gets the option descriptors.
- getOptionDescriptors(String) - Method in class chemaxon.marvin.io.MolExportModule
-
Gets an array of option descriptors for the specified format.
- getOptionDescriptors(String, String, List<OptionDescriptor>) - Method in class chemaxon.marvin.io.MolExportModule
-
Gets an array of option descriptors.
- getOptionDescriptors(ResourceBundle, String, String, List<OptionDescriptor>) - Static method in class chemaxon.marvin.io.MolExportModule
-
Gets an array of option descriptors.
- getOptions() - Method in class chemaxon.formats.MolImporter
-
Gets the import options.
- getOptions() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
-
Gets the import options.
- getOptions() - Method in class chemaxon.marvin.io.MolExportModule
-
Returns the output options.
- getOptions() - Method in class chemaxon.marvin.io.MRecordImporter
-
Gets the options for the import module.
- getOptions() - Method in interface chemaxon.marvin.io.MRecordReader
-
Gets the import options.
- getOptionSign() - Method in class chemaxon.marvin.io.MolExportModule
-
Gets the sign of the options.
- getOptionsPane(int) - Method in class chemaxon.marvin.plugin.PluginFactory
-
Gets the options pane for a plugin, loads it if needed.
- getOptionsPane() - Method in class chemaxon.marvin.plugin.PluginFactory.PluginRecord
-
- getOptionsToDeselect() - Method in class chemaxon.marvin.util.OptionDescriptor
-
Gets the options that must be deselected if this option is selected.
- getOptionsToDisable() - Method in class chemaxon.marvin.util.OptionDescriptor
-
Gets the options that must be switched off if this option is selected.
- getOptionsToEnable() - Method in class chemaxon.marvin.util.OptionDescriptor
-
Gets the options that must be switched off if this option is selected.
- getOrCreateWorksheet(String) - Method in class chemaxon.formats.documents.jchemexcel.JChemExcelAPI
-
- getOrientation() - Method in enum chemaxon.marvin.alignment.AlignmentProperties
-
- getOrientationType() - Method in class chemaxon.marvin.alignment.Alignment
-
- getOriginalMolecule() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
- getOsVersionStr() - Static method in class com.chemaxon.version.VersionInfo
-
Returns the OS version information as string.
- getOtherAtom(MolAtom) - Method in class chemaxon.struc.MolBond
-
Gets the other end of the bond.
- getOtherCrossingBond(MolBond) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
-
Gets the other bond if a bond is a crossing bond in a ladder-type polimer
bracket.
- getOtherEnd() - Method in class chemaxon.struc.graphics.MEFlowBasePoint
-
Gets the atom at the other end point.
- getOwnerCount() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the current number of owners.
- getPageFormat(String) - Method in class chemaxon.marvin.common.UserSettings
-
Gets the specified PageFormat
- getPageNumber() - Method in class chemaxon.naming.DocumentExtractor.Hit
-
Deprecated.
For document formats that have a notion of page (for instance PDF),
this method returns the page the hit occurs on.
- getPageSettings() - Method in class chemaxon.struc.MDocument
-
Gets the page settings of multipage molecular document.
- getPalette() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
Returns the used built-in palette.
- getPaletteString() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
Returns the string identifier of the used built-in palette.
- getParameter(String) - Method in class chemaxon.marvin.beans.MarvinPane
-
Gets a parameter.
- getParameterPanel() - Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
-
Returns the parameter panel.
- getParameterPanel(int) - Method in class chemaxon.marvin.plugin.PluginFactory
-
Gets the parameter panel for a plugin, loads it if needed.
- getParameterPanel() - Method in class chemaxon.marvin.plugin.PluginFactory.PluginRecord
-
- getParameters(Properties) - Method in class chemaxon.marvin.plugin.gui.OptionsPane
-
Returns the parameters set by the user.
- getParameters(Properties) - Method in class chemaxon.marvin.plugin.gui.ParameterPanel
-
Returns the plugin parameters.
- getParameters(Properties) - Method in interface chemaxon.marvin.plugin.ParameterPanelHandler
-
Returns the plugin parameters.
- getParams() - Method in class chemaxon.marvin.beans.MarvinPane
-
Gets the parameter string.
- getParent() - Method in class chemaxon.struc.MolAtom
-
Return the molecule graph that contains this atom.
- getParent() - Method in class chemaxon.struc.MolBond
-
Gets the parent graph.
- getParent() - Method in class chemaxon.struc.MoleculeGraph
-
Gets the parent graph that contains this substructure.
- getParentDocument() - Method in class chemaxon.struc.MoleculeGraph
-
Gets the document or the document of the parent graph.
- getParentLine() - Method in class chemaxon.struc.graphics.MMidPoint
-
Gets the parent line.
- getParentMolecule() - Method in class chemaxon.struc.Sgroup
-
Gets the parent molecule.
- getParentRect() - Method in class chemaxon.struc.graphics.MRectanglePoint
-
Gets the parent rectangle.
- getParentSgroup() - Method in class chemaxon.struc.Sgroup
-
Gets the parent S-group.
- getParentSgroupGraph() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
- getParity(int) - Method in class chemaxon.struc.MoleculeGraph
-
Computes the parity of an atom of the Molecule instance based on both
the coordinates of the neighboring atoms and the stereo information
of the bonds to those.
- getParity(int) - Method in class chemaxon.struc.RgMolecule
-
Computes the parity of an atom of the RgMolecule instance based on both
the coordinates of the neighboring atoms and the stereo information
of the bonds to those.
- getParity(int) - Method in class chemaxon.struc.RxnMolecule
-
Computes the parity of an atom of the RxnMolecule instance based on both
the coordinates of the neighboring atoms and the stereo information
of the bonds to those.
- getParity(int) - Method in interface chemaxon.struc.Smolecule
-
Gets the parity of an atom.
- getParityType(int) - Method in class chemaxon.struc.MoleculeGraph
-
Gets parity type.
- getPartialAtomCharge(int) - Method in class chemaxon.marvin.space.AtomProperty.MoleculeAtomProperty
-
- getPartialAtomCharge(int) - Method in class chemaxon.marvin.space.AtomProperty.SmoleculeAtomProperty
-
- getPath() - Method in class chemaxon.formats.MolInputStream
-
Gets the path or URL of the file.
- getPeptideDisplayType() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the current peptide display type
- getpH() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
-
Returns the pH where the major microspecies should be taken.
- getpH() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
-
Returns the pH where the major microspecies should be taken.
- getpH() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns the pH where the major microspecies should be taken.
- getPharmacophore() - Method in class chemaxon.marvin.alignment.Pharmacophore3D
-
- getpHs() - Method in class chemaxon.marvin.calculations.HBDAPlugin
-
Returns the pH array.
- getpHs() - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
-
Returns the pH array.
- getpHs() - Method in class chemaxon.marvin.calculations.logDPlugin
-
Returns the pH array.
- getpHs() - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Returns the pH array.
- getpI() - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
-
Returns the isoelectric point.
- getPiCharge(int) - Method in class chemaxon.marvin.calculations.ChargePlugin
-
Returns the pi charge of a specified atom.
- getPiece(String) - Method in class chemaxon.marvin.beans.MSketchPane
-
Gets the current molecule piece in the specified format.
- getPiOEN(int) - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
-
Returns the pi orbital electronegativity of a specified atom.
- getpKa(int) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Returns the most significant pKa value for the given atom index.
- getpKa(int, int) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
- getpKaPrefixType() - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Returns the pKa prefix type.
- getpKaType(int) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
- getpKaValues(int, int) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Returns the pKa values for the given atom index and pKa type.
- getPlaceholderText() - Method in class chemaxon.marvin.services.DynamicArgument
-
Returns the value placeholder text.
- getPlacementOrigin(DPoint3) - Method in class chemaxon.struc.sgroup.DataSgroup
-
If isAbsolutePlacement is false it calculates the middle point of the
coordinates of atoms this S-group is associated to.
- getPlainText() - Method in class chemaxon.struc.graphics.MTextDocument
-
Gets the document as plain text.
- getPlainText() - Method in class chemaxon.struc.graphics.MTextDocument.Portion
-
Gets the selected text as a plain text string.
- getPlattIndex() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Calculates the Platt index of the molecule which is equal to the total
sum of the edge degrees of a molecular graph.
- getPlugin() - Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
-
Returns the plugin.
- getPlugin() - Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
-
Returns the calculator plugin object.
- getPlugin() - Method in exception chemaxon.marvin.plugin.concurrent.PluginExecutionException
-
Returns the plugin object.
- getPlugin(int) - Method in class chemaxon.marvin.plugin.PluginFactory
-
Gets a plugin, loads it if needed.
- getPlugin() - Method in class chemaxon.marvin.plugin.PluginFactory.PluginRecord
-
- getPluginIDs() - Method in class chemaxon.jep.Evaluator
-
- getPluginIndex(String) - Method in class chemaxon.marvin.plugin.PluginFactory
-
Gets a plugin index from record key.
- getPluginList() - Static method in class chemaxon.license.LicenseManager
-
Returns the list of the plugin identifiers known by the license manager.
- getPluginParameters() - Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
-
Returns the plugin parameter table (this should be set in the plugin).
- getPluginResource(String) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns the plugin JAR as resource URL,
given the JAR file path relatively to the "plugins" directory.
- getPoint(int) - Method in class chemaxon.struc.graphics.MAtomSetPoint
-
Gets the point.
- getPoint(int) - Method in class chemaxon.struc.graphics.MChemicalStruct
-
Gets a point of the object.
- getPoint(int) - Method in class chemaxon.struc.graphics.MEFlow
-
Gets a point of the line.
- getPoint(int) - Method in class chemaxon.struc.graphics.MEFlowBasePoint
-
Gets the point.
- getPoint(int) - Method in class chemaxon.struc.graphics.MPolyline
-
Gets the clone of a point of the line.
- getPoint(int) - Method in class chemaxon.struc.MObject
-
Gets a point of the object.
- getPoint(int) - Method in class chemaxon.struc.MPoint
-
Gets the point.
- getPointCount() - Method in class chemaxon.struc.graphics.MChemicalStruct
-
Gets the number of points (atoms).
- getPointCount() - Method in class chemaxon.struc.graphics.MPolyline
-
Gets the number of points.
- getPointCount() - Method in class chemaxon.struc.MObject
-
Gets the number of points.
- getPointCount() - Method in class chemaxon.struc.MPoint
-
Gets the number of points.
- getPointRef(int, CTransform3D) - Method in class chemaxon.struc.graphics.MPolyline
-
Gets a reference to a point or midpoint in the polyline.
- getPointRef(int, CTransform3D) - Method in class chemaxon.struc.graphics.MRectangle
-
Gets an internal selectable point of the rectangle.
- getPointRef(int, CTransform3D) - Method in class chemaxon.struc.graphics.MRoundedRectangle
-
Gets an internal selectable point of the rectangle.
- getPointRef(int, CTransform3D) - Method in class chemaxon.struc.MObject
-
Gets a reference to a point of the object.
- getPointRef(int, CTransform3D) - Method in class chemaxon.struc.MPoint
-
Gets a point of the line.
- getPointRefCount() - Method in class chemaxon.struc.graphics.MEFlow
-
Gets the number of point references.
- getPointRefCount() - Method in class chemaxon.struc.graphics.MPolyline
-
Gets the number of point references.
- getPointRefCount() - Method in class chemaxon.struc.graphics.MRectangle
-
Gets the number of internal selectable point references.
- getPointRefCount() - Method in class chemaxon.struc.graphics.MRoundedRectangle
-
Gets the number of internal selectable point references.
- getPointRefCount() - Method in class chemaxon.struc.MObject
-
Gets the number of point references.
- getPointRefCount() - Method in class chemaxon.struc.MPoint
-
Gets the number of point references.
- getPoints() - Method in class chemaxon.struc.graphics.MPolyline
-
Gets the points.
- getPoints() - Method in class chemaxon.struc.MoleculeGraph
-
Gets an array containing the atom coordinates.
- getPoints(int) - Method in class chemaxon.struc.prop.MHCoords3DProp
-
Gets the Hydrogen locations for an atom.
- getPolarizability(int) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
-
Returns the atom polarizability value.
- getPopupMenusEnabled() - Method in class chemaxon.marvin.beans.MarvinPane
-
Are popup menus enabled?
- getPortion(int, int) - Method in class chemaxon.struc.graphics.MTextDocument
-
Gets a portion of the document.
- getPortion(int, int) - Method in class chemaxon.struc.graphics.MTextDocument.Portion
-
Gets a portion of the text relative to this portion.
- getPortName() - Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor
-
Returns the port name
- getPos() - Method in class chemaxon.struc.sgroup.DataSgroup
-
Gets the data display DASP position (0...9).
- getPosition() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
-
Gets the current position.
- getPosition() - Method in exception chemaxon.marvin.io.MRecordParseException
-
Gets the position of the error.
- getPosition() - Method in class chemaxon.marvin.space.monitor.PositionMonitor
-
Returns the monitor's position.
- getPosition() - Method in class chemaxon.struc.graphics.MTextDocument.Section
-
Gets the position in the document.
- getPositionInPolyline() - Method in class chemaxon.struc.graphics.MMidPoint
-
Gets the position in the polyline.
- getPositionInRect() - Method in class chemaxon.struc.graphics.MRectanglePoint
-
Gets the position in the rectangle.
- getPositionsString() - Method in class chemaxon.naming.DocumentExtractor.Hit
-
Deprecated.
- getPossibleAtomCenteredStereoAtoms(MoleculeGraph) - Static method in class chemaxon.calculations.stereo.Stereochemistry
-
Returns the indexes of atom-centered stereoactive atoms.
- getPossibleAtomCenteredStereoAtomsWithNoParity(MoleculeGraph) - Static method in class chemaxon.calculations.stereo.Stereochemistry
-
Returns the indexes of atoms that have the possibility to have
tetrahedral stereo and have no exact parity set on them.
- getPossibleAttachmentPoints(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
-
- getPossibleRotatableBondCount() - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
-
Rotatable bond count before the atrop isomer calculation.
- getPreBreakingChars() - Method in class chemaxon.struc.graphics.MTextBox
-
Gets the breaking characters before that the text in the text
box can be broken if it doesn't fit into the text box.
- getPreferredIUPACName() - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
-
Returns the preferred IUPAC name.
- getPreferredLabelDir(CTransform3D, int) - Method in class chemaxon.struc.MolAtom
-
Gets the preferred direction for an additional label.
- getPreferredSize() - Method in class chemaxon.marvin.beans.MViewPane
-
Gets the preferred size of the component.
- getPreferredView() - Method in class chemaxon.marvin.io.MolImportModule
-
Specifies which view style is preferred (for instance in MarvinView) for this format.
- getPrefix() - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
-
Returns the code assist invoke prefix
- getPrefix() - Method in exception chemaxon.naming.NameFormatException
-
The part of the input name that was recognized, or null.
- getPreviousNormalTextSectionIndex() - Method in class chemaxon.struc.graphics.MTextBox
-
Gets the index of the last `normal' text section before the
current subscript/superscript section.
- getPrimaryIndexes() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AtomSelection
-
Gets the primary indexes.
- getPrimaryMolecule() - Method in class chemaxon.struc.MDocument
-
Gets the primary molecule object.
- getPrimaryMolecules() - Method in class chemaxon.struc.MDocument
-
Gets an array containing the primary molecule objects.
- getPrimitives() - Method in class chemaxon.marvin.space.SurfaceComponent
-
Returns the primitives (for example triangles) of the surface.
- getPrincipalPolarizabilityComponents() - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
-
- getPriority() - Method in class chemaxon.fixers.StructureFixerDescriptor
-
Returns the fixer priority.
- getPriority(String) - Method in class chemaxon.formats.MFileFormat
-
- getPriority() - Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor
-
Gets the priority of the
MTransferable object by exporting to clipboard.
- getProbeRadius() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
Returns the probe radius the surface computing will use.
- getProduct(int) - Method in class chemaxon.struc.RxnMolecule
-
Gets a product.
- getProductCount() - Method in class chemaxon.struc.RxnMolecule
-
Gets the number of products.
- getProductList(boolean) - Static method in class chemaxon.license.LicenseManager
-
Returns the list of the product identifiers known by the license manager.
- getProductName() - Method in class chemaxon.calculations.dipole.DipoleCalculator
-
- getProductName() - Method in class chemaxon.calculations.nmr.NMRCalculator
-
- getProductName() - Method in class chemaxon.marvin.calculations.AlignmentPlugin
-
- getProductName() - Method in class chemaxon.marvin.calculations.ChargePlugin
-
Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() - Method in class chemaxon.marvin.calculations.ConformerPlugin
-
Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
-
- getProductName() - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() - Method in class chemaxon.marvin.calculations.HBDAPlugin
-
Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
-
Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() - Method in class chemaxon.marvin.calculations.IonChargePlugin
-
Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
-
Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
-
Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() - Method in class chemaxon.marvin.calculations.logDPlugin
-
Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() - Method in class chemaxon.marvin.calculations.logPPlugin
-
Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
-
Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
-
Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() - Method in class chemaxon.marvin.calculations.MSAPlugin
-
Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
-
Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
-
Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() - Method in class chemaxon.marvin.calculations.RefractivityPlugin
-
Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() - Method in class chemaxon.marvin.calculations.ResonancePlugin
-
- getProductName() - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
-
Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
-
- getProductName() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() - Method in class chemaxon.marvin.calculations.TPSAPlugin
-
- getProductName() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns the product identifier of the plugin as given by
LicenseManager.
- getProducts() - Method in class chemaxon.struc.RxnMolecule
-
Gets all products in an array.
- getProgessLength() - Method in class chemaxon.checkers.runner.BasicCheckerRunner
-
- getProgessLength() - Method in interface chemaxon.checkers.runner.CheckerRunner
-
- getProgressBar() - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
-
- getProgressMonitor(Component) - Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
-
- getPropArraySize() - Method in class chemaxon.struc.MDocument.Prop
-
Gets the array size.
- getPropArraySize() - Method in class chemaxon.struc.MProp
-
Gets the array size.
- getPropArraySize() - Method in class chemaxon.struc.prop.MDoubleArrayProp
-
Gets the array size.
- getPropArraySize() - Method in class chemaxon.struc.prop.MHashProp
-
Gets the array size.
- getPropArraySize() - Method in class chemaxon.struc.prop.MIntegerArrayProp
-
Gets the array size.
- getPropArraySize() - Method in class chemaxon.struc.prop.MListProp
-
Gets the array size.
- getProperties() - Method in class chemaxon.checkers.result.AtomQueryPropertyCheckerResult
-
Returns the flag which can used to identify which properties should be
fixed.
- getPropertiesDescriptionChangedByOtherApp() - Method in class chemaxon.marvin.common.UserSettings
-
The method collects the changes in the config file, if its timestamp was changed.
- getProperty(String) - Method in class chemaxon.marvin.common.UserSettings
-
Returns the value for the given key.
- getProperty(String) - Method in class chemaxon.struc.MolAtom
-
Returns the property value to which the specified property key is mapped
at this atom, or null if this atom has no mapping for this property key.
- getProperty(String) - Method in class chemaxon.struc.MolBond
-
Returns the property value to which the specified property key is mapped
at this bond, or null if this bond has no mapping for this property key.
- getProperty(String) - Method in class chemaxon.struc.Molecule
-
- getPropertyChangeSupport() - Method in interface chemaxon.marvin.services.ServiceDescriptorEditor
-
- getPropertyContainer() - Method in class chemaxon.marvin.io.MRecord
-
Gets the properties.
- getPropertyCount() - Method in class chemaxon.struc.Molecule
-
Gets the total number of RDfile/SDfile properties.
- getPropertyDescriptors(Class<?>, Vector<PropertyDescriptor>) - Method in class chemaxon.marvin.beans.MarvinPaneBeanInfo
-
Puts the descriptors of the common Marvin bean properties into the specified Vector.
- getPropertyDescriptors() - Method in class chemaxon.marvin.beans.MSketchPaneBeanInfo
-
Returns the property descriptor array.
- getPropertyDescriptors() - Method in class chemaxon.marvin.beans.MViewPaneBeanInfo
-
Returns the property descriptor array.
- getPropertyKey(int) - Method in class chemaxon.struc.Molecule
-
Gets an RDfile/SDfile property key.
- getPropertyKeys() - Method in class chemaxon.struc.Molecule
-
- getPropertyMap() - Method in class chemaxon.marvin.common.UserSettings
-
Shortcut to getPropertyMap(UserSettings.PROPERTY_TYPE_ALL)
- getPropertyMap(String) - Method in class chemaxon.marvin.common.UserSettings
-
Returns a map of properties from the given type.
- getPropertyObject(String) - Method in class chemaxon.struc.Molecule
-
Gets an RDfile/SDfile property object.
- getPropertyText(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
-
Returns molecule properties is text form.
- getPropList() - Method in class chemaxon.struc.MPropertyContainer
-
Gets the list of basic properties.
- getPropType() - Method in class chemaxon.struc.MDocument.Prop
-
Gets the type name of the property.
- getPropType() - Method in class chemaxon.struc.MProp
-
Gets the type name of the property.
- getPropType() - Method in class chemaxon.struc.prop.MBooleanProp
-
Gets the type name of the property.
- getPropType() - Method in class chemaxon.struc.prop.MDoubleArrayProp
-
Gets the type name of the property.
- getPropType() - Method in class chemaxon.struc.prop.MDoubleProp
-
Gets the type name of the property.
- getPropType() - Method in class chemaxon.struc.prop.MHashProp
-
Gets the type name of the property.
- getPropType() - Method in class chemaxon.struc.prop.MHCoords3DProp
-
Gets the type name of the property.
- getPropType() - Method in class chemaxon.struc.prop.MIntegerArrayProp
-
Gets the type name of the property.
- getPropType() - Method in class chemaxon.struc.prop.MIntegerProp
-
Gets the type name of the property.
- getPropType() - Method in class chemaxon.struc.prop.MListProp
-
Gets the type name of the property.
- getPropType() - Method in class chemaxon.struc.prop.MMoleculeProp
-
Gets the type name of the property.
- getPropType() - Method in class chemaxon.struc.prop.MObjectProp
-
Gets the type name of the property.
- getPropType() - Method in class chemaxon.struc.prop.MStringProp
-
Gets the type name of the property.
- getPropValue() - Method in class chemaxon.struc.MDocument.Prop
-
Gets the property value as an object.
- getPropValue() - Method in class chemaxon.struc.MProp
-
Gets the property value as an object.
- getPropValue() - Method in class chemaxon.struc.prop.MBooleanProp
-
Gets the property value as an object.
- getPropValue() - Method in class chemaxon.struc.prop.MDoubleArrayProp
-
Gets the property value as an object.
- getPropValue() - Method in class chemaxon.struc.prop.MDoubleProp
-
Gets the property value as an object.
- getPropValue() - Method in class chemaxon.struc.prop.MHashProp
-
Gets the property value as an object.
- getPropValue() - Method in class chemaxon.struc.prop.MHCoords3DProp
-
Gets the property value as an object.
- getPropValue() - Method in class chemaxon.struc.prop.MIntegerArrayProp
-
Gets the property value as an object.
- getPropValue() - Method in class chemaxon.struc.prop.MIntegerProp
-
Gets the property value as an object.
- getPropValue() - Method in class chemaxon.struc.prop.MListProp
-
Gets the property value as an object.
- getPropValue() - Method in class chemaxon.struc.prop.MMoleculeProp
-
Gets the property value as an object.
- getPropValue() - Method in class chemaxon.struc.prop.MObjectProp
-
Gets the property value as an object.
- getPropValue() - Method in class chemaxon.struc.prop.MStringProp
-
Gets the property value as an object.
- getPropXSDType() - Method in class chemaxon.struc.MDocument.Prop
-
Gets the XSD type name of the property.
- getPropXSDType() - Method in class chemaxon.struc.MProp
-
Gets the XSD type name of the property.
- getPropXSDType() - Method in class chemaxon.struc.prop.MBooleanProp
-
Gets the XSD type name of the property.
- getPropXSDType() - Method in class chemaxon.struc.prop.MCollectionProp
-
Gets the XSD type name of the property.
- getPropXSDType() - Method in class chemaxon.struc.prop.MDoubleArrayProp
-
Gets the XSD type name of the property.
- getPropXSDType() - Method in class chemaxon.struc.prop.MDoubleProp
-
Gets the XSD type name of the property.
- getPropXSDType() - Method in class chemaxon.struc.prop.MHCoords3DProp
-
Gets the XSD type name of the property.
- getPropXSDType() - Method in class chemaxon.struc.prop.MIntegerArrayProp
-
Gets the XSD type name of the property.
- getPropXSDType() - Method in class chemaxon.struc.prop.MIntegerProp
-
Gets the XSD type name of the property.
- getPropXSDType() - Method in class chemaxon.struc.prop.MMoleculeProp
-
Gets the XSD type name of the property.
- getPropXSDType() - Method in class chemaxon.struc.prop.MObjectProp
-
Gets the XSD type name of the property.
- getPropXSDType() - Method in class chemaxon.struc.prop.MStringProp
-
Gets the XSD type name of the property.
- getQProp(String) - Method in class chemaxon.struc.MolAtom
-
Gets a query property.
- getQPropAsInt(String) - Method in class chemaxon.struc.MolAtom
-
Gets a query property as an integer.
- getQPropAsInt(int, String) - Method in interface chemaxon.struc.Smolecule
-
Gets a query property as an integer.
- getQPropMinMax(String) - Method in class chemaxon.struc.MolAtom
-
Gets the minimum and maximum possible values of a query property.
- getQPropNames() - Method in class chemaxon.struc.MolAtom
-
Gets the names of query properties with non-null values.
- getQPropNameSet() - Method in class chemaxon.struc.MolAtom
-
Gets the names of query properties with non-null values, or null if no
query properties are set.
- getQueryAromaticity() - Method in class chemaxon.struc.MolAtom
-
Gets the aromatic/aliphatic query property.
- getQueryCode() - Method in class chemaxon.struc.sgroup.DataSgroup
-
Gets the program code of the query option.
- getQueryLabel() - Method in class chemaxon.struc.MolAtom
-
Gets the string representation of the query atom
- getQueryMode() - Method in class chemaxon.formats.MolImporter
-
Gets query mode.
- getQueryMode() - Method in class chemaxon.marvin.io.MRecordImporter
-
Gets the query mode.
- getQueryMoleculeErrorMessage(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
-
- getQueryOp() - Method in class chemaxon.struc.sgroup.DataSgroup
-
Gets the data query operator.
- getQuerystr() - Method in class chemaxon.struc.MolAtom
-
- getQuerystr() - Method in class chemaxon.struc.MolBond
-
Gets the query properties.
- getQuerystr() - Method in class chemaxon.struc.QueryBond
-
Gets the query properties.
- getQueryString() - Method in class chemaxon.struc.MolAtom
-
Returns s the query string assigned to this atom.
- getRadical() - Method in class chemaxon.struc.MolAtom
-
- getRadical(int) - Method in interface chemaxon.struc.Smolecule
-
Gets the radical value of an atom.
- getRadicalCount() - Method in class chemaxon.struc.MolAtom
-
Gets the number of free electrons.
- getRadicalCount(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
- getRadicalValue() - Method in class chemaxon.struc.MolAtom
-
- getRadius() - Method in class chemaxon.marvin.space.PharmacophoreArrow
-
Returns the radius of the arrow.
- getRadius() - Method in class chemaxon.marvin.space.PharmacophorePoint
-
Returns the radius of the PharmacophorePoint in angstroms.
- getRainbowPalette() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
-
Returns the color palette that is used when the coloring mode of the component
is rainbow coloring.
- getRandicIndex() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Calculates the Randic index or molecular connectivity index as the
harmonic sum of the geometric means of the node degrees for each edge.
- getRangeMax() - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
Maximal y value of the NMR spectrum function.
- getRangeMin() - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
Minimal y value of the NMR spectrum function.
- getRawValueAt(double) - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
Returns the value of the unscaled NMR spectrum function at a given x point.
- getRCSBLink(String) - Static method in class chemaxon.marvin.space.MSpaceEasy
-
Returns the URL of the RCSB database
- getRCSBLink(String, boolean) - Static method in class chemaxon.marvin.space.MSpaceEasy
-
Returns the URL of the RCSB database
- getReactant(int) - Method in class chemaxon.struc.RxnMolecule
-
Gets a reactant.
- getReactantCount() - Method in class chemaxon.struc.RxnMolecule
-
Gets the number of reactants.
- getReactants() - Method in class chemaxon.struc.RxnMolecule
-
Gets all reactants in an array.
- getReaction() - Method in class chemaxon.jep.context.ReactionContext
-
Returns the reaction.
- getReaction(MoleculeGraph) - Static method in class chemaxon.struc.RxnMolecule
-
Returns the reaction represented by the given molecule if exists,
otherwise null.
- getReactionArrow() - Method in class chemaxon.struc.RxnMolecule
-
Gets a two-element array containing the endpoints of the reaction arrow.
- getReactionArrow(boolean) - Method in class chemaxon.struc.RxnMolecule
-
Gets the reaction arrow of this reaction with the possibility to
generate an arrow if the arrow is not yet set.
- getReactionArrowList() - Method in class chemaxon.struc.RxnMolecule
-
Gets the list of the reaction arrows of this reaction.
- getReactionArrowType() - Method in class chemaxon.struc.RxnMolecule
-
Gets the reaction arrow type.
- getReactionArrowTypeName() - Method in class chemaxon.struc.RxnMolecule
-
Gets the reaction arrow type name.
- getReactionSmarts() - Method in class chemaxon.checkers.result.SubstructureCheckerResult
-
Returns the reactionSmarts
- getReactionSmarts() - Method in class chemaxon.checkers.SubstructureChecker
-
Returns the reactionSmarts
- getReactionSteps() - Method in class chemaxon.struc.RxnMolecule
-
Divides this reaction into simple step reactions if this is a multistep
reaction.
- getReactionStereo() - Method in class chemaxon.struc.MolAtom
-
Gets the reaction stereo property describing how the stereo configuration
of the atom changes during the reaction.
- getReactionSupport() - Method in class chemaxon.marvin.beans.MSketchPane
-
Is reaction drawing supported?
- getReadGlobalGUIProperties() - Method in class chemaxon.marvin.beans.MarvinPane
-
- getRealBondCount() - Method in class chemaxon.struc.MolAtom
-
Gets the number of bonds connected to "real" atoms.
- getRealEigenValue() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
-
- getRealRotatableBondCount() - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
-
Rotatable bond count (atrop bonds excluded)
- getRecognizedFormat() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
-
Gets the recognized file format.
- getRecognizedFormat() - Method in interface chemaxon.marvin.io.MRecordReader
-
Gets the recognized file format.
- getRecognizer(int, int) - Method in class chemaxon.formats.recognizer.RecognizerList
-
Deprecated.
Gets an element of the recognizer list at the specified level.
- getRecordCount() - Method in class chemaxon.formats.MolImporter
-
Gets the current record number.
- getRecordCount() - Method in class chemaxon.marvin.io.ArrayMDocSource
-
Gets the current record number.
- getRecordCount() - Method in class chemaxon.marvin.io.MDocSource
-
Gets the current record number.
- getRecordCountMax() - Method in class chemaxon.formats.MolImporter
-
Gets the total number of records read.
- getRecordCountMax() - Method in class chemaxon.marvin.io.ArrayMDocSource
-
Gets the total number of records.
- getRecordCountMax() - Method in class chemaxon.marvin.io.MDocSource
-
Gets the total number of records.
- getRecordIDBackground(int) - Method in class chemaxon.marvin.beans.MViewPane
-
Gets the highlight color of a record.
- getRecordIDForeground(int) - Method in class chemaxon.marvin.beans.MViewPane
-
Gets the foreground color of a record.
- getRecordIndex() - Method in exception chemaxon.marvin.view.MDocStorage.RecordUnavailableException
-
Gets the requested, unavailable record index.
- getRecordIndexMax() - Method in exception chemaxon.marvin.view.MDocStorage.RecordUnavailableException
-
Gets the maximum available record index.
- getRecordIndexMin() - Method in exception chemaxon.marvin.view.MDocStorage.RecordUnavailableException
-
Gets the minimum available record index.
- getRecordNumber() - Method in class chemaxon.marvin.io.MRecordReader.Position
-
Gets the record number.
- getRecordReader() - Method in class chemaxon.marvin.io.MRecordImporter
-
Gets the record reader.
- getReferenceAndRotatedFused() - Method in class chemaxon.marvin.alignment.AlignRigidEasy
-
- getReferenceWithNewCoordinates() - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
-
- getReflogDs() - Method in class chemaxon.marvin.calculations.logDPlugin
-
Returns the reference logD array.
- getRefpHs() - Method in class chemaxon.marvin.calculations.logDPlugin
-
Returns the reference pH array.
- getRefractivity() - Method in class chemaxon.marvin.calculations.RefractivityPlugin
-
Returns the refractivity value.
- getRefractivityHIncrement(int) - Method in class chemaxon.marvin.calculations.RefractivityPlugin
-
Returns the refractivity increment on the H atoms attached to a given atom.
- getRefractivityIncrement(int) - Method in class chemaxon.marvin.calculations.RefractivityPlugin
-
Returns the refractivity increment for a given atom.
- getRelativeNegativity() - Method in class chemaxon.struc.MolAtom
-
Check negativity compared to the neighbors.
- getRemark() - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
Returns the calculation remark: if no results (no result types) then
returns remark, otherwise returns null.
- getRemark() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Returns a warning message in case of arithmetical overflow
(the number of enumerated structures exceeds
Long.MAX_VALUE),
null otherwise.
- getRemark() - Method in class chemaxon.marvin.calculations.ResonancePlugin
-
Returns a warning message if there are no resonants,
null otherwise.
- getRemark() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Returns a warning message if there are no tautomers,
null otherwise.
- getRemark() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns the calculation remark:
if no results (no result types) then returns remark,
otherwise returns null.
- getRemark() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns the calculation remark.
- getRemark() - Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
-
Returns the calculation remark.
- getRemark() - Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
-
Returns the calculation remark.
- getRendering() - Method in class chemaxon.marvin.beans.MarvinPane
-
Gets the rendering style.
- getRendering() - Method in class chemaxon.marvin.MolPrinter
-
Returns the rendering style of atoms and bonds.
- getRenderingQuality() - Method in class chemaxon.marvin.space.GraphicComponent
-
Returns the actual rendering quality of the component.
- getRepeatingUnitAtom(int) - Method in class chemaxon.struc.sgroup.MultipleSgroup
-
Gets a paradigmatic repeating unit atom.
- getRepeatingUnitAtomCount() - Method in class chemaxon.struc.sgroup.MultipleSgroup
-
Gets the number of atoms in the pararadigmatic repeating unit.
- getRepeatingUnitAtoms() - Method in class chemaxon.struc.sgroup.MultipleSgroup
-
Gets the repeating unit atoms.
- getReporter() - Method in class chemaxon.checkers.StructureCheck
-
Gets the reporter used by the check procedure.
- getRepresentationClass() - Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor
-
- getRequestMethod() - Method in class chemaxon.marvin.services.json.JsonServiceDescriptor
-
Gets the HTTP method of the request.
- getResidueAtomId() - Method in class chemaxon.struc.MolAtom
-
Gets the residue atom identifier.
- getResidueSeq() - Method in class chemaxon.struc.MolAtom
-
Gets the residue sequence number.
- getResidueType() - Method in class chemaxon.struc.MolAtom
-
Gets the residue type.
- getResidueTypeId(int) - Method in class chemaxon.marvin.space.AtomProperty.MoleculeAtomProperty
-
- getResidueTypeId(int) - Method in class chemaxon.marvin.space.AtomProperty.SmoleculeAtomProperty
-
- getResourceBundle(String) - Static method in class chemaxon.marvin.beans.MarvinPane
-
Utility method to get a resource bundle.
- getResult(Object, int) - Method in class chemaxon.marvin.calculations.ChargePlugin
-
Returns the result item for the specified type and index.
- getResult(Object, int) - Method in class chemaxon.marvin.calculations.ConformerPlugin
-
Returns the result item for the specified key and index.
- getResult(Object, int) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
-
Returns the result item for the specified key and index.
- getResult(Object, String) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
-
Returns the atom count of a specific atom.
- getResult(Object, int) - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
Returns the result item for the specified key and index.
- getResult(Object, String) - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
Returns the distance, angle or dihedral of 2, 3 or 4 atoms if type is set
to "distance", "angle" or "diheral".
- getResult(Object, int) - Method in class chemaxon.marvin.calculations.HBDAPlugin
-
Returns the result item for the specified type and index.
- getResult(Object, int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
-
Returns the result item for the specified key and index.
- getResult(Object, int) - Method in class chemaxon.marvin.calculations.IonChargePlugin
-
Returns the result item for the specified type and index.
- getResult(Object, int) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
-
Returns the result item for the specified key and index.
- getResult(Object, String) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
-
Returns the result item for the specified pH.
- getResult(Object, int) - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
-
Returns the result item for the specified key and index.
- getResult(Object, int) - Method in class chemaxon.marvin.calculations.logDPlugin
-
Returns the result item for the specified type and index.
- getResult(Object, String) - Method in class chemaxon.marvin.calculations.logDPlugin
-
Returns the result item for the specified pH.
- getResult(Object, int) - Method in class chemaxon.marvin.calculations.logPPlugin
-
Returns the result item for the specified key and index.
- getResult(Object, int) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
-
Returns the microsepcies if pH is different from
Double.NaN, otherwise returns the input molecule itself.
- getResult(Object, int) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Returns the result item for the specified key and index.
- getResult(Object, String) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Returns the enumerated structures.
- getResult(Object, int) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
-
Returns the result item for the specified key and index.
- getResult(Object, int) - Method in class chemaxon.marvin.calculations.MSAPlugin
-
Returns the result item for the specified key and index.
- getResult(Object, int) - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
-
Returns the result item for the specified type and index.
- getResult(Object, int) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Returns the result item for the specified key and index.
- getResult(Object, String) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Returns the result item for the specified type ("acidic" or "basic")
and the specified strength index ("1" means the strongest value,
"2" means the second strongest value, etc.) given in the argument string.
- getResult(Object, int) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
-
Returns the result item for the specified type and index.
- getResult(Object, int) - Method in class chemaxon.marvin.calculations.RefractivityPlugin
-
Returns the result item for the specified key and index.
- getResult(Object, int) - Method in class chemaxon.marvin.calculations.ResonancePlugin
-
Returns the result item for the specified key and index.
- getResult(Object, int) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
-
Returns the result item for the specified key and index.
- getResult() - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
-
- getResult(Object, int) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
-
- getResult(Object, int) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Returns the result item for the specified key and index.
- getResult(Object, int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns the result item for the specified key and index.
- getResult(Object, String) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns the shortest path between two atoms if type is set ot "shortestPath",
returns connectivity info if type is set to "connected".
- getResult(Object, int) - Method in class chemaxon.marvin.calculations.TPSAPlugin
-
Returns the result item for the specified key and index.
- getResult(Object, int) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns the result item for the specified type and index.
- getResult(Object, String) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns the result item for the specified argument string.
- getResult(int) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns the result item for the specified type and index.
- getResult(String) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns the result item for the specified argument string.
- getResult(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
-
Returns the result string for the given molecule.
- getResult() - Method in class chemaxon.marvin.plugin.concurrent.DefaultPluginWorkUnit
-
Returns the cached results.
- getResult() - Method in class chemaxon.marvin.plugin.concurrent.PluginWorkUnit
-
- getResult() - Method in class chemaxon.marvin.plugin.concurrent.ReusablePluginWorkUnit
-
Returns the plugin object itself.
- getResultantImplicitHCharge(int) - Method in class chemaxon.marvin.calculations.ChargePlugin
-
Returns the implicit H charge around a central atom
- getResultAsRGB(Object, int, Object) - Method in class chemaxon.marvin.calculations.HBDAPlugin
-
Returns the specified result color(s) as int format (alpha<<24 + red<<16 +
green<<8 + blue).
- getResultAsRGB(Object, int, Object) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Returns the specified result color as int format (alpha<<24 + red<<16 + green<<8 + blue):
RED for acidic pKa, BLUE for basic pKa.
- getResultAsRGB(Object, int, Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns the specified result color as int format
(alpha<<24 + red<<16 + green<<8 + blue).
- getResultAsRGB(int, Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns the specified result color as int format (alpha<<24 + red<<16 + green<<8 + blue).
- getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.ChargePlugin
-
Returns the specified result in String format.
- getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.ConformerPlugin
-
Returns the specified result in String format.
- getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
-
Returns the specified result in String format.
- getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
Returns the specified result in String format.
- getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.HBDAPlugin
-
Returns the specified result in String format.
- getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
-
Returns the specified result in String format.
- getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.IonChargePlugin
-
Returns the specified result in String format.
- getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
-
Returns the specified result in String format.
- getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
-
Returns the specified result in String format.
- getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.logDPlugin
-
Returns the specified result in String format.
- getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.logPPlugin
-
Returns the specified result in String format.
- getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
-
Returns the specified result molecule in SMILES format.
- getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Returns the specified result in String format.
- getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
-
Returns the specified result in String format.
- getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.MSAPlugin
-
Returns the specified result in String format.
- getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
-
Returns the specified result in String format.
- getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Returns the specified result in String format.
- getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
-
Returns the specified result in String format.
- getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.RefractivityPlugin
-
Returns the specified result in String format.
- getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.ResonancePlugin
-
Returns the specified result in String format.
- getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
-
Returns the specified result in String format.
- getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
-
- getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Returns the specified result in String format.
- getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns the specified result in String format.
- getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.TPSAPlugin
-
Returns the specified result in String format.
- getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns the specified result in String format.
- getResultAsString(int, Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns the specified result in String format for the first result type.
- getResultComponent() - Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
-
Returns the result component for display.
- getResultCount(Object) - Method in class chemaxon.marvin.calculations.ChargePlugin
-
Returns the number of result items for the given result type.
- getResultCount(Object) - Method in class chemaxon.marvin.calculations.ConformerPlugin
-
Returns the number of result items for the given result key.
- getResultCount(Object) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
-
Returns the number of result items for the given result key.
- getResultCount(Object) - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
Returns the number of result items for the given result key.
- getResultCount(Object) - Method in class chemaxon.marvin.calculations.HBDAPlugin
-
Returns the number of result items for the given result type.
- getResultCount(Object) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
-
Returns the number of result items for the given result key.
- getResultCount(Object) - Method in class chemaxon.marvin.calculations.IonChargePlugin
-
Returns the number of result items for the given result key.
- getResultCount(Object) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
-
Returns the number of result items for the given result key.
- getResultCount(Object) - Method in class chemaxon.marvin.calculations.logDPlugin
-
Returns the number of result items for the given result key.
- getResultCount(Object) - Method in class chemaxon.marvin.calculations.logPPlugin
-
Returns the number of result items for the given result key.
- getResultCount(Object) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
-
Returns the number of result items: 1.
- getResultCount(Object) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Returns the number of result items for the given result key.
- getResultCount(Object) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
-
Returns the number of result items for the given result key.
- getResultCount(Object) - Method in class chemaxon.marvin.calculations.MSAPlugin
-
Returns the number of result items for the given result key.
- getResultCount(Object) - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
-
Returns the number of result items for the given result type.
- getResultCount(Object) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Returns the number of result items for the given result key.
- getResultCount(Object) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
-
Returns the number of result items for the given result key.
- getResultCount(Object) - Method in class chemaxon.marvin.calculations.RefractivityPlugin
-
Returns the number of result items for the given result key.
- getResultCount(Object) - Method in class chemaxon.marvin.calculations.ResonancePlugin
-
Returns the number of result items for the given result key.
- getResultCount(Object) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
-
Returns the number of result items for the given result key.
- getResultCount() - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
-
- getResultCount(Object) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Returns the number of result items for the given result key.
- getResultCount(Object) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns the number of result items for the given result key.
- getResultCount(Object) - Method in class chemaxon.marvin.calculations.TPSAPlugin
-
Returns the number of result items for the given result key.
- getResultCount(Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns the number of result items for the given result key.
- getResultCount() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns the number of result items for the first result type.
- getResultDomain(Object) - Method in class chemaxon.marvin.calculations.ChargePlugin
-
- getResultDomain(Object) - Method in class chemaxon.marvin.calculations.ConformerPlugin
-
Returns the calculation domain.
- getResultDomain(Object) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
-
- getResultDomain(Object) - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
- getResultDomain(Object) - Method in class chemaxon.marvin.calculations.HBDAPlugin
-
- getResultDomain(Object) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
-
- getResultDomain(Object) - Method in class chemaxon.marvin.calculations.IonChargePlugin
-
- getResultDomain(Object) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
-
Returns the calculation domain.
- getResultDomain(Object) - Method in class chemaxon.marvin.calculations.logDPlugin
-
- getResultDomain(Object) - Method in class chemaxon.marvin.calculations.logPPlugin
-
- getResultDomain(Object) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
-
- getResultDomain(Object) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Returns the calculation domain.
- getResultDomain(Object) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
-
Returns the calculation domain.
- getResultDomain(Object) - Method in class chemaxon.marvin.calculations.MSAPlugin
-
- getResultDomain(Object) - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
-
- getResultDomain(Object) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
- getResultDomain(Object) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
-
- getResultDomain(Object) - Method in class chemaxon.marvin.calculations.RefractivityPlugin
-
- getResultDomain(Object) - Method in class chemaxon.marvin.calculations.ResonancePlugin
-
Returns the calculation domain.
- getResultDomain(Object) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
-
Returns the calculation domain.
- getResultDomain(Object) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
-
- getResultDomain(Object) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Returns the calculation domain.
- getResultDomain(Object) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
- getResultDomain(Object) - Method in class chemaxon.marvin.calculations.TPSAPlugin
-
- getResultDomain(Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
- getResultDomain() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
- getResultDomain() - Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
-
Returns the domain for the first result type.
- getResultList() - Method in class chemaxon.checkers.runner.BasicCheckerRunner
-
- getResultList() - Method in interface chemaxon.checkers.runner.CheckerRunner
-
- getResultMessage() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns the plugin calculation error message,
error or warning.
- getResultMessage() - Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
-
Returns the plugin calculation error message,
error or warning.
- getResultMolecule() - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
-
- getResultMolecule() - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
-
The result molecule will be 3D and aromatized version of the input
molecules.
- getResultMolecule() - Method in class chemaxon.marvin.calculations.AlignmentPlugin
-
- getResultMolecule() - Method in class chemaxon.marvin.calculations.ChargePlugin
-
Returns the result molecule for display.
- getResultMolecule() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
-
Returns the result molecule for display.
- getResultMolecule() - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
Returns the result molecule for display.
- getResultMolecule() - Method in class chemaxon.marvin.calculations.HBDAPlugin
-
Returns the result molecule for display.
- getResultMolecule() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
-
Returns the result molecule for display.
- getResultMolecule() - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
-
Returns the result molecule for display.
- getResultMolecule() - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
-
Returns the result molecule for display.
- getResultMolecule() - Method in class chemaxon.marvin.calculations.logPPlugin
-
Returns the result molecule for display.
- getResultMolecule() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
-
Returns the major microspecies for display.
- getResultMolecule() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Returns the result molecule for display.
- getResultMolecule() - Method in class chemaxon.marvin.calculations.MSAPlugin
-
Returns the result molecule for display.
- getResultMolecule() - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
-
Returns the result molecule for display.
- getResultMolecule() - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Returns the result molecule for display.
- getResultMolecule() - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
-
Returns the result molecule for display.
- getResultMolecule() - Method in class chemaxon.marvin.calculations.RefractivityPlugin
-
Returns the result molecule for display.
- getResultMolecule() - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
-
Get result structure
- getResultMolecule() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns the result molecule for display.
- getResultMolecule() - Method in class chemaxon.marvin.calculations.TPSAPlugin
-
Returns the result molecule for display.
- getResultMolecule() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns the result molecule for display.
- getResultMolecule(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
-
Returns the decorated result molecule for the given target molecule.
- getResultMolecules() - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
Returns the result molecules, molecular results are set in the first
molecule, atomic results are set in subsequent molecules as atom labels.
- getResultMolecules() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns the result molecules, molecular results are set in the first molecule,
atomic results are set in subsequent molecules as atom labels.
- getResultMolecules() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns the result molecule array for display.
- getResultMolecules(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
-
Returns the result molecules for the given target molecule.
- getResults(Object) - Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
-
Returns result items for the given result type.
- getResultsAsRGB(Object, int, Object) - Method in class chemaxon.marvin.calculations.HBDAPlugin
-
Returns the specified result color(s) as int format (alpha<<24 + red<<16 +
green<<8 + blue).
- getResultsAsRGB(Object, int, Object) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
-
Returns the specified result color(s) as int format
(alpha<<24 + red<<16 + green<<8 + blue).
- getResultsAsRGB(Object, int, Object) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Returns the specified result color(s) as int format
(alpha<<24 + red<<16 + green<<8 + blue).
- getResultsAsRGB(Object, int, Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns the specified result color(s) as int format
(alpha<<24 + red<<16 + green<<8 + blue).
- getResultsAsRGB(int, Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns the specified result color(s) as int format
(alpha<<24 + red<<16 + green<<8 + blue).
- getResultsAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.HBDAPlugin
-
Returns the specified result in GUI-specific String format: A for acceptor,
D for donor.
- getResultsAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
-
Returns the specified results in String format.
- getResultsAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Returns the specified result with possible subresults
(both pKa values instead of the most significant pKa) in String format.
- getResultsAsString(Object, int, Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns the specified result with possible subresults.
- getResultsAsString(int, Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns the specified result with possible subresults.
- getResultSource() - Method in class chemaxon.marvin.calculations.ConformerPlugin
-
Returns the result as a document source object.
- getResultSource() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Returns the result as a document source object.
- getResultSource() - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
-
Returns the result as a document source object.
- getResultSource() - Method in class chemaxon.marvin.calculations.ResonancePlugin
-
Returns the result as a document source object.
- getResultSource() - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
-
Returns the result as a document source object.
- getResultSource() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Returns the result as a document source object.
- getResultSource() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns the result as a document source object.
- getResultTypes() - Method in class chemaxon.marvin.calculations.AlignmentPlugin
-
Returns the result types.
- getResultTypes() - Method in class chemaxon.marvin.calculations.ChargePlugin
-
Returns the result types (possible types: "sigma", "pi", "total").
- getResultTypes() - Method in class chemaxon.marvin.calculations.ConformerPlugin
-
Returns the result types.
- getResultTypes() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
-
Returns the result types.
- getResultTypes() - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
Returns the result types.
- getResultTypes() - Method in class chemaxon.marvin.calculations.HBDAPlugin
-
Returns the result types.
- getResultTypes() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
-
Returns the result types.
- getResultTypes() - Method in class chemaxon.marvin.calculations.IonChargePlugin
-
Returns the result types (possible type: "charge").
- getResultTypes() - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
-
Returns the result types.
- getResultTypes() - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
-
Returns the result types.
- getResultTypes() - Method in class chemaxon.marvin.calculations.logDPlugin
-
Returns the result types.
- getResultTypes() - Method in class chemaxon.marvin.calculations.logPPlugin
-
Returns the result types.
- getResultTypes() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
-
Returns the result types (possible types: "majority-ms").
- getResultTypes() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Returns the result types.
- getResultTypes() - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
-
Returns the result types.
- getResultTypes() - Method in class chemaxon.marvin.calculations.MSAPlugin
-
Returns the result types.
- getResultTypes() - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
-
Returns the result types (possible types: "sigma", "pi").
- getResultTypes() - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Returns the result types (possible types: pKa, acidic, basic, msdistr).
- getResultTypes() - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
-
Returns the result types (possible types: sigma, pi, total).
- getResultTypes() - Method in class chemaxon.marvin.calculations.RefractivityPlugin
-
Returns the result types.
- getResultTypes() - Method in class chemaxon.marvin.calculations.ResonancePlugin
-
Returns the result types.
- getResultTypes() - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
-
Returns the result types.
- getResultTypes() - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
-
- getResultTypes() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Returns the result types.
- getResultTypes() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns the result types.
- getResultTypes() - Method in class chemaxon.marvin.calculations.TPSAPlugin
-
Returns the result types.
- getResultTypes() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns the result types.
- getReturnTypes() - Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor
-
Returns the array of return types
- getRgroup() - Method in class chemaxon.struc.MolAtom
-
Gets the R-group ID.
- getRgroupAttachmentPointOrder() - Method in class chemaxon.struc.MolAtom
-
Gets the attachment point order of an R-group attachment point.
- getRgroupBridgeIds() - Method in class chemaxon.struc.RgMolecule
-
Returns the r-group bridge id pairs.
- getRgroupBridgeMembers(int, int) - Method in class chemaxon.struc.RgMolecule
-
Returns the corresponding r-group bridge members for the given r-group
bridge id pair.
- getRgroupBridges() - Method in class chemaxon.struc.RgMolecule
-
Returns the r-group bridges, the id pairs and the corresponding r-group
bridge members.
- getRgroupCount() - Method in class chemaxon.struc.RgMolecule
-
Gets the number of R-groups.
- getRgroupId(int) - Method in class chemaxon.struc.RgMolecule
-
Gets the ID of an R-group.
- getRgroupId(int) - Method in interface chemaxon.struc.Smolecule
-
Gets the R-group identifier of an atom.
- getRgroupIndex(long) - Method in class chemaxon.struc.RgMolecule
-
Gets the R-group index from the R-group member ID.
- getRgroupMember(int, int) - Method in class chemaxon.struc.RgMolecule
-
Gets an R-group member.
- getRgroupMemberCount(int) - Method in class chemaxon.struc.RgMolecule
-
Gets the number of R-group members.
- getRgroupMemberG(int, int) - Method in class chemaxon.struc.RgMolecule
-
Gets an R-group member.
- getRgroupMemberID(MolAtom) - Method in class chemaxon.struc.RgMolecule
-
Gets the unique indentifier of the R-group member that contains the
specified atom.
- getRgroupMemberIndex(long) - Method in class chemaxon.struc.RgMolecule
-
Gets the R-group member index from the R-group member ID.
- getRgroups() - Method in class chemaxon.checkers.result.RgroupCheckerResult
-
Returns a
List of
RgroupInfo objects with R-atoms and R-group members
affected by the problem
- getRight() - Method in class chemaxon.marvin.space.GraphicCell
-
Returns the x coordinate of the right edge of the cell.
- getRightBracket(CTransform3D) - Method in class chemaxon.struc.graphics.MBracket
-
- getRightName() - Method in class chemaxon.struc.sgroup.SgroupAtom
-
Set the string that will be shown at the right side of the molecule.
- getRingAtomCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns the ring atom count.
- getRingBondCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns the ring bond count.
- getRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns the ring count.
- getRingCount(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Calculates the number of rings (SSSR smallest set of smallest rings) of a
given size in the molecule.
- getRingCountOfAtom(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Calculates the number of rings (SSSR smallest set of smallest rings) an
atom is part of.
- getRingCountOfSize(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
- getRings() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Identifies the rings in the molecule.
- getRings(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Identifies rings in the molecule having a given size.
- getRingSystemCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns the number of ring systems.
- getRingSystemCount(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns the number of ring systems having a given size (number of
rings) in the molecule.
- getRingSystemCountOfSize(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
- getRingSystems() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Identifies the ring systems in the molecule.
- getRingSystems(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Indentifies the ring systems in the molecule having a given size (number
of rings).
- getRlogic(int) - Method in class chemaxon.struc.RgMolecule
-
Gets R-logic flags.
- getRlogicRange(int) - Method in class chemaxon.struc.RgMolecule
-
Gets R-logic occurrence range.
- getRLogicVisible() - Method in class chemaxon.marvin.common.UserSettings
-
Tells whether the R-logic is visible if exists
- getRmsd() - Method in class chemaxon.marvin.alignment.Alignment
-
- getRmsd() - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
-
- getRmsd() - Method in class chemaxon.marvin.alignment.MMPAlignmentResult
-
- getRoot() - Method in class chemaxon.struc.RgMolecule
-
Gets the root structure.
- getRootG() - Method in class chemaxon.struc.RgMolecule
-
Gets the root structure.
- getRootSgroups() - Method in class chemaxon.struc.Molecule
-
Gets root s-groups (groups that are not embedded into another s-group).
- getRotatableBondCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns the rotatable bond count.
- getRotatedCoordinates() - Method in class chemaxon.marvin.alignment.AlignRigidEasy
-
- getRotatedMolecule() - Method in class chemaxon.marvin.alignment.AlignRigidEasy
-
- getRotateMatrix() - Method in class chemaxon.marvin.space.GraphicCell
-
Returns the matrix of rotation.
- getRotationMatrix(int) - Method in class chemaxon.marvin.beans.MViewPane
-
Gets the rotation part of the transformation matrix.
- getRotBondCount() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
-
- getRow(int) - Static method in class chemaxon.struc.MolAtom
-
The row or or period of an element in the periodic system.
- getRow(int) - Static method in class chemaxon.struc.PeriodicSystem
-
The row or or period of an element in the periodic system.
- getRowCount() - Method in class chemaxon.marvin.space.GraphicScene
-
Returns the number of rows in the scene.
- getRowHeight() - Method in class chemaxon.marvin.view.swing.TableOptions
-
Gets the row height.
- getRSChiralCenters(Molecule) - Static method in class chemaxon.checkers.StereoCheckUtility
-
Gets the (R) and (S) chiral centers of the molecule
- getrsChiralCenters(Molecule) - Static method in class chemaxon.checkers.StereoCheckUtility
-
Gets the (r) and (s) stereo centers of the molecule
- getSaveGlobalGUIProperties() - Method in class chemaxon.marvin.beans.MarvinPane
-
Checks whether we have to read GUI properties from a .MRV file
- getSaveGUIPropertiesInMRV() - Method in class chemaxon.marvin.common.UserSettings
-
- getSaveLoadZoomFactorToMRV() - Method in class chemaxon.marvin.common.UserSettings
-
Tells if marvin save the zoom factor to mrv or not.
- getScaffoldOrientatedHit(Molecule, Molecule) - Static method in class chemaxon.util.HitDisplayUtil
-
Only for internal use!
- getScaffoldOrientatedHit(Molecule, Molecule, int[]) - Static method in class chemaxon.util.HitDisplayUtil
-
Returns an aligned (rotated) version of molToAlign that contains
scaffold - possibly in the same position or optimally close to it.
- getScaffoldOrientatedHit(Molecule, Molecule, int[][]) - Static method in class chemaxon.util.HitDisplayUtil
-
Returns an aligned (rotated) version of molToAlign that contains scaffold - possibly in the same position or
optimally close to it.
- getScale() - Method in class chemaxon.marvin.beans.MSketchPane
-
Returns the scale factor of the current magnification.
- getScale() - Method in class chemaxon.marvin.MolPrinter
-
Returns the scale factor in units of regular bond length.
- getScale() - Method in class chemaxon.struc.CTransform3D
-
Gets the scale factor.
- getScale() - Method in class chemaxon.struc.graphics.MTextAttributes
-
Gets the relative size of the font compared to the base font.
- getScaledAWTFont(Float) - Method in class chemaxon.struc.graphics.MFont
-
Gets an AWT font instance after scaling.
- getScriptCount(int, int) - Method in class chemaxon.struc.graphics.MTextDocument
-
Gets the number of subscripts or superscripts on the last normal
character.
- getSecondaryIndexes() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AtomSelection
-
Gets the secondary indexes.
- getSecondaryStructureType(int) - Method in class chemaxon.marvin.space.AtomProperty.MoleculeAtomProperty
-
Gets the type of the secondary structure element which the current
atom belongs to.
- getSecondaryStructureType(int) - Method in class chemaxon.marvin.space.AtomProperty.SmoleculeAtomProperty
-
- getSection(int) - Method in class chemaxon.struc.graphics.MTextDocument
-
Gets a section of the document.
- getSectionCount() - Method in class chemaxon.struc.graphics.MTextDocument
-
Gets the number of sections in the document.
- getSectionIndexOfCharAt(int) - Method in class chemaxon.struc.graphics.MTextDocument
-
Gets the section index of a character.
- getSectionShiftY(int) - Method in class chemaxon.struc.graphics.MTextDocument
-
Gets the y shift of a section.
- getSelectedAtom(int) - Method in class chemaxon.marvin.space.MoleculeComponent
-
- getSelectedAtoms(int, String) - Method in class chemaxon.marvin.view.MDocStorage
-
Gets the selected atom indices.
- getSelectedElements() - Method in class chemaxon.marvin.space.monitor.Monitor
-
Returns the set of the monitored items.
- getSelectedFieldCount() - Method in class chemaxon.marvin.view.swing.TableOptions
-
Gets the number of selected fields.
- getSelectedFields() - Method in class chemaxon.marvin.view.swing.TableOptions
-
Get selected fields array which are selected in Table Options dialog box
- getSelectedFieldTypes() - Method in class chemaxon.marvin.view.swing.TableOptions
-
Get type array of selected field types.
- getSelectedIndex() - Method in class chemaxon.marvin.beans.MViewPane
-
Gets the index of the molecule that is selected by the user.
- getSelectedItem() - Method in class chemaxon.marvin.space.monitor.Label
-
- getSelectedString() - Method in class chemaxon.struc.graphics.MTextBox
-
Gets the selected substring.
- getSelection() - Method in class chemaxon.marvin.beans.MSketchPane
-
Gets a clone of the selection.
- getSelection() - Method in class com.chemaxon.calculations.stereoanal.ErrorReport
-
Returns the selection of atoms.
- getSelection() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AtropStereoCenter
-
- getSelection() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter
-
- getSelection() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter
-
- getSelection() - Method in interface com.chemaxon.calculations.stereoanal.stereocenters.StereoCenter
-
Gets a selection which contains index of center atom and indexes of ligands.
- getSelection() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter
-
- getSelectionEndColumn() - Method in class chemaxon.struc.graphics.MTextBox
-
Gets the selection's end column number.
- getSelectionEndPos() - Method in class chemaxon.struc.graphics.MTextBox
-
Gets the selection's end position.
- getSelectionEndRow() - Method in class chemaxon.struc.graphics.MTextBox
-
Gets the selection's end row number.
- getSelectionStartColumn() - Method in class chemaxon.struc.graphics.MTextBox
-
Gets the selection's start column number.
- getSelectionStartPos() - Method in class chemaxon.struc.graphics.MTextBox
-
Gets the selection's start position.
- getSelectionStartRow() - Method in class chemaxon.struc.graphics.MTextBox
-
Gets the selection's start row number.
- getSeparator(int) - Method in class chemaxon.marvin.plugin.PluginFactory
-
Gets if a separator is required after the plugin menuitem in the Tools menu.
- getServiceDescriptorConfigurationAsStream() - Static method in class chemaxon.marvin.services.ServiceDescriptorTools
-
- getServiceDescriptorConfigurationAsStream(UserSettings) - Static method in class chemaxon.marvin.services.ServiceDescriptorTools
-
- getServiceDescriptorConfigurationAsStream(String) - Static method in class chemaxon.marvin.services.ServiceDescriptorTools
-
Returns the service descriptor configuration stream from path, or null.
- getServiceDescriptorEditorProvider(String) - Static method in class chemaxon.marvin.services.ServiceDescriptorTools
-
- getServiceDescriptorReader(String) - Static method in class chemaxon.marvin.services.ServiceDescriptorTools
-
- getServiceDescriptorWriter(String) - Static method in class chemaxon.marvin.services.ServiceDescriptorTools
-
- getServiceDialogProvider(String) - Static method in class chemaxon.marvin.services.ServiceDescriptorTools
-
- getServiceHandler() - Method in class chemaxon.marvin.services.httpservice.HTTPServiceDescriptor
-
- getServiceHandler() - Method in class chemaxon.marvin.services.json.JsonServiceDescriptor
-
- getServiceHandler() - Method in class chemaxon.marvin.services.localservice.LocalServiceDescriptor
-
- getServiceHandler() - Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor
-
- getServiceHandler() - Method in class chemaxon.marvin.services.xmlrpcservice.XMLRPCServiceDescriptor
-
- getServicesConfigurationPath() - Method in class chemaxon.jep.Evaluator
-
Returns the custom services configuration path.
- getServicesConfigURL() - Method in class chemaxon.marvin.common.UserSettings
-
Returns the URL of configuration for Services in marvin sketch
- getSet() - Method in class chemaxon.struc.graphics.MTextAttributes
-
Gets the set of attributes used.
- getSetColor(int) - Method in class chemaxon.marvin.beans.MarvinPane
-
Deprecated.
as of Marvin 3.3, replaced by getAtomSetColor
- getSetSeq() - Method in class chemaxon.struc.MolAtom
-
Gets the atom set sequence number.
- getSetSeq() - Method in class chemaxon.struc.MolBond
-
Gets the bond set.
- getSeverity() - Method in class chemaxon.checkers.StructureCheckerDescriptor
-
Returns the severity
- getSgroup(int) - Method in class chemaxon.struc.Molecule
-
Gets an S-group.
- getSgroup() - Method in class chemaxon.struc.sgroup.SgroupAtom
-
Gets the S-group corresponding to this superatom.
- getSgroupArray() - Method in class chemaxon.struc.Molecule
-
Gets the array of S-groups.
- getSgroupCount() - Method in class chemaxon.struc.Molecule
-
Gets the number of S-groups.
- getSgroupGraph() - Method in class chemaxon.struc.Sgroup
-
Gets a COPY of the molecule graph.
- getSgroupGraph() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Gets the molecule graph as a selection.
- getSgroupIterator() - Method in class chemaxon.struc.Molecule
-
Returns an iterator over the s-groups in this molecule in proper
sequence.
- getSgroupLigands() - Method in class chemaxon.struc.Molecule
-
Gets the S-group's ligands if the structure represents an S-group.
- getSgroups() - Method in class chemaxon.checkers.result.SgroupCheckerResult
-
Returns a
List which contains the affected groups of the problem
- getSgroupType(String) - Static method in class chemaxon.marvin.io.formats.mdl.MolfileUtil
-
Gets the S-group type.
- getSgroupType() - Method in class chemaxon.struc.Sgroup
-
Gets the S-group type.
- getShapes(CTransform3D) - Method in class chemaxon.struc.graphics.MBracket
-
- getShapeScore() - Method in class chemaxon.marvin.alignment.MMPAlignmentResult
-
- getShapeTanimoto() - Method in class chemaxon.marvin.alignment.MMPAlignmentResult
-
- getShapeTanimoto() - Method in class chemaxon.marvin.alignment.PairwiseAlignment
-
- getShapeTanimoto() - Method in interface chemaxon.marvin.alignment.PairwiseComparison
-
- getShapeTanimoto() - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D
-
- getSheetName() - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
Returns the sheet name the structures added to.
- getShifts() - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
Returns chemical shifts.
- getShiftX() - Method in class chemaxon.marvin.space.GraphicCell
-
Returns the shifting value of the x direction.
- getShiftX(int) - Method in class chemaxon.marvin.space.GraphicScene
-
Returns corrected shifting value of the given cell.
- getShiftY() - Method in class chemaxon.marvin.space.GraphicCell
-
Returns the shifting value of the y direction.
- getShiftY(int) - Method in class chemaxon.marvin.space.GraphicScene
-
Returns corrected shifting value of the given cell.
- getShortestPath(int, int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Calculates the shortest topological path (number of bonds) between two
atoms.
- getShortName() - Method in enum chemaxon.struc.SgroupType
-
- getShowLogPercentage() - Method in class chemaxon.marvin.calculations.pKaPlugin
-
- getSigmaCharge(int) - Method in class chemaxon.marvin.calculations.ChargePlugin
-
Returns the sigma charge of a specified atom.
- getSigmaOEN(int) - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
-
Returns the sigma orbital electronegativity of a specified atom.
- getSimilarityScoreDisplay() - Method in class chemaxon.util.HitColoringAndAlignmentOptions
-
Returns the mode of similarity score display.
- getSimpleName() - Method in class chemaxon.marvin.services.httpservice.HTTPServiceDescriptor
-
- getSimpleName() - Method in class chemaxon.marvin.services.json.JsonServiceDescriptor
-
- getSimpleName() - Method in class chemaxon.marvin.services.localservice.LocalServiceDescriptor
-
- getSimpleName() - Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor
-
- getSimpleName() - Method in class chemaxon.marvin.services.xmlrpcservice.XMLRPCServiceDescriptor
-
- getSimplifiedMolecule() - Method in class chemaxon.struc.Molecule
-
Gets the simplified molecule object.
- getSimpView() - Method in class chemaxon.marvin.beans.MSketchPane
-
- getSingleMsDistribution(int) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
- getSink() - Method in class chemaxon.struc.graphics.MEFlow
-
Gets the destination of the electron-flow arrow (MolAtom, MolBond, or
MolAtom[2] for incipient bond).
- getSinkAtom() - Method in class chemaxon.struc.graphics.MEFlow
-
Gets the atom at the sink of this arrow.
- getSinkAtoms() - Method in class chemaxon.struc.graphics.MEFlow
-
Gets the atom or atoms at the arrow sink.
- getSinkBond() - Method in class chemaxon.struc.graphics.MEFlow
-
Gets the bond at the sink of this arrow.
- getSize() - Method in class chemaxon.marvin.view.MDocStorage
-
Gets the total number of entries.
- getSizeDouble() - Method in class chemaxon.struc.graphics.MFont
-
Gets the font size.
- getSketchAnyBond() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the default any bond drawing style in the sketcher.
- getSketchArrowHeadLength() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the current arrow head length.
- getSketchArrowHeadWidth() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the current arrow head width.
- getSketchArrowTailLength() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the current arrow tail length.
- getSketchArrowTailWidth() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the current arrow tail width.
- getSketchCarbonVisibility() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the default carbon displaying style in the sketcher.
- getSketchColorScheme() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the sketcher's default color scheme.
- getSketchImplicitH() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the display method of implicit hydrogens for the sketcher.
- getSketchLigandOrderVisibility() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the default ligand order displaying style in the sketcher.
- getSketchLoadWorkingDir() - Method in class chemaxon.marvin.common.UserSettings
-
Based on the preferences this funtion returns the proper working directory for the
MarvinSketch application's load filechooser.
- getSketchMode() - Method in class chemaxon.marvin.beans.MSketchPane
-
Gets the sketching mode.
- getSketchMolbg2d() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the sketcher's default 2D molecule background color.
- getSketchMolbg3d() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the sketcher's default 3D molecule background color.
- getSketchRecentFileList() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the recent files' list at marvinsketch, the last item is the most recent.
- getSketchRecentFileListSize() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the recent file list requested size, based on a preferences setting
- getSketchRendering2d() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the rendering style for the 2D sketcher.
- getSketchRendering3d() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the rendering style for the 3D sketcher.
- getSketchSaveWorkingDir() - Method in class chemaxon.marvin.common.UserSettings
-
Not implemented yet don't use it.
- getSkip(int) - Method in class chemaxon.struc.graphics.MPolyline
-
Gets the distance of the (visible) head or tail from the corresponding
line end point.
- getSmallestRing() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Identifies the smallest ring (number of stoms) in the molecule.
- getSmallestRingSize() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns the smallest ring size.
- getSmallestRingSizeForIdx() - Method in class chemaxon.struc.MoleculeGraph
-
Get the smallest ring size in which the atom
(specified with it's index) can be located.
- getSmallestRingSizeOfAtom(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns the size of smallest ring containing the specified atom.
- getSmallestRingSystem() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Identifies the smallest ring system (number of rings) in the molecule.
- getSmallestRingSystemSize() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns the size of the smallest ring system (number of rings) in the molecule.
- getSMILESFontSize() - Method in class chemaxon.marvin.view.swing.TableOptions
-
Gets the SMILES font size.
- getSmolecule() - Method in class chemaxon.calculations.ElementalAnalyser
-
Retrieves the input molecule
- getSmoleculeAtomProperty() - Method in class chemaxon.marvin.space.AtomProperty
-
- getSolubility() - Method in interface com.chemaxon.calculations.solubility.SolubilityResult
-
Returns the solubility value.
- getSolubility(SolubilityUnit) - Method in interface com.chemaxon.calculations.solubility.SolubilityResult
-
Returns the solubility value.
- getSolubilityCategory() - Method in interface com.chemaxon.calculations.solubility.SolubilityResult
-
Returns the solubility category.
- getSolubilityCategory(SolubilityCategories) - Method in interface com.chemaxon.calculations.solubility.SolubilityResult
-
Returns the solubility category.
- getSortedMicrospecies(int) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
-
Returns the microspecies molecule,
sorted by descreasing distribution at the given pH.
- getSortedMsDistribution(int) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
-
Returns the microspecies distribution,
sorted by descreasing distribution at the given pH.
- getSortedSgroups() - Method in class chemaxon.struc.Molecule
-
Gets the sorted S-groups in parent-child order.
- getSortedValues(int, double[], int[]) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
- getSource() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
-
- getSource() - Method in interface chemaxon.checkers.result.StructureCheckerResult
-
- getSource() - Method in class chemaxon.struc.graphics.MEFlow
-
Gets the origin of the electron-flow arrow (MolAtom or MolBond).
- getSourceAtom() - Method in class chemaxon.struc.graphics.MEFlow
-
Gets the atom at the source of this arrow.
- getSourceAtoms() - Method in class chemaxon.struc.graphics.MEFlow
-
Gets the atom or atoms at the arrow source.
- getSourceBond() - Method in class chemaxon.struc.graphics.MEFlow
-
Gets the bond at the source of this arrow.
- getSpecResult(Molecule, String) - Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
-
Returns a specific plugin result corresponding to the given molecule
and argument string.
- getSSSR() - Method in class chemaxon.struc.MoleculeGraph
-
Gets the Smallest Set of Smallest Ring atom indexes array.
- getSSSRBonds() - Method in class chemaxon.struc.MoleculeGraph
-
Gets the Smallest Set of Smallest Ring bond indexes array.
- getSSSRBondsAsBitSet() - Method in class chemaxon.struc.MoleculeGraph
-
Gets the Smallest Set of Smallest Ring edges as an array of BitSets, one BitSet for each ring.
- getSSSRBondSet() - Method in class chemaxon.struc.MoleculeGraph
-
Get SSSR bond index bitset.
- getSSSRBondSetInLong() - Method in class chemaxon.struc.MoleculeGraph
-
- getSSSRIdxesForAtoms() - Method in class chemaxon.struc.MoleculeGraph
-
Get the sssr ring indexes in which the atom
(specified with it's index) can be located.
- getStandardError(Object, int) - Method in class chemaxon.marvin.calculations.logPPlugin
-
- getStartAt() - Method in class chemaxon.marvin.view.swing.TableOptions
-
Get the index number of the molecule that is the first to be displayed.
- getStartColumn() - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
- getStartLineCount() - Method in class chemaxon.marvin.io.MRecord
-
Gets the line number at the starting point.
- getStartPos() - Method in class chemaxon.struc.graphics.MTextDocument.Portion
-
Gets the position of the first character.
- getStartPosition() - Method in class chemaxon.marvin.io.MRecord
-
Gets the start position in the input file.
- getStartPosition() - Method in class chemaxon.struc.MDocument
-
Gets the starting position of this document in the input file.
- getStartPosition() - Method in class chemaxon.struc.Molecule
-
Gets the starting position of this molecule in the input file.
- getStatus() - Method in class chemaxon.marvin.alignment.Alignment
-
- getSteps() - Method in enum chemaxon.marvin.alignment.AtropIsomerDetector.Accuracy
-
- getStereo(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Calculates absolute stereo configuration of the given atom.
- getStereo(int, int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Calculates absolute stereo configuration of the given double bond.
- getStereo1(MolAtom) - Method in class chemaxon.struc.MolBond
-
Gets wedge bond type relative to the specified chiral atom.
- getStereo2(int, int, int, int) - Method in class chemaxon.struc.MoleculeGraph
-
Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
- getStereo2(MolAtom, int, int, MolAtom) - Method in class chemaxon.struc.MoleculeGraph
-
Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
- getStereo2(MolBond, MolAtom, MolAtom) - Method in class chemaxon.struc.MoleculeGraph
-
Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
- getStereo2(MolBond, MolAtom, MolAtom, boolean) - Method in class chemaxon.struc.MoleculeGraph
-
Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
- getStereo2(MolBond) - Method in class chemaxon.struc.MoleculeGraph
-
- getStereo2(MolBond, MolAtom, int, int, MolAtom) - Method in class chemaxon.struc.MoleculeGraph
-
Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
- getStereo2(MolBond, MolAtom, int, int, MolAtom, boolean) - Method in class chemaxon.struc.MoleculeGraph
-
Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
- getStereo2(MolBond, MolAtom, MolAtom, boolean) - Method in class chemaxon.struc.RgMolecule
-
Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
- getStereoActiveParts() - Method in interface chemaxon.struc.CIPStereoDescriptorIface
-
- getStereoCare() - Method in class chemaxon.struc.MolAtom
-
Reports double bond stereo care information on the connected bonds.
- getStereoCenter() - Method in class com.chemaxon.calculations.stereoanal.ErrorReport
-
Returns an optional of stereo centers.
- getStereoCenters() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.EnhancedStereoGroup
-
- getStereoDoubleBondCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Calculates the number of stereo double bonds.
- getStereoGroupNumber() - Method in class chemaxon.struc.MolAtom
-
Gets the stereochemical group number for AND and OR groups of the
enhanced stereo representation.
- getStereoGroupType() - Method in class chemaxon.struc.MolAtom
-
Gets the stereochemical group type for the enhanced stereo
representation.
- getStereoisomer(int) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
-
Returns a stereoisomer.
- getStereoisomerCount() - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
-
Returns the number of different stereoisomers.
- getStereoisomers() - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
-
Returns the stereoisomers in a Molecule[] array.
- getStereoValue() - Method in interface chemaxon.struc.CIPStereoDescriptorIface
-
- getStericEffectIndex(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Calculates topological steric effect index (TSEI) of an atom from
covalent radii values and topological distances.
- getStericHindrance(int) - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
Calculates hindrance of an atom from covalent radii values and distances.
- getStickdst() - Method in class chemaxon.marvin.beans.MSketchPane
-
Gets the sticking distance.
- getStickThickness() - Method in class chemaxon.marvin.beans.MarvinPane
-
Gets the stick thickness.
- getStickThickness() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the stick diameter for ball and stick mode.
- getStickThickness() - Method in class chemaxon.marvin.MolPrinter
-
Gets the 3D stick's diameter.
- getStoredParameters(Properties) - Method in class chemaxon.marvin.plugin.gui.ParameterPanel
-
Returns the stored parameters.
- getStoredParameters(Properties) - Method in interface chemaxon.marvin.plugin.ParameterPanelHandler
-
Returns the stored parameters.
- getStrategy() - Method in class chemaxon.checkers.runner.BasicCheckerRunner
-
Returns the strategy to use.
- getStrictMolecule() - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
- getString() - Method in class chemaxon.marvin.io.MRecord
-
Gets the record text as string.
- getString() - Method in class chemaxon.struc.graphics.MFont
-
Gets the string representation.
- getString() - Method in class chemaxon.struc.graphics.MTextDocument.Section
-
Gets the text string.
- getString(String) - Method in class chemaxon.struc.MPropertyContainer
-
- getStringFromClipboard() - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
-
Returns the String data from the clipboard contents, if the clipboard contains a Transferable
that provides support to
DataFlavor.stringFlavor
- getStructurallogPIncrement() - Method in class chemaxon.marvin.calculations.logPPlugin
-
Returns the structural logP increment.
- getStructure(int) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
-
Returns a structure.
- getStructure(int) - Method in class chemaxon.marvin.calculations.ResonancePlugin
-
Returns a resonant structure.
- getStructure(int) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Returns a tautomer.
- getStructureCellHeight() - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
- getStructureCellWidth() - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
- getStructureColumnIndex() - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
- getStructureColumnName() - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
- getStructureCount() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Returns the number of all enumerated structures,
-1 in case of arithmetical overflow
(if the number would exceed
Long.MAX_VALUE).
- getStructureCount() - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
-
Returns the number of different structures.
- getStructureCount() - Method in class chemaxon.marvin.calculations.ResonancePlugin
-
Returns the number of different resonant structures.
- getStructureCount() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Returns the number of different tautomers.
- getStructureID() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Returns the structure ID used in Markush code (enumeration ID) generation.
- getStructures() - Method in class chemaxon.checkers.result.SubstructureCheckerResult
-
Returns the structures
- getStructures() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Returns the enumerated structures.
- getStructures() - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
-
Returns all structures.
- getStructures() - Method in class chemaxon.marvin.calculations.ResonancePlugin
-
Returns resonant structures in Molecule[] array.
- getStructures() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
- getStyle() - Method in class chemaxon.struc.graphics.MFont
-
Gets the font style.
- getSubFormatPriority(String) - Static method in class chemaxon.formats.MFileFormat
-
Gets the priority of the specified subformat name.
- getSubGraphCount() - Method in class chemaxon.struc.MoleculeGraph
-
Gets the number of all "submolecules".
- getSubGraphCount() - Method in class chemaxon.struc.RgMolecule
-
Gets the number of all "submolecules".
- getSubGraphCount() - Method in class chemaxon.struc.RxnMolecule
-
Gets the number of all "submolecules".
- getSubGraphs() - Method in class chemaxon.struc.MoleculeGraph
-
Gets all "submolecules".
- getSubGraphs(MoleculeGraph[], int) - Method in class chemaxon.struc.MoleculeGraph
-
Gets all "submolecules".
- getSubGraphs(MoleculeGraph[], int) - Method in class chemaxon.struc.RgMolecule
-
Gets all "submolecules".
- getSubGraphs(MoleculeGraph[], int) - Method in class chemaxon.struc.RxnMolecule
-
Gets all "submolecules".
- getSubLevel() - Method in class chemaxon.struc.graphics.MTextAttributes
-
Gets the subscript/superscript level.
- getSubscript() - Method in class chemaxon.struc.sgroup.DataSgroup
-
Gets the subscript for non-superatom S-groups.
- getSubscript() - Method in class chemaxon.struc.Sgroup
-
Gets the subscript for non-superatom S-groups.
- getSubscript() - Method in class chemaxon.struc.sgroup.MultipleSgroup
-
Gets the subscript.
- getSubType() - Method in class chemaxon.struc.Sgroup
-
Gets polymer S-group subtype.
- getSuperAtom() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Gets the superatom.
- getSuperscript() - Method in class chemaxon.struc.Sgroup
-
Gets the superscript for non-superatom S-groups.
- getSuperscript() - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
-
Gets the superscript for Sru S-groups.
- getSupportedDescriptors() - Method in interface chemaxon.marvin.services.ServiceDescriptorEditorProvider
-
Returns a set of supported ServiceDescriptor classes.
- getSurface() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
Returns the surface.
- getSurfaceArea() - Method in class chemaxon.marvin.calculations.MSAPlugin
-
- getSurfaceArea() - Method in class chemaxon.marvin.calculations.TPSAPlugin
-
Returns the surface area.
- getSurfacePrecision() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
Returns the grid resolution from which the surface is computed.
- getSurfaceSimplificationEnabled() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
Returns true if Surface Simplification is enabled.
- getSurfaceSmoothnessFactor() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
Surfaces can be smoothed by the following algorithm:
Paul Bourke: Surface Relaxation and Smoothing
http://astronomy.swin.edu.au/~pbourke/modelling/relax/
This algorithm has a smoothness factor.
- getSurfaceThreshold() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
Returns the isovalue/threshold of the surface.
- getSurfaceType(String) - Static method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- getSurfaceType() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
Returns the type of the surface.
- getSurfaceTypeString(int) - Static method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- getSymbol() - Method in class chemaxon.struc.MolAtom
-
Gets the element symbol.
- getSymbol(int) - Static method in class chemaxon.struc.PeriodicSystem
-
Symbol of the element
- getSymbol() - Method in class chemaxon.struc.sgroup.SgroupAtom
-
Gets the abbreviated group symbol.
- getSymbolTable() - Method in class chemaxon.jep.Evaluator
-
Returns the symbol table of predefined constants (molecules, molecule sets
and other constants defined in the built-in and the user-defined jep.script).
- getSzegedIndex() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Calculates the Szeged index of the molecule.
- getT(int) - Method in class chemaxon.marvin.beans.MViewPane
-
Gets a text field value in a GridBagView table.
- getT(int, int) - Method in class chemaxon.marvin.view.MDocStorage
-
Gets a text field in a record.
- getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class chemaxon.marvin.beans.MViewEditor
-
Sets up the editor component.
- getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class chemaxon.marvin.beans.MolRenderer
-
The implementation of this method sets up the rendering component to display the passed-in
molecule, and then returns the component.
- getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class chemaxon.marvin.beans.MViewRenderer
-
The implementation of this method sets up the rendering component to display the passed-in
molecule, and then returns the component.
- getTableOptions() - Method in class chemaxon.marvin.view.swing.TableSupport
-
Gets the table options component.
- getTableSupport() - Method in class chemaxon.marvin.beans.MViewPane
-
Gets an object that helps to build and use a viewer table.
- getTableText(String, String[], double[][]) - Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
-
Returns table in string form.
- getTabScale() - Method in class chemaxon.marvin.beans.MViewPane
-
Gets the magnification in the molecule cells.
- getTabScale(int) - Method in class chemaxon.marvin.beans.MViewPane
-
Gets the magnification for a molecule cell.
- getTag() - Method in class chemaxon.struc.sgroup.DataSgroup
-
Gets the tag character for footnote display (or space if blank).
- getTailCrossingBonds() - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
-
Gets the tail crossing bonds.
- getTCenter() - Method in class chemaxon.struc.graphics.MRectangle
-
Gets the transformed point.
- getTemporaryObject(String) - Method in class chemaxon.struc.MolAtom
-
Gets a temporary object.
- getTerminalBondDeletionStyle() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the terminal bon deletion style.
- getText() - Method in class chemaxon.marvin.space.monitor.Label
-
Returns the explicit text of the label, or null if there is no explicit label set.
- getText() - Method in class chemaxon.struc.graphics.MTextBox
-
Gets the text stored.
- getTextAttributesAtCursor() - Method in class chemaxon.struc.graphics.MTextBox
-
Gets the common attributes of the text on the cursor.
- getTextDocument() - Method in class chemaxon.struc.graphics.MTextBox
-
Gets the text document.
- getThickness() - Method in class chemaxon.struc.graphics.MPolyline
-
Gets the line thickness.
- getThrowable() - Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
-
Returns the throwable object.
- getThrowable() - Method in interface chemaxon.util.iterator.MoleculeIterator
-
- getTitle() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Returns the frame title.
- getTitle() - Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
-
Returns the frame title.
- getToolBar(JTextPane) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Returns the default toolbar for textPane instance
NOTE: textPane have to be created with this factory
- getToolbarConfigPath() - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
-
Returns the toolbar configuration path
- getTop() - Method in class chemaxon.marvin.space.GraphicCell
-
Returns the y coordinate of the top of the cell.
- getTopLeftIndex() - Method in class chemaxon.marvin.beans.MViewPane
-
Gets the index of the top left cell.
- getTopLevelContainer() - Method in class chemaxon.marvin.beans.MarvinPane
-
- getTOption() - Method in class chemaxon.struc.graphics.MRectangle
-
Gets the transformation options.
- getTotalCharge(int) - Method in class chemaxon.marvin.calculations.ChargePlugin
-
Returns the total charge of a specified atom.
- getTotalCharge() - Method in class chemaxon.struc.MoleculeGraph
-
Gets the total (formal) charge of the molecule.
- getTotalCharge() - Method in class chemaxon.struc.Sgroup
-
Calculates the sum of the charge values on the atoms in this S-group.
- getTotalPiEnergy() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
-
- getTPSA() - Method in class chemaxon.marvin.calculations.TPSAPlugin
-
- getTraditionalName() - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
-
Returns the traditional IUPAC name.
- getTrainingIds() - Static method in class chemaxon.marvin.calculations.logPPlugin
-
Returns the id's of available logP trainings.
- getTransferableFor(Molecule, Properties) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
-
- getTransferableFor(Molecule, Properties, String) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
-
- getTransferData(DataFlavor) - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
-
Returns the result of the transfer operation.
- getTransferDataFlavors() - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
-
Returns the DataFlavors supported by the actual implementation.
- getTransformationCenter() - Method in class chemaxon.marvin.space.GraphicCell
-
Returns the transformation center.
- getTransformationCenter() - Method in class chemaxon.marvin.space.GraphicScene
-
Returns the center of transformation of the active cell or null
if there is no active cell.
- getType() - Method in class chemaxon.checkers.AromaticityErrorChecker
-
Returns the type of the aromatization
- getType() - Method in class chemaxon.marvin.services.ServiceArgument
-
Returns the argument type
- getType(int) - Method in class chemaxon.marvin.space.AtomProperty.MoleculeAtomProperty
-
- getType(int) - Method in class chemaxon.marvin.space.AtomProperty.SmoleculeAtomProperty
-
- getType() - Method in class chemaxon.marvin.util.OptionDescriptor
-
Gets the option type.
- getType() - Method in interface chemaxon.struc.CIPStereoDescriptorIface
-
- getType() - Method in class chemaxon.struc.graphics.MBracket
-
Gets the bracket type.
- getType() - Method in class chemaxon.struc.MolBond
-
Gets the bond type.
- getType(MoleculeGraph) - Method in class chemaxon.struc.RxnMolecule
-
Checks whether the atoms in the selection are all in reactants, products or agents.
- getType() - Method in class chemaxon.struc.Sgroup
-
- getType(String) - Static method in enum chemaxon.struc.SgroupType
-
Returns an SgroupType for the given short name.
- getType() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.EnhancedStereo
-
Gets the type of enhanced stereo flag.
- getTypes() - Method in class chemaxon.checkers.AtomTypeChecker
-
Returns the checked atom types
- getTypeString(Object) - Method in class chemaxon.marvin.calculations.ChargePlugin
-
Returns a string representation of the given type.
- getTypeString(Object) - Method in class chemaxon.marvin.calculations.ConformerPlugin
-
Returns a string representation of the given type.
- getTypeString(Object) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
-
Returns a string representation of the given type.
- getTypeString(Object) - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
Returns a string representation of the given type.
- getTypeString(Object) - Method in class chemaxon.marvin.calculations.HBDAPlugin
-
Returns a string representation of the given type.
- getTypeString(Object) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
-
Returns a string representation of the given type.
- getTypeString(Object) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
-
Returns a string representation of the given type.
- getTypeString(Object) - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
-
Returns a string representation of the given type.
- getTypeString(Object) - Method in class chemaxon.marvin.calculations.logPPlugin
-
Returns a string representation of the given type.
- getTypeString(Object) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Returns a string representation of the given type.
- getTypeString(Object) - Method in class chemaxon.marvin.calculations.MSAPlugin
-
Returns a string representation of the given type.
- getTypeString(Object) - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
-
Returns a string representation of the given type.
- getTypeString(Object) - Method in class chemaxon.marvin.calculations.RefractivityPlugin
-
Returns a string representation of the given type.
- getTypeString(Object) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
-
Returns a string representation of the given type.
- getTypeString(Object) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
-
Returns a string representation of the given type.
- getTypeString(Object) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns a string representation of the given type.
- getTypeString(Object) - Method in class chemaxon.marvin.calculations.TPSAPlugin
-
Returns a string representation of the given type.
- getTypeString(Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns a string representation of the given type.
- getUndefinedRSChiralCenters(Molecule) - Static method in class chemaxon.checkers.StereoCheckUtility
-
Gets the undefined (R) and (S) chiral centers of the molecule
- getUndefinedrsChiralCenters(Molecule) - Static method in class chemaxon.checkers.StereoCheckUtility
-
Gets the undefined (r) and (s) stereo centers of the molecule
- getUndo() - Method in class chemaxon.marvin.beans.MSketchPane
-
Gets the maximum undo depth.
- getUnguessableFormat(String) - Static method in class chemaxon.formats.MFileFormatUtil
-
Gets the file format from the file name extension for formats that
are not guessable from the file content.
- getUnit() - Method in class chemaxon.calculations.dipole.DipoleResult
-
Returns the dipole moment unit.
- getUnit() - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder
-
Gets the NMR unit.
- getUnit() - Method in class chemaxon.calculations.nmr.NMRCalculator
-
Returns NMR spectrum unit.
- getUnit() - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
Returns the unit type.
- getUnits() - Method in class chemaxon.struc.sgroup.DataSgroup
-
Gets the unit of this data field.
- getUpperLimit() - Method in enum com.chemaxon.calculations.solubility.DefaultSolubilityCategory
-
- getUpperLimit() - Method in class com.chemaxon.calculations.solubility.SolubilityCategories.UndefinedSolubilityCategory
-
- getUpperLimit() - Method in interface com.chemaxon.calculations.solubility.SolubilityCategory
-
The upper limit of category.
- getUsableObject(UOID) - Method in class chemaxon.marvin.space.GraphicComponent
-
Returns the component that the given UOID identifies.
- getUsableObject(UOID) - Method in class chemaxon.marvin.space.MacroMoleculeComponent
-
- getUsableObjectId(MacroMoleculeComponent.MoleculeVisualizer) - Method in class chemaxon.marvin.space.MacroMoleculeComponent
-
- getUserSettings() - Method in class chemaxon.marvin.beans.MarvinPane
-
Gets the user settings object.
- getUserTypes() - Method in class chemaxon.marvin.calculations.logPPlugin
-
Returns the user defined result types.
- getValence() - Method in class chemaxon.struc.MolAtom
-
Gets the valence.
- getValence(int) - Method in interface chemaxon.struc.Smolecule
-
Gets the valence.
- getValenceCheckOptions() - Method in class chemaxon.struc.MoleculeGraph
-
Returns the options for valence checking.
- getValenceCheckOptions() - Method in class chemaxon.struc.RgMolecule
-
Returns the options for valence checking.
- getValenceCheckState() - Method in class chemaxon.struc.MoleculeGraph
-
Deprecated.
As of Marvin 6.0, replaced by MoleculeGraph.getValenceCheckOptions() and
MoleculeGraph.isValenceCheckEnabled().
Usage:
// Same as getValenceCheckState() == ValenceCheckState.OFF:
isValenceCheckEnabled() == true;
// Same as getValenceCheckState() == ValenceCheckState.AMBIGUOUS_AROMATIC_ATOMS_IGNORED:
getValenceCheckOptions.isLocalAromatic() == true;
// Same as getValenceCheckState() == ValenceCheckState.FULL:
getValenceCheckOptions.isLocalAromatic() == false;
- getValenceProp() - Method in class chemaxon.struc.MolAtom
-
Gets the valence property.
- getValenceProperty(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
- getValencePropMinMax() - Method in class chemaxon.struc.MolAtom
-
Gets the minimum and maximum possible values of the valence property.
- getValidationResultLabel(JTextPane) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Returns a
JLabel instance, dinamically showing validation result of textPane
NOTE: will validate against Molecular Context.
- getValidationResultLabel(JTextPane, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Returns a
JLabel instance, dinamically showing validation result of textPane
NOTE: textPane have to be created with this factory
- getValidationResultLabelForReactionContext(JTextPane) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Returns a
JLabel instance, dinamically showing validation result of textPane
NOTE: will validate against Reaction Context.
- getValidSinkAtomPairsForMolecule(Molecule, MolAtom) - Static method in class chemaxon.struc.graphics.MEFlow
-
Deprecated.
As of Marvin 6.1, replaced by
EFlowPlacementValidators.getValidSinkAtomPairs(Molecule, MolAtom)
.
- getValidSinkAtomPairsForMolecule(Molecule, MolBond) - Static method in class chemaxon.struc.graphics.MEFlow
-
Deprecated.
As of Marvin 6.1, replaced by
EFlowPlacementValidators.getValidSinkAtomPairs(Molecule, MolBond)
.
- getValidSinkAtomsForMolecule(Molecule, MolAtom) - Static method in class chemaxon.struc.graphics.MEFlow
-
Deprecated.
As of Marvin 6.1, replaced by
EFlowPlacementValidators.getValidSinkAtoms(Molecule, MolAtom)
.
- getValidSinkAtomsForMolecule(Molecule, MolBond) - Static method in class chemaxon.struc.graphics.MEFlow
-
Deprecated.
As of Marvin 6.1, replaced by
EFlowPlacementValidators.getValidSinkAtoms(Molecule, MolBond)
.
- getValidSinkBondsForMolecule(Molecule, MolAtom) - Static method in class chemaxon.struc.graphics.MEFlow
-
Deprecated.
As of Marvin 6.1, replaced by
EFlowPlacementValidators.getValidSinkBonds(Molecule, MolAtom)
.
- getValidSinkBondsForMolecule(Molecule, MolBond) - Static method in class chemaxon.struc.graphics.MEFlow
-
Deprecated.
As of Marvin 6.1, replaced by
EFlowPlacementValidators.getValidSinkBonds(Molecule, MolBond)
.
- getValidSourceAtomPairsForMolecule(Molecule) - Static method in class chemaxon.struc.graphics.MEFlow
-
Deprecated.
As of Marvin 6.1, replaced by
EFlowPlacementValidators.getValidSourceAtomPairs(Molecule)
.
- getValidSourceAtomsForMolecule(Molecule) - Static method in class chemaxon.struc.graphics.MEFlow
-
Deprecated.
As of Marvin 6.1, replaced by
EFlowPlacementValidators.getValidSourceAtoms(Molecule)
.
- getValidSourceBondsForMolecule(Molecule) - Static method in class chemaxon.struc.graphics.MEFlow
-
Deprecated.
As of Marvin 6.1, replaced by
EFlowPlacementValidators.getValidSourceBonds(Molecule)
.
- getValue() - Method in class chemaxon.marvin.services.ServiceArgument
-
Returns the argument value
- getValue() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AtropStereoCenter
-
- getValue() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter
-
- getValue() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter
-
- getValue() - Method in interface com.chemaxon.calculations.stereoanal.stereocenters.StereoCenter
-
- getValue() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter
-
- getValueAt(double) - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
Returns the value of the NMR spectrum function at a given x point.
- getVanDerWaalsRadius(int) - Static method in class chemaxon.struc.PeriodicSystem
-
Van der Waals radius of the element in Angstroms.
- getVDWSA() - Method in class chemaxon.marvin.calculations.MSAPlugin
-
Returns van der Waals surface area.
- getVerboseLevel() - Method in class chemaxon.marvin.space.GraphicCell
-
Gets the verbose level.
- getVerboseLevel() - Method in class chemaxon.marvin.space.GraphicScene
-
Gets the verbose level.
- getVersion() - Static method in class com.chemaxon.version.VersionInfo
-
Returns the product version.
- getVertexCount() - Method in class chemaxon.marvin.space.SurfaceComponent
-
Returns the number of allocated vertices in the SurfaceComponent.
- getVertexX(int) - Method in class chemaxon.marvin.space.SurfaceComponent
-
Returns the x coordinate of the ith vertex.
- getVertexY(int) - Method in class chemaxon.marvin.space.SurfaceComponent
-
Returns the y coordinate of the ith vertex.
- getVertexZ(int) - Method in class chemaxon.marvin.space.SurfaceComponent
-
Returns the z coordinate of the ith vertex.
- getVerticalAlignment() - Method in class chemaxon.struc.graphics.MTextBox
-
Gets the vertical alignment.
- getViewAnyBond() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the default any bond drawing style in the viewer.
- getViewCarbonVisibility() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the default carbon displaying style in the viewer.
- getViewColorScheme() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the viewer's default color scheme.
- getViewHandlerType() - Method in class chemaxon.marvin.view.swing.TableOptions
-
Gets the view handler type.
- getViewImplicitH() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the display method of implicit hydrogens for the viewer.
- getViewLayout() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the table layout of the Viewer.
- getViewLigandOrderVisibility() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the default ligand order displaying style in the viewer.
- getViewLoadWorkingDir() - Method in class chemaxon.marvin.common.UserSettings
-
Based on the preferences this funtion returns the proper working directory for the MarvinView
application's load filechooser.
- getViewMolbg2d() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the viewer's default molecule background color for 2D.
- getViewMolbg3d() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the viewer's default molecule background color for 3D.
- getViewNavmode2d() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the navigation mode for the 2D viewer.
- getViewNavmode3d() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the navigation mode for the 3D viewer.
- getViewportHeight() - Method in class chemaxon.marvin.space.GraphicScene
-
Returns the phisical height of the viewport.
- getViewportWidth() - Method in class chemaxon.marvin.space.GraphicScene
-
Returns the phisical width of the viewport.
- getViewRecentFileList() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the recent files' list in MarvinView, the last item is the most recent.
- getViewRecentFileListSize() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the recent file list requested size, based on a preferences setting
- getViewRendering2d() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the rendering style for the 2D viewer.
- getViewRendering3d() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the rendering style for the 3D viewer.
- getViewSaveWorkingDir() - Method in class chemaxon.marvin.common.UserSettings
-
Not implemented yet, don't use it.
- getVisibleAtomCount() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- getVisibleAtomCount() - Method in class chemaxon.marvin.space.MoleculeComponent
-
Returns the number of atoms currently visible.
- getVisibleButtonB(int) - Method in class chemaxon.marvin.beans.MViewPane
-
Gets the i-th button in the visible area of the viewer.
- getVisibleButtonC(int) - Method in class chemaxon.marvin.beans.MViewPane
-
Gets the i-th checkbox in the visible area of the viewer.
- getVisibleCellComponent(int) - Method in class chemaxon.marvin.beans.MViewPane
-
Gets the canvas of the specified cell in a GridBag layout based table.
- getVisibleCellCount() - Method in class chemaxon.marvin.beans.MViewPane
-
Gets the number of the visible cells in a GridBag layout based table.
- getVisibleCellIndex(int) - Method in class chemaxon.marvin.beans.MViewPane
-
Determines the visible cell index of a cell
- getVisibleCoords(MolAtom) - Method in class chemaxon.struc.Molecule
-
Returns the coordinates of the given atom (contained in the molecule).
- getVisibleCoords(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
-
Returns the coordinates of the given atom (contained in the molecule).
- getVisiblePointRef(int, CTransform3D) - Method in class chemaxon.struc.graphics.MBracket
-
Gets an internal selectable point of the rectangle.that is visible when highlighting.
- getVisiblePointRefCount() - Method in class chemaxon.struc.graphics.MBracket
-
Gets the number of internal selectable point references that are visible when highlighting.
- getVisualizable() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
-
- getVolume() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
-
- getVolume() - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
- getVolumeScore() - Method in class chemaxon.marvin.alignment.Alignment
-
- getVolumeTanimoto() - Method in class chemaxon.marvin.calculations.AlignmentPlugin
-
- getWarningMessage() - Method in class chemaxon.marvin.calculations.AlignmentPlugin
-
Returns the calculation warning information message.
- getWarningMessage() - Method in class chemaxon.marvin.calculations.ConformerPlugin
-
Returns a warning message if there are no conformers, null
otherwise.
- getWarningMessage() - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
Returns a warning message if lowest energy conformer calculation was unsuccessful
or aborted by user, null otherwise.
- getWarningMessage() - Method in class chemaxon.marvin.calculations.HBDAPlugin
-
Returns the calculation warning information message if no H-bond donor/acceptor atoms found,
returns the empty string otherwise.
- getWarningMessage() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
-
Returns the calculation warning information message.
- getWarningMessage() - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
-
Returns the calculation warning information message
if no isoelectric point exists, returns the empty string otherwise.
- getWarningMessage() - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Returns the calculation warning information message.
- getWarningMessage() - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
-
Returns a warning message if there are no stereoisomers, null
otherwise.
- getWarningMessage() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
- getWarningMessage() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns the calculation warning information message.
- getWebServiceName() - Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor
-
Returns the service name
- getWeights() - Method in class chemaxon.struc.graphics.MAtomSetPoint
-
Gets the atom weights used in average location calculation.
- getWidth() - Method in class chemaxon.marvin.space.GraphicCell
-
Returns the width of the cell.
- getWienerIndex() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Calculates the Wiener index of the molecule, which is the average
topological atom distance (half of the sumof all atom distances) in the
molecule.
- getWienerPolarity() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Calculates the Wiener polarity number of the molecule, which is the
number of 3 bond length distances in the molecule.
- getWinScale() - Method in class chemaxon.marvin.beans.MViewPane
-
Gets the magnification in the zoom windows.
- getWireThickness() - Method in class chemaxon.marvin.beans.MarvinPane
-
Gets the line thickness for wireframe mode.
- getWireThickness() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the bond thickness in wireframe mode.
- getWireThickness() - Method in class chemaxon.marvin.MolPrinter
-
Gets the line thickness for wireframe mode.
- getWord(ByteBuffer, int) - Method in class chemaxon.marvin.io.PositionedInputStream
-
- getWordsRead() - Method in class chemaxon.naming.DocumentExtractor.ProgressInfo
-
Deprecated.
- getWorkbook() - Method in class chemaxon.formats.documents.jchemexcel.JChemExcelAPI
-
Returns the Workbook object model instance
- getWorkbook() - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
Returns the Workbook object model instance
- getWorkOnBackGround() - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
-
Returns whether the subsystem works on the current thread or on a background thread.
- getWrapperException(Exception) - Method in class chemaxon.marvin.plugin.concurrent.PluginWorkUnit
-
Returns a wrapper exception to be returned.
- getWrapperException(Exception) - Method in class chemaxon.marvin.plugin.concurrent.ReusablePluginWorkUnit
-
Returns a wrapper exception to be returned.
- getWrongLengthBonds() - Method in class chemaxon.checkers.result.BondLengthCheckerResult
-
Returns the internal representation of the bond length checker result, which contains all information required
to fix bond length errors.
- getWsdlURI() - Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor
-
Returns the WSDL URI
- getX(int) - Method in class chemaxon.marvin.space.AtomProperty.MoleculeAtomProperty
-
- getX(int) - Method in class chemaxon.marvin.space.AtomProperty.SmoleculeAtomProperty
-
- getX() - Method in class chemaxon.struc.MolAtom
-
Gets the X coordinate.
- getX() - Method in class chemaxon.struc.sgroup.DataSgroup
-
Gets the X coordinate.
- getXState() - Method in class chemaxon.struc.Sgroup
-
Gets the expanded/contracted state.
- getY(int) - Method in class chemaxon.marvin.space.AtomProperty.MoleculeAtomProperty
-
- getY(int) - Method in class chemaxon.marvin.space.AtomProperty.SmoleculeAtomProperty
-
- getY() - Method in class chemaxon.struc.MolAtom
-
Gets the Y coordinate.
- getY() - Method in class chemaxon.struc.sgroup.DataSgroup
-
Gets the Y coordinate.
- getZ(int) - Method in class chemaxon.marvin.space.AtomProperty.MoleculeAtomProperty
-
- getZ(int) - Method in class chemaxon.marvin.space.AtomProperty.SmoleculeAtomProperty
-
- getZ() - Method in class chemaxon.struc.MolAtom
-
Gets the Z coordinate.
- getZCoordinateTo2DPart() - Method in class chemaxon.marvin.space.GraphicComponent
-
Returns a third, z coordinate in order to display 2D parts in proper order.
- getZCoordinateTo2DPart() - Method in class chemaxon.marvin.space.monitor.Label
-
Returns a third, z coordinate in order to display 2D parts in proper order.
- gl - Variable in class chemaxon.marvin.space.GraphicComponent
-
must be accessible in derived classes
- glColor() - Method in class chemaxon.marvin.space.GraphicComponent
-
Sets the default/constant color of the component for drawing.
- GLInfo - Static variable in class chemaxon.marvin.space.GraphicScene
-
- GlobalLocationControl - Class in chemaxon.marvin.space.monitor
-
This control is to change the location say translate a GraphicComponent
in the global coordinate system.
- GlobalLocationControl(Monitor) - Constructor for class chemaxon.marvin.space.monitor.GlobalLocationControl
-
Creates a new instance of GlobalLocationControl
- GlobalOrientationControl - Class in chemaxon.marvin.space.monitor
-
This control is to change the orientation say rotate a GraphicComponent
in the global coordinate system.
- GlobalOrientationControl(Monitor) - Constructor for class chemaxon.marvin.space.monitor.GlobalOrientationControl
-
Creates a new instance of GlobalOrientationControl
- gltext - Variable in class chemaxon.marvin.space.monitor.Label
-
This is to draw labels in the viewing plane.
- glu - Variable in class chemaxon.marvin.space.GraphicComponent
-
- GRAPH_INVARIANTS - Static variable in class chemaxon.marvin.view.ViewParameterConstants
-
Identifier of parameter: "grinv".
- GRAPH_INVARIANTS_VISIBLE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter: "grinvVisible".
- GraphicCell - Class in chemaxon.marvin.space
-
GraphicCell is a rectangular part of the OpenGL2 canvas containing GraphicComponents.
- GraphicCell() - Constructor for class chemaxon.marvin.space.GraphicCell
-
Creates a new instance of GraphicCell.
- GraphicCell(GL2, GLU) - Constructor for class chemaxon.marvin.space.GraphicCell
-
Creates a new instance of GraphicCell.
- graphicCell - Variable in class chemaxon.marvin.space.GraphicComponent
-
which cell of the scene is this component displayed in
- GraphicComponent - Class in chemaxon.marvin.space
-
GraphicComponents are the basic objects what MarvinSpace can visualize and handle.
- GraphicComponent() - Constructor for class chemaxon.marvin.space.GraphicComponent
-
Creates an empty object.
- GraphicScene - Class in chemaxon.marvin.space
-
GraphicScene is the main "entry point" to MarvinSpace.
- GraphicScene() - Constructor for class chemaxon.marvin.space.GraphicScene
-
Creates a hardware accelerated and double buffered GraphicScene.
- GraphicScene(int, int) - Constructor for class chemaxon.marvin.space.GraphicScene
-
Creates a hardware accelerated and double buffered GraphicScene.
- graphInvariant() - Method in class chemaxon.calculations.stereo.Stereochemistry
-
- graphInvariant() - Method in class chemaxon.calculations.TopologyAnalyser
-
- GRID_MAPPING - Static variable in class chemaxon.marvin.space.SurfaceColoring
-
Coloring by mapping values form a grid to the surface.
- GRINV_DONT_STORE - Static variable in class chemaxon.struc.MoleculeGraph
-
Graph invariant option to instruct that the graph invariant should not be
stored in MoleculeGraph.
- GRINV_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Show graph invariants flag.
- GRINV_NOHYDROGEN - Static variable in class chemaxon.struc.MoleculeGraph
-
Graph invariant option for ignoring explicit hydrogens.
- GRINV_OLDSTEREO - Static variable in class chemaxon.struc.MoleculeGraph
-
Graph invariant option for calculating graph invariants using the old
stereo method.
- GRINV_STEREO - Static variable in class chemaxon.struc.MoleculeGraph
-
Graph invariant option for calculating graph invariants using stereo
information.
- GRINV_USEMAPS - Static variable in class chemaxon.struc.MoleculeGraph
-
Graph invariant option for calculating graph invariants considering
atom maps also.
- GRINV_VALUE_OPTIONS - Static variable in class chemaxon.struc.MoleculeGraph
-
Unified mask of graph invariant options affecting grinv value.
- grinvCC - Variable in class chemaxon.struc.MoleculeGraph
-
Graph invariant change count.
- GROUP_SCHEME - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Group color scheme in display option flags.
- GROUP_SCHEME_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Group color scheme.
- GROUPTYPE_ALTERNATING_COPOLYMER_GROUP - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
- GROUPTYPE_ANYPOLYMER_GROUP - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
- GROUPTYPE_BLOCK_COPOLYMER_GROUP - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
- GROUPTYPE_COMPONENT_GROUP - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
- GROUPTYPE_COPOLYMER_GROUP - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
- GROUPTYPE_CROSSLINK_GROUP - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
- GROUPTYPE_GENERIC_GROUP - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
- GROUPTYPE_GRAFT_GROUP - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
- GROUPTYPE_MER_GROUP - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
- GROUPTYPE_MODIFICATION_GROUP - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
- GROUPTYPE_MONOMER_GROUP - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
- GROUPTYPE_MULTIPLE_GROUP - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
- GROUPTYPE_ORDERED_MIXTURE_GROUP - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
- GROUPTYPE_RANDOM_COPOLYMER_GROUP - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
- GROUPTYPE_RANGE_GROUP - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
- GROUPTYPE_SRU_GROUP - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
- GROUPTYPE_SUPERATOM_GROUP - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
- GROUPTYPE_UNORDERED_MIXTURE_GROUP - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
- guessPeptideFormat(String) - Static method in class chemaxon.formats.recognizer.PeptideRecognizer
-
Deprecated.
as of Marvin 2014.07.21.0 intended for internal use
- GZIP - Static variable in class chemaxon.formats.MFileFormat
-
GZIPped file.
- I - Static variable in class chemaxon.core.ChemConst
-
- icell - Variable in class chemaxon.marvin.plugin.CalculatorPluginDisplay
-
The viewer cell index (0 for sketcher).
- ICON_PATH - Static variable in class chemaxon.checkers.StructureCheckerDescriptor
-
icon path of checker
- ignoreConfigurationErrors - Variable in class chemaxon.checkers.StructureCheckOptions
-
Ignores configuration errors - errors found in input files does not cause the execution to stop on the input file, just skips
the actual structure and tries the next - printing error message on the standard error
- ignoreDrawProperties - Variable in class chemaxon.marvin.space.monitor.Label
-
- ignoreDrawProperties(boolean) - Method in class chemaxon.marvin.space.monitor.Label
-
Sets the label whether it accepts draw properties or not.
- ignoreErrors - Variable in class chemaxon.checkers.StructureCheckOptions
-
Ignores errors - errors found in input files does not cause the execution to stop on the input file, just skips
the actual structure and tries the next - printing error message on the standard error
- IMAGE_IMPORT_SERVICE_URL - Static variable in class chemaxon.marvin.common.ParameterConstants
-
- IMAGE_SAVE_FORMAT - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter: "imageSaveFormat".
- IMAGE_SAVE_URL - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter: "imageSaveURL".
- IMAGE_SHOW_URL - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter: "imageShowURL".
- ImageExportUtil - Class in chemaxon.util
-
Utility functions to create format parameter string for molecule export and for usage of .NET
based EMF generator.
- IMPLICIT_H - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter: "implicitH".
- IMPLICITH_ALL - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Display implicit hydrogens on all atoms.
- IMPLICITH_ALL_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Display implicit hydrogens on all atoms.
- IMPLICITH_HETERO - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Display implicit hydrogens only on heteroatoms.
- IMPLICITH_HETERO_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Display implicit hydrogens only on heteroatoms.
- IMPLICITH_HETEROTERM - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Display implicit hydrogens only on hetero and terminal atoms.
- IMPLICITH_HETEROTERM_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Display implicit hydrogens only on hetero and terminal atoms.
- IMPLICITH_LEVELS - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Array of implicit Hydrogen visibility levels.
- IMPLICITH_MASK - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Implicit hydrogen visibility mask.
- IMPLICITH_OFF - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Do not display any implicit hydrogens.
- IMPLICITH_OFF_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Do not display any implicit hydrogens.
- implicitizeHydrogens(int) - Method in class chemaxon.struc.MoleculeGraph
-
- implicitizeHydrogens(int, MolAtom[]) - Method in class chemaxon.struc.MoleculeGraph
-
- implicitizeHydrogens(int, MolAtom[], boolean) - Method in class chemaxon.struc.MoleculeGraph
-
- implicitizeHydrogens0(int, MolAtom[], boolean) - Method in class chemaxon.struc.Molecule
-
- implicitizeHydrogens0(int, MolAtom[], boolean) - Method in class chemaxon.struc.MoleculeGraph
-
- IMPORT_CONVERSION - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter: "importConv".
- IMPORT_ENABLED - Static variable in class chemaxon.marvin.view.ViewParameterConstants
-
Identifier of parameter: "importEnabled".
- importDoc(byte[]) - Static method in class chemaxon.formats.MolImporter
-
Reads a document from a byte array.
- importDoc(byte[], String, String) - Static method in class chemaxon.formats.MolImporter
-
Reads a document from a byte array.
- importer - Variable in class chemaxon.marvin.io.formats.MoleculeImporter
-
The wrapped importer.
- importMol(byte[]) - Static method in class chemaxon.formats.MolImporter
-
Read a molecule from a byte array.
- importMol(byte[], String, String) - Static method in class chemaxon.formats.MolImporter
-
Read a molecule from a byte array.
- importMol(byte[], Molecule) - Static method in class chemaxon.formats.MolImporter
-
Read a molecule from a byte array.
- importMol(byte[], String, String, Molecule) - Static method in class chemaxon.formats.MolImporter
-
Read a molecule from a byte array.
- importMol(String) - Static method in class chemaxon.formats.MolImporter
-
Read a molecule from a string.
- importMol(String, String) - Static method in class chemaxon.formats.MolImporter
-
Read a molecule from a string.
- importMol(String, ImportOptions) - Static method in class chemaxon.formats.MolImporter
-
Read a molecule from a string with the given options.
- importMol(String, String, String) - Static method in class chemaxon.formats.MolImporter
-
- importMol(String, Molecule) - Static method in class chemaxon.formats.MolImporter
-
Read a molecule from a string.
- importMol(String, String, String, Molecule) - Static method in class chemaxon.formats.MolImporter
-
- In - Static variable in class chemaxon.core.ChemConst
-
- IN_INPUT_ORDER - Static variable in class chemaxon.util.concurrent.processors.ConcurrentProcessors
-
- inAtomList(int, int) - Method in interface chemaxon.struc.Smolecule
-
Tests whether the specified element is in the atom list.
- incGrinvCC() - Method in class chemaxon.struc.MoleculeGraph
-
Increases the graph invariant change count and sets
grinv to null.
- incGrinvCC(boolean) - Method in class chemaxon.struc.MoleculeGraph
-
- incGrinvCCOnly() - Method in class chemaxon.struc.MoleculeGraph
-
Increases the graph invariant change count, but does not change grinv.
- INCHI - Static variable in class chemaxon.formats.MFileFormat
-
IUPAC InChI files.
- INCHIKEY - Static variable in class chemaxon.formats.MFileFormat
-
IUPAC InChIKey.
- INCLUDE_ALL_ATOMS - Static variable in class chemaxon.util.iterator.IteratorFactory
-
Include all atoms: chemical atoms, explicit hydrogen, multicenter, lone
pair and pseudo atoms in atom iterations.
- INCLUDE_ALL_BONDS - Static variable in class chemaxon.util.iterator.IteratorFactory
-
Include all bonds: covalent and coordinate bonds in bond iteration.
- INCLUDE_CHEMICAL_ATOMS - Static variable in class chemaxon.util.iterator.IteratorFactory
-
- INCLUDE_CHEMICAL_ATOMS_ONLY - Static variable in class chemaxon.util.iterator.IteratorFactory
-
Include only chemical atoms in iteration, skip multicenters, lone pairs
and pseudo atoms.
- Incomplecule - Interface in chemaxon.struc
-
Ancestor of molecule classes and interfaces.
- INCORRECT_AROMATIC_NITROGEN_REMARK - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
-
Incorrect aromatic nitrogen remark.
- incQProp(String) - Method in class chemaxon.struc.MolAtom
-
Increments the value of a query property.
- incQueryAromaticity() - Method in class chemaxon.struc.MolAtom
-
Increments the value of the query aromaticity property.
- incValenceProp() - Method in class chemaxon.struc.MolAtom
-
Increments the value of the valence property.
- indexOf(MObject) - Method in class chemaxon.struc.MDocument
-
Searches for an object in the document or in the chemical structure that
belongs to the document.
- indexOf(MolBond) - Method in class chemaxon.struc.MolAtom
-
Returns the index of the specified bond in this atom.
- indexOf(Sgroup) - Method in class chemaxon.struc.Molecule
-
Gets the array index of an S-group.
- indexOf(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
-
Gets the index of the specified atom.
- indexOf(MolBond) - Method in class chemaxon.struc.MoleculeGraph
-
Gets the index of the specified bond.
- indexOf(MolAtom) - Method in class chemaxon.struc.RgMolecule
-
Gets the index of the specified node in the graph union.
- indexOf(MolBond) - Method in class chemaxon.struc.RgMolecule
-
Gets the index of the specified edge in the graph union.
- indexOf(MolAtom) - Method in class chemaxon.struc.RxnMolecule
-
Gets the index of the specified node in the graph union.
- indexOf(MolBond) - Method in class chemaxon.struc.RxnMolecule
-
Gets the index of the specified edge in the graph union.
- indexOf(MolAtom) - Method in class chemaxon.struc.Sgroup
-
Gets the atom index in the S-group graph.
- indexOf(MolBond) - Method in class chemaxon.struc.Sgroup
-
Gets the bond index in the S-group graph.
- indexOf(MolBond) - Method in class chemaxon.struc.sgroup.SgroupAtom
-
Returns the index of the specified bond in this atom.
- indexOfButtonB(AbstractButton) - Method in class chemaxon.marvin.beans.MViewPane
-
Gets the index of the button on the visible area of the viewer.
- indexOfButtonC(AbstractButton) - Method in class chemaxon.marvin.beans.MViewPane
-
Gets the index of the checkbox in the visible area of the viewer.
- indexOfReferenced(MolBond) - Method in class chemaxon.struc.MolAtom
-
Returns the index of the referenced bond in this atom.
- indicesOf(String) - Method in class chemaxon.formats.recognizer.RecognizerList
-
Deprecated.
Gets the level and the index of the specified format.
- init(MolPanel) - Method in class chemaxon.marvin.beans.MarvinPane
-
Initializes the content pane.
- init(MolPanel, boolean) - Method in class chemaxon.marvin.beans.MarvinPane
-
Initializes the content pane.
- init(GLAutoDrawable) - Method in class chemaxon.marvin.space.GraphicScene
-
Called by the drawable immediately after the OpenGL2 context is initialized for the first
time.
- initAction(Action, ResourceBundle, String, KeyStroke) - Static method in class chemaxon.marvin.beans.MarvinPane
-
Deprecated.
as of Marvin 3.3.1, replaced by SwingUtil.initAction
- initAction(Action, ResourceBundle, String, KeyStroke) - Static method in class chemaxon.marvin.util.SwingUtil
-
Initializes an action from information in a resource.
- initBrackets() - Method in class chemaxon.struc.Sgroup
-
Initializes the list of brackets in this S-group.
- initButton(AbstractButton, ResourceBundle, String) - Static method in class chemaxon.marvin.beans.MarvinPane
-
Deprecated.
as of Marvin 3.3.1, replaced by SwingUtil.initButton
- initButton(AbstractButton, ResourceBundle, String) - Static method in class chemaxon.marvin.util.SwingUtil
-
Utility method to initialize a button from information in a resource.
- initButton(AbstractButton, ResourceBundle, String, boolean) - Static method in class chemaxon.marvin.util.SwingUtil
-
Utility method to initialize a button from information in a resource.
- initCtrlShortcutForMac(JMenuItem) - Static method in class chemaxon.marvin.util.SwingUtil
-
Deprecated.
does nothing.
- initDraw() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- initDraw() - Method in class chemaxon.marvin.space.MoleculeComponent
-
Initializes gl related drawing variables, for example display lists.
- initDraw() - Method in class chemaxon.marvin.space.PharmacophoreArrow
-
- initDraw() - Method in class chemaxon.marvin.space.PharmacophorePoint
-
Initializes all internal data structure needed for drawing the component.
- initFields() - Method in class chemaxon.marvin.view.swing.TableOptions
-
Initialize field information before update.
- INITIAL_CAPACITY - Static variable in class chemaxon.struc.MoleculeGraph
-
Initial capacity of the atoms and bonds vectors.
- initialised - Variable in class chemaxon.marvin.space.MacroMoleculeComponent
-
- initialize() - Method in class chemaxon.checkers.ComponentChecker
-
Empty default implementation
- initInApplet() - Static method in class chemaxon.marvin.util.SwingUtil
-
Deprecated.
does nothing.
- initMolImport(MolInputStream) - Method in class chemaxon.marvin.io.formats.mdl.MolImport
-
Initializes the import module.
- initMolImport(MRecord, String) - Method in class chemaxon.marvin.io.MolImportModule
-
Initializes the import module.
- initMolImport(MolInputStream) - Method in class chemaxon.marvin.io.MolImportModule
-
Initializes the import module.
- initProgressMonitor(String, int, int) - Method in interface chemaxon.common.util.MProgressMonitor
-
Create a progress monitor.
- initVariables(boolean) - Method in class chemaxon.marvin.alignment.AlignmentMolecule
-
- InputProducer<V> - Interface in chemaxon.util.concurrent
-
Source of the input data.
- inputProducers - Variable in class chemaxon.util.concurrent.marvin.CompositeInputProducer
-
The input producer array.
- insert(int, String, MTextAttributes) - Method in class chemaxon.struc.graphics.MTextDocument
-
Inserts a string.
- insertAtom(int, MolAtom) - Method in class chemaxon.struc.MoleculeGraph
-
- insertBond(int, MolBond) - Method in class chemaxon.struc.MolAtom
-
Inserts a bond at a specified index.
- insertBond(int, MolBond) - Method in class chemaxon.struc.MoleculeGraph
-
- insertBond(int, MolBond) - Method in class chemaxon.struc.sgroup.SgroupAtom
-
- insertBondInOrder(MolBond, MolBond[]) - Method in class chemaxon.struc.MoleculeGraph
-
Insert a bond in the order specified as the second argument.
- insertNullAtoms(int, int) - Method in class chemaxon.struc.MoleculeGraph
-
Insert nulls into the atom array.
- insertNullAtoms(int, int) - Method in class chemaxon.struc.RgMolecule
-
Insert nulls into the atom array.
- insertNullBonds(int, int) - Method in class chemaxon.struc.MoleculeGraph
-
Insert nulls into the bond array.
- insertNullBonds(int, int) - Method in class chemaxon.struc.RgMolecule
-
Insert nulls into the bond array.
- insertText(String) - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Inserts the given string to textPane at caret position.
- insideLabel(double, double) - Method in class chemaxon.struc.MolAtom
-
Tests whether the specified point is inside the atom label.
- INSTABLE_TAUTOMERIC_FORM_REMARK - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
-
Instable tautomeric form remark.
- INSTANT_JCHEM - Static variable in class chemaxon.license.LicenseManager
-
Identifier of product: Instant JChem
- INSTANT_JCHEM_SERVER - Static variable in class chemaxon.license.LicenseManager
-
Identifier of product: Instant JChem Server
- INSTANT_JCHEM_VIZ - Static variable in class chemaxon.license.LicenseManager
-
Identifier of product: Instant JChem VIZ
- intValue() - Method in class chemaxon.struc.prop.MIntegerProp
-
Gets the integer value.
- INVALID_LINKNODE_MESSAGE - Static variable in class chemaxon.struc.MoleculeGraph
-
- InvalidChecker - Class in chemaxon.checkers
-
An extremal checker implementation
indicating error in the configuration imported from XML or action string
- InvalidChecker(String) - Constructor for class chemaxon.checkers.InvalidChecker
-
Initializes an invalid structure checker instance
- invert() - Method in class chemaxon.struc.CTransform3D
-
Inverts the matrix.
- invertSelection(int) - Method in class chemaxon.marvin.space.GraphicCell
-
The previously picked part of the component will be selected
if it was unselected and vice versa.
- invertSelection() - Method in class chemaxon.marvin.space.GraphicComponent
-
Sets the previously picked but unprocessed element to be selected if it was not set and vice versa.
- invertSelection(ComponentElement) - Method in class chemaxon.marvin.space.GraphicComponent
-
Sets the the given part of the component to be selected if it was not set and vice versa.
- invertSelection(UOID) - Method in class chemaxon.marvin.space.GraphicScene
-
The previously picked part of the component will be selected
if it was unselected and vice versa.
- invertSelection() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
-
Sets the previously picked but unprocessed element to be selected if it was not set and vice versa.
- invertSelection() - Method in class chemaxon.marvin.space.MoleculeComponent
-
Sets the the given part of the component to be selected if it was not set and vice versa.
- INVISIBLE_SETS - Static variable in class chemaxon.marvin.common.ParameterConstants
-
- invokeAndWait(Callable<T>) - Static method in class chemaxon.marvin.util.SwingUtil
-
Calls SwingUtilities.invokeLater() for a Callable by wrapping it into a FutureTask object,
blocks until it is finished and returns the result (calling FutureTask.get()).
- invokeAndWait(Runnable) - Method in interface chemaxon.marvin.view.TaskScheduler
-
Enqueues a task on the scheduler's thread and waits for its completion.
- invokeLater(Callable<T>) - Static method in class chemaxon.marvin.util.SwingUtil
-
Calls SwingUtilities.invokeLater() for a Callable by wrapping it into a FutureTask object.
- invokeLater(Runnable, int) - Method in interface chemaxon.marvin.view.TaskScheduler
-
Enqueues a task on the scheduler's thread.
- ionChargeOf(int) - Static method in class chemaxon.struc.MolAtom
-
Gets the ion charge.
- IonChargePlugin - Class in chemaxon.marvin.calculations
-
Plugin class for charge calculation on ionized microspecies.
- IonChargePlugin() - Constructor for class chemaxon.marvin.calculations.IonChargePlugin
-
Constructor.
- ionizer - Variable in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
-
- Ir - Static variable in class chemaxon.core.ChemConst
-
- irm - Variable in class chemaxon.marvin.space.GraphicComponent
-
Inverse of the Rotation matrix represented by a GeomCalc matrix.
- is3d() - Method in class chemaxon.struc.CTransform3D
-
Tests whether the transformation is 3D.
- isAbsoluteLabelsVisible() - Method in class chemaxon.marvin.MolPrinter
-
Is 'Absolute' label visible?.
- isAbsolutePlacement() - Method in class chemaxon.struc.sgroup.DataSgroup
-
Gets whether the placement of this attached data is absolute or relative
to the objects it is attached.
- isAbsoluteStereoRelevant(Molecule) - Static method in class chemaxon.checkers.StructureCheckerHelper
-
Determines if molecule contains a stereo center with no enhanced stereo
property.
- isAbsStereo() - Method in class chemaxon.struc.MoleculeGraph
-
Gets the absolute stereoconfiguration flag.
- isAbsStereo() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
-
Gets the absolute stereoconfiguration flag.
- isAcceptableGraph(MoleculeGraph) - Static method in class chemaxon.struc.sgroup.MultipleSgroup
-
Decides whether the given molecule graph can be the graph of a multiple s-group.
- isAcceptablePolymerGraph(MoleculeGraph) - Static method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
-
Checks if the given molecular graph can be the graph of a polymer SRU
- isAcceptableRSRUGraph(MoleculeGraph) - Static method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
-
Checks if the given molecular graph can be the graph of an RSRU
- isAcceptableSru(String) - Static method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
-
- isAcceptedOptionName(String) - Static method in class chemaxon.util.HitColoringAndAlignmentOptions
-
Checks if the given option name can be a hit coloring and alignment option.
- isAcceptedSpecialLigand(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
- isAcceptor(int) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D
-
- isAcceptor() - Method in class chemaxon.marvin.space.PharmacophorePoint
-
- isActinideMetal(int) - Static method in class chemaxon.struc.PeriodicSystem
-
Checks if the given atom is an actinide metal
Actinium is included.
- isActive() - Method in class chemaxon.marvin.space.GraphicCell
-
Returns true if this cell is the active cell of the entire scene.
- isActiveCell(int) - Method in class chemaxon.marvin.space.GraphicScene
-
Returns true if the cell having cellIndex is the active cell of the scene.
- isAddServices() - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
-
Returns true if services are displayed in the popup list
- isAdvancedSave() - Method in class chemaxon.marvin.common.UserSettings
-
Gets wether the useres uses advanced save or not.
- isAliphaticAtom(int) - Method in class chemaxon.calculations.Ring
-
Determines if an atom is not a member of an aromatic ring.
- isAliphaticAtom(int) - Method in class chemaxon.calculations.TopologyAnalyser
-
- isAliphaticAtom(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns true if aliphatic atom.
- isAliphaticBond(int) - Method in class chemaxon.calculations.Ring
-
Determines if a bond is not a member of an aromatic ring.
- isAliphaticRC(int) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D
-
- isAlkaliMetal(int) - Static method in class chemaxon.struc.PeriodicSystem
-
Checks if the given atom is an alkali (group I.) metal.
- isAlkalineEarthMetal(int) - Static method in class chemaxon.struc.PeriodicSystem
-
Checks if the given atom is an alkaline earth (group II.) metal.
- isAllowTraditionalNitrogen() - Method in class chemaxon.checkers.ValenceErrorChecker
-
Gets whether the checker allows traditional N representation
- isAmbiguousStereo() - Method in class chemaxon.struc.MolAtom
-
Check if the atom has ambiguous stereo wedge configuration.
- isAminoAcidBondColoringEnabled() - Method in class chemaxon.marvin.common.UserSettings
-
Gets wether the user uses peptide bridge coloring or not.
- isAminoAcidBondColoringEnabled() - Method in class chemaxon.marvin.MolPrinter
-
Is peptide bridge coloring enabled?
- isAnchor(int) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D
-
- isAnimated(int) - Method in class chemaxon.marvin.beans.MViewPane
-
Selected cell is animated or not.
- isAnimSync() - Method in class chemaxon.marvin.beans.MViewPane
-
Gets the animation synchronization.
- isAnionic() - Method in class chemaxon.marvin.space.PharmacophorePoint
-
- isAntialiasEnabled() - Method in class chemaxon.marvin.space.GraphicScene
-
Returns true if full-screen antialias is enabled.
- isApproximateCount() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Returns true if count is approximate due to multiple position bonds with
multicenters of variable size, false otherwise.
- isAromatic(int[], Molecule) - Static method in class chemaxon.checkers.StructureCheckerHelper
-
Determines if a ring in the molecule is aromatic or not
- isAromatic(int) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D
-
- isAromatic() - Method in class chemaxon.marvin.space.PharmacophorePoint
-
- isAromaticAtom(int) - Method in class chemaxon.calculations.Ring
-
Determines if an atom is a member of an aromatic ring.
- isAromaticAtom(int) - Method in class chemaxon.calculations.TopologyAnalyser
-
- isAromaticAtom(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns true if aromatic atom.
- isAromaticBond(int) - Method in class chemaxon.calculations.Ring
-
Determines if a bond is a member of an aromatic ring.
- isAromaticityChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker
-
Gets the option determining if the checker detects aromaticity atom query
properties or not.
- isAromaticRC(int) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D
-
- isAromaticSMILESSubset(int) - Static method in class chemaxon.struc.MolAtom
-
Is the atom can be aromatic according to the daylight specification:
Only atoms on the following list can be considered aromatic:
C, N, O, P, S, As, Se, and * (wildcard).
- isAromatize() - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
-
Deprecated.
- isArrow() - Method in class chemaxon.struc.graphics.MPolyline
-
Checks if it is an arrow.
- isAsymmetricAtom(int) - Method in class chemaxon.calculations.stereo.Stereochemistry
-
Determines if an atom is asymmetric or not.
- isAsymmetricAtom(int) - Method in class chemaxon.calculations.TopologyAnalyser
-
- isAsymmetricAtom(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns true if asymmetric atom.
- isAtom(Object) - Static method in class chemaxon.struc.graphics.MEFlow
-
Gets whether the arrow's terminus is at an atom.
- isAtom() - Method in class chemaxon.struc.MoleculeGraph
-
Deprecated.
As of Marvin 14.7.7, no replacement.
Not supported feature.
- isAtom() - Method in class chemaxon.struc.RgMolecule
-
Deprecated.
As of Marvin 14.7.7, no replacement.
Not supported feature.
- isAtom() - Method in class chemaxon.struc.RxnMolecule
-
Deprecated.
As of Marvin 14.7.7, no replacement.
Not supported feature.
- isAtomFaded(int) - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- isAtomFaded(int) - Method in class chemaxon.marvin.space.MoleculeComponent
-
Tells whether the atom is faded or not.
- isAtomicSymbol(String) - Static method in class chemaxon.struc.PeriodicSystem
-
Returns whether the given string corresponds to an atomic number of
an element in the periodic system specified by its symbol.
- isAtomInRing(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
- isAtomMappingVisible() - Method in class chemaxon.marvin.beans.MarvinPane
-
Determines the visibility of the atom mapping.
- isAtomMappingVisible() - Method in class chemaxon.marvin.MolPrinter
-
Returns true if atom mapping is visible.
- isAtomNumbersVisible() - Method in class chemaxon.marvin.beans.MarvinPane
-
Deprecated.
in 6.2.0. Use getAtomNumberingType() instead.
- isAtomNumbersVisible() - Method in class chemaxon.marvin.MolPrinter
-
Deprecated.
in 6.2.0. Use getAtomNumberingType instead.
- isAtomPropertiesVisible() - Method in class chemaxon.marvin.common.UserSettings
-
Tells wheter the atom properties are visible or not if exist.
- isAtomPropertiesVisible() - Method in class chemaxon.marvin.MolPrinter
-
Get the atom properties visibility
- isAtomSetColorModeSet() - Method in class chemaxon.struc.MDocument
-
Decides whether the atomset coloring mode is set.
- isAtomSymbolsVisible() - Method in class chemaxon.marvin.beans.MarvinPane
-
Tests the visibility of the atom symbols in 3D.
- isAtomSymbolsVisible() - Method in class chemaxon.marvin.MolPrinter
-
Returns the atom symbol visibility of 3D mode.
- isAtomVisible(int) - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- isAtomVisible(int) - Method in class chemaxon.marvin.space.MoleculeComponent
-
Returns if the atom is visible or hidden.
- isAttachmentAtom(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Checks whether the given atom is an attachment atom or not.
- isAutoCheckStructure() - Method in class chemaxon.marvin.common.UserSettings
-
Tells whether the automatic structure checking is enabled or not
- isAutoHeight() - Method in class chemaxon.struc.graphics.MTextBox
-
Gets if it is autoHeight.
- isAutomaticFogEnabled() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the state of automatic fog calculation mode.
- isAutoPopup() - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
-
Returns the auto popup behaviour
- isAutoSize() - Method in class chemaxon.struc.graphics.MTextBox
-
- isAvailable() - Method in class chemaxon.checkers.AbstractStructureChecker
-
- isAvailable() - Method in class chemaxon.checkers.InvalidChecker
-
- isAvailable() - Method in interface chemaxon.checkers.StructureChecker
-
Returns true if the checker is available, and can be used
- isAvailable() - Method in class chemaxon.checkers.SubstructureChecker
-
- isBarredAtom(int) - Method in class chemaxon.calculations.TopologyAnalyser
-
Determines if an atom is is part of a certain functional group with high
rotational barrier (amides, thioamides, sulphonamides).
- isBold() - Method in class chemaxon.struc.graphics.MFont
-
Tests whether the font is bold.
- isBold() - Method in class chemaxon.struc.MolBond
-
Decides whether this bond is bold or not.
- isBond(Object) - Static method in class chemaxon.struc.graphics.MEFlow
-
Gets whether the arrow's terminus is at a bond.
- isBond() - Method in class chemaxon.struc.MoleculeGraph
-
Deprecated.
As of Marvin 14.7.7, no replacement.
Not supported feature.
- isBond() - Method in class chemaxon.struc.RgMolecule
-
Deprecated.
As of Marvin 14.7.7, no replacement.
Not supported feature.
- isBond() - Method in class chemaxon.struc.RxnMolecule
-
Deprecated.
As of Marvin 14.7.7, no replacement.
Not supported feature.
- isBondDraggedAlong() - Method in class chemaxon.marvin.beans.MSketchPane
-
Is the currently used bond shown at the mouse cursor?
- isBondDraggedAlong() - Method in class chemaxon.marvin.common.UserSettings
-
Is the currently used bond shown at the mouse cursor?
- isBondLengthVisible() - Method in class chemaxon.marvin.beans.MarvinPane
-
Gets the bond length display option.
- isBondLengthVisible() - Method in class chemaxon.marvin.MolPrinter
-
Return whether the bond length is visible or not.
- isBondParallelWith(MolBond) - Method in class chemaxon.struc.MoleculeGraph
-
Checks if there is a bond parallel (having same endpoints) with the given bond in this
MoleculeGraph.
- isBoundTo(MolAtom) - Method in class chemaxon.struc.MolAtom
-
Checks if this MolAtom is connected to another one or not.
- isBracketCrossingBond(MolBond) - Method in class chemaxon.struc.Sgroup
-
- isBracketVisible() - Method in class chemaxon.struc.Sgroup
-
Tests whether the bracket is visible.
- isBracketVisible() - Method in class chemaxon.struc.sgroup.MultipleSgroup
-
Tests whether the bracket is visible.
- isBracketVisible() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Tests whether the bracket is visible.
- isBridgeHeadAtom(MoleculeGraph, int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
-
Deprecated.
as of Marvin 5.11.1, replaced by
TopologyUtil.isBridgeHeadAtom(MoleculeGraph, int)
- isCanceled() - Method in class chemaxon.checkers.runner.BasicCheckerRunner
-
Returns the canceled
- isCanceled() - Method in interface chemaxon.common.util.MProgressMonitor
-
Tests whether the user canceled the dialog.
- isCanceled() - Method in interface chemaxon.util.Cancelable
-
- isCationic() - Method in class chemaxon.marvin.space.PharmacophorePoint
-
- isCell() - Method in class chemaxon.marvin.space.CellOrComponentId
-
Returns true if this id identifies a cell.
- isChainAtom(int) - Method in class chemaxon.calculations.Ring
-
Determines if an atom a ring bond or a chain bond.
- isChainAtom(int) - Method in class chemaxon.calculations.TopologyAnalyser
-
- isChainAtom(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns true if chain atom.
- isChainBond(int) - Method in class chemaxon.calculations.Ring
-
Determines if a bond is a ring bond or a chain bond.
- isChainBond(int) - Method in class chemaxon.calculations.TopologyAnalyser
-
- isChainBond(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Determines if a bond is a ring bond or a chain bond.
- isChargeCalc() - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
-
Returns true if pH-Charge calculation.
- isChargeWithCircle() - Method in class chemaxon.marvin.MolPrinter
-
Get the visibility of Charge with Circle
- isCheckerActionHelpPrinting() - Method in class chemaxon.checkers.StructureCheck
-
Returns whether the checker action help text needs to be printed.
- isChecking() - Method in class chemaxon.checkers.runner.BasicCheckerRunner
-
- isChecking() - Method in interface chemaxon.checkers.runner.CheckerRunner
-
This function identifies the state of the checker thread
- isChildOf(MObject) - Method in class chemaxon.struc.graphics.MMidPoint
-
Is this object a children of another one?
- isChildOf(MObject) - Method in class chemaxon.struc.graphics.MRectanglePoint
-
Is this object a children of another one?
- isChildOf(MObject) - Method in class chemaxon.struc.MObject
-
Is this object a children of another one?
- isChildOf(MObject) - Method in class chemaxon.struc.MPoint
-
Is this object a children of another one?
- isChiral() - Method in class chemaxon.calculations.stereo.Stereochemistry
-
Determines if the molecule contains an atom with R or S stereo
configuration.
- isChiral() - Method in class chemaxon.calculations.TopologyAnalyser
-
- isChiral(Molecule) - Static method in class chemaxon.checkers.StructureCheckerHelper
-
Determines if the molecule contains an atom with R or S stereo
configuration.
- isChiralCenter(int) - Method in class chemaxon.calculations.stereo.Stereochemistry
-
Determines if an atom can be a tetrahedral stereogenic center.
- isChiralCenter(int) - Method in class chemaxon.calculations.TopologyAnalyser
-
- isChiralCenter(int) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
-
Determines if an atom can be a tetrahedral stereogenic center.
- isChiralCenter(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Determines if an atom can be a tetrahedral stereogenic center.
- isCleanable() - Method in class chemaxon.formats.MolExporter
-
Tests whether cleaning is meaningful for the chosen output format.
- isCleanable() - Method in class chemaxon.marvin.io.MolExportModule
-
Tests whether 2D or 3D cleaning is meaningful for this output format.
- isCleanHOptionEnabled() - Method in class chemaxon.marvin.common.UserSettings
-
Returns true if the H option for cleaning is enabled.
- isCleanNeeded() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Returns true if clean is needed for GUI display.
- isClearClipboardBeforeExport() - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
-
Returns whether the subsystem clears the clipboard before a copy operation.
- isClipped() - Method in class chemaxon.marvin.space.SurfaceComponent
-
Returns true if there are clipping planes enabled that will clip part
of the surface during drawing.
- isCloseEnabled() - Method in class chemaxon.marvin.beans.MSketchPane
-
Determines if the File->Close menu item is enabled or not.
- isCollinear(DPoint3, DPoint3, DPoint3) - Static method in class chemaxon.struc.DPoint3
-
Checks whether three 3D points can be connected with a line.
- isCollinear(MolAtom) - Method in class chemaxon.struc.MolBond
-
Returns whether atom is collinear with the bond or not.
- isColoringEnabled() - Method in class chemaxon.util.HitColoringAndAlignmentOptions
-
Specifies if substructure hit coloring should be used.
- isColorMapperEnabled() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- isComment(String) - Static method in class chemaxon.formats.recognizer.SMILESRecognizer
-
Deprecated.
- isCompatible(MTextAttributes, MTextAttributes, MFont) - Method in class chemaxon.struc.graphics.MTextAttributes
-
Tests whether two attribute sets are compatible.
- isComponent() - Method in class chemaxon.marvin.space.CellOrComponentId
-
Returns true if this id identifies a component.
- isComponentPart() - Method in class chemaxon.marvin.space.ComponentElement
-
Returns true if the if the component is a structured component.
- isConfirmExit() - Method in class chemaxon.marvin.beans.MSketchPane
-
Gets whether the confirmation dialog will be appear or not by exit.
- isConjugated() - Method in class chemaxon.struc.MolBond
-
Gets the conjugation state of the bond set by the conjugation modul.
- isConnected() - Method in class chemaxon.calculations.TopologyAnalyser
-
Determines if the molecule is a connected graph or not.
- isConnected(int, int) - Method in class chemaxon.calculations.TopologyAnalyser
-
Determines if two atoms are members of a connected graph or not.
- isConnected(int, int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns true if two atoms are in the same connected component,
false for atoms of disconnected structures.
- isConnectedGraph() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Determines if the molecule is a connected graph or not.
- isConnectionCountChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker
-
Gets the option determining if the checker detects connection count atom
query properties or not.
- isContracted() - Method in class chemaxon.struc.sgroup.MultipleSgroup
-
Is this S-group contracted?
- isContracted() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Decides whether this S-group is contracted or not.
- isControllable(String) - Method in class chemaxon.marvin.space.GraphicComponent
-
A component must return true if it allows itself to be controlled
by the given type controller.
- isControllable(String) - Method in class chemaxon.marvin.space.MacroMoleculeComponent
-
Returns whether controling by the given type of controller is allowed to the component.
- isControllable(String) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
Returns whether controling by the given type of controller is allowed to the component.
- isControllable(String) - Method in class chemaxon.marvin.space.MoleculeComponent
-
Returns whether controling by the given type of controller is allowed to the component.
- isControllable(String) - Method in class chemaxon.marvin.space.PharmacophoreArrow
-
Returns whether controling by the given type of controller is allowed to the component.
- isControllable(String) - Method in class chemaxon.marvin.space.PharmacophorePoint
-
Returns whether controling by the given type of controller is allowed to the component.
- isCoordDependent() - Method in class chemaxon.struc.MProp
-
Tests whether the property depends on the molecular coordinates.
- isCoordinate() - Method in class chemaxon.struc.MolBond
-
Tests whether the bond is coordinate.
- isCopyAsTransferable() - Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor
-
Determines whether the
MTransferable is appearing as an option in the Copy As dialog.
- isCorrect(StructureCheckerResult) - Method in class chemaxon.checkers.ReactionChecker
-
This method determines if a component of the reaction correct or not.
- isCorrect(StructureCheckerResult) - Method in class chemaxon.checkers.ReactionMapErrorChecker
-
- isCoupled() - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder
-
Tells whether the spectrum is coupled.
- isCoupled() - Method in class chemaxon.calculations.nmr.NMRCalculator
-
Coupled/decoupled spectrum.
- isCouplingNeeded() - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
Returns whether spin-spin couplings are taken into account.
- isCreateRingCenters() - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
-
- isCrossingBond(MolBond) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
-
Decides whether the bond is a crossing bond in a ladder-type polymer bracket.
- isCubeLine(String, int) - Static method in class chemaxon.formats.recognizer.CubeRecognizer
-
Deprecated.
Checks if it is a cube line:
an integer followed by floats.
- isCumulatedDoubleBond() - Method in class chemaxon.checkers.RingStrainErrorChecker
-
Returns the detectCummulatedDoubleBonds
- isCurrentFontDefault() - Method in class chemaxon.struc.graphics.MTextBox
-
Tests whether the default font is used.
- isCurrentFontRegular() - Method in class chemaxon.struc.graphics.MTextBox
-
Tests whether the current font is regular.
- isCxSMILESLine(String) - Static method in class chemaxon.formats.recognizer.SMILESRecognizer
-
Deprecated.
Checks if a line is a ChemAxon Extended
SMILES/SMARTS format.
- isDataDetached() - Method in class chemaxon.struc.sgroup.DataSgroup
-
Gets whether the data should be displayed close to the objects or
separately (detached).
- isDataFlavorSupported(DataFlavor) - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
-
- isDaylightFormatWithoutOptions(String) - Static method in class chemaxon.checkers.StructureCheckerHelper
-
Returns true if daylight format with options supported, false otherwise
- isDefault() - Method in class chemaxon.struc.graphics.MTextAttributes
-
Tests whether all attributes have default values.
- isDefaultSelected() - Method in class chemaxon.marvin.util.OptionDescriptor
-
Tests whether the option is selected by default.
- isDefaultTransferable() - Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor
-
Determines whether the
MTransferable instance should be used by the default copy
operation.
- isDehidrogenize() - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
-
Deprecated.
The explicit Hydrogens are not removed from the original
input structure. No need to use.
- isDescendantOf(Sgroup) - Method in class chemaxon.struc.Sgroup
-
Decides whether this is a descendant of another sgroup.
- isDetachable() - Method in class chemaxon.marvin.beans.MViewPane
-
Gets the detachable property.
- isDetectCumulatedDoubleBonds() - Method in class chemaxon.checkers.RingStrainErrorChecker
-
Returns the detectCummulatedDoubleBonds
- isDetectTransDoubleBonds() - Method in class chemaxon.checkers.RingStrainErrorChecker
-
Returns the detectTransDoubleBonds
- isDetectTripleBonds() - Method in class chemaxon.checkers.RingStrainErrorChecker
-
Returns the detectTripleBonds
- isDialogVisible() - Method in interface chemaxon.common.util.MProgressMonitor
-
Tests whether the dialog is visible.
- isDisplayChargeWithCircle() - Method in class chemaxon.marvin.common.UserSettings
-
- isDisplayLabelsAndBoxes() - Method in class chemaxon.util.HitColoringAndAlignmentOptions
-
Gets whether bounding boxes and labels are to be displayed for
the components of the search.
- isDisplayLonePairsAsLine() - Method in class chemaxon.marvin.common.UserSettings
-
- isDistancerangeSet() - Method in enum chemaxon.marvin.alignment.AlignmentProperties
-
- isDndTransferable() - Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor
-
- isDocumentExport() - Method in class chemaxon.marvin.io.MolExportModule
-
Tests if this export module is document export instead of a simple
molecule export.
- isDocumentImporter() - Method in class chemaxon.marvin.io.MolImportModule
-
Tests whether this module is a document importer or not.
- isDone() - Method in class chemaxon.checkers.StructureCheck
-
This function returns true when command line process finished without any
error
- isDonor(int) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D
-
- isDonor() - Method in class chemaxon.marvin.space.PharmacophorePoint
-
- isDoodle() - Method in class chemaxon.checkers.runner.BasicCheckerRunner
-
Returns the isDoodle
- isDraggable() - Method in class chemaxon.marvin.beans.MViewPane
-
Determines whether mouse dragged evens are allowed or not.
- isEditable(int, Molecule, String) - Method in class chemaxon.marvin.io.MFieldAccessor
-
Tests whether a field is editable or not.
- isEditable() - Method in class chemaxon.struc.graphics.MTextBox
-
Determines if this text box's content can be edited by the user.
- isEmpty() - Method in class chemaxon.jep.context.ReactionContext
-
Returns true if the context is empty.
- isEmpty() - Method in class chemaxon.struc.graphics.MChemicalStruct
-
A chemical structure object is empty if the molecule graph is empty.
- isEmpty() - Method in class chemaxon.struc.graphics.MPolyline
-
A polyline becomes empty if it has less than 2 points.
- isEmpty() - Method in class chemaxon.struc.graphics.MTextBox
-
A text box is empty if the string contains only whitespace.
- isEmpty() - Method in class chemaxon.struc.MDocument
-
Tests whether the document is empty:
the main molecule object in the document is empty
no graphic object is included (neither simple nor extra)
- isEmpty() - Method in class chemaxon.struc.MObject
-
An object may become empty if all the children are removed.
- isEmpty() - Method in class chemaxon.struc.Molecule
-
Tests whether the molecule is empty.
- isEmpty() - Method in class chemaxon.struc.MoleculeGraph
-
Tests whether the molecule graph is empty.
- isEmpty() - Method in class chemaxon.struc.RgMolecule
-
Ask if the molecule is empty or not.
- isEmpty() - Method in class chemaxon.struc.RxnMolecule
-
Ask if the reaction is empty or not.
- isEmpty() - Method in class chemaxon.struc.Sgroup
-
Is it an empty S-group?
- isEnabledT(int, int) - Method in class chemaxon.marvin.view.MDocStorage
-
Tests whether a text field is enabled.
- isEnableTranslateAndRotate() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
-
- isEndReached() - Method in class chemaxon.formats.MolImporter
-
Tests whether the end of input is already reached.
- isEndReached() - Method in class chemaxon.marvin.io.ArrayMDocSource
-
Tests whether the end of input is already reached.
- isEndReached() - Method in class chemaxon.marvin.io.MDocSource
-
Tests whether the end of input is already reached.
- isEndReached() - Method in exception chemaxon.marvin.view.MDocStorage.RecordUnavailableException
-
Tests whether the end of storage is reached.
- isErrorOccured() - Method in class chemaxon.checkers.StructureCheck
-
Returns whether structure error found in the input files.
- isExcluded() - Method in class chemaxon.marvin.space.PharmacophorePoint
-
- isExcludedAtom(MolAtom) - Method in class chemaxon.util.iterator.IteratorFactory
-
By overriding this method, the inclusion pattern of IteratorFactory can
be rewritten to exclude more atoms, than it would normally.
- isExcludedBond(MolBond) - Method in class chemaxon.util.iterator.IteratorFactory
-
By overriding this method, the inclusion pattern of IteratorFactory can
be rewritten to exclude more bonds, than it would normally.
- isExitCanceled() - Method in class chemaxon.marvin.beans.MarvinPane
-
Check whether exiting is allowed or not.
- isExpandable(int) - Method in class chemaxon.struc.Molecule
-
Tests if the molecule is expandable with the specified options.
- isExpanded() - Method in interface chemaxon.struc.sgroup.Expandable
-
Is this S-group expanded?
- isExpanded() - Method in class chemaxon.struc.sgroup.MultipleSgroup
-
Is this S-group expanded?
- isExpanded() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Is this S-group expanded?
- isExperimentalEnabled() - Method in class chemaxon.marvin.beans.MarvinPane
-
Tests whether experimental features are enabled.
- isExpertMode() - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
-
Returns the expert mode
- isExplicitConnectionCountChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker
-
Gets the option determining if the checker detects explicit connection
count atom query properties or not.
- isExplicitHVisible() - Method in class chemaxon.marvin.MolPrinter
-
Deprecated.
As of Marvin 5.5.1 this method always returns true. This method will be removed
in a future release.
- isExtraObject(MObject) - Method in class chemaxon.struc.MDocument
-
Decides whether a graphic object belongs to the main chemical structure
of the document.
- isEZLabelsVisible() - Method in class chemaxon.marvin.MolPrinter
-
Returns the visibility state of absolute double bond stereo configuration labels.
- isEzVisible() - Method in class chemaxon.marvin.beans.MarvinPane
-
Gets the E/Z display option.
- isEZVisible() - Method in class chemaxon.marvin.common.UserSettings
-
Are E/Z labels visible?
- isEzVisible() - Method in class chemaxon.marvin.MolPrinter
-
- isFallBackToBasic() - Method in class chemaxon.checkers.runner.AdvancedCheckerRunner
-
Returns true if runner should fall back to basic runner when preferred fix failed.
- isFiltered() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Return true if molecule filter is set.
- isFixed(int) - Method in class chemaxon.marvin.view.MDocStorage
-
Tests whether a record is fixed.
- isFixerActionHelpPrinting() - Method in class chemaxon.checkers.StructureCheck
-
Returns whether the fixer action help text needs to be printed.
- isFixing() - Method in class chemaxon.checkers.StructureCheck
-
Returns whether structure checker needs to fix invalid structures
automatically.
- isFlagSet(long) - Method in class chemaxon.formats.MFileFormat
-
Checks whether the format has a given (set of) flag(s) set.
- isFlipped() - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
-
Decides whether this sgroup is flipped.
- isFontDefault(MFont) - Method in class chemaxon.struc.graphics.MTextAttributes
-
Tests whether the default font is used.
- isFontDefaultInRange(int, int) - Method in class chemaxon.struc.graphics.MTextDocument
-
Tests whether the default font is used in the specified range.
- isFontRegular() - Method in class chemaxon.struc.graphics.MTextAttributes
-
Tests whether the default font is used.
- isFontRegularInRange(int, int) - Method in class chemaxon.struc.graphics.MTextDocument
-
Tests whether the default font is used in the specified range.
- isFractionQuicklyAvailable(double) - Method in class chemaxon.marvin.view.MDocStorage
-
Tests whether the specified fraction of the total (estimated) number of records is quickly
available.
- isFreeAttachAtom(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Checks whether the specified atom has free attachment point.
- isFreeLegalAttachAtom(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
- isFull() - Method in class chemaxon.marvin.space.monitor.Monitor
-
Returns true if the monitor is full and can measure.
- isGenerateDistanceRanges() - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
-
- isGeneric() - Method in class chemaxon.struc.MolAtom
-
Tests whether the atom is a generic atom.
- isGenNameShown() - Method in class chemaxon.marvin.view.swing.TableOptions
-
Are IUPAC names shown in the table?
- isGLInitialized() - Method in class chemaxon.marvin.space.GraphicScene
-
Returns true if the OpenGL2 canvas is already initialized.
- isGrabbingEnabled() - Method in class chemaxon.formats.MolImporter
-
Deprecated.
as of Marvin 6.2. It has no effect on the code.
- isGraphicComponent() - Method in class chemaxon.marvin.space.GraphicComponent
-
- isGraphicComponent() - Method in class chemaxon.marvin.space.MoleculeComponent
-
- isGraphInvariantVisible() - Method in class chemaxon.marvin.MolPrinter
-
Return whether the graph invariant is visible or not.
- isGrinv() - Method in class chemaxon.marvin.beans.MarvinPane
-
Deprecated.
as of Marvin 3.5, use isGrinvVisible() instead
- isGrinvCCValid() - Method in class chemaxon.struc.MoleculeGraph
-
Tests whether the graph invariant change count is valid.
- isGrinvCCValid() - Method in class chemaxon.struc.SelectionMolecule
-
Tests whether the graph invariant change count is valid.
- isGrinvVisible() - Method in class chemaxon.marvin.beans.MarvinPane
-
Gets the visibility of the graph invariants.
- isGUIContracted() - Method in class chemaxon.struc.Molecule
-
- isH(int) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D
-
- isHalogen(int) - Static method in class chemaxon.struc.PeriodicSystem
-
Checks if the given atom is a halogen.
- isHashed() - Method in class chemaxon.struc.MolBond
-
Decides whether this bond is hashed or not.
- isHelpPrinting() - Method in class chemaxon.checkers.StructureCheck
-
Returns whether the help text needs to be printed.
- isHierarchic() - Method in class chemaxon.struc.MPropertyContainer
-
- isHighlighted() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- isHighlighted() - Method in class chemaxon.marvin.space.MoleculeComponent
-
This functionality is currently unavailable.
- isHighlighted() - Method in class chemaxon.marvin.space.PharmacophoreArrow
-
Returns true if the component is highlighted.
- isHighlighted() - Method in class chemaxon.marvin.space.PharmacophorePoint
-
Returns true if the component is highlighted.
- isHighlighted(MObject) - Method in class chemaxon.struc.MDocument
-
Is the specified object currently highlighted?
- isHinderedBiarylBridgeBond(int) - Method in class chemaxon.calculations.TopologyAnalyser
-
Determines if a bond bridges two aryl systems having more than two ortho
substituents.
- isHomologyEnumerated() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Indicates if homology groups are enumerated or not.
- isHydrogenCountChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker
-
Gets the option determining if the checker detects hydrogen count atom
query properties or not.
- isHydrophobic(int) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D
-
- isHydrophobic() - Method in class chemaxon.marvin.space.PharmacophorePoint
-
- isImplicitHcountImportant(MolAtom) - Static method in class chemaxon.marvin.io.MolExportModule
-
Checks whether the number of implicit hydrogens is important
information for an atom or not.
- isImplicitHcountImportant(MoleculeGraph) - Method in class chemaxon.marvin.io.MolExportModule
-
Checks whether the number of implicit hydrogens is important information
for the atoms of mol or not.
- isImplicitHydrogenCountChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker
-
Gets the option determining if the checker detects implicit hydrogen
count atom query properties or not.
- isImplicitHydrogenMode() - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
Returns implicit hydrogen mode.
- isImplicitizableH(int) - Method in class chemaxon.struc.MolAtom
-
Tests whether the hydrogen atom is implicitizable or not.
- isIn3D() - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
-
Returns true if structures are returned in 3D.
- isIncipBond(Object) - Static method in class chemaxon.struc.graphics.MEFlow
-
Gets whether the arrow's sink is at an incipient bond.
- isIncompleteReaction() - Method in class chemaxon.struc.RgMolecule
-
Check whether the reaction is incomplete or not.
- isIncompleteReaction() - Method in class chemaxon.struc.RxnMolecule
-
Check whether the reaction is incomplete or not.
- isInputAvailable() - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
-
Checks that the implementation supports input from clipboard.
- isInputAvailable() - Method in interface chemaxon.marvin.modules.datatransfer.MTransferable
-
Checks that the implementation supports input from clipboard.
- isInputMoleculeAromatized() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns true if the input molecule has aromatic bond.
- isInternalSelectable() - Method in class chemaxon.struc.MObject
-
Is it a selection only internal object?
- isInternalSelectable() - Method in class chemaxon.struc.MPoint
-
Is it a selection only internal object?
- isItalic() - Method in class chemaxon.struc.graphics.MFont
-
Tests whether the font is italic.
- isKeepMapping() - Method in class com.chemaxon.mapper.AutoMapper
-
Returns if the mapper will keep the initial mapping or not.
- isKeepMapping() - Method in class com.chemaxon.mapper.AutoMapper.Options
-
- isLanthanideMetal(int) - Static method in class chemaxon.struc.PeriodicSystem
-
Checks if the given atom is a lanthanide metal
Lanthanum is included.
- isLargeMolecule() - Method in class chemaxon.struc.MoleculeGraph
-
Returns true if large molecule
(number of atoms exceeds 1000).
- isLastLine() - Method in class chemaxon.formats.recognizer.Recognizer
-
Tests whether it is the last line of file.
- isLegalAttachment(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
- isLicensed() - Method in class chemaxon.calculations.Ring
-
This method is for internal use only.
- isLicensed() - Method in class chemaxon.calculations.TopologyAnalyser
-
- isLicensed() - Method in class chemaxon.checkers.AbstractStructureChecker
-
- isLicensed(String) - Static method in class chemaxon.license.LicenseManager
-
Returns true if the license manager recognizes the given product to be licensed.
- isLicensed() - Method in class chemaxon.marvin.alignment.AlignRigidEasy
-
- isLicensed() - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
-
- isLicensed() - Method in class chemaxon.marvin.calculations.ChargePlugin
-
Returns true if the plugin is licensed.
- isLicensed() - Method in class chemaxon.marvin.calculations.HBDAPlugin
-
Returns true if the plugin is licensed.
- isLicensed() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
-
Returns true if the plugin is licensed.
- isLicensed() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
-
- isLicensed() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
- isLicensed() - Method in class chemaxon.marvin.calculations.MSAPlugin
-
Returns true if the plugin is licensed.
- isLicensed() - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
-
Returns true if the plugin is licensed.
- isLicensed() - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
-
Returns true if the plugin is licensed.
- isLicensed() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns true if the plugin is licensed.
- isLigand() - Method in class chemaxon.marvin.space.MoleculeComponent
-
- isLigandErrorVisible() - Method in class chemaxon.marvin.common.UserSettings
-
Tells wheter the bond's ligand error is visible or not.
- isLigandErrorVisible() - Method in class chemaxon.marvin.MolPrinter
-
Gets the bond's ligand error visibility
- isLinkNode() - Method in class chemaxon.struc.MolAtom
-
The atom is a link node if the maximum number of repetitions is nonzero.
- isLoadedMolModified() - Method in class chemaxon.marvin.beans.MSketchPane
-
Determines whether the original molecule that is loaded in is modified or not.
- isLocalAromatic() - Method in class chemaxon.core.calculations.valencecheck.ValenceCheckOptions
-
Do not calculate valence for ambiguous aromatic atoms behaving
like aromatic Nitrogens (e.g.
- isLogging() - Method in class chemaxon.checkers.StructureCheck
-
Returns whether there is a log file available for logging.
- isLonePairAsLine() - Method in class chemaxon.marvin.MolPrinter
-
Get the visibility of Lone Pairs: dots/line
- isLonePairAutoCalc() - Method in class chemaxon.marvin.common.UserSettings
-
Returns the state of the automatic lone pair calculation.
- isLonePairsAutoCalculated() - Method in class chemaxon.marvin.MolPrinter
-
Returns the state of the automatic calculation of lone pairs.
- isLonePairsVisible() - Method in class chemaxon.marvin.MolPrinter
-
Returns the visibility state of lone pairs.
- isLP(int) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D
-
- isMacromoleculePart() - Method in class chemaxon.marvin.space.MoleculeComponent
-
Tells whether this MoleculeComponent is a visualizer of a ligand in a complex
or an independent small molecule.
- isMappable() - Method in class chemaxon.struc.MolAtom
-
Checks if this atom it a mappable.
- isMarkBonds() - Method in class com.chemaxon.mapper.AutoMapper
-
Returns if the mapper marks the reaction center bonds or not.
- isMarkBonds() - Method in class com.chemaxon.mapper.AutoMapper.Options
-
- isMarvinCompMode() - Method in class chemaxon.marvin.io.formats.smiles.SmartsAtomQuerifier
-
Marvin compatibility mode.
- isMergedComponent(MoleculeGraph) - Method in class chemaxon.struc.RxnMolecule
-
Check whether given molecule is reaction component with a set of intentionally merged fragments or not.
- isMetal(int) - Static method in class chemaxon.struc.PeriodicSystem
-
Decides whether the element is a metal.
- isMetalloid(int) - Static method in class chemaxon.struc.PeriodicSystem
-
Checks if the given atom is a metalloid.
- isMinimumHeightSet() - Method in class chemaxon.struc.graphics.MTextBox
-
Gets if it is minimumHeightSet.
- isMolecular() - Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
-
Returns true if molecule output.
- isMolecule() - Method in class chemaxon.struc.MoleculeGraph
-
Deprecated.
as of Marvin 14.7.7, no replacement.
Usage:
use myObject instanceof Molecule instead
- isMolMovie() - Method in class chemaxon.formats.MolImporter
-
Are the imported molecules merged into one multi-set molecule?
- isMolNameShown() - Method in class chemaxon.marvin.view.swing.TableOptions
-
Are molecule names shown in the table?
- isMPLabelsVisible() - Method in class chemaxon.marvin.MolPrinter
-
Returns the visibility state of M/P labels.
- isMPVisible() - Method in class chemaxon.marvin.beans.MarvinPane
-
Gets the M/P display option.
- isMPVisible() - Method in class chemaxon.marvin.common.UserSettings
-
- isMsCalc() - Method in class chemaxon.marvin.calculations.HBDAPlugin
-
Returns true if microspecies calculation.
- isMsCalc() - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Returns true if microspecies calculation.
- isMsCalc() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns true if microspecies calculation.
- isMSpaceDisplayLabelOnlyOnHeavyAtoms() - Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
-
Returns if mspace should display label only on heavy atoms.
- isMultiChiral() - Method in class chemaxon.struc.MoleculeGraph
-
Returns the multiple chirality flag.
- isMultipleDisplay() - Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
-
Returns true if results for more molecules can be displayed
in a single component, false if each molecule should be displayed
in a separate component.
- isMultiSet() - Method in class chemaxon.formats.MolImporter
-
Are the imported molecules merged into one multi-set molecule?
- isMultiThreadedRunEnabled() - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
For internal use only.
- isMultiThreadedRunEnabled() - Method in class chemaxon.marvin.calculations.MSAPlugin
-
For internal use only.
- isMultiThreadedRunEnabled() - Method in class chemaxon.marvin.calculations.ResonancePlugin
-
For internal use only.
- isMultiThreadedRunEnabled() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
For internal use only.
- isMultiThreadedRunEnabled() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
For internal use only.
- isNegative(int) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D
-
- isNegligible(double[]) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
- isNegligibleResult(Object, int, Object) - Method in class chemaxon.marvin.calculations.HBDAPlugin
-
Returns whether the result can be ignored.
- isNegligibleResult(Object, int, Object) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Returns whether the result can be ignored.
- isNegligibleResult(Object, int, Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns whether the result can be ignored.
- isNobleGas(int) - Static method in class chemaxon.struc.PeriodicSystem
-
Checks if the given atom is a noble gas.
- isNonPreferredStereoAtom(MoleculeGraph) - Static method in class chemaxon.marvin.util.CleanUtil
-
Check if the atoms in the molecule is in SP2 hybridization state and
has wedge whose getAtom1 is the specified atom, but wiggly
bonds next to double bonds are allowed.
- IsoelectricPointPlugin - Class in chemaxon.marvin.calculations
-
Plugin class for isoelectric point and pH - charge distribution calculation.
- IsoelectricPointPlugin() - Constructor for class chemaxon.marvin.calculations.IsoelectricPointPlugin
-
Constructor.
- isOK() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns true if no calculation error,
false on error.
- isOK() - Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
-
Returns true if the calculation has run without error.
- isOkActionEnabled() - Method in class chemaxon.marvin.plugin.gui.ParameterPanel
-
- isOkActionEnabled() - Method in interface chemaxon.marvin.plugin.ParameterPanelHandler
-
Returns true if "OK" button is enabled.
- isolate(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
-
- isolate(MolBond) - Method in class chemaxon.struc.MoleculeGraph
-
- ISOMERS_PLUGIN_GROUP - Static variable in class chemaxon.license.LicenseManager
-
Identifier of plugin: Isomers Plugin Group
- isOneLetterPeptideDisplay() - Method in class chemaxon.marvin.MolPrinter
-
Decides whether the Peptide display settings set to one letter.
- isOnlyFirstAtomInStereoCalculation() - Method in class chemaxon.struc.MoleculeGraph
-
Get how parity module interpret wedes.
- isOptionsPaneLoaded(int) - Method in class chemaxon.marvin.plugin.PluginFactory
-
Returns true is options pane is loaded for plugin,
false otherwise.
- isOrderedComponentSgroup() - Method in class chemaxon.struc.Sgroup
-
Returns if the Sgroup is ordered component Sgroup.
- isOtherMetal(int) - Static method in class chemaxon.struc.PeriodicSystem
-
Checks if the given atom is an "other metal", group IIIa-Va metal.
- ISOTOPE_H - Static variable in class chemaxon.struc.MolAtom
-
Include Hydrogen isotope(s).
- IsotopeChecker - Class in chemaxon.checkers
-
IsotopeChecker detects isotopes (non-elemental atoms).
- IsotopeChecker() - Constructor for class chemaxon.checkers.IsotopeChecker
-
Default constructor
- isotopeComposition(int) - Method in class chemaxon.calculations.ElementalAnalyser
-
Gets the molecular composition (w/w%).
- isotopeComposition(int, boolean) - Method in class chemaxon.calculations.ElementalAnalyser
-
Gets the molecular composition (w/w%).
- IsotopeFixer - Class in chemaxon.fixers
-
- IsotopeFixer() - Constructor for class chemaxon.fixers.IsotopeFixer
-
Deprecated.
- isotopeFormula() - Method in class chemaxon.calculations.ElementalAnalyser
-
Calculates the molecular formula (isotopes are separated).
- isotopeFormula(boolean) - Method in class chemaxon.calculations.ElementalAnalyser
-
Calculates the molecular formula (isotopes are separated).
- isotopeType(int, int) - Static method in class chemaxon.struc.MolAtom
-
Gets the type of an isotope.
- isOutputCleanable(String) - Static method in class chemaxon.formats.MFileFormatUtil
-
Tests whether the specified output format is cleanable.
- isOverflowCalculation() - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Returns true if overflow calculation:
maximum number of ionizable atoms exceeded and protein ionization invoked.
- isPartSelected(MoleculeGraph) - Method in class chemaxon.struc.Sgroup
-
Decides if part of the sgroup is selected or not.
- isPositionVariation() - Method in class chemaxon.struc.MolBond
-
Decides whether this bond is a position variation bond.
- isPositive(int) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D
-
- isPrintEnabled() - Method in class chemaxon.marvin.beans.MarvinPane
-
Determines if the File->Print menu item is enabled or not.
- isPropertyRecord() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
-
- isPropertyRecord() - Method in interface chemaxon.marvin.io.MRecordReader
-
- isPseudo() - Method in class chemaxon.struc.MolAtom
-
Tests whether if the atom is a pseudo atom.
- isQProp() - Method in class chemaxon.struc.MolAtom
-
Tests whether this object represents a query property.
- isQuery() - Method in class chemaxon.struc.MolAtom
-
Tests whether it is a query atom.
- isQuery() - Method in class chemaxon.struc.MolBond
-
Tests whether it is query bond or has query property:
any
single or double
single or aromatic
double or aromatic
smarts bond
ring or chain topology
For more information on smarts bond and query bonds, see
The JChem Query Guide
- isQuery() - Method in class chemaxon.struc.MoleculeGraph
-
Indicates if the molecule has query features: query atoms or query bonds.
- isQuery() - Method in class chemaxon.struc.RgMolecule
-
Indicates if the molecule has query features.
- isQuery() - Method in class chemaxon.struc.RxnMolecule
-
Indicates if the molecule has query features: query atoms or query bonds.
- isQueryDisplay() - Method in class chemaxon.util.HitColoringAndAlignmentOptions
-
Gets whether the query should be displayed in
the upper left corner along with the hit.
- isRandomEnumeration() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Returns true if random enumeration is requested.
- isReaction() - Method in class chemaxon.struc.Molecule
-
Checks if the structure represents a reaction or not.
- isReaction() - Method in class chemaxon.struc.RgMolecule
-
Checks if the structure represents a reaction or not.
- isReaction() - Method in class chemaxon.struc.RxnMolecule
-
Checks if the structure represents a reaction or not.
- isReactionArrow(MoleculeGraph) - Method in class chemaxon.struc.MObject
-
- isReactionErrorVisible() - Method in class chemaxon.marvin.beans.MSketchPane
-
Deprecated.
As of Version 5.3.2, this method is deprecated and has no replacement. It will be
removed in a future version of Marvin.
Are reaction errors highlighted?
- isRealAtom(MolAtom) - Static method in class chemaxon.checkers.StructureCheckerUtility
-
Gets whether the provided atom represents an atom (and not something that
should not be an atom)
- isRealAtomParent() - Method in class chemaxon.struc.MoleculeGraph
-
Can it be a real atom parent?
- isRealAtomParent() - Method in class chemaxon.struc.RgMolecule
-
R-group molecule objects cannot be real node parents.
- isRealAtomParent() - Method in class chemaxon.struc.RxnMolecule
-
Reaction molecules cannot be real node parents.
- isRealAtomParent() - Method in class chemaxon.struc.SelectionMolecule
-
Selection molecules are not real atom parents.
- isRemovable() - Method in class chemaxon.struc.MolBond
-
Deprecated.
As of Marvin 6.2, no replacement.
Not supported feature.
- isRemovable() - Method in class chemaxon.struc.Sgroup
-
Decides whether an S-group should be ungrouped if its structure changes.
- isRemoveUnusedDefitions() - Method in class chemaxon.util.HitColoringAndAlignmentOptions
-
Gets whether unused definitions should be removed or not.
- isRepeatingUnitAtom(MolAtom) - Method in class chemaxon.struc.sgroup.MultipleSgroup
-
Checks if the specified atom object is in the paradigmatic repeating
unit or not.
- isReporting() - Method in class chemaxon.checkers.StructureCheck
-
Returns whether help text is printed.
- isRestH(int) - Method in class chemaxon.struc.RgMolecule
-
Informs whether the restH condition is set to the referenced R-group
definition.
- isRewindable() - Method in class chemaxon.formats.MolImporter
-
Tests whether rewinding (seeking backwards) is possible in the
underlying input stream.
- isRewindable() - Method in class chemaxon.marvin.io.ArrayMDocSource
-
Tests whether rewinding (seeking backwards) is possible.
- isRewindable() - Method in class chemaxon.marvin.io.MDocSource
-
Tests whether rewinding (seeking backwards) is possible.
- isRewindable() - Method in class chemaxon.marvin.view.MDocStorage
-
Tests whether the document storage is rewindable.
- isRgrouped(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns true if molecule with R-groups.
- isRgroupsVisible() - Method in class chemaxon.marvin.beans.MarvinPane
-
Determines the visibility of R-group defintions.
- isRgroupsVisible() - Method in class chemaxon.marvin.MolPrinter
-
Decides whether the R-group definitions are visible.
- isRing() - Method in class chemaxon.struc.MoleculeGraph
-
Deprecated.
As of Marvin 14.7.7, no replacement.
Not supported feature.
- isRingAtom(int) - Method in class chemaxon.calculations.Ring
-
Determines if an atom a ring bond or a chain bond.
- isRingAtom(int) - Method in class chemaxon.calculations.TopologyAnalyser
-
- isRingAtom(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Returns true if ring atom.
- isRingBond(int) - Method in class chemaxon.calculations.Ring
-
Determines if a bond is a ring bond or a chain bond.
- isRingBond(int) - Method in class chemaxon.calculations.TopologyAnalyser
-
- isRingBond(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Determines if a bond is a ring bond or a chain bond.
- isRingBond(int) - Method in class chemaxon.struc.MoleculeGraph
-
Is this bond in ring?
- isRingBondCountChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker
-
Gets the option determining if the checker detects ring bond count atom
query properties or not.
- isRingCountChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker
-
Gets the option determining if the checker detects ring count atom query
properties or not.
- isRLogicVisible() - Method in class chemaxon.marvin.MolPrinter
-
Is R-logic visible?.
- isRotatableBond(int) - Method in class chemaxon.calculations.TopologyAnalyser
-
Determines if a bond is a rotatable or not
- isRotatableBond(int) - Method in class chemaxon.marvin.alignment.RotatableBondDetector
-
Not flexible if:
double, aromatic, triple bond
single bond neighboring a triple like at cyanide
chain end bonds
amide
thioamide: -C(=S)-NR2
sulphonamide R-S(=O)2-NR2
aniline N : C(aromatic)-N(sp3)
aromatic amidine : C(aromatic)-C(=NH)-NH2
aromatic nitroso : C(aromatic)-N=O
aromatic nitro : C(aromatic)-NO2 (although at some substituent
position it may be rotatable)
C(aromatic)-N(amide) flexible Warning there are three intentional but
unexpected feature:
Ring bonds may be rotatable also.
- isRotatableBond(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Determines if a bond is a rotatable or not
- isSameParityClass(int, int, int, int, int, int, int, int) - Static method in class chemaxon.struc.MolAtom
-
Calculates if chirality centers in the structure and the query
belong to the same parity class.
- isSaveIniEnabled() - Method in class chemaxon.marvin.beans.MarvinPane
-
Automatically saves user settings to an initialization file.
- isSearchAll() - Method in class chemaxon.checkers.RatomChecker
-
Gets the option determining if the checker detects all R-atoms or not.
- isSearchBridgehead() - Method in class chemaxon.checkers.ExplicitHydrogenChecker
-
Returns if the checker search for bridgehead explicit hydrogens
- isSearchCharged() - Method in class chemaxon.checkers.ExplicitHydrogenChecker
-
Returns if the checker search for charged explicit hydrogens
- isSearchCircularReference() - Method in class chemaxon.checkers.RgroupReferenceErrorChecker
-
Deprecated.
Sets the option determining if the checker detects nested R-atoms
referencing to their own R-groups directly or in circularly or not.
- isSearchContracted() - Method in class chemaxon.checkers.AbbreviatedGroupChecker
-
Returns if the checker is searching for contracted SGroups or not
- isSearchDefaultValence() - Method in class chemaxon.checkers.ValencePropertyChecker
-
Returns if the checker detects valence properties with the default
valence of the current atom type.
- isSearchDisconnected() - Method in class chemaxon.checkers.RatomChecker
-
Gets the option determining if the checker detects R-atoms not connected
to any other atoms or not.
- isSearchExpanded() - Method in class chemaxon.checkers.AbbreviatedGroupChecker
-
Returns if the checker is searching for expanded SGroups or not
- isSearchGeneric() - Method in class chemaxon.checkers.RatomChecker
-
Gets the option determining if the checker detects R-atoms without
identifier numbers or not.
- isSearchHConnected() - Method in class chemaxon.checkers.ExplicitHydrogenChecker
-
Returns if the checker search for H connected explicit hydrogens
- isSearchIsotopic() - Method in class chemaxon.checkers.ExplicitHydrogenChecker
-
Returns if the checker search for isotopic explicit hydrogens
- isSearchLinker() - Method in class chemaxon.checkers.RatomChecker
-
Gets the option determining if the checker detects R-atoms with more than
one connection or not.
- isSearchLonely() - Method in class chemaxon.checkers.ExplicitHydrogenChecker
-
Returns if the checker search for lonely explicit hydrogens
- isSearchMapped() - Method in class chemaxon.checkers.ExplicitHydrogenChecker
-
Returns if the checker search for mapped explicit hydrogens
- isSearchMissingRatom() - Method in class chemaxon.checkers.RgroupReferenceErrorChecker
-
Deprecated.
- isSearchMissingRgroup() - Method in class chemaxon.checkers.RgroupReferenceErrorChecker
-
Deprecated.
Gets the option determining if the checker detects missing R-groups or
not.
- isSearchNested() - Method in class chemaxon.checkers.RatomChecker
-
Gets the option determining if the checker detects R-atoms within
R-groups or not.
- isSearchNonDefaultValence() - Method in class chemaxon.checkers.ValencePropertyChecker
-
Returns if the checker detects valence properties with a non-default
valence of the current atom type.
- isSearchPolymerEndGroup() - Method in class chemaxon.checkers.ExplicitHydrogenChecker
-
Returns if the checker search for polymer end group explicit hydrogens
- isSearchRadical() - Method in class chemaxon.checkers.ExplicitHydrogenChecker
-
Returns if the checker search for radical explicit hydrogens
- isSearchSelfReference() - Method in class chemaxon.checkers.RgroupReferenceErrorChecker
-
Deprecated.
- isSearchSgroup() - Method in class chemaxon.checkers.ExplicitHydrogenChecker
-
Returns if the checker search for S-group explicit hydrogens
- isSearchSgroupEnd() - Method in class chemaxon.checkers.ExplicitHydrogenChecker
-
Returns if the checker search for S-group end explicit hydrogens
- isSearchUnusedRgroup() - Method in class chemaxon.checkers.RgroupReferenceErrorChecker
-
Deprecated.
Gets the option determining if the checker detects unused R-groups or
not.
- isSearchValenceError() - Method in class chemaxon.checkers.ExplicitHydrogenChecker
-
Returns if the checker search for valence errored explicit hydrogens
- isSearchWedged() - Method in class chemaxon.checkers.ExplicitHydrogenChecker
-
Returns if the checker search for wedged explicit hydrogens
- isSeekable() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
-
Tests whether the record reader is seekable.
- isSeekable() - Method in class chemaxon.marvin.io.MRecordImporter
-
Tests whether the record reader is seekable.
- isSeekable() - Method in interface chemaxon.marvin.io.MRecordReader
-
Tests whether the record reader is seekable.
- isSeekable() - Method in class chemaxon.marvin.io.PositionedInputStream
-
Tests whether the stream is seekable.
- isSelectable() - Method in class chemaxon.marvin.beans.MViewPane
-
Are the cells selectable?
- isSelectableNow() - Method in class chemaxon.struc.graphics.MMidPoint
-
- isSelectableNow() - Method in class chemaxon.struc.graphics.MRectanglePoint
-
- isSelectableNow() - Method in class chemaxon.struc.MObject
-
Is the object selectable now?
- isSelected() - Method in class chemaxon.marvin.space.GraphicComponent
-
Tells whether the component is being selected or not.
- isSelected(ComponentElement) - Method in class chemaxon.marvin.space.GraphicComponent
-
Tells whether a part of the component is selected.
- isSelected() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- isSelected(ComponentElement) - Method in class chemaxon.marvin.space.MoleculeComponent
-
Returns true if the given item is selected.
- isSelected() - Method in class chemaxon.marvin.space.MoleculeComponent
-
Returns true if the whole component is selected.
- isSelected() - Method in class chemaxon.struc.MObject
-
Is the object selected?
- isSelected() - Method in class chemaxon.struc.MolAtom
-
Tests whether this atom is selected.
- isSelected(MoleculeGraph) - Method in class chemaxon.struc.Sgroup
-
Is the sgroup or part of the sgroup selected?
- isSelectedAtom(int) - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- isSelectedAtom(int) - Method in class chemaxon.marvin.space.MoleculeComponent
-
Returns true if the atom with the given index is selected.
- isSelectedComponent(int) - Method in class chemaxon.marvin.space.GraphicCell
-
Tells whether the given component is selected.
- isSelfReference(MProp) - Method in class chemaxon.struc.MoleculeGraph
-
Tests whether the specified property is a self reference to the molecule.
- isSelfReference(MProp) - Method in class chemaxon.struc.MPropertyContainer
-
Tests whether a property is a self reference to the containing
molecule.
- isSelfReference(MProp) - Method in class chemaxon.struc.RgMolecule
-
Tests whether the specified property is a self reference to the molecule.
- isSetColoringEnabled() - Method in class chemaxon.marvin.beans.MarvinPane
-
Is the atom/bond set coloring enabled?
- isSetColoringEnabled() - Method in class chemaxon.marvin.MolPrinter
-
Returns true if atoms and bonds are colored according to the color of the pre-defined set
they belong to.
- isSgroup() - Method in class chemaxon.struc.Molecule
-
Deprecated.
As of Marvin 14.7.7, no replacement.
Not supported feature.
- isShowMultiMoleculeOnEditSource() - Method in class chemaxon.marvin.common.UserSettings
-
- isSimilarTo(MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
-
Tests if the molecule graph is similar to another graph.
- isSimpleMolecule() - Method in class chemaxon.struc.MDocument
-
Tests whether the document is equivalent to a simple molecule.
- isSingleCellLabelShown() - Method in class chemaxon.marvin.view.swing.TableOptions
-
Tests whether label should be shown for a single cell.
- isSingleStepReaction() - Method in class chemaxon.struc.RxnMolecule
-
Decides wheter this reaction is a singlestep or multistep reaction.
- isSizeFinal() - Method in class chemaxon.marvin.view.MDocStorage
-
Tests whether the storage size is final.
- isSketchWindowOpened(int) - Method in class chemaxon.marvin.beans.MViewPane
-
Checks whether the molecule from the specified cell is opened in a sketcher window or not.
- isSmallestRingSizeChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker
-
Gets the option determining if the checker detects smallest ring size
atom query properties or not.
- isSMILESShown() - Method in class chemaxon.marvin.view.swing.TableOptions
-
Are SMILES strings shown in the table?
- isSmoothBackgroundEnabled() - Method in class chemaxon.marvin.space.GraphicScene
-
Returns true if the background is enabled to be smooth, so that
it does not have a homogenous color.
- isSpecBeilsteinGeneric(String) - Static method in class chemaxon.marvin.io.formats.mdl.MolfileUtil
-
Tests whether the specified symbol is a Beilstein Generic except
A, Q and X.
- isSpecialAtom(MolAtom) - Static method in class chemaxon.checkers.StructureCheckerUtility
-
Gets whether the provided atom is special
- isSpecIsotopeSymbolPreferred() - Method in class chemaxon.struc.MolAtom
-
Tests whether special symbol is used.
- isSpecIsotopeSymbolUsed() - Method in class chemaxon.struc.MolAtom
-
Tests whether special symbol is used.
- isStarAtom(MolAtom) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
-
Decides whether an atom is a star atom in this S-group.
- isStartupSelectorShown() - Method in class chemaxon.marvin.common.UserSettings
-
- isStereo(Molecule) - Static method in class chemaxon.checkers.StereoCheckUtility
-
Gets whether the molecule is stereo
- isStreamOutput() - Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
-
Returns true if stream output.
- isSubFormatOf(String, String) - Static method in class chemaxon.formats.MFileFormatUtil
-
Tests whether a format is a sub-format of another format.
- isSubsetChangable() - Method in class chemaxon.marvin.view.swing.TableOptions
-
Returns whether startAt and maxSize can be changed.
- isSubstitutionCountChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker
-
Gets the option determining if the checker detects substitution count
atom query properties or not.
- isSupportedTransferFormat(String) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
-
Checks whether the given format is available in the current environment or not.
- isSymmetric() - Method in class chemaxon.struc.MoleculeGraph
-
Tests whether the molecule graph is symmetric.
- isTerminal(MolBond) - Static method in class chemaxon.checkers.StructureCheckerHelper
-
This method returns true if the
MolBond represented by molBond
parameter is terminal in a
Molecule structure, false otherwise
- isTerminalAtom() - Method in class chemaxon.struc.MolAtom
-
Determines whether it is a terminal atom or not.
- isThicknessSet() - Method in class chemaxon.struc.graphics.MPolyline
-
Checks if the line thickness is set.
- isThreeLetterPeptideDisplay() - Method in class chemaxon.marvin.MolPrinter
-
Decides whether the Peptide display settings set to three letter.
- isTotalSelected(MoleculeGraph) - Method in class chemaxon.struc.Sgroup
-
Decides if the whole sgroup is selected or not.
- isTotalSelected(MoleculeGraph) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Decides if the whole superatom sgroup is selected or not.
- isTraditionalNitrogensAllowed() - Method in class chemaxon.core.calculations.valencecheck.ValenceCheckOptions
-
Returns if the traditional way of the ylidene
and nitro groups if true the N in CN(=O)=O, CN(C)(C)=O,
CN(=C)=O and c1ccccn1=O is accepted if false they are marked
as valence error.
- isTransDoubleBond() - Method in class chemaxon.checkers.RingStrainErrorChecker
-
Returns the detectTransDoubleBonds
- isTransformable() - Method in class chemaxon.struc.graphics.MAtomSetPoint
-
Is it a transformable object?
- isTransformable() - Method in class chemaxon.struc.graphics.MEFlowBasePoint
-
Is it a transformable object?
- isTransformable() - Method in class chemaxon.struc.graphics.MRectanglePoint
-
- isTransformable() - Method in class chemaxon.struc.MObject
-
Is it a transformable object?
- isTransformationEnabled() - Method in class chemaxon.marvin.common.UserSettings
-
Gets the transformation enabled/disabled.
- isTransitionMetal(int) - Static method in class chemaxon.struc.PeriodicSystem
-
Checks if the given atom is a transition metal, IB-VIIIB.
- isTransparent() - Method in class chemaxon.marvin.MolPrinter
-
Returns the transparency state of the painting.
- isTransparentBackgroundEnabled() - Method in class chemaxon.marvin.space.GraphicScene
-
Returns true if the background is transparent.
- isTripleBond() - Method in class chemaxon.checkers.RingStrainErrorChecker
-
Returns the detectTripleBonds
- isUndecided(Object) - Static method in class chemaxon.jep.ChemJEP
-
Returns whether the result object is undecided.
- isUnitDisplayed() - Method in class chemaxon.struc.sgroup.DataSgroup
-
Gets whether the units string should be displayed.
- isUnsaturationChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker
-
Gets the option determining if the checker detects unsaturation atom
query properties or not.
- isURL(String) - Static method in class chemaxon.marvin.space.MSpaceEasy
-
Tells whether the given path is an URL (Uniform Resource Locator) or not.
- isURLOrFileName(String) - Static method in class chemaxon.formats.MFileFormatUtil
-
Tests whether the specified string is an URL (absolute or relative)
or file name.
- isValenceCheckEnabled() - Method in class chemaxon.struc.MoleculeGraph
-
Determines whether valence check is enabled on this molecule graph.
- isValenceErrorVisible() - Method in class chemaxon.marvin.beans.MSketchPane
-
Are valence errors highlighted?
- isValenceErrorVisible() - Method in class chemaxon.marvin.common.UserSettings
-
Are valence errors visible?
- isValenceErrorvisible() - Method in class chemaxon.marvin.MolPrinter
-
Returns the visibility state of valence errors.
- isValenceErrorVisibleInView() - Method in class chemaxon.marvin.beans.MViewPane
-
Are valence errors highlighted?
- isValenceErrorVisibleInView() - Method in class chemaxon.marvin.common.UserSettings
-
Are valence errors visible in MarvinView?
- isValencePropertyVisible() - Method in class chemaxon.marvin.common.UserSettings
-
Tells wheter the atom valence property is visible or not.
- isValencePropertyVisible() - Method in class chemaxon.marvin.MolPrinter
-
Gets the atom valence property visibility
- isValid() - Method in class chemaxon.checkers.AbbreviatedGroupChecker
-
Excluded object is initialized.
- isValid() - Method in class chemaxon.checkers.AbstractStructureChecker
-
- isValid() - Method in class chemaxon.checkers.InvalidChecker
-
- isValid(InputStream) - Static method in class chemaxon.checkers.runner.configuration.reader.XMLBasedConfigurationReader
-
Checks whether the contents of the provided input stream is a valid
configuration XML
- isValid() - Method in interface chemaxon.checkers.StructureChecker
-
Returns true if the checker's configuration is valid, false otherwise
- isValid() - Method in class chemaxon.checkers.SubstructureChecker
-
- isValid() - Method in class chemaxon.marvin.services.DynamicArgument
-
- isValid() - Method in class chemaxon.marvin.services.ServiceArgument
-
Returns true if service argument is valid
- isValid() - Method in interface chemaxon.marvin.services.ServiceDescriptorEditor
-
Returns true if editor represents a valid descriptor in current state
- isValid(MProp) - Method in class chemaxon.struc.MPropertyContainer
-
Tests whether a coordinate dependent property is still valid.
- isvalidateSgroupsAtCreation() - Method in class chemaxon.marvin.common.UserSettings
-
Is the validation of the possible sgroups and allow only the chemically correct ones on
sgroups creation and edit dialog.
- isValidLinkNode(int, int, int) - Method in class chemaxon.struc.MoleculeGraph
-
Checks whether the specified link atom is valid or not.
- isValidSourceAndSinkForMolecule(Object, Object, Molecule) - Static method in class chemaxon.struc.graphics.MEFlow
-
Deprecated.
As of Marvin 6.1, replaced by
EFlowPlacementValidators.isValidFlow(MolAtom, MolAtom, Molecule)
or one of the other implementations instead.
- isValidSourceForMolecule(Object, Molecule) - Static method in class chemaxon.struc.graphics.MEFlow
-
Deprecated.
As of Marvin 6.1, replaced by
EFlowPlacementValidators.isValidSource(MolAtom, Molecule)
or
EFlowPlacementValidators.isValidSource(MolAtom[], Molecule)
or
EFlowPlacementValidators.isValidSource(MolBond, Molecule)
.
- isVerbose() - Method in class chemaxon.marvin.space.GraphicCell
-
Gets the verbose level.
- isVerbose() - Method in class chemaxon.marvin.space.GraphicScene
-
Gets the verbose level.
- isViewAtomMarkEnabled() - Method in class chemaxon.marvin.common.UserSettings
-
Returns true if atom mark and highlight is enabled in View.
- isViewWindowOpened(int) - Method in class chemaxon.marvin.beans.MViewPane
-
Checks whether the view canvas of the specified cell is detached into a separate window or
not.
- isVisible() - Method in class chemaxon.marvin.space.ComponentElement
-
Returns true if the ComponentElement is visible in the component.
- isVisible() - Method in class chemaxon.marvin.space.GraphicComponent
-
Returns true if this component is allowed to be drawn.
- isVisible(ComponentElement) - Method in class chemaxon.marvin.space.GraphicComponent
-
Returns true if the specified part of the component is allowed to be drawn.
- isVisible() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
-
Returns true if any of its visualizers is visible.
- isVisible(ComponentElement) - Method in class chemaxon.marvin.space.MacroMoleculeComponent
-
Returns true if the gien ComponentElement is visible.
- isVisible() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- isVisible() - Method in class chemaxon.marvin.space.MoleculeComponent
-
Returns true if this component is allowed to be drawn.
- isVisible(ComponentElement) - Method in class chemaxon.marvin.space.MoleculeComponent
-
Returns true if the given item is visible.
- isVisible() - Method in class chemaxon.marvin.space.monitor.Monitor
-
A monitor is visible if all of its selected components are visible,
and it is not hidden explicitly.
- isVisible(ComponentElement) - Method in class chemaxon.marvin.space.monitor.PositionMonitor
-
Returns true, because a PositionMonitor cannot be hidden.
- isVisible() - Method in class chemaxon.struc.Sgroup
-
Checks whether this group is 'visible' (all parents are expanded in case
of superatom S-groups) or not.
- isVolumeVisible() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
Tells whether the volumetric data is shown or not.
- isZoomToScaffoldOnLoad() - Method in class chemaxon.marvin.common.UserSettings
-
- ITALIC - Static variable in class chemaxon.struc.graphics.MFont
-
Italic font style.
- ITEM_COUNT - Static variable in class chemaxon.marvin.space.monitor.Label
-
- items - Variable in class chemaxon.marvin.plugin.gui.ParameterPanel
-
- iterator() - Method in class chemaxon.marvin.io.MDocSource
-
Gets a molecule iterator for this document source.
- iterator(Iterator<Molecule>) - Static method in class com.chemaxon.mapper.AutoMapper
-
Returns an iterator that will return the mapped molecules from the specified iterator.
NOTE: the returned iterator provides the same molecule instances with maps added
- iterator(Iterator<Molecule>, AutoMapper.Options) - Static method in class com.chemaxon.mapper.AutoMapper
-
Returns an iterator that will return the mapped molecules from the specified iterator using the specified number
of threads for mapping.
NOTE: the returned iterator provides the same molecule instances with maps added
- iterator(Iterator<Molecule>, Mapper<RxnMolecule>...) - Static method in class com.chemaxon.mapper.AutoMapper
-
Returns an iterator that will return the mapped molecules from the specified iterator using the specified mappers
for mapping.
- IteratorFactory - Class in chemaxon.util.iterator
-
The
IteratorFactory class provides implementations of
Iterator to ease the handling of atoms and bonds used in
Molecule objects and its descendants.
- IteratorFactory(Molecule, int, int) - Constructor for class chemaxon.util.iterator.IteratorFactory
-
Constructs an iterator factory for the specified molecule with a
specified atom and bond related behavior.
- IteratorFactory(Molecule) - Constructor for class chemaxon.util.iterator.IteratorFactory
-
Constructs an iterator factory for the specified molecule with default
atom and bond related behavior to include all atoms and bonds.
- IteratorFactory(MoleculeGraph) - Constructor for class chemaxon.util.iterator.IteratorFactory
-
Constructs an iterator factory for the specified molecule with default
atom and bond related behavior to include all atoms and bonds.
- IteratorFactory.AtomIterator - Class in chemaxon.util.iterator
-
The AtomIterator class provides an iterator for the atoms of
the specified molecule of the factory according to the atom related
behavior set in the factory.
- IteratorFactory.AtomIterator() - Constructor for class chemaxon.util.iterator.IteratorFactory.AtomIterator
-
Constructs an atom iterator for the specified molecule of the factory
according to the atom related behavior set in the factory.
- IteratorFactory.AtomNeighbourIterator - Class in chemaxon.util.iterator
-
The AtomNeighbourIterator class provides an iterator to
process the atoms connecting to a specified atom according to the atom
and bond related behavior of this factory.
- IteratorFactory.AtomNeighbourIterator(MolAtom) - Constructor for class chemaxon.util.iterator.IteratorFactory.AtomNeighbourIterator
-
Constructs an iterator to process the atoms connecting to the
specified atom according to the atom and bond related behavior of
this factory.
- IteratorFactory.BondIterator - Class in chemaxon.util.iterator
-
The BondIterator class provides an iterator to process the
bonds of the specified molecule in this factory according to the bond
related behavior of this factory.
- IteratorFactory.BondIterator() - Constructor for class chemaxon.util.iterator.IteratorFactory.BondIterator
-
Constructs an iterator to process the bonds of the specified molecule
in this factory according to the bond related behavior of this
factory.
- IteratorFactory.BondNeighbourIterator - Class in chemaxon.util.iterator
-
The BondNeighbourIterator class provides an iterator to
process the bonds connecting to the specified atom according to the atom
and bond related behavior of this factory.
- IteratorFactory.BondNeighbourIterator(MolAtom) - Constructor for class chemaxon.util.iterator.IteratorFactory.BondNeighbourIterator
-
Constructs an iterator to process the bonds connecting to the
specified atom.
- IteratorFactory.NeighbourIterator<E> - Class in chemaxon.util.iterator
-
The NeighbourIterator class provides an iterator to process
the bonds connecting to the specified atom according to the atom and bond
related behavior of this factory.
- IteratorFactory.NeighbourIterator(MolAtom) - Constructor for class chemaxon.util.iterator.IteratorFactory.NeighbourIterator
-
Constructs an iterator to process the bonds connecting to the
specified atom.
- IteratorFactory.RgComponentIterator - Class in chemaxon.util.iterator
-
The RgComponentIterator class provides an iterator to
process the rgroup definition components in the specified molecule of the
factory.
- IteratorFactory.RgComponentIterator() - Constructor for class chemaxon.util.iterator.IteratorFactory.RgComponentIterator
-
Constructs an iterator to process the rgroup definition components,
if the specified molecule in the factory is an RgMolecule, the
iterator is empty otherwise.
- IteratorFactory.RxnComponentIterator - Class in chemaxon.util.iterator
-
The RxnComponentIterator class provides an iterator to
process the components (reactant, product and agent components) in the
reaction molecule of the factory.
- IteratorFactory.RxnComponentIterator() - Constructor for class chemaxon.util.iterator.IteratorFactory.RxnComponentIterator
-
Constructs an iterator to process the components (reactant, product
and agent components), if the specified molecule in the factory is an
RxnMolecule, the iterator is empty otherwise.
- IteratorFactory.SgroupIterator - Class in chemaxon.util.iterator
-
The SgroupIterator class provides an iterator for the
s-groups of the specified molecule of the factory.
- IteratorFactory.SgroupIterator() - Constructor for class chemaxon.util.iterator.IteratorFactory.SgroupIterator
-
Constructs an s-group iterator for the specified molecule of the
factory.
- IUPAC_NAMING_PLUGIN - Static variable in class chemaxon.license.LicenseManager
-
Identifier of plugin: IUPAC Naming Plugin
- IUPACNamingPlugin - Class in chemaxon.marvin.calculations
-
IUPAC name generator plugin.
- IUPACNamingPlugin() - Constructor for class chemaxon.marvin.calculations.IUPACNamingPlugin
-
- m00 - Variable in class chemaxon.struc.CTransform3D
-
The m00 element of the matrix.
- m01 - Variable in class chemaxon.struc.CTransform3D
-
The m01 element of the matrix.
- m02 - Variable in class chemaxon.struc.CTransform3D
-
The m02 element of the matrix.
- m03 - Variable in class chemaxon.struc.CTransform3D
-
The m03 element of the matrix.
- m10 - Variable in class chemaxon.struc.CTransform3D
-
The m10 element of the matrix.
- m11 - Variable in class chemaxon.struc.CTransform3D
-
The m11 element of the matrix.
- m12 - Variable in class chemaxon.struc.CTransform3D
-
The m12 element of the matrix.
- m13 - Variable in class chemaxon.struc.CTransform3D
-
The m13 element of the matrix.
- m20 - Variable in class chemaxon.struc.CTransform3D
-
The m20 element of the matrix.
- m21 - Variable in class chemaxon.struc.CTransform3D
-
The m21 element of the matrix.
- m22 - Variable in class chemaxon.struc.CTransform3D
-
The m22 element of the matrix.
- m23 - Variable in class chemaxon.struc.CTransform3D
-
The m23 element of the matrix.
- m30 - Variable in class chemaxon.struc.CTransform3D
-
The m30 element of the matrix.
- m31 - Variable in class chemaxon.struc.CTransform3D
-
The m31 element of the matrix.
- m32 - Variable in class chemaxon.struc.CTransform3D
-
The m32 element of the matrix.
- m33 - Variable in class chemaxon.struc.CTransform3D
-
The m33 element of the matrix.
- MacroMoleculeComponent - Class in chemaxon.marvin.space
-
MacroMoleculeComponent is a visualizer of complex structures.
- MacroMoleculeComponent() - Constructor for class chemaxon.marvin.space.MacroMoleculeComponent
-
Creates a new instance of MacroMoleculeComponent
- MacroMoleculeComponent(MacroMolecule) - Constructor for class chemaxon.marvin.space.MacroMoleculeComponent
-
Creates a new instance of MacroMoleculeComponent
- MacroMoleculeComponent.MoleculeVisualizer - Interface in chemaxon.marvin.space
-
- main(String[]) - Static method in class chemaxon.checkers.StructureCheck
-
- main(String[]) - Static method in class chemaxon.formats.MdlCompressor
-
Main program.
- main(String[]) - Static method in class chemaxon.formats.MolConverter
-
Main method.
- main(String[]) - Static method in class chemaxon.jep.Evaluator
-
The command line version entry point.
- main(String[]) - Static method in class chemaxon.naming.DocumentExtractor
-
Deprecated.
Expects the name of a plain text file as the first argument
(or from the standard input when absent).
- main(String[]) - Static method in class chemaxon.util.DotfileUtil
-
Print the ChemAxon dotdir absolute path.
- mainMChemicalStruct - Variable in class chemaxon.struc.MDocument
-
- mainMMoleculeMovie - Variable in class chemaxon.struc.MDocument
-
- mainWithoutExit(String[]) - Static method in class chemaxon.formats.MolConverter
-
Same as main(), but never calls System.exit().
- MajorMicrospeciesAccessorPlugin - Class in chemaxon.marvin.calculations
-
Common base class for all plugins with possible major microspecies input.
- MajorMicrospeciesAccessorPlugin() - Constructor for class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
-
Constructor.
- MajorMicrospeciesPlugin - Class in chemaxon.marvin.calculations
-
Plugin class that calculates the major microspecies on a given pH.
- MajorMicrospeciesPlugin() - Constructor for class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
-
Constructor.
- makeColor(String) - Static method in class chemaxon.struc.MObject
-
- makeEditMenu(Container) - Method in class chemaxon.marvin.beans.MViewPane
-
Adds menu items to the specified Edit menu.
- makeHelpMenu(Container) - Method in class chemaxon.marvin.beans.MViewPane
-
- makeItSimilar(MoleculeGraph) - Method in class chemaxon.struc.Molecule
-
Copies some properties of this molecule to the other one specified as
argument.
- makeItSimilar(MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
-
Copies some properties of this molecule to the other one specified as
argument.
- makeItSimilar(MoleculeGraph) - Method in class chemaxon.struc.RgMolecule
-
Copies some properties of this molecule to the other one specified as
argument.
- makeItSimilar(MoleculeGraph) - Method in class chemaxon.struc.RxnMolecule
-
Copies some properties of this molecule to the other one specified as
argument.
- makeRecentFileListMenu(Container) - Method in class chemaxon.marvin.beans.MViewPane
-
Read the recent file list from marvin.properties, and add it to the specified parent menu.
- makeSaveAsMenu(Container) - Method in class chemaxon.marvin.beans.MViewPane
-
Creates the "Save As" menu and adds it to the specified parent menu.
- makeStructureMenu(Container) - Method in class chemaxon.marvin.beans.MViewPane
-
- makeTableMenu(Container) - Method in class chemaxon.marvin.view.swing.TableSupport
-
Creates Table menu items.
- makeToolsMenu() - Method in class chemaxon.marvin.beans.MViewPane
-
- makeViewMenu(Container) - Method in class chemaxon.marvin.beans.MViewPane
-
Adds menu items to the specified View menu.
- manuallySetNormals(boolean) - Method in class chemaxon.marvin.space.SurfaceComponent
-
If this is set by true, we do not want to explicitly set normal vectors,
but SurfaceComponent will compute them automatically.
- map(RxnMolecule) - Method in class com.chemaxon.mapper.AutoMapper
-
Maps the reaction.
- map(T) - Method in interface com.chemaxon.mapper.Mapper
-
Marks the matching parts of item with the same identifier.
- MapMoleculeFixer - Class in chemaxon.fixers
-
- MapMoleculeFixer() - Constructor for class chemaxon.fixers.MapMoleculeFixer
-
- MAPPED_H - Static variable in class chemaxon.struc.MolAtom
-
Mapped Hydrogen atom(s).
- Mapper<T> - Interface in com.chemaxon.mapper
-
Provides support for mapping parts of <T> instances by finding the matching parts and mark them with the same
identifier.
- Mapper.MappingStyle - Enum in com.chemaxon.mapper
-
Available mapping styles by
Mapper
- mapPropertyFile(String, float, float) - Method in class chemaxon.marvin.space.MSpaceEasy
-
Maps the given property file (Gaussian or Charmm) to a previously read or computed
molecular surface and sets minimum and maximum values as visualization setting of the
surface coloring.
- mapPropertyToSurface(VolumetricData) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
Coloring surface based on the given grid.
- mapPropertyToSurface(Grid) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- mapReaction(Molecule...) - Static method in class com.chemaxon.mapper.AutoMapper
-
Maps the reactions in the specified collection using multiple threads if possible.
- mapReaction(AutoMapper.Options, Molecule...) - Static method in class com.chemaxon.mapper.AutoMapper
-
Maps the reactions in the specified collection using the specified options.
- mapReaction(Mapper<RxnMolecule>[], Molecule...) - Static method in class com.chemaxon.mapper.AutoMapper
-
Maps the reactions in the specified collection using the specified mappers in multiple threads.
- mapReaction(Collection<Molecule>) - Static method in class com.chemaxon.mapper.AutoMapper
-
Maps the reactions in the specified collection using multiple threads if possible.
- mapReaction(Collection<Molecule>, AutoMapper.Options) - Static method in class com.chemaxon.mapper.AutoMapper
-
Maps the reactions in the specified collection using the specified options.
- mapReaction(Collection<Molecule>, Mapper<RxnMolecule>...) - Static method in class com.chemaxon.mapper.AutoMapper
-
Maps the reactions in the specified collection using the specified mappers in multiple threads.
- mapReaction(MolImporter, MolExporter) - Static method in class com.chemaxon.mapper.AutoMapper
-
Reads the reactions from the importer, maps them, and writes to the exporter.
- mapReaction(MolImporter, MolExporter, AutoMapper.Options) - Static method in class com.chemaxon.mapper.AutoMapper
-
Reads the reactions from the importer, maps them, and writes to the exporter.
- mapReaction(MolImporter, MolExporter, Mapper<RxnMolecule>...) - Static method in class com.chemaxon.mapper.AutoMapper
-
Reads the reactions from the importer, maps them, and writes to the exporter.
- MapReactionFixer - Class in chemaxon.fixers
-
- MapReactionFixer() - Constructor for class chemaxon.fixers.MapReactionFixer
-
Default constructor
- MARKUSH_EDITOR - Static variable in class chemaxon.license.LicenseManager
-
Identifier of product: Markush Editor
- MARKUSH_ENUM_PLUGIN - Static variable in class chemaxon.license.LicenseManager
-
Identifier of plugin: Markush Enumeration Plugin
- MARKUSH_REDUCTION - Static variable in class chemaxon.util.HitColoringAndAlignmentOptions
-
Constant value specifying, that in case of markush searching
the markush structure is expanded according to the query
structure.
- MARKUSH_REDUCTION_HGEXPANSION - Static variable in class chemaxon.util.HitColoringAndAlignmentOptions
-
Constant value specifying, that in case of markush searching
the markush structure is expanded according to the query
structure and homology groups are also replaced by the query structure
matching on them.
- MARKUSH_SEARCH - Static variable in class chemaxon.license.LicenseManager
-
Identifier of product: Markush Search
- markushDisplayMode - Variable in class chemaxon.util.HitColoringAndAlignmentOptions
-
- MarkushEnumerationPlugin - Class in chemaxon.marvin.calculations
-
Plugin class for enumerating Markush molecules.
- MarkushEnumerationPlugin() - Constructor for class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Constructor.
- MARVIN_APPLETS - Static variable in class chemaxon.license.LicenseManager
-
Identifier of product: Marvin Applets
- MARVIN_BEANS - Static variable in class chemaxon.license.LicenseManager
-
Identifier of product: Marvin Beans
- MARVIN_CONFIG_DEFAULT_PATH - Static variable in class chemaxon.marvin.common.UserSettings
-
The default configuration file path inside the chemaxon settings directory in user home.
- MarvinPane - Class in chemaxon.marvin.beans
-
Ancestor of the Marvin Beans.
- MarvinPane() - Constructor for class chemaxon.marvin.beans.MarvinPane
-
Constructor.
- MarvinPaneBeanInfo - Class in chemaxon.marvin.beans
-
Ancestor of Marvin's BeanInfo classes that are needed by GUI builders.
- MarvinPaneBeanInfo() - Constructor for class chemaxon.marvin.beans.MarvinPaneBeanInfo
-
- MarvinTransferable - Class in chemaxon.marvin.modules.datatransfer
-
Abstract Adapter implementation of the MTransferable interface used by Marvin.
- MarvinTransferable() - Constructor for class chemaxon.marvin.modules.datatransfer.MarvinTransferable
-
- mass() - Method in class chemaxon.calculations.ElementalAnalyser
-
Calculates the molecular weight of the molecule.
- massPrecision() - Method in class chemaxon.calculations.ElementalAnalyser
-
Calculates the precision of the molecular weight (number of decimal
digits).
- matches(String, long, long) - Method in class chemaxon.formats.MFileFormat
-
Tests whether the format matches the specified pattern.
- MAtomSetPoint - Class in chemaxon.struc.graphics
-
Point fixed to the location of one or more atoms.
- MAtomSetPoint() - Constructor for class chemaxon.struc.graphics.MAtomSetPoint
-
Contructs an empty point object.
- MAtomSetPoint(MolAtom[]) - Constructor for class chemaxon.struc.graphics.MAtomSetPoint
-
Contructs a point object.
- MAtomSetPoint(MAtomSetPoint) - Constructor for class chemaxon.struc.graphics.MAtomSetPoint
-
Copy constructor.
- MAX_LINE_LENGTH - Static variable in class chemaxon.marvin.plugin.CalculatorPluginDisplay
-
Maximum desired line length used to form multi-line text.
- MAX_NUMBER_OF_COMPONENTS_PER_CELL - Static variable in class chemaxon.marvin.space.GraphicCell
-
- MAX_RECENT_FILE_LIST_SIZE - Static variable in class chemaxon.marvin.common.UserSettings
-
The maximum size of sketchRecentFileList
- MAX_SCALE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter: "maxscale".
- maxAbsOxStateOf(int) - Static method in class chemaxon.struc.MolAtom
-
Gets the oxidation state that has the maximum absolute value
- MAXIMAL_DISTANCE_LIMIT - Static variable in class chemaxon.checkers.StructureCheckerHelper
-
This constant represents the the upper bound of bond length for ChemAxon
built-in StructureChecker implementations
- maximumItemCount() - Method in class chemaxon.marvin.space.monitor.AngleMonitor
-
Returns 3 as the angle is measured between 3 elements.
- maximumItemCount() - Method in class chemaxon.marvin.space.monitor.DihedralMonitor
-
Returns 4, as measuring dihedral is defined on 4 components.
- maximumItemCount() - Method in class chemaxon.marvin.space.monitor.DistanceMonitor
-
Returns 2 as distance can be measured between 2 elements.
- maximumItemCount() - Method in class chemaxon.marvin.space.monitor.Label
-
Returns 1, because this is the maximun number of selected elements.
- maximumItemCount() - Method in class chemaxon.marvin.space.monitor.Monitor
-
Returns the number of items necessary for monitoring.
- maximumItemCount() - Method in class chemaxon.marvin.space.monitor.PositionMonitor
-
Returns 1, because this is the maximun number of selected elements.
- maxScale(Rectangle) - Method in class chemaxon.marvin.MolPrinter
-
Calculates the maximum scaling factor for fitting the image in the specified rectangle.
- maxScale(Dimension) - Method in class chemaxon.marvin.MolPrinter
-
Calculates the maximum scaling factor for fitting the image in a rectangle of the specified
size.
- maxx() - Method in class chemaxon.marvin.space.BoundingBox
-
Returns the maximum x coordinate of the box.
- maxy() - Method in class chemaxon.marvin.space.BoundingBox
-
Returns the maximum y coordinate of the box.
- maxz() - Method in class chemaxon.marvin.space.BoundingBox
-
Returns the maximum z coordinate of the box.
- MBooleanProp - Class in chemaxon.struc.prop
-
String property.
- MBooleanProp(boolean) - Constructor for class chemaxon.struc.prop.MBooleanProp
-
Constructs a property.
- MBooleanProp(String) - Constructor for class chemaxon.struc.prop.MBooleanProp
-
Constructs a property.
- MBracket - Class in chemaxon.struc.graphics
-
Bracket object.
- MBracket() - Constructor for class chemaxon.struc.graphics.MBracket
-
Constructs a bracket.
- MBracket(MPoint, MPoint) - Constructor for class chemaxon.struc.graphics.MBracket
-
Constructs a bracket with the specified corner points.
- MBracket(MPoint, MPoint, Color) - Constructor for class chemaxon.struc.graphics.MBracket
-
Constructs a bracket with the specified corner points and color.
- MBracket(MBracket) - Constructor for class chemaxon.struc.graphics.MBracket
-
Copy constructor.
- MCES - Static variable in class chemaxon.license.LicenseManager
-
Identifier of product: MCES
- MChemicalStruct - Class in chemaxon.struc.graphics
-
Molecule graph object.
- MChemicalStruct(MoleculeGraph) - Constructor for class chemaxon.struc.graphics.MChemicalStruct
-
Contructs a molecule graph object.
- MChemicalStruct(MChemicalStruct) - Constructor for class chemaxon.struc.graphics.MChemicalStruct
-
Copy constructor.
- MCollectionProp - Class in chemaxon.struc.prop
-
Collection of properties.
- MCollectionProp() - Constructor for class chemaxon.struc.prop.MCollectionProp
-
- Md - Static variable in class chemaxon.core.ChemConst
-
- MDL_DOWNWEDGE_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
MDL style down wedge orientation.
- MDL_EXPAND - Static variable in interface chemaxon.struc.sgroup.Expandable
-
MDL like multiple group expansion flag.
- MdlCompressor - Class in chemaxon.formats
-
Molfile compression.
- MdlCompressor(InputStream, OutputStream, int) - Constructor for class chemaxon.formats.MdlCompressor
-
Create a(n un)compressor for the specified input and output streams.
- MDocSource - Class in chemaxon.marvin.io
-
Marvin document source.
- MDocSource() - Constructor for class chemaxon.marvin.io.MDocSource
-
- MDocStorage - Class in chemaxon.marvin.view
-
Sparse dynamic document storage and reader.
- MDocStorage() - Constructor for class chemaxon.marvin.view.MDocStorage
-
Constructs a document storage.
- MDocStorage(int) - Constructor for class chemaxon.marvin.view.MDocStorage
-
Constructs a document storage.
- MDocStorage.CancellationException - Exception in chemaxon.marvin.view
-
Exception indicating that records are not available because the user cancelled file reading.
- MDocStorage.Listener - Interface in chemaxon.marvin.view
-
Document production listener.
- MDocStorage.RecordUnavailableException - Exception in chemaxon.marvin.view
-
Requested record is not available in the source.
- MDocument - Class in chemaxon.struc
-
Marvin document.
- MDocument(MoleculeGraph) - Constructor for class chemaxon.struc.MDocument
-
Creates a document for the specified molecule graph.
- MDocument(Molecule[]) - Constructor for class chemaxon.struc.MDocument
-
Creates a document for the specified molecule animation.
- MDocument(MDocument) - Constructor for class chemaxon.struc.MDocument
-
Copy constructor.
- MDocument(MDocument, boolean) - Constructor for class chemaxon.struc.MDocument
-
Copy constructor.
- MDocument.CheckerMark - Class in chemaxon.struc
-
Provides informations for Structure Checker higlight
- MDocument.CheckerMark(MolAtom[], MolBond[], Color) - Constructor for class chemaxon.struc.MDocument.CheckerMark
-
- MDocument.Prop - Class in chemaxon.struc
-
Property that stores an MDocument.
- MDocument.Prop() - Constructor for class chemaxon.struc.MDocument.Prop
-
- MDoubleArrayProp - Class in chemaxon.struc.prop
-
Double array property.
- MDoubleArrayProp(double[]) - Constructor for class chemaxon.struc.prop.MDoubleArrayProp
-
Constructs a property object from a double array.
- MDoubleArrayProp(String, int, int) - Constructor for class chemaxon.struc.prop.MDoubleArrayProp
-
Constructs a double array property from a string value.
- MDoubleProp - Class in chemaxon.struc.prop
-
Double floating point property.
- MDoubleProp(double) - Constructor for class chemaxon.struc.prop.MDoubleProp
-
Constructs a property object from a double floating point value.
- MDoubleProp(String) - Constructor for class chemaxon.struc.prop.MDoubleProp
-
Constructs a double floating point property from a string value.
- MEAN_VALUE - Static variable in class chemaxon.marvin.space.SurfaceColoring
-
Will the mean of the affecting properties be mapped onto the surface.
- measure - Variable in class chemaxon.marvin.space.monitor.MeasurementMonitor
-
- measureFrameRate() - Method in class chemaxon.marvin.space.GraphicScene
-
Measures frame rate of drawing.
- measurement() - Method in class chemaxon.marvin.space.monitor.AngleMonitor
-
Does the angle measurement.
- measurement() - Method in class chemaxon.marvin.space.monitor.DihedralMonitor
-
Measures the dihedral.
- measurement() - Method in class chemaxon.marvin.space.monitor.DistanceMonitor
-
Measures the distance.
- measurement - Variable in class chemaxon.marvin.space.monitor.MeasurementMonitor
-
- measurement() - Method in class chemaxon.marvin.space.monitor.MeasurementMonitor
-
Returns the measurement measured by the monitor as a double.
- MeasurementMonitor - Class in chemaxon.marvin.space.monitor
-
Monitor that measures something on its elements.
- MeasurementMonitor() - Constructor for class chemaxon.marvin.space.monitor.MeasurementMonitor
-
Creates a new instance of MeasureMonitor
- MEDIUM_FONT_SIZE - Static variable in class chemaxon.marvin.space.monitor.Label
-
- mediumPrecisions - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- MEFlow - Class in chemaxon.struc.graphics
-
Electron flow arrow.
Representing the movement of one or two electrons in a reaction as a curved
arrow.
Electron flow can start from any atom or bond, but not from any atom pairs
that has no connection bond.
The logic of the electron flows:
If the source is an Atom, the sink can be:
any Atom
Bond connected to this Atom
an atom pair from this atom and any other atom (incipient bond)
If the source is a Bond, the sink can be:
one of the Atoms on the end of this Bond
a Bond connected to this Bond (has common ending Atom)
an atom pair from one of the Atoms on the end of this Bond and any other
atom (incipient bond)
If only the sink/source is in an sgroup, the sink/source must be the
attachment point.
- MEFlow() - Constructor for class chemaxon.struc.graphics.MEFlow
-
Contructs an empty 2 electron flow arrow.
- MEFlow(int) - Constructor for class chemaxon.struc.graphics.MEFlow
-
Contructs an empty electron flow arrow.
- MEFlow(MPoint, MPoint, int) - Constructor for class chemaxon.struc.graphics.MEFlow
-
Contructs an electron flow arrow with the specified endpoints.
- MEFlow(MEFlow) - Constructor for class chemaxon.struc.graphics.MEFlow
-
Copy constructor.
- MEFlowBasePoint - Class in chemaxon.struc.graphics
-
Electron flow arrow base point.
- MEFlowBasePoint() - Constructor for class chemaxon.struc.graphics.MEFlowBasePoint
-
Contructs an empty point object.
- MEFlowBasePoint(MolAtom, MPoint) - Constructor for class chemaxon.struc.graphics.MEFlowBasePoint
-
Contructs a point object.
- MEFlowBasePoint(MEFlowBasePoint) - Constructor for class chemaxon.struc.graphics.MEFlowBasePoint
-
Copy constructor.
- MEllipse - Class in chemaxon.struc.graphics
-
Ellipse object.
- MEllipse() - Constructor for class chemaxon.struc.graphics.MEllipse
-
Constructs an ellipse.
- MEllipse(MPoint, MPoint) - Constructor for class chemaxon.struc.graphics.MEllipse
-
Constructs a ellipse with the specified corner points.
- MEllipse(MPoint, MPoint, Color) - Constructor for class chemaxon.struc.graphics.MEllipse
-
Constructs a ellipse with the specified corner points and color.
- MEllipse(MEllipse) - Constructor for class chemaxon.struc.graphics.MEllipse
-
Copy constructor.
- MENU_CUSTOMIZATION_FILE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter: "menuconfig".
- MENUBAR - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter: "menubar".
- menubar - Variable in class chemaxon.marvin.space.MSpaceEasy
-
- MERGE_DISTANCE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter: "mergedst".
- mergeAtoms(MolAtom, MolAtom) - Method in class chemaxon.struc.Molecule
-
Deprecated.
As of Marvin 6.2, use MergeUtil.mergeAtoms(MolAtom, MolAtom, boolean) instead.
- mergeAtoms(MolAtom, MolAtom) - Method in class chemaxon.struc.MoleculeGraph
-
Deprecated.
As of Marvin 6.2, use MergeUtil.mergeAtoms(MolAtom, MolAtom, boolean) instead.
- mergeAtoms(MolAtom, MolAtom) - Method in class chemaxon.struc.RgMolecule
-
Deprecated.
As of Marvin 6.2, use MergeUtil.mergeAtoms(MolAtom, MolAtom, boolean) instead.
- mergeAtoms(MolAtom, MolAtom) - Method in class chemaxon.struc.RxnMolecule
-
Deprecated.
As of Marvin 6.2, use MergeUtil.mergeAtoms(MolAtom, MolAtom, boolean) instead.
- mergeBrackets(MolBond, MolBond) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
-
Sets the crossing bonds of this sgroup so that
they will share a common bracket.
- mergeComponentParts(MoleculeGraph, int, boolean) - Method in class chemaxon.struc.RxnMolecule
-
Finds those component parts that are contained in the molecule graph m and
creates a new component containing all atoms of m, splitting them from the previous merges.
- mergeFrags(int, int, int) - Method in class chemaxon.struc.MoleculeGraph
-
Merges two connected components of the given fragmentation type.
- mergeProperties(UserSettings, MPropertyContainer, Rectangle) - Static method in class chemaxon.util.ImageExportUtil
-
Merge the properties of UserSettings with the GUI properties.
If both has a value for a given key, the value stored in GUI properties will be used.
- MESH_TYPE - Static variable in class chemaxon.marvin.space.SurfaceComponent
-
- METABOLIZER - Static variable in class chemaxon.license.LicenseManager
-
Identifier of product: Metabolizer
- MetalloceneCheckerResult - Class in chemaxon.checkers.result
-
- MetalloceneCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, StructureCheckerErrorType, Molecule, String, String, String, String, Icon, List<List<MolAtom>>, List<MolAtom>) - Constructor for class chemaxon.checkers.result.MetalloceneCheckerResult
-
Deprecated.
use MetalloceneCheckerResult.MetalloceneCheckerResult(StructureChecker, List, List, StructureCheckerErrorType, Molecule, String, String, String, String, Icon, List, List, int) instead
- MetalloceneCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, StructureCheckerErrorType, Molecule, String, String, String, String, Icon, List<List<MolAtom>>, List<MolAtom>, int) - Constructor for class chemaxon.checkers.result.MetalloceneCheckerResult
-
Constructor which initialize all the properties.
- MetalloceneErrorChecker - Class in chemaxon.checkers
-
MetalloceneErrorChecker detects metallocenes represented in ionic or covalently bonded formats,
that are not coordinate multicenters.
- MetalloceneErrorChecker() - Constructor for class chemaxon.checkers.MetalloceneErrorChecker
-
Default constructor
- MetalloceneFixer - Class in chemaxon.fixers
-
A descendant of
AbstractStructureFixer which converts a single incorrectly drawn
metallocene into multicenter based coordinate bond representation.
- MetalloceneFixer() - Constructor for class chemaxon.fixers.MetalloceneFixer
-
- METHOD_KLOP - Static variable in class chemaxon.marvin.calculations.logDPlugin
-
logP calculation method "KLOP"
- METHOD_KLOP - Static variable in class chemaxon.marvin.calculations.logPPlugin
-
logP calculation method "KLOP"
- METHOD_PHYS - Static variable in class chemaxon.marvin.calculations.logDPlugin
-
logP calculation method: "PHYS"
- METHOD_PHYS - Static variable in class chemaxon.marvin.calculations.logPPlugin
-
logP calculation method: "PHYS"
- METHOD_USER_DEFINED - Static variable in class chemaxon.marvin.calculations.logDPlugin
-
User defined logP calculation method
- METHOD_USER_DEFINED - Static variable in class chemaxon.marvin.calculations.logPPlugin
-
User defined logP calculation method
- METHOD_VG - Static variable in class chemaxon.marvin.calculations.logDPlugin
-
logP calculation method "VG"
- METHOD_VG - Static variable in class chemaxon.marvin.calculations.logPPlugin
-
logP calculation method "VG"
- METHOD_WEIGHTED - Static variable in class chemaxon.marvin.calculations.logDPlugin
-
Weighted logP calculation method
- METHOD_WEIGHTED - Static variable in class chemaxon.marvin.calculations.logPPlugin
-
Weighted logP calculation method
- MFieldAccessor - Class in chemaxon.marvin.io
-
Abstract class for extracting fields (properties) from input and storing them.
- MFieldAccessor() - Constructor for class chemaxon.marvin.io.MFieldAccessor
-
- MFileFormat - Class in chemaxon.formats
-
File format descriptor class.
- MFileFormat(String, String, String, String, String, String, String, String, long) - Constructor for class chemaxon.formats.MFileFormat
-
Creates a format descriptor.
- MFileFormatUtil - Class in chemaxon.formats
-
File format related utility functions.
- MFileFormatUtil() - Constructor for class chemaxon.formats.MFileFormatUtil
-
- MFont - Class in chemaxon.struc.graphics
-
Font wrapper class that does not require an X server.
- MFont(String, int, double) - Constructor for class chemaxon.struc.graphics.MFont
-
Contructs a font.
- MFont(String) - Constructor for class chemaxon.struc.graphics.MFont
-
Parses a font from a string.
- MFont(MFont) - Constructor for class chemaxon.struc.graphics.MFont
-
Copy constructor.
- MFont(Font) - Constructor for class chemaxon.struc.graphics.MFont
-
Create a wrapper for the specified AWT font.
- Mg - Static variable in class chemaxon.core.ChemConst
-
- MHashProp - Class in chemaxon.struc.prop
-
Linked hash map of properties.
- MHashProp() - Constructor for class chemaxon.struc.prop.MHashProp
-
Constructs a property object from an integer value.
- MHashProp(MHashProp, Set) - Constructor for class chemaxon.struc.prop.MHashProp
-
Copy constructor.
- MHCoords3DProp - Class in chemaxon.struc.prop
-
3D coordinates array property.
- MHCoords3DProp(Map<MolAtom, DPoint3[]>, MoleculeGraph) - Constructor for class chemaxon.struc.prop.MHCoords3DProp
-
Constructs a property object from a map.
- MHCoords3DProp(Map<Integer, DPoint3[]>, long) - Constructor for class chemaxon.struc.prop.MHCoords3DProp
-
Constructs a property object from a map.
- MHCoords3DProp(String) - Constructor for class chemaxon.struc.prop.MHCoords3DProp
-
Constructs a point array property from a string value.
- MIN_RECENT_FILE_LIST_SIZE - Static variable in class chemaxon.marvin.common.UserSettings
-
The minimum size of sketchRecentFileList
- MIN_RING_SIZE_FOR_TRANS_DB - Static variable in class chemaxon.struc.MoleculeGraph
-
The minimal size of the ring for the existence of TRANS double bond.
- MINIMAL_ATOM_DISTANCE_LIMIT - Static variable in class chemaxon.checkers.StructureCheckerHelper
-
This constant represents the minimal allowed atom distance (distance here
means euclidean distance) between two atoms for ChemAxon built-in
StructureChecker implementations
- MINIMAL_DISTANCE_LIMIT - Static variable in class chemaxon.checkers.StructureCheckerHelper
-
This constant represents the minimal allowed bond distance (distance here
means euclidean distance) between two bonds and the lower bound of bond
length for ChemAxon built-in StructureChecker implementations
- MinMaxDistance - Class in chemaxon.marvin.alignment
-
Calculates the minimum or maximum intermolecular Cartesian distance between
atoms by rotating flexible bonds.
- MinMaxDistance() - Constructor for class chemaxon.marvin.alignment.MinMaxDistance
-
- MIntegerArrayProp - Class in chemaxon.struc.prop
-
Integer array property.
- MIntegerArrayProp(int[]) - Constructor for class chemaxon.struc.prop.MIntegerArrayProp
-
Constructs a property object from an integer value.
- MIntegerArrayProp(String, int, int) - Constructor for class chemaxon.struc.prop.MIntegerArrayProp
-
Constructs an integer array property from a string value.
- MIntegerProp - Class in chemaxon.struc.prop
-
Integer property.
- MIntegerProp(int) - Constructor for class chemaxon.struc.prop.MIntegerProp
-
Constructs a property object from an integer value.
- MIntegerProp(String) - Constructor for class chemaxon.struc.prop.MIntegerProp
-
Constructs an integer property from a string value.
- minx() - Method in class chemaxon.marvin.space.BoundingBox
-
Returns the minimum x coordinate of the box.
- miny() - Method in class chemaxon.marvin.space.BoundingBox
-
Returns the minimum y coordinate of the box.
- minz() - Method in class chemaxon.marvin.space.BoundingBox
-
Returns the minimum z coordinate of the box.
- MissingAtomMapChecker - Class in chemaxon.checkers
-
MissingAtomMapChecker detects unmapped atoms.
- MissingAtomMapChecker() - Constructor for class chemaxon.checkers.MissingAtomMapChecker
-
Default constructor
- MissingRGroupChecker - Class in chemaxon.checkers
-
- MissingRGroupChecker() - Constructor for class chemaxon.checkers.MissingRGroupChecker
-
Initializes the checker
- MListProp - Class in chemaxon.struc.prop
-
Property list property.
- MListProp() - Constructor for class chemaxon.struc.prop.MListProp
-
Constructs a property object from a list.
- MListProp(MListProp, Set) - Constructor for class chemaxon.struc.prop.MListProp
-
Copy constructor.
- MM_MASK - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Mouse motion mask in display option flags.
- MM_MODES - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Mouse motion modes.
- MM_OFFSET - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Mouse motion mode offset in display option flags.
- MM_ROT3D - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
3D rotation motion mode.
- MM_ROTZ - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
2D rotation (about Z axis) motion mode.
- MM_ZOOM - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Zoom mouse motion mode.
- MM_ZOOMROT - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Zoom-rotate mouse motion mode.
- mmc - Variable in class chemaxon.marvin.space.MoleculeComponent
-
- MMF_FIELD - Static variable in class chemaxon.marvin.view.swing.TableOptions
-
Main molecule is a field in at least one record.
- MMF_NOT_FIELD - Static variable in class chemaxon.marvin.view.swing.TableOptions
-
Main molecule is not a field in at least one record.
- MMF_UNSET - Static variable in class chemaxon.marvin.view.swing.TableOptions
-
Not yet decided whether the main molecule is a field or not.
- MMidPoint - Class in chemaxon.struc.graphics
-
Middle point in a line.
- MMidPoint(MPolyline, int, double, double, double) - Constructor for class chemaxon.struc.graphics.MMidPoint
-
Contructs a middle point object.
- MMidPoint(MMidPoint) - Constructor for class chemaxon.struc.graphics.MMidPoint
-
Copy constructor.
- MMidPoint.Sticky - Class in chemaxon.struc.graphics
-
Fixed middle point that can be a point of a polyline.
- MMidPoint.Sticky(MPolyline, int) - Constructor for class chemaxon.struc.graphics.MMidPoint.Sticky
-
Constructor.
- MMidPoint.Sticky(MMidPoint) - Constructor for class chemaxon.struc.graphics.MMidPoint.Sticky
-
Copy constructor.
- MMoleculeProp - Class in chemaxon.struc.prop
-
Molecule property.
- MMoleculeProp(Molecule) - Constructor for class chemaxon.struc.prop.MMoleculeProp
-
Constructs a property object from a molecule.
- MMPAlignment - Class in chemaxon.marvin.alignment
-
3D Molecular alignment that uses the maximum common substructure to align a pair of
structures.
- MMPAlignment(Molecule, Molecule, MMPAlignmentProperties) - Constructor for class chemaxon.marvin.alignment.MMPAlignment
-
Constructs an MMPAlignment object for later alignment of two structures.
- MMPAlignment(Molecule, Molecule) - Constructor for class chemaxon.marvin.alignment.MMPAlignment
-
Constructs an MMPAlignment object for later alignment of two structures.
- MMPAlignmentProperties - Class in chemaxon.marvin.alignment
-
Input property settings for MMPAlignment.
- MMPAlignmentProperties() - Constructor for class chemaxon.marvin.alignment.MMPAlignmentProperties
-
Constructs a MMPAlignmentProperties object with the options:
FlexibilityMode.KEEP_FIRST_RIGID_SECOND_FLEXIBLE_EXTRA,
AlignmentAccuracyMode.ACCURATE, and MCS similarity limit :0.3
- MMPAlignmentProperties(AlignmentProperties.FlexibilityMode, AlignmentAccuracyMode, double) - Constructor for class chemaxon.marvin.alignment.MMPAlignmentProperties
-
Constructs a MMPAlignmentProperties object.
- MMPAlignmentProperties(AlignmentProperties.FlexibilityMode, AlignmentAccuracyMode, double, int) - Constructor for class chemaxon.marvin.alignment.MMPAlignmentProperties
-
Constructs a MMPAlignmentProperties object.
- MMPAlignmentProperties(AlignmentProperties.FlexibilityMode, AlignmentAccuracyMode, double, boolean) - Constructor for class chemaxon.marvin.alignment.MMPAlignmentProperties
-
Constructs a MMPAlignmentProperties object.
- MMPAlignmentProperties(AlignmentProperties.FlexibilityMode, AlignmentAccuracyMode, double, boolean, int) - Constructor for class chemaxon.marvin.alignment.MMPAlignmentProperties
-
Constructs a MMPAlignmentProperties object.
- MMPAlignmentProperties(AlignmentProperties.FlexibilityMode, AlignmentAccuracyMode) - Constructor for class chemaxon.marvin.alignment.MMPAlignmentProperties
-
Deprecated.
- MMPAlignmentResult - Class in chemaxon.marvin.alignment
-
Results of the MMPAlignment process.
- Mn - Static variable in class chemaxon.core.ChemConst
-
- Mo - Static variable in class chemaxon.core.ChemConst
-
- MObject - Class in chemaxon.struc
-
Paintable object.
- MObject(Color, Color, Color) - Constructor for class chemaxon.struc.MObject
-
Contructs a paintable object with the specified color.
- MObject(MObject) - Constructor for class chemaxon.struc.MObject
-
Copy constructor.
- MObjectProp - Class in chemaxon.struc.prop
-
Property that stores any object.
- MObjectProp(Object) - Constructor for class chemaxon.struc.prop.MObjectProp
-
Constructs a property object.
- MObjectProp(String) - Constructor for class chemaxon.struc.prop.MObjectProp
-
Constructs a property from a string value.
- mode - Variable in class chemaxon.checkers.StructureCheckOptions
-
The mode of the structure check (only check or fixes too)
- mode - Variable in class chemaxon.marvin.space.monitor.Monitor
-
- MODE_MOVING - Static variable in class chemaxon.marvin.space.GraphicScene
-
- MODE_NORMAL - Static variable in class chemaxon.marvin.space.GraphicCell
-
- MODE_PICK - Static variable in class chemaxon.marvin.space.GraphicCell
-
- MODE_STANDING - Static variable in class chemaxon.marvin.space.GraphicScene
-
- MODEL_LARGE - Static variable in class chemaxon.marvin.calculations.pKaPlugin
-
Calculation model: large (always precise, can take more time).
- MODEL_SMALL - Static variable in class chemaxon.marvin.calculations.pKaPlugin
-
Calculation model: small (precise up to the specified number of ionizable atoms).
- modifiesOrigin - Variable in class chemaxon.marvin.space.GraphicComponent
-
Tells whether this component modifies the transformation center of the cell
or not.
- MOL - Static variable in class chemaxon.formats.MFileFormat
-
MDL Molfiles and Rgfiles.
- mol - Variable in class chemaxon.marvin.space.AtomProperty.MoleculeAtomProperty
-
- mol - Variable in class chemaxon.marvin.space.MoleculeComponent
-
- MOL2 - Static variable in class chemaxon.formats.MFileFormat
-
Tripos Mol2 files.
- MOL_LOADER_FINISHED_EVENT - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter: "molLoaderFinishedEvent".
- MOL_V3_OUT - Static variable in class chemaxon.formats.MFileFormat
-
MDL Extended Molfiles and Rgfiles.
- MolAligner - Class in chemaxon.util
-
Tool for aligning a target molecule to a pattern molecule.
- MolAligner() - Constructor for class chemaxon.util.MolAligner
-
Creates a new MolAligner object.
- MolAligner(Molecule, Molecule) - Constructor for class chemaxon.util.MolAligner
-
Creates a new MolAligner object while setting the pattern and target
molecules
- MolAtom - Class in chemaxon.struc
-
Atom object and the properties of the elements.
- MolAtom(int, double, double, double) - Constructor for class chemaxon.struc.MolAtom
-
Construct an atom.
- MolAtom(double, double) - Constructor for class chemaxon.struc.MolAtom
-
Construct a carbon atom at the specified location.
- MolAtom(int) - Constructor for class chemaxon.struc.MolAtom
-
Construct an atom of the specified type at the origin.
- MolBond - Class in chemaxon.struc
-
Chemical bond.
- MolBond(MolAtom, MolAtom, int) - Constructor for class chemaxon.struc.MolBond
-
Construct a bond between two atoms.
- MolBond(MolBond) - Constructor for class chemaxon.struc.MolBond
-
Copy constructor.
- MolBond(MolAtom, MolAtom) - Constructor for class chemaxon.struc.MolBond
-
Construct a single bond between two atoms.
- MolCondition - Interface in chemaxon.jep
-
Deprecated.
Will be removed soon.
- MolContext - Class in chemaxon.jep.context
-
Expression evaluation context containing a single molecule.
- MolContext() - Constructor for class chemaxon.jep.context.MolContext
-
Constructor.
- MolContext(Molecule) - Constructor for class chemaxon.jep.context.MolContext
-
Creates a MolContext with the given input molecule.
- MolConverter - Class in chemaxon.formats
-
Converts between molecule file formats.
- MolConverter(MolConverter.Builder) - Constructor for class chemaxon.formats.MolConverter
-
Creates a MolConverter object.
- MolConverter(InputStream, OutputStream, String, boolean) - Constructor for class chemaxon.formats.MolConverter
-
Creates a MolConverter object.
- MolConverter(InputStream, String, String, boolean) - Constructor for class chemaxon.formats.MolConverter
-
Use this constructor if you do not need output buffering but want to
determine output file positions.
- MolConverter(List<Object>, OutputStream, String, boolean) - Constructor for class chemaxon.formats.MolConverter
-
- MolConverter(List<Object>, String, String, boolean) - Constructor for class chemaxon.formats.MolConverter
-
- MolConverter(List<Object>, List<String>, String, String, boolean) - Constructor for class chemaxon.formats.MolConverter
-
- MolConverter(MolConverter.Options) - Constructor for class chemaxon.formats.MolConverter
-
- MolConverter(List<Object>, List<String>, OutputStream, String, boolean) - Constructor for class chemaxon.formats.MolConverter
-
- MolConverter(List<Object>, List<String>, OutputStream, String, boolean, String[]) - Constructor for class chemaxon.formats.MolConverter
-
- MolConverter(List<Object>, List<String>, OutputStream, String, boolean, String[], String) - Constructor for class chemaxon.formats.MolConverter
-
- MolConverter.Builder - Class in chemaxon.formats
-
MolConverter builder.
- MolConverter.Builder() - Constructor for class chemaxon.formats.MolConverter.Builder
-
Constructs an empty Builder object.
- MolConverter.Options - Class in chemaxon.formats
-
- MolConverter.Options() - Constructor for class chemaxon.formats.MolConverter.Options
-
Deprecated.
- MOLECULAR_DESCRIPTORS - Static variable in class chemaxon.license.LicenseManager
-
Identifier of product: Molecular Descriptors
- MolecularDynamicsPlugin - Class in chemaxon.marvin.calculations
-
Molecular Dynamics plugin.
- MolecularDynamicsPlugin() - Constructor for class chemaxon.marvin.calculations.MolecularDynamicsPlugin
-
Creates a new instance of MolecularDynamicsPlugin
- MolecularSurfaceComponent - Class in chemaxon.marvin.space
-
Class that represents a surface of a molecule.
- MolecularSurfaceComponent() - Constructor for class chemaxon.marvin.space.MolecularSurfaceComponent
-
Creates a new instance of MolecularSurfaceComponent without setting anything.
- MolecularSurfaceComponent(MoleculeIterators.MoleculeInterface, VolumetricData) - Constructor for class chemaxon.marvin.space.MolecularSurfaceComponent
-
Creates a MolecularSurfaceComponent from the given MoleculeInterface and VolumetricData,
which usually comes from a Gaussian Cube file.
- MolecularSurfaceComponent(MoleculeIterators.MoleculeInterface, VolumetricData, float) - Constructor for class chemaxon.marvin.space.MolecularSurfaceComponent
-
Creates a MolecularSurfaceComponent from the given MoleculeInterface and VolumetricData,
which usually comes from a Gaussian Cube file.
- MolecularSurfaceComponent(ArrayList) - Constructor for class chemaxon.marvin.space.MolecularSurfaceComponent
-
Creates a MolecularSurfaceComponent to the given list of MoleculeInterfaces
and MoleculeVisualizers.
- MolecularSurfaceComponent(ArrayList, String) - Constructor for class chemaxon.marvin.space.MolecularSurfaceComponent
-
Creates a MolecularSurfaceComponent to the given list of MoleculeInterfaces
and MoleculeVisualizers.
- molecule - Variable in class chemaxon.checkers.runner.BasicCheckerRunner
-
- MOLECULE - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter: "mol".
- molecule - Variable in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
-
The
Molecule which will be transferred to the clipboard.
- MOLECULE - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
-
Calculation domain type: calculation refers to the molecule.
- Molecule - Class in chemaxon.struc
-
Molecule class.
- Molecule(Molecule, int, int) - Constructor for class chemaxon.struc.Molecule
-
Construct a molecule or fragment with the specified number of atoms
and bonds.
- Molecule(Molecule, MolAtom) - Constructor for class chemaxon.struc.Molecule
-
Construct a molecule consisting of a single atom (node).
- Molecule(Molecule, MolBond) - Constructor for class chemaxon.struc.Molecule
-
Construct a molecule consisting of a single bond (edge).
- Molecule() - Constructor for class chemaxon.struc.Molecule
-
Construct a 2 dimensional molecule.
- MOLECULE_BACKGROUND - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter: "molbg".
- MOLECULE_CHANGED - Static variable in class chemaxon.marvin.view.ViewParameterConstants
-
Identifier of parameter: "molChanged".
- MOLECULE_FORMAT - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter: "molFormat".
- MoleculeChargeChecker - Class in chemaxon.checkers
-
MoleculeChargeChecker detects molecules where the sum of the formal atom
charges is not zero.
- MoleculeChargeChecker() - Constructor for class chemaxon.checkers.MoleculeChargeChecker
-
Default constructor
- MoleculeComponent - Class in chemaxon.marvin.space
-
MoleculeComponent is the basic visualizer of simple molecules in MarvinSpace.
- MoleculeComponent() - Constructor for class chemaxon.marvin.space.MoleculeComponent
-
Creates a new instance of MoleculeComponent.
- MoleculeComponent(Molecule) - Constructor for class chemaxon.marvin.space.MoleculeComponent
-
Creates a new instance of MoleculeComponent from the given molecule.
- MoleculeComponent(MacroMolecule.HeteroComponent, MacroMoleculeComponent) - Constructor for class chemaxon.marvin.space.MoleculeComponent
-
Creates a new instance of MoleculeComponent from the given
HeteroComponent and MacroMoleculeComponent;
this class can be used as a visualizer of a ligand.
- MoleculeGraph - Class in chemaxon.struc
-
A graph consisting of MolAtom nodes and MolBond edges.
- MoleculeGraph(MoleculeGraph, int, int) - Constructor for class chemaxon.struc.MoleculeGraph
-
Construct a molecule or fragment with the specified number of atoms
and bonds.
- MoleculeGraph() - Constructor for class chemaxon.struc.MoleculeGraph
-
Construct a 2 dimensional molecule.
- MoleculeGraph.ValenceCheckState - Enum in chemaxon.struc
-
- MoleculeImporter - Class in chemaxon.marvin.io.formats
-
Molecule importer.
- MoleculeImporter(String) - Constructor for class chemaxon.marvin.io.formats.MoleculeImporter
-
Constructs a new importer for the file.
- MoleculeImporter(String, String) - Constructor for class chemaxon.marvin.io.formats.MoleculeImporter
-
Constructs a new importer for the file.
- MoleculeImporter(File) - Constructor for class chemaxon.marvin.io.formats.MoleculeImporter
-
Constructs a new importer for the file.
- MoleculeImporter(File, String) - Constructor for class chemaxon.marvin.io.formats.MoleculeImporter
-
Constructs a new importer for the file.
- MoleculeImporter(InputStream) - Constructor for class chemaxon.marvin.io.formats.MoleculeImporter
-
Constructs a new importer for the input stream.
- MoleculeImporter(InputStream, String) - Constructor for class chemaxon.marvin.io.formats.MoleculeImporter
-
Constructs a new importer for the stream.
- MoleculeImporter(InputStream, String, String) - Constructor for class chemaxon.marvin.io.formats.MoleculeImporter
-
Constructs a new importer for the stream.
- MoleculeIterator - Interface in chemaxon.util.iterator
-
Molecule iterator.
- MoleculeIteratorFactory - Class in chemaxon.util.iterator
-
Molecule iterator factory.
- MoleculeIteratorFactory() - Constructor for class chemaxon.util.iterator.MoleculeIteratorFactory
-
- MOLECULES - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
-
Calculation domain type: calculation refers to multiple molecule output.
- MoleculeUtil - Class in chemaxon.marvin.util
-
Deprecated.
as of Marvin 5.11.1
- MoleculeUtil() - Constructor for class chemaxon.marvin.util.MoleculeUtil
-
Deprecated.
- MolExport - Class in chemaxon.marvin.io.formats.mdl
-
Exports MDL Molfile, SDfile, RGfile, RDfile, Rxnfile and
(ChemAxon) compressed molfile.
- MolExport() - Constructor for class chemaxon.marvin.io.formats.mdl.MolExport
-
Constructor.
- MolExporter - Class in chemaxon.formats
-
Molecule exporter class.
- MolExporter(String, String, int, String[], String) - Constructor for class chemaxon.formats.MolExporter
-
Creates a molecule exporter.
- MolExporter(String, String) - Constructor for class chemaxon.formats.MolExporter
-
Creates a molecule exporter.
- MolExporter(OutputStream, String, boolean, String[], String) - Constructor for class chemaxon.formats.MolExporter
-
Creates a molecule exporter.
- MolExporter(OutputStream, String) - Constructor for class chemaxon.formats.MolExporter
-
Creates a molecule exporter.
- MolExporter(OutputStream, String, boolean, String[]) - Constructor for class chemaxon.formats.MolExporter
-
Creates a molecule exporter.
- MolExporter(OutputStream, String, String) - Constructor for class chemaxon.formats.MolExporter
-
Creates a molecule exporter.
- MolExportException - Exception in chemaxon.marvin.io
-
Molecule export exception.
- MolExportException(String) - Constructor for exception chemaxon.marvin.io.MolExportException
-
Creates a molecule export exception with the specified message.
- MolExportException(String, Throwable) - Constructor for exception chemaxon.marvin.io.MolExportException
-
Creates a molecule export exception with the specified message and
cause.
- MolExportException(Throwable) - Constructor for exception chemaxon.marvin.io.MolExportException
-
Creates a molecule export exception with the specified cause.
- MolExportModule - Class in chemaxon.marvin.io
-
Abstract base class of molecule export modules.
- MolExportModule() - Constructor for class chemaxon.marvin.io.MolExportModule
-
- MolfileUtil - Class in chemaxon.marvin.io.formats.mdl
-
MDL molfile related utility methods.
- MolfileUtil() - Constructor for class chemaxon.marvin.io.formats.mdl.MolfileUtil
-
- MolFilter - Interface in chemaxon.util
-
Molecule filter.
- MolFormatException - Exception in chemaxon.formats
-
Something's wrong with a molecule file format.
- MolFormatException() - Constructor for exception chemaxon.formats.MolFormatException
-
Creates a molecule format exception.
- MolFormatException(String) - Constructor for exception chemaxon.formats.MolFormatException
-
Creates a molecule format exception with the specified message.
- MolFormatException(String, Throwable) - Constructor for exception chemaxon.formats.MolFormatException
-
Creates a molecule format exception with the specified message and
cause.
- MolFormatException(Throwable) - Constructor for exception chemaxon.formats.MolFormatException
-
Creates a molecule format exception with the specified cause.
- MolFragLoader - Class in chemaxon.marvin.util
-
Molecule fragment loader.
- MolFragLoader() - Constructor for class chemaxon.marvin.util.MolFragLoader
-
Constructor.
- MolFragLoader(MolImporter) - Constructor for class chemaxon.marvin.util.MolFragLoader
-
Constructor: sets the molecule fragment iterator
from the specified importer.
- MolFragLoader(MoleculeIterator) - Constructor for class chemaxon.marvin.util.MolFragLoader
-
Constructor: sets the molecule fragment iterator.
- MolFragLoader.RgroupAttachmentCountFilter - Class in chemaxon.marvin.util
-
Molecule filter which accepts molecules with a specified number of R-group attachments.
- MolFragLoader.RgroupAttachmentCountFilter(int) - Constructor for class chemaxon.marvin.util.MolFragLoader.RgroupAttachmentCountFilter
-
Contructor.
- molID - Variable in class chemaxon.marvin.alignment.AlignmentMolecule
-
- MolImageSize - Class in chemaxon.marvin.util
-
Deprecated.
since 5.5 use ImageExport methods to get this data if you need it. this class will be
deleted in a future release.
- MolImageSize() - Constructor for class chemaxon.marvin.util.MolImageSize
-
Deprecated.
- MolImageSize(int, int, double) - Constructor for class chemaxon.marvin.util.MolImageSize
-
Deprecated.
- MolImageSize(MolImageSize) - Constructor for class chemaxon.marvin.util.MolImageSize
-
Deprecated.
- MolImport - Class in chemaxon.marvin.io.formats.mdl
-
Imports MDL Molfile, SDfile, RGfile, RDfile, Rxnfile and
(ChemAxon) compressed molfile.
- MolImport() - Constructor for class chemaxon.marvin.io.formats.mdl.MolImport
-
- MolImporter - Class in chemaxon.formats
-
Molecule file importer.
- MolImporter(InputStream) - Constructor for class chemaxon.formats.MolImporter
-
Create a molecule importer for an input stream.
- MolImporter(InputStream, String) - Constructor for class chemaxon.formats.MolImporter
-
Create a molecule importer for an input stream.
- MolImporter(InputStream, String, String) - Constructor for class chemaxon.formats.MolImporter
-
Create a molecule importer for an input stream.
- MolImporter(InputStream, String, String, String) - Constructor for class chemaxon.formats.MolImporter
-
Create a molecule importer for an input stream.
- MolImporter(File, String) - Constructor for class chemaxon.formats.MolImporter
-
Create a molecule importer for a file.
- MolImporter(File) - Constructor for class chemaxon.formats.MolImporter
-
Create a molecule importer for a file.
- MolImporter(String) - Constructor for class chemaxon.formats.MolImporter
-
Create a molecule importer for a file.
- MolImporter(String, Object, String) - Constructor for class chemaxon.formats.MolImporter
-
Create a molecule importer with a progress monitor.
- MolImportModule - Class in chemaxon.marvin.io
-
Base class of Molecule import modules.
- MolImportModule() - Constructor for class chemaxon.marvin.io.MolImportModule
-
- MolImportModule.PreferredView - Enum in chemaxon.marvin.io
-
- MolInputProducer - Class in chemaxon.util.concurrent.marvin
-
- MolInputProducer() - Constructor for class chemaxon.util.concurrent.marvin.MolInputProducer
-
Constructor.
- MolInputProducer(MolImporter) - Constructor for class chemaxon.util.concurrent.marvin.MolInputProducer
-
Constructor.
- MolInputProducer(MolImporter[]) - Constructor for class chemaxon.util.concurrent.marvin.MolInputProducer
-
Constructor.
- MolInputStream - Class in chemaxon.formats
-
Molecule input stream that has the ability to determine the input file
format.
- MolInputStream(InputStream) - Constructor for class chemaxon.formats.MolInputStream
-
Create a molecule input stream from an ordinary one,
and determine the format.
- MolInputStream(InputStream, String) - Constructor for class chemaxon.formats.MolInputStream
-
Create a molecule input stream from an ordinary one,
If null is specified as the fmt argument, then the file format is
determined automatically.
- MolInputStream(InputStream, String, String) - Constructor for class chemaxon.formats.MolInputStream
-
Create a molecule input stream from an ordinary one,
If null is specified as the fmt argument, then the file format is
determined automatically.
- MolInputStream(InputStream, String, String, String) - Constructor for class chemaxon.formats.MolInputStream
-
Create a molecule input stream from an ordinary one,
If null is specified as the fmt argument, then the file format is
determined automatically.
- MOLMOVIE - Static variable in class chemaxon.formats.MFileFormatUtil
-
Read multi-molecule files as movies.
- molPanel - Variable in class chemaxon.marvin.beans.MarvinPane
-
Underlying panel.
- MolPrinter - Class in chemaxon.marvin
-
Molecule renderer that can draw a molecule to a graphics context using various display settings.
- MolPrinter() - Constructor for class chemaxon.marvin.MolPrinter
-
Constructs a molecule renderer for an empty molecule.
- MolPrinter(MoleculeGraph) - Constructor for class chemaxon.marvin.MolPrinter
-
Constructs a molecule renderer for the specified molecule.
- MolPrinter(MDocument) - Constructor for class chemaxon.marvin.MolPrinter
-
Constructs a molecule renderer for the specified document.
- MolRenderer - Class in chemaxon.marvin.beans
-
MolRenderer is a simple TableCellRenderer component based on MolPrinter that can be used to
render Molecule objects in JTables.
- MolRenderer() - Constructor for class chemaxon.marvin.beans.MolRenderer
-
- molToScreenCoords(DPoint3, Point2D) - Method in class chemaxon.marvin.MolPrinter
-
Converts molecular coordinates to 2D screen coordinates.
- monitor - Variable in class chemaxon.marvin.space.monitor.Control
-
- Monitor - Class in chemaxon.marvin.space.monitor
-
The Monitor is for "watching" something in the scene.
- Monitor() - Constructor for class chemaxon.marvin.space.monitor.Monitor
-
Creates a new instance of Monitor.
- MONO_SCHEME - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Monochrome color scheme in display option flags.
- MONO_SCHEME_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Monochrome color scheme.
- MORE_ENABLED - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter: "moreEnabled".
- MORE_ERROR_MESSAGE - Static variable in class chemaxon.checkers.StructureCheckerDescriptor
-
multiple error message for checker
- motionMode - Variable in class chemaxon.marvin.space.GraphicComponent
-
Indicates if the component is in standing or in moving mode.
- mousex - Variable in class chemaxon.marvin.space.GraphicComponent
-
Mouse position in picking mode.
- mousey - Variable in class chemaxon.marvin.space.GraphicComponent
-
Mouse position in picking mode.
- moveCorners(double, double) - Method in class chemaxon.struc.MolAtom
-
Translates the coordinates of the atom label.
- moveMainMoleculeGraphToFront() - Method in class chemaxon.struc.MDocument
-
Move the main molecule graph to the top of stack.
- moveMoleculeMovieToFront() - Method in class chemaxon.struc.MDocument
-
Move the molecule movie (if exists) to the top of stack.
- moveObject(MObject, int) - Method in class chemaxon.struc.MDocument
-
Move an object to another place in the stack.
- moveTo(DPoint3) - Method in class chemaxon.struc.MoleculeGraph
-
Move the molecule.
- MP_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter: "mpVisible".
- MP_VISIBLE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter: "mpVisible" property.
- MPoint - Class in chemaxon.struc
-
Point object.
- MPoint(double, double, double) - Constructor for class chemaxon.struc.MPoint
-
Contructs a point object.
- MPoint(double, double) - Constructor for class chemaxon.struc.MPoint
-
Contructs a point object.
- MPoint(DPoint3) - Constructor for class chemaxon.struc.MPoint
-
Constructs a point object.
- MPoint(MPoint) - Constructor for class chemaxon.struc.MPoint
-
Copy constructor.
- MPolyline - Class in chemaxon.struc.graphics
-
Polyline object.
- MPolyline() - Constructor for class chemaxon.struc.graphics.MPolyline
-
Contructs an empty line.
- MPolyline(MPoint, MPoint) - Constructor for class chemaxon.struc.graphics.MPolyline
-
Contructs a line with the specified endpoints.
- MPolyline(MPoint, MPoint, Color, Color) - Constructor for class chemaxon.struc.graphics.MPolyline
-
Contructs a line with the specified endpoints.
- MPolyline(boolean, Color, Color) - Constructor for class chemaxon.struc.graphics.MPolyline
-
Creates a closed polyline.
- MPolyline(MPolyline) - Constructor for class chemaxon.struc.graphics.MPolyline
-
Copy constructor.
- MPolyline(MPolyline, MPoint) - Constructor for class chemaxon.struc.graphics.MPolyline
-
Contructs a polyline from the specified starting polyline and endpoint.
- MProgressMonitor - Interface in chemaxon.common.util
-
Progress monitor interface.
- MProp - Class in chemaxon.struc
-
Property base class.
- MProp() - Constructor for class chemaxon.struc.MProp
-
- MPropertyContainer - Class in chemaxon.struc
-
Property container.
- MPropertyContainer() - Constructor for class chemaxon.struc.MPropertyContainer
-
Creates an empty property container.
- MPropHandler - Class in chemaxon.marvin.io
-
Property factory.
- MPropHandler() - Constructor for class chemaxon.marvin.io.MPropHandler
-
- MRecord - Class in chemaxon.marvin.io
-
Record in a multi-molecule file.
- MRecord() - Constructor for class chemaxon.marvin.io.MRecord
-
Default constructor.
- MRecord(long, long, int, String, MPropertyContainer, int[]) - Constructor for class chemaxon.marvin.io.MRecord
-
Creates a record.
- MRecord(long, long, int, String, MPropertyContainer, int[], int) - Constructor for class chemaxon.marvin.io.MRecord
-
Creates a record.
- MRecord(long, long, int, String, MPropertyContainer, int[], int, String) - Constructor for class chemaxon.marvin.io.MRecord
-
Creates a record.
- MRecordImporter - Class in chemaxon.marvin.io
-
Marvin molecule file reader.
- MRecordImporter(MolInputStream, String) - Constructor for class chemaxon.marvin.io.MRecordImporter
-
Creates a reader for the specified molecule input stream in concurrent mode.
- MRecordParseException - Exception in chemaxon.marvin.io
-
Record reading exception.
- MRecordParseException(MRecordReader.Position, String) - Constructor for exception chemaxon.marvin.io.MRecordParseException
-
Creates an exception with the specified message.
- MRecordParseException(MRecordReader.Position, String, Throwable) - Constructor for exception chemaxon.marvin.io.MRecordParseException
-
Creates an exception with the specified message and cause.
- MRecordParseException(MRecordReader.Position, Throwable) - Constructor for exception chemaxon.marvin.io.MRecordParseException
-
Creates an exception with the specified cause.
- MRecordReader - Interface in chemaxon.marvin.io
-
Marvin record reader.
- MRecordReader.Position - Class in chemaxon.marvin.io
-
Position in the input file.
- MRecordReader.Position(int, int) - Constructor for class chemaxon.marvin.io.MRecordReader.Position
-
Creates a locator.
- MRectangle - Class in chemaxon.struc.graphics
-
Rectangle object.
- MRectangle() - Constructor for class chemaxon.struc.graphics.MRectangle
-
Constructs a rectangle.
- MRectangle(MPoint, MPoint) - Constructor for class chemaxon.struc.graphics.MRectangle
-
Constructs a rectangle with the specified corner points.
- MRectangle(MPoint, MPoint, Color, Color) - Constructor for class chemaxon.struc.graphics.MRectangle
-
Constructs a rectangle with the specified corner points.
- MRectangle(MRectangle) - Constructor for class chemaxon.struc.graphics.MRectangle
-
Copy constructor.
- MRectanglePoint - Class in chemaxon.struc.graphics
-
Rectangle point object.
- MRectanglePoint(MRectangle, int, double, double, double) - Constructor for class chemaxon.struc.graphics.MRectanglePoint
-
Contructs a rectangle corner point object.
- MRectanglePoint(MRectanglePoint) - Constructor for class chemaxon.struc.graphics.MRectanglePoint
-
Copy constructor.
- MRectanglePoint.Sticky - Class in chemaxon.struc.graphics
-
Fixed rectangle point that can be a point of a polyline.
- MRectanglePoint.Sticky(MRectangle, int) - Constructor for class chemaxon.struc.graphics.MRectanglePoint.Sticky
-
Constructor.
- MRectanglePoint.Sticky(MRectanglePoint) - Constructor for class chemaxon.struc.graphics.MRectanglePoint.Sticky
-
Copy constructor.
- MRoundedRectangle - Class in chemaxon.struc.graphics
-
Rounded rectangle object.
- MRoundedRectangle() - Constructor for class chemaxon.struc.graphics.MRoundedRectangle
-
Constructs a rounded rectangle
- MRoundedRectangle(MPoint, MPoint) - Constructor for class chemaxon.struc.graphics.MRoundedRectangle
-
Constructs a rounded rectangle with the specified corner points.
- MRoundedRectangle(MPoint, MPoint, double, double) - Constructor for class chemaxon.struc.graphics.MRoundedRectangle
-
Constructs a rounded rectangle with the specified corner points.
- MRoundedRectangle(MPoint, MPoint, Color) - Constructor for class chemaxon.struc.graphics.MRoundedRectangle
-
Constructs a rounded rectangle with the specified corner points and color.
- MRoundedRectangle(MPoint, MPoint, double, double, Color) - Constructor for class chemaxon.struc.graphics.MRoundedRectangle
-
Constructs a rounded rectangle with the specified corner points and color.
- MRoundedRectangle(MRoundedRectangle) - Constructor for class chemaxon.struc.graphics.MRoundedRectangle
-
Copy constructor.
- MRV - Static variable in class chemaxon.formats.MFileFormat
-
Chemaxon Marvin Document.
- MSAPlugin - Class in chemaxon.marvin.calculations
-
Plugin class for molecular surface area calculation.
- MSAPlugin() - Constructor for class chemaxon.marvin.calculations.MSAPlugin
-
Constructor.
- MSBMP - Static variable in class chemaxon.formats.MFileFormat
-
Windows Bitmap format.
- MSelectionDocument - Class in chemaxon.struc
-
Selection document.
- MSelectionDocument(SelectionMolecule) - Constructor for class chemaxon.struc.MSelectionDocument
-
Creates a document for the specified molecule graph.
- MSelectionDocument(MSelectionDocument) - Constructor for class chemaxon.struc.MSelectionDocument
-
Copy constructor.
- MSketch - Class in chemaxon.marvin.beans
-
Java independent serialization of the sketcher bean.
- MSketch() - Constructor for class chemaxon.marvin.beans.MSketch
-
Constructor used for deserialization.
- MSketch(MSketchPane) - Constructor for class chemaxon.marvin.beans.MSketch
-
Constructor used for serialization.
- MSketchPane - Class in chemaxon.marvin.beans
-
The MarvinSketch Bean.
- MSketchPane() - Constructor for class chemaxon.marvin.beans.MSketchPane
-
Constructs the sketcher.
- MSketchPane(UserSettings) - Constructor for class chemaxon.marvin.beans.MSketchPane
-
Constructs the sketcher with the specified user settings object.
- MSketchPane(UserSettings, boolean) - Constructor for class chemaxon.marvin.beans.MSketchPane
-
Constructs the sketcher with the specified user settings object.
- MSketchPane(UserSettings, boolean, JComponent) - Constructor for class chemaxon.marvin.beans.MSketchPane
-
Constructs the sketcher with the specified user settings object.
- MSketchPaneBeanInfo - Class in chemaxon.marvin.beans
-
MarvinSketch bean information.
- MSketchPaneBeanInfo() - Constructor for class chemaxon.marvin.beans.MSketchPaneBeanInfo
-
- MSPACE_CONFIG_DEFAULT_PATH - Static variable in class chemaxon.marvin.space.GraphicScene
-
- MSpaceEasy - Class in chemaxon.marvin.space
-
Easy-to-use functions of MarvinSpace, customizable gui for applets and
applications.
- MSpaceEasy(boolean) - Constructor for class chemaxon.marvin.space.MSpaceEasy
-
Creates the JPanel with the OpenGL2 canvas, but does not embed it in any
swing container.
- MSpaceEasy(int, int, boolean) - Constructor for class chemaxon.marvin.space.MSpaceEasy
-
Creates the JPanel with the OpenGL2 canvas, but does not embed it in any
swing container.
- MSpaceEasy(boolean, boolean, URL) - Constructor for class chemaxon.marvin.space.MSpaceEasy
-
Creates the JPanel with the OpenGL2 canvas, but does not embed it in any
swing container.
- MSpaceEasy(int, int, boolean, boolean, URL) - Constructor for class chemaxon.marvin.space.MSpaceEasy
-
Creates the JPanel with the OpenGL2 canvas, but does not embed it in any
swing container.
- MStringProp - Class in chemaxon.struc.prop
-
String property.
- MStringProp(String) - Constructor for class chemaxon.struc.prop.MStringProp
-
Constructs a property.
- Mt - Static variable in class chemaxon.core.ChemConst
-
- MTextAttributes - Class in chemaxon.struc.graphics
-
Text attributes.
- MTextAttributes(int, int, Color, MFont, double, double, double) - Constructor for class chemaxon.struc.graphics.MTextAttributes
-
Constructs a attributes object.
- MTextBox - Class in chemaxon.struc.graphics
-
Text box object.
- MTextBox() - Constructor for class chemaxon.struc.graphics.MTextBox
-
Contructs an empty text box.
- MTextBox(MTextBox) - Constructor for class chemaxon.struc.graphics.MTextBox
-
Copy constructor.
- MTextDocument - Class in chemaxon.struc.graphics
-
Text document consisting of sections with different attributes.
- MTextDocument() - Constructor for class chemaxon.struc.graphics.MTextDocument
-
Constructs an empty document.
- MTextDocument(String) - Constructor for class chemaxon.struc.graphics.MTextDocument
-
Constructs a document from the specified string.
- MTextDocument(MTextDocument) - Constructor for class chemaxon.struc.graphics.MTextDocument
-
Copy constructor.
- MTextDocument.Portion - Class in chemaxon.struc.graphics
-
Selected text.
- MTextDocument.Section - Class in chemaxon.struc.graphics
-
Plain text section with uniform attributes.
- MTextDocument.Section(int, String) - Constructor for class chemaxon.struc.graphics.MTextDocument.Section
-
Constructs a text section.
- MTextDocument.Section(int, String, MTextAttributes) - Constructor for class chemaxon.struc.graphics.MTextDocument.Section
-
Constructs a text section.
- MTextDocument.Section(MTextDocument.Section) - Constructor for class chemaxon.struc.graphics.MTextDocument.Section
-
Copy constructor.
- MTransferable - Interface in chemaxon.marvin.modules.datatransfer
-
The interface of Marvin transferable implementations.
- MTransformable - Interface in chemaxon.struc
-
Interface for 3D transformable classes.
- mul(CTransform3D) - Method in class chemaxon.struc.CTransform3D
-
Multiplies by another matrix.
- MULTICENTER - Static variable in class chemaxon.struc.MolAtom
-
"Atomic number" of a central atom of a MulticenterSgroup.
- MultiCenterChecker - Class in chemaxon.checkers
-
MultiCenterChecker detects structures containing multicenter atoms.
- MultiCenterChecker() - Constructor for class chemaxon.checkers.MultiCenterChecker
-
Default constructor
- MulticenterSgroup - Class in chemaxon.struc.sgroup
-
Multicenter S-group to represent complexes like
markush ring structures, ferrocenes, metallocenes...
- MulticenterSgroup(Molecule) - Constructor for class chemaxon.struc.sgroup.MulticenterSgroup
-
Constructs a Multicenter S-group.
- MulticenterSgroup(MulticenterSgroup, Molecule, Sgroup) - Constructor for class chemaxon.struc.sgroup.MulticenterSgroup
-
Copy constructor.
- MulticenterSgroup(MulticenterSgroup, Molecule, Sgroup, int[]) - Constructor for class chemaxon.struc.sgroup.MulticenterSgroup
-
Copy constructor.
- MultiComponentChecker - Class in chemaxon.checkers
-
MultiComponentChecker detects structures containing disconnected components/fragments.
- MultiComponentChecker() - Constructor for class chemaxon.checkers.MultiComponentChecker
-
Default constructor
- MULTIPLE - Static variable in class chemaxon.formats.MolExporter
-
Use this flag to produce multiple output files.
- MultipleSgroup - Class in chemaxon.struc.sgroup
-
Multiple S-group.
- MultipleSgroup(Molecule, boolean) - Constructor for class chemaxon.struc.sgroup.MultipleSgroup
-
Constructs a multiple S-group.
- MultipleSgroup(MultipleSgroup, Molecule, Sgroup, int[]) - Constructor for class chemaxon.struc.sgroup.MultipleSgroup
-
Copy constructor.
- MultipleStereocenterChecker - Class in chemaxon.checkers
-
- MultipleStereocenterChecker() - Constructor for class chemaxon.checkers.MultipleStereocenterChecker
-
Initializes a multiple stereo checker
- MULTISET - Static variable in class chemaxon.formats.MFileFormatUtil
-
The multi-molecule file really contains multiple atom sets of one
molecule.
- MView - Class in chemaxon.marvin.beans
-
Java independent serialization of the viewer bean.
- MView() - Constructor for class chemaxon.marvin.beans.MView
-
Constructor used for deserialization.
- MView(MViewPane) - Constructor for class chemaxon.marvin.beans.MView
-
Constructor used for serialization.
- MViewEditor - Class in chemaxon.marvin.beans
-
MViewEditor is an implementation of AbstractCellEditor and TableCellEditor that can be used to
assign a cell editor to Molecule objects in JTables.
- MViewEditor() - Constructor for class chemaxon.marvin.beans.MViewEditor
-
Creates the cell editor.
- MViewPane - Class in chemaxon.marvin.beans
-
The MarvinView Bean.
- MViewPane() - Constructor for class chemaxon.marvin.beans.MViewPane
-
Constructs the viewer.
- MViewPane(UserSettings) - Constructor for class chemaxon.marvin.beans.MViewPane
-
Constructs the viewer with the specified user settings.
- MViewPaneBeanInfo - Class in chemaxon.marvin.beans
-
MarvinView bean information.
- MViewPaneBeanInfo() - Constructor for class chemaxon.marvin.beans.MViewPaneBeanInfo
-
- MViewParams - Class in chemaxon.marvin.beans
-
MViewParams is a helper tool to generate parameter string to MViewPane.
- MViewParams() - Constructor for class chemaxon.marvin.beans.MViewParams
-
For each new parameter generation a new MViewParams instance is necessary to be created.
- MViewRenderer - Class in chemaxon.marvin.beans
-
MViewRenderer is a TableCellRenderer component that can be used to render Molecule objects in
JTables.
- MViewRenderer() - Constructor for class chemaxon.marvin.beans.MViewRenderer
-
Creates the cell renderer.
- R_GROUPS_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter: "rgroupsVisible".
- Ra - Static variable in class chemaxon.core.ChemConst
-
- RA_IN_EXPAND - Static variable in class chemaxon.struc.Sgroup
-
Atom removal in expand.
- RA_REMOVE_EXCEPT_RU - Static variable in class chemaxon.struc.Sgroup
-
Replace without duplicating.
- RacemateChecker - Class in chemaxon.checkers
-
A descendant of
AtomChecker detecting asymmetric tetrahedral atoms without
specific stereochemistry.
- RacemateChecker() - Constructor for class chemaxon.checkers.RacemateChecker
-
Creates a new RacemateChecker instance.
- racemicStereoCenters() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
-
Calculates the racemic tetrahedral stereogenic centers.
- racemicStereoCentersWithAttachedData() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
-
Calculates the racemic tetrahedral stereogenic centers (with attached data).
- RacemicTetrahedralFilter - Class in com.chemaxon.calculations.stereoanal.filters.tetrahedral
-
Filter for racemic tetrahedral centers.
- RacemicTetrahedralFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.tetrahedral.RacemicTetrahedralFilter
-
- RAD1 - Static variable in class chemaxon.struc.MolAtom
-
Monovalent radical center.
- RAD2 - Static variable in class chemaxon.struc.MolAtom
-
Divalent radical center.
- RAD2_SINGLET - Static variable in class chemaxon.struc.MolAtom
-
Divalent radical center with singlet electronic configuration.
- RAD2_TRIPLET - Static variable in class chemaxon.struc.MolAtom
-
Divalent radical center with triplet electronic configuration.
- RAD3 - Static variable in class chemaxon.struc.MolAtom
-
Trivalent radical center.
- RAD3_DOUBLET - Static variable in class chemaxon.struc.MolAtom
-
Trivalent radical center with doublet electronic configuration.
- RAD3_QUARTET - Static variable in class chemaxon.struc.MolAtom
-
Trivalent radical center with quartet electronic configuration.
- RAD4 - Static variable in class chemaxon.struc.MolAtom
-
Invalid value for radical center for students.
- RAD_COUNT_MASK - Static variable in class chemaxon.struc.MolAtom
-
Radical's free electron count bits in flags for valid radical values.
- RAD_MASK - Static variable in class chemaxon.struc.MolAtom
-
Radical value bits in flags.
- RAD_OFF - Static variable in class chemaxon.struc.MolAtom
-
Radical value offset in flags.
- RADICAL_CHAR - Static variable in class chemaxon.struc.MolAtom
-
- RADICAL_H - Static variable in class chemaxon.struc.MolAtom
-
Include radical Hydrogen atom(s).
- RadicalChecker - Class in chemaxon.checkers
-
- RadicalChecker() - Constructor for class chemaxon.checkers.RadicalChecker
-
Default constructor
- radicalCoordsLabel - Static variable in class chemaxon.struc.graphics.MEFlowBasePoint
-
- radicalState - Static variable in class chemaxon.struc.graphics.MEFlow
-
- RADIUS_CONSTANT - Static variable in class chemaxon.marvin.space.SurfaceColoring
-
Is the atom property range a fix value
- RADIUS_VDW - Static variable in class chemaxon.marvin.space.SurfaceColoring
-
Is the atom property range the van der Waals radius
- RADIUS_VDW_EXTENDED - Static variable in class chemaxon.marvin.space.SurfaceColoring
-
Is the atom property range the van der Waals radius plus a fix value (for example the probe radius)
- RAINBOW_MODE - Static variable in class chemaxon.marvin.space.MacroMoleculeComponent
-
- randicIndex() - Method in class chemaxon.calculations.TopologyAnalyser
-
Calculates the Randic index or molecular connectivity index as the
harmonic sum of the geometric means of the node degrees for each edge.
- randomizeRotatableDihedrals(Molecule, Random) - Static method in class chemaxon.marvin.alignment.Alignment
-
Rotates rotatable bonds by a random dihedral angle value.
- RareElementChecker - Class in chemaxon.checkers
-
A descendant of
AtomTypeChecker detecting structures containing elements which
are usually rare in organic/drug molecules.
- RareElementChecker() - Constructor for class chemaxon.checkers.RareElementChecker
-
Default constructor
- RATOM - Static variable in class chemaxon.jep.context.ReactionContext
-
- RatomChecker - Class in chemaxon.checkers
-
- RatomChecker() - Constructor for class chemaxon.checkers.RatomChecker
-
Creates a new anyChecker instance detecting all R-atoms.
- RatomChecker(Map<String, String>) - Constructor for class chemaxon.checkers.RatomChecker
-
Creates a new anyChecker instance reading checking options from the
params argument.
- Rb - Static variable in class chemaxon.core.ChemConst
-
- RC_CHANGE - Static variable in class chemaxon.struc.MolBond
-
The bond (order) has changed in the reaction.
- RC_MAKE_AND_CHANGE - Static variable in class chemaxon.struc.MolBond
-
The bond is created and changed.
- RC_MAKE_OR_BREAK - Static variable in class chemaxon.struc.MolBond
-
The bond is made or broken in the reaction.
- RC_NOT_CENTER - Static variable in class chemaxon.struc.MolBond
-
The bond is not a reacting center.
- RC_NOT_MODIFIED - Static variable in class chemaxon.struc.MolBond
-
The bond is not modified in the reaction.
- RC_REACTING_CENTER - Static variable in class chemaxon.struc.MolBond
-
The bond is a reacting center.
- RC_UNMAPPED - Static variable in class chemaxon.struc.MolBond
-
Unmapped bond in reacting center.
- RDF - Static variable in class chemaxon.formats.MFileFormat
-
MDL RDfiles.
- Re - Static variable in class chemaxon.core.ChemConst
-
- REACTANT - Static variable in class chemaxon.jep.context.ReactionContext
-
- REACTANTS - Static variable in class chemaxon.struc.RxnMolecule
-
"Reactant" structure type.
- REACTING_CENTER_MASK - Static variable in class chemaxon.struc.MolBond
-
Mask for reacting center bits.
- ReactingCenterBondMarkChecker - Class in chemaxon.checkers
-
Checker detects bonds with reacting center bond marks.
- ReactingCenterBondMarkChecker() - Constructor for class chemaxon.checkers.ReactingCenterBondMarkChecker
-
Default constructor
- REACTION_ERROR_VISIBLE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Deprecated.
As of Version 5.3.2, this method is deprecated and has no replacement. It will be
removed in a future version of Marvin.
- REACTION_SUPPORT - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter: "reactionSupport".
- reactionArrow - Variable in class chemaxon.marvin.plugin.CalculatorPluginDisplay
-
The reaction arrow endpoints, null if not a reaction.
- ReactionChecker - Class in chemaxon.checkers
-
Descendants of ReactionChecker detect reaction scheme problems.
- ReactionChecker(StructureCheckerErrorType, StructureChecker) - Constructor for class chemaxon.checkers.ReactionChecker
-
Default constructor.
- ReactionCheckerResult - Class in chemaxon.checkers.result
-
Deprecated.
- ReactionCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, List<Long>, StructureCheckerErrorType, Molecule, String, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.ReactionCheckerResult
-
Deprecated.
use ReactionCheckerResult.ReactionCheckerResult(StructureChecker, List, List, List, StructureCheckerErrorType, Molecule, String, String, String, String, Icon, int) instead
- ReactionCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, List<Long>, StructureCheckerErrorType, Molecule, String, String, String, String, Icon, int) - Constructor for class chemaxon.checkers.result.ReactionCheckerResult
-
Deprecated.
Constructor which initialize all the properties.
- ReactionContext - Class in chemaxon.jep.context
-
Expression evaluation context to evaluate reaction conditions.
- ReactionContext() - Constructor for class chemaxon.jep.context.ReactionContext
-
Constructor.
- ReactionContext(RxnMolecule) - Constructor for class chemaxon.jep.context.ReactionContext
-
Constructs a reaction context with specified reaction.
- ReactionContext(boolean) - Constructor for class chemaxon.jep.context.ReactionContext
-
Deprecated.
Copy feature is no longer required.
Constructor.
- ReactionMapErrorChecker - Class in chemaxon.checkers
-
A descendant of
ReactionChecker detecting reactions with invalid mapping.
Reaction components should contain at least two mapped atoms, otherwise they are considered
incorrectly mapped.
- ReactionMapErrorChecker() - Constructor for class chemaxon.checkers.ReactionMapErrorChecker
-
Default constructor
- REACTOR - Static variable in class chemaxon.license.LicenseManager
-
Identifier of product: Reactor
- read() - Method in class chemaxon.formats.MolImporter
-
Read the next molecule.
- read(Molecule) - Method in class chemaxon.formats.MolImporter
-
- read() - Method in class chemaxon.marvin.io.formats.MoleculeImporter
-
- read() - Method in class chemaxon.marvin.io.PositionedInputStream
-
Reads a character.
- read(byte[], int, int) - Method in class chemaxon.marvin.io.PositionedInputStream
-
Reads a byte array.
- read(MolImporter) - Method in class chemaxon.util.concurrent.marvin.MolInputProducer
-
- read16doubles(ObjectInput) - Method in class chemaxon.struc.CTransform3D
-
Reads the 4x4 matrix components as double precision floating point
numbers.
- read16floats(ObjectInput) - Method in class chemaxon.struc.CTransform3D
-
Reads the 4x4 matrix components as single precision floating point
numbers.
- readAttribute(String, String) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Reads an attribute from JAR manifest.
- readDoc(MDocument, Molecule) - Method in class chemaxon.formats.MolImporter
-
- readDoc(ObjectInput) - Static method in class chemaxon.marvin.beans.MarvinPane
-
- readDoc() - Method in class chemaxon.marvin.io.MRecordImporter
-
Reads the next document.
- readDocument(MDocument) - Method in class chemaxon.marvin.io.MolImportModule
-
Reads the next document.
- readExternal(ObjectInput) - Method in class chemaxon.marvin.beans.MarvinPane
-
Restores object state.
- readExternal(ObjectInput) - Method in class chemaxon.marvin.beans.MSketch
-
Restores the sketcher's state.
- readExternal(ObjectInput) - Method in class chemaxon.marvin.beans.MSketchPane
-
Restores object state.
- readExternal(ObjectInput) - Method in class chemaxon.marvin.beans.MView
-
Restores the viewer's state.
- readExternal(ObjectInput) - Method in class chemaxon.marvin.beans.MViewPane
-
Restores object state.
- readExternal(ObjectInput) - Method in class chemaxon.struc.CTransform3D
-
Deserializes a transformation matrix.
- readExternal(ObjectInput) - Method in class chemaxon.struc.DPoint3
-
Deserializes a 3D point.
- readExternal(ObjectInput) - Method in class chemaxon.struc.graphics.MTextAttributes
-
- readExternal(ObjectInput) - Method in class chemaxon.struc.graphics.MTextDocument
-
Restores the document.
- readExternal(ObjectInput) - Method in class chemaxon.struc.MPropertyContainer
-
Restores the property container's state.
- readFromString(String) - Method in class chemaxon.struc.graphics.MTextDocument
-
Reads the document from a string.
- readLine() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
-
Reads the next line.
- readLine() - Method in class chemaxon.marvin.io.PositionedInputStream
-
Reads a line.
- readMol(Molecule) - Method in class chemaxon.formats.MolImporter
-
- readMol(ObjectInput) - Static method in class chemaxon.marvin.beans.MarvinPane
-
- readMol(Molecule) - Method in class chemaxon.marvin.io.formats.mdl.MolImport
-
Reads a molecule from MDL mol/sdf/rxn file.
- readMol(Molecule) - Method in class chemaxon.marvin.io.MolImportModule
-
Reads the next molecule.
- readMol(Molecule) - Method in class chemaxon.marvin.io.MRecordImporter
-
Reads the next molecule.
- readMolMovie(MDocument) - Method in class chemaxon.marvin.io.MRecordImporter
-
Reads molecules as a movie.
- readMultiSet(Molecule) - Method in class chemaxon.marvin.io.MRecordImporter
-
Reads molecules as one multi-set molecule.
- readPDB(String) - Method in class chemaxon.marvin.space.MSpaceEasy
-
Reads a protein given as String.
- readPDF(File) - Static method in class chemaxon.naming.DocumentExtractor
-
Deprecated.
Creates a DocumentExtractor to process the given PDF document.
- readPDF(InputStream) - Static method in class chemaxon.naming.DocumentExtractor
-
Deprecated.
Creates a DocumentExtractor to process the given PDF document.
- readPropertyFile(String) - Method in class chemaxon.marvin.space.MSpaceEasy
-
- readRecordAsText() - Method in class chemaxon.formats.MolImporter
-
Reads the next molecule in text format without creating a
Molecule object.
- readRecordAsText() - Method in class chemaxon.marvin.io.MRecordImporter
-
Reads the next record.
- readResources(Class<?>, String) - Static method in class chemaxon.marvin.beans.MarvinPane
-
Reads resources from the specified file.
- readServiceDescriptors(InputStream) - Method in interface chemaxon.marvin.services.ServiceDescriptorReader
-
Returns a list of configured
ServiceDescriptor objects from specified
InputStream
- readWorkbook(InputStream) - Static method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
Loads a workbook from an InputStream
- ready() - Method in class chemaxon.marvin.space.BoundingBox
-
It has to be called after passing all coordinates to the box.
- RearomatizeFixer - Class in chemaxon.fixers
-
- RearomatizeFixer() - Constructor for class chemaxon.fixers.RearomatizeFixer
-
- rearrangeSgroups(int[]) - Method in class chemaxon.struc.Molecule
-
Orders S-groups in the vector of S-groups in the given order corresponding
to the given new indexes.
- rebuildStructures() - Method in class chemaxon.struc.RxnMolecule
-
For each structure (reactant or product) determines
whether it should be a reactant or a product depending
on its the relative position to the reaction arrow.
- rebuildStructures(DPoint3[], int) - Method in class chemaxon.struc.RxnMolecule
-
Sets the reaction arrow.
- recalcCentralAtom() - Method in class chemaxon.struc.sgroup.MulticenterSgroup
-
Recalculates and sets the coordinates of the central atom of this sgroup.
- recalcReactionArrow() - Method in class chemaxon.struc.RxnMolecule
-
Recalculates the coordinates of the reaction arrow from the reactants and products,
forced recalculation.
- receiveNotificationOnCoordinateChange(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicComponent
-
Notifies the current object that the coordinates of the given component
have been changed.
- receiveNotificationOnCoordinateChange(GraphicComponent) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
The molecule will notify the surface when its coordinates change.
- receiveNotificationOnCoordinateChange(GraphicComponent) - Method in class chemaxon.marvin.space.monitor.Label
-
When the coordinates of the labeled object change, the label refreshes
its coordinates relatively.
- receiveNotificationOnCoordinateChange(GraphicComponent) - Method in class chemaxon.marvin.space.monitor.MeasurementMonitor
-
Gets notification from its selected components if their coordinates have been
changed.
- receiveNotificationOnCoordinateChange(GraphicComponent) - Method in class chemaxon.marvin.space.monitor.Monitor
-
Gets notification from its selected components if their coordinates have been
changed.
- receiveNotificationOnInvisibility(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicComponent
-
Notifies the current object that the given component is not visible.
- receiveNotificationOnInvisibility(GraphicComponent) - Method in class chemaxon.marvin.space.monitor.Monitor
-
If the component to that this monitor is assigned becomes hidden,
this monitor will also behave so.
- receiveNotificationOnSelection(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicComponent
-
Notifies the current object that the given component became selected.
- receiveNotificationOnUnSelection(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicComponent
-
Notifies the current object that the given component became unselected.
- receiveNotificationOnVisibility(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicComponent
-
Notifies the current object that the given component became visible.
- receiveNotificationOnVisibility(GraphicComponent) - Method in class chemaxon.marvin.space.monitor.Monitor
-
If the component to that this monitor is assigned becomes visible,
this monitor will also behave so.
- recognizeOneLineFormat(String) - Static method in class chemaxon.formats.MFileFormatUtil
-
Recognize a one-line string as CxSMILES, CxSMARTS, AbbrevGroup,
Peptide or IUPAC name.
- Recognizer - Class in chemaxon.formats.recognizer
-
File format recognizer.
- Recognizer() - Constructor for class chemaxon.formats.recognizer.Recognizer
-
- RecognizerList - Class in chemaxon.formats.recognizer
-
Deprecated.
as of Marvin 2014.07.21.0 not used
- reCreate() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- reCreate() - Method in class chemaxon.marvin.space.MoleculeComponent
-
- RECURSIVE_UNGROUP - Static variable in class chemaxon.struc.Molecule
-
Ungroup and expand (if possible) the child S-groups.
- RED - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
-
Constant storing the red rgb value (the acidic pKa result color).
- redo() - Method in class chemaxon.marvin.beans.MSketchPane
-
Invokes a redo command.
- redraw() - Method in class chemaxon.marvin.space.GraphicScene
-
Redraws the entire scene.
- refersTo(GraphicComponent) - Method in class chemaxon.marvin.space.monitor.Monitor
-
Retruns true if component is between the selected elements.
- REFRACTIVITY_PLUGIN - Static variable in class chemaxon.license.LicenseManager
-
Identifier of plugin: Refractivity Plugin
- RefractivityPlugin - Class in chemaxon.marvin.calculations
-
Plugin class for refractivity calculation.
- RefractivityPlugin() - Constructor for class chemaxon.marvin.calculations.RefractivityPlugin
-
Constructor.
- refresh() - Static method in class chemaxon.license.LicenseManager
-
Re-reads licenses from the default locations.
- refresh() - Method in class chemaxon.marvin.space.GraphicScene
-
- refresh() - Method in class chemaxon.marvin.space.monitor.Label
-
The monitor refreshes its coordinates from the selected item's coordinates.
- refresh() - Method in class chemaxon.marvin.space.monitor.MeasurementMonitor
-
Deletes the position and the value of the measurement to recount.
- refresh() - Method in class chemaxon.marvin.space.monitor.PositionMonitor
-
The monitor refreshes its coordinates from the selected item's coordinates.
- refresh() - Method in class chemaxon.marvin.space.MSpaceEasy
-
Makes all unprocessed event to be processed and makes the graphic canvas redraw.
- refreshColoring() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- regenBonds() - Method in class chemaxon.struc.MoleculeGraph
-
Regenerates the bond vector: remove its elements, then put the bond
objects from the atoms into it.
- regenBonds() - Method in class chemaxon.struc.RgMolecule
-
Regenerate the edge vectors: remove their elements, then put the edge
objects from the nodes into it.
- regenBonds() - Method in class chemaxon.struc.RxnMolecule
-
Regenerate the edge vectors: remove their elements, then put the edge
objects from the nodes into it.
- regenCtabs() - Method in class chemaxon.struc.MoleculeGraph
-
Regenerates connection table and bond table.
- regenCtabs() - Method in class chemaxon.struc.SelectionMolecule
-
Regenerates connection table and bond table.
- regenGearch() - Method in class chemaxon.struc.MoleculeGraph
-
Recreate graph search results object.
- registerFormat(MFileFormat) - Static method in class chemaxon.formats.MFileFormatUtil
-
Registers a user defined file format.
- registerNativeNames() - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
-
Registers the Native names supported by the implementation.
- registerNativeNames() - Method in interface chemaxon.marvin.modules.datatransfer.MTransferable
-
Registers the Native names supported by the implementation.
- REGISTRATION_SYSTEM - Static variable in class chemaxon.license.LicenseManager
-
Identifier of product: Structure Checker
- REGULAR_DOUBLE - Static variable in class chemaxon.struc.RxnMolecule
-
Regular double reaction arrow type.
- REGULAR_SINGLE - Static variable in class chemaxon.struc.RxnMolecule
-
Regular single reaction arrow type.
- RelativeStereoChecker - Class in chemaxon.checkers
-
- RelativeStereoChecker() - Constructor for class chemaxon.checkers.RelativeStereoChecker
-
Initializes relative stereo checker
- relativeX - Variable in class chemaxon.marvin.space.monitor.Label
-
- relativeY - Variable in class chemaxon.marvin.space.monitor.Label
-
- releaseBaseMElectrons() - Method in class chemaxon.struc.graphics.MEFlow
-
- releaseNewEMFGenerator() - Static method in class chemaxon.util.ImageExportUtil
-
Releases and disposes native resources needed by the .NET based EMF generator.
- releasePermanentResources() - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
-
Releases all clipboard related native libraries and resources.
- reload() - Method in class chemaxon.fixers.StructureFixerFactory
-
Deprecated.
Forces reload of configuration on next fixer list request.
- reloadCodeCompletionData() - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Forces all CodeAssist instances created with this factory to reload the code completion data.
- reloadDefaultMap() - Static method in class chemaxon.checkers.StructureCheckerFactory
-
Deprecated.
Forces reload of factory data.
- reloadDefaults() - Static method in class chemaxon.fixers.StructureFixerFactory
-
Deprecated.
Forces reload of factory defaults.
- reloadParameters() - Method in class chemaxon.marvin.plugin.gui.ParameterPanel
-
Reloads previously stored parameters to parameter panel.
- reloadParameters() - Method in interface chemaxon.marvin.plugin.ParameterPanelHandler
-
Reloads previously stored parameters to parameter panel.
- RemovalDate - Enum in com.chemaxon.common.annotations
-
- remove(String) - Method in class chemaxon.formats.recognizer.RecognizerList
-
Deprecated.
Removes the recognizer with the specified codename.
- remove(NameConverter) - Static method in class chemaxon.naming.NameConverters
-
Remove the converter from the converter list.
- remove(int, int) - Method in class chemaxon.struc.graphics.MTextDocument
-
Deletes a substring in the document.
- remove(MProp) - Method in class chemaxon.struc.MPropertyContainer
-
Removes a property.
- remove(int) - Method in class chemaxon.struc.prop.MListProp
-
Removes an element.
- remove() - Method in class chemaxon.util.iterator.IteratorFactory.AtomIterator
-
Removes the next atom in the iteration.
- remove() - Method in class chemaxon.util.iterator.IteratorFactory.BondIterator
-
Removes the next bond in the iteration.
- remove() - Method in class chemaxon.util.iterator.IteratorFactory.NeighbourIterator
-
The remove operation is not supported by this Iterator
implementation.
- remove() - Method in class chemaxon.util.iterator.IteratorFactory.RgComponentIterator
-
The remove operation is not supported by this Iterator
implementation.
- remove() - Method in class chemaxon.util.iterator.IteratorFactory.RxnComponentIterator
-
The remove operation is not supported by this Iterator
implementation.
- remove() - Method in class chemaxon.util.iterator.IteratorFactory.SgroupIterator
-
Removes the next s-group in the iteration.
- removeActionListener(ActionListener) - Method in class chemaxon.marvin.beans.MarvinPane
-
Removes an action listener.
- removeActionListener(ActionListener) - Method in class chemaxon.marvin.view.swing.TableOptions
-
Removes an action listener.
- RemoveAliasFixer - Class in chemaxon.fixers
-
- RemoveAliasFixer() - Constructor for class chemaxon.fixers.RemoveAliasFixer
-
- removeAll() - Method in class chemaxon.struc.Molecule
-
Removes all the atoms and bonds.
- removeAll() - Method in class chemaxon.struc.MoleculeGraph
-
Removes all the atoms and bonds.
- removeAll() - Method in class chemaxon.struc.RgMolecule
-
Remove all the atoms and bonds from the root structure, and from all
the R-groups.
- removeAll() - Method in class chemaxon.struc.RxnMolecule
-
Remove all the atoms and bonds from the root structure, and from all
the R-groups.
- removeAllAttachmentPoints() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Removes all of the attachment points of the Superatom s-group.
- removeAllBonds() - Method in class chemaxon.struc.MolAtom
-
Removes all bonds.
- removeAllBonds(boolean) - Method in class chemaxon.struc.MolAtom
-
Removes all bonds.
- removeAllBonds() - Method in class chemaxon.struc.Molecule
-
Removes all bonds.
- removeAllBonds() - Method in class chemaxon.struc.MoleculeGraph
-
Removes all bonds.
- removeAllBonds() - Method in class chemaxon.struc.RgMolecule
-
Remove all bonds from the root structure, and from all
the R-groups.
- removeAllBonds() - Method in class chemaxon.struc.RxnMolecule
-
Removes all bonds from the reactants, products and agents.
- removeAllBonds() - Method in class chemaxon.struc.sgroup.SgroupAtom
-
Remove all edges.
- removeAllBonds(boolean) - Method in class chemaxon.struc.sgroup.SgroupAtom
-
Removes all edges.
- removeAllComponents() - Method in class chemaxon.marvin.space.GraphicCell
-
Removes all components from the cell.
- removeAllComponents() - Method in class chemaxon.marvin.space.GraphicScene
-
Removes all component from the scene and clears the selection panel.
- removeAllComponents(Class) - Method in class chemaxon.marvin.space.GraphicScene
-
Removes all component from the scene and clears the selection panel.
- removeAllComponents() - Method in class chemaxon.marvin.space.MSpaceEasy
-
Removes all components from the scene.
- removeAllConstraints() - Method in class chemaxon.marvin.alignment.Alignment
-
- removeAllExcept(String) - Method in class chemaxon.formats.recognizer.RecognizerList
-
Deprecated.
Removes all recognizers except the specified.
- removeAllExcept(long, long) - Method in class chemaxon.formats.recognizer.RecognizerList
-
Deprecated.
Removes all recognizers except those with the specified flags.
- removeAllMolecules() - Method in class chemaxon.marvin.alignment.Alignment
-
before every new alignment the molecules have to be removed.
- removeAllMolecules() - Method in class chemaxon.marvin.alignment.PairwiseAlignment
-
- removeAllMolecules() - Method in interface chemaxon.marvin.alignment.PairwiseComparison
-
- removeAllMolecules() - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D
-
- removeAllPairs() - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
-
Removes all user defined atom pairs.
- removeAllProperty() - Method in class chemaxon.marvin.common.UserSettings
-
Removes all property that are stored in this UserSettings object.
- removeAllSgroups() - Method in class chemaxon.struc.Molecule
-
Removes all S-groups.
- removeAssociation(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicComponent
-
Removes the dependency of the given component from this component.
- removeAtom(MolAtom) - Method in class chemaxon.struc.graphics.MEFlow
-
- removeAtom(MolAtom) - Method in class chemaxon.struc.MDocument
-
Removes an atom from all the chemical graphs and removes all
graphics objects that contain its reference.
- removeAtom(MolAtom, int) - Method in class chemaxon.struc.MDocument
-
Removes an atom from all the chemical graphs and removes all
graphics objects that contain its reference.
- removeAtom(MolAtom) - Method in class chemaxon.struc.MObject
-
Removes the atom from the corresponding molecule object.
- removeAtom(MolAtom, int) - Method in class chemaxon.struc.Molecule
-
Removes an atom and its bonds by reference.
- removeAtom(int, int) - Method in class chemaxon.struc.Molecule
-
Removes an atom and its bonds by index.
- removeAtom(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
-
Removes an atom and its bonds by reference.
- removeAtom(int) - Method in class chemaxon.struc.MoleculeGraph
-
Removes an atom and its bonds by index.
- removeAtom(MolAtom, int) - Method in class chemaxon.struc.MoleculeGraph
-
Removes an atom and its bonds with extra clean-up options.
- removeAtom(int, int) - Method in class chemaxon.struc.MoleculeGraph
-
Removes an atom and its bonds with extra clean-up options.
- removeAtom(MolAtom, int) - Method in class chemaxon.struc.RgMolecule
-
Removes an atom and its bonds from the root structure and from all the
R-groups.
- removeAtom(int, int) - Method in class chemaxon.struc.RgMolecule
-
Removes an atom and its bonds from the root structure.
- removeAtom(MolAtom, int) - Method in class chemaxon.struc.RxnMolecule
-
Removes an atom from the reactants, products or agents.
- removeAtom(int, int) - Method in class chemaxon.struc.RxnMolecule
-
Removes an atom from the reactants, products or agents.
- removeAtom(MolAtom) - Method in class chemaxon.struc.SelectionMolecule
-
Removes an atom and its bonds.
- removeAtom(int) - Method in class chemaxon.struc.SelectionMolecule
-
Removes an atom and its bonds from the graph.
- removeAtom(MolAtom, int) - Method in class chemaxon.struc.sgroup.MultipleSgroup
-
Removes an atom from the S-group.
- removeAtom(MolAtom) - Method in class chemaxon.struc.Sgroup
-
Removes an atom and its bonds from the S-group.
- removeAtom(MolAtom, int) - Method in class chemaxon.struc.Sgroup
-
Removes an atom and its bonds from the S-group.
- removeAtom(Sgroup, MolAtom, int) - Static method in class chemaxon.struc.Sgroup
-
- removeAtom(MolAtom, int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Removes an atom from the S-group.
- removeAtom(int) - Method in interface chemaxon.struc.WSmolecule
-
Removes an atom.
- removeAtomAliases(Molecule) - Static method in class chemaxon.marvin.alignment.MMPAlignment
-
Utility for preprocessing structure for alignment.
- RemoveAtomFixer - Class in chemaxon.fixers
-
- RemoveAtomFixer() - Constructor for class chemaxon.fixers.RemoveAtomFixer
-
- removeAtomFromChildren(Sgroup, MolAtom) - Method in class chemaxon.struc.Molecule
-
Removes the parameter atom from the parameter S-group and it's
descendants.
- removeAtomFromGraphs(MolAtom) - Method in class chemaxon.struc.MDocument
-
Removes the specified node from all molecule graphs.
- RemoveAtomMapFixer - Class in chemaxon.fixers
-
- RemoveAtomMapFixer() - Constructor for class chemaxon.fixers.RemoveAtomMapFixer
-
- RemoveAtomQueryPropertyFixer - Class in chemaxon.fixers
-
- RemoveAtomQueryPropertyFixer() - Constructor for class chemaxon.fixers.RemoveAtomQueryPropertyFixer
-
- RemoveAtomValueFixer - Class in chemaxon.fixers
-
- RemoveAtomValueFixer() - Constructor for class chemaxon.fixers.RemoveAtomValueFixer
-
- RemoveAttachedDataFixer - Class in chemaxon.fixers
-
- RemoveAttachedDataFixer() - Constructor for class chemaxon.fixers.RemoveAttachedDataFixer
-
- removeAttachmentPoint(int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Removes the attachment point with the given order.
- removeAttachmentPoints(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Removes all attachment points of the given attachment atom.
- removeBond(MolBond) - Method in class chemaxon.struc.MolAtom
-
Removes a bond by reference.
- removeBond(MolBond, boolean) - Method in class chemaxon.struc.MolAtom
-
Removes a bond by reference.
- removeBond(int) - Method in class chemaxon.struc.MolAtom
-
Removes a bond.
- removeBond(int, boolean) - Method in class chemaxon.struc.MolAtom
-
Removes a bond.
- removeBond(MolBond, int) - Method in class chemaxon.struc.Molecule
-
Removes a bond by reference.
- removeBond(int, int) - Method in class chemaxon.struc.Molecule
-
Removes a bond by index.
- removeBond(MolBond) - Method in class chemaxon.struc.MoleculeGraph
-
Removes a bond by reference.
- removeBond(int) - Method in class chemaxon.struc.MoleculeGraph
-
Removes a bond by index.
- removeBond(MolBond, int) - Method in class chemaxon.struc.MoleculeGraph
-
Removes a bond by reference.
- removeBond(int, int) - Method in class chemaxon.struc.MoleculeGraph
-
Removes a bond by index.
- removeBond(MolBond, int) - Method in class chemaxon.struc.RgMolecule
-
Remove a bond from the root structure, and from all the R-groups.
- removeBond(int, int) - Method in class chemaxon.struc.RgMolecule
-
Remove a bond from the root structure.
- removeBond(MolBond, int) - Method in class chemaxon.struc.RxnMolecule
-
Removes a bond from the reactants, products or agents.
- removeBond(int, int) - Method in class chemaxon.struc.RxnMolecule
-
Removes an edge from a reactant, agent or product.
- removeBond(MolBond) - Method in class chemaxon.struc.SelectionMolecule
-
Removes a bond by reference.
- removeBond(int) - Method in class chemaxon.struc.SelectionMolecule
-
Removes a bond from the graph.
- removeBond(MolBond) - Method in class chemaxon.struc.Sgroup
-
Removes a bond from the S-group.
- removeBond(int, boolean) - Method in class chemaxon.struc.sgroup.SgroupAtom
-
Removes a bond.
- removeBond(MolBond, boolean) - Method in class chemaxon.struc.sgroup.SgroupAtom
-
Removes a bond by reference.
- removeBond(MolBond) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Removes a the given bond from the S-group.
- removeBond(int) - Method in interface chemaxon.struc.WSmolecule
-
Removes a bond.
- RemoveBondFixer - Class in chemaxon.fixers
-
- RemoveBondFixer() - Constructor for class chemaxon.fixers.RemoveBondFixer
-
- removeBonds() - Method in class chemaxon.struc.Sgroup
-
Removes the edge references.
- removeChild(MObject) - Method in class chemaxon.struc.graphics.MPolyline
-
- removeChild(MObject) - Method in class chemaxon.struc.graphics.MRectangle
-
- removeChild(MObject) - Method in class chemaxon.struc.MObject
-
Removes a child object.
- removeChildSgroup(Sgroup) - Method in class chemaxon.struc.Sgroup
-
Removes an S-group from the children list.
- RemoveChiralFlagFixer - Class in chemaxon.fixers
-
A
StructureFixer implementation which removes absolute stereo property from the molecule.
- RemoveChiralFlagFixer() - Constructor for class chemaxon.fixers.RemoveChiralFlagFixer
-
- removeColorsFromMolecules() - Method in class chemaxon.struc.MDocument
-
Removes coloring from all molecular objects in the document.
- removeComponent(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicCell
-
Removes the component and all associated components from the cell.
- removeComponent(Class) - Method in class chemaxon.marvin.space.GraphicCell
-
- removeComponent(int) - Method in class chemaxon.marvin.space.GraphicCell
-
Removes the component which has the given index,
and all of its associated components from the cell.
- removeComponent(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicScene
-
Removes a component from the scene.
- removeComponent(UOID) - Method in class chemaxon.marvin.space.GraphicScene
-
Removes a component from the scene.
- removeComponent(GraphicComponent) - Method in class chemaxon.marvin.space.MSpaceEasy
-
Activates the container cell of the component, removes it from the scene,
and also from the selection panel if that exists.
- removeComponent(int, int) - Method in class chemaxon.struc.RxnMolecule
-
Removes a reactant, product or agent.
- removeCTflagFromSmallRings(MoleculeGraph) - Static method in class chemaxon.marvin.util.CleanUtil
-
Remove CIS|TRANS flag from bonds in rings smaller than size 8.
- removeDependentRgroupDefinition(int) - Method in class chemaxon.struc.RgMolecule
-
Removes the dependent R-group definition of the referenced R-group
definition.
- removeElectronsOf(MolAtom) - Method in class chemaxon.struc.MDocument
-
Removes the Electron containers belongs to targetAtom,
- removeElectronToAtomMapping(MolAtom, MElectronContainer) - Method in class chemaxon.struc.graphics.MChemicalStruct
-
- removeEmptyComponents() - Method in class chemaxon.struc.RxnMolecule
-
Checks all the componentes and removes those that are empty
(node count is zero).
- RemoveExplicitHydrogenFixer - Class in chemaxon.fixers
-
- RemoveExplicitHydrogenFixer() - Constructor for class chemaxon.fixers.RemoveExplicitHydrogenFixer
-
- removeExplicitLonePairs() - Method in class chemaxon.struc.MoleculeGraph
-
- removeGraphicComponent(MacroMoleculeComponent.MoleculeVisualizer) - Method in class chemaxon.marvin.space.MacroMoleculeComponent
-
- removeGroupedAtom(MoleculeGraph, MolAtom, MolBond[], int) - Static method in class chemaxon.struc.Sgroup
-
Removes an atom from the molecule and remove its specified bonds.
- removeHAtoms(MoleculeGraph, int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
-
Deprecated.
since Marvin 5.11 use
convertExplicitHToImplicit(MoleculeGraph, int) instead
- removeHAtoms(MoleculeGraph) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
-
Deprecated.
since Marvin 5.11 use
convertExplicitHToImplicit(MoleculeGraph) instead
- removeHAtoms(MoleculeGraph, MolAtom[], int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
-
Deprecated.
since Marvin 5.11 use
convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int) instead
- removeHAtoms(MoleculeGraph, MolAtom[], int, boolean) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
-
Deprecated.
since Marvin 5.11 use convertExplicitHToImplicit(MoleculeGraph, MolAtom[],
int, boolean) instead
- removeHelperProperties(Molecule) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
- RemoveInvalidChiralFlagFixer - Class in chemaxon.fixers
-
A
StructureFixer implementation which removes absolute stereo property from the molecule.
- RemoveInvalidChiralFlagFixer() - Constructor for class chemaxon.fixers.RemoveInvalidChiralFlagFixer
-
- removeIsolatedAtoms() - Method in class chemaxon.struc.MoleculeGraph
-
Removes the null atom entries in the atoms array
and sets the index fields appropriately.
- removeIsolatedBonds() - Method in class chemaxon.struc.MoleculeGraph
-
Removes the null bond entries in the bonds array
and sets the index fields appropriately.
- removeLeavingGroup(int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Deprecated.
As of Marvin 6.2, no replacement.
Not supported feature.
- removeListener(MDocStorage.Listener) - Method in class chemaxon.marvin.view.MDocStorage
-
Removes a listener.
- removeLonePairs(MoleculeGraph) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
-
Deprecated.
since Marvin 5.11 use
convertExplicitLonePairsToImplicit(MoleculeGraph) instead
- removeLonePairs(Molecule) - Static method in class chemaxon.marvin.alignment.MMPAlignment
-
Utility for preprocessing structure for alignment.
- removeMolecules() - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
-
- removeNotify() - Method in class chemaxon.struc.graphics.MMidPoint
-
Point removed from a document.
- removeNotify(MDocument) - Method in class chemaxon.struc.graphics.MPolyline
-
- removeNotify() - Method in class chemaxon.struc.graphics.MRectanglePoint
-
Point removed from a document.
- removeNotify() - Method in class chemaxon.struc.MObject
-
- removeNotify(MDocument) - Method in class chemaxon.struc.MObject
-
Called when the object is removed from a document.
- removeObject(MObject) - Method in class chemaxon.struc.MDocument
-
Removes an object from the document or from the chemical structure of the document.
- removeObject(int) - Method in class chemaxon.struc.MDocument
-
Removes an object from the document.
- removeObject(MObject) - Method in class chemaxon.struc.Molecule
-
- removeObject(MObject) - Method in class chemaxon.struc.MSelectionDocument
-
Removes an object from the document.
- removeObject(int) - Method in class chemaxon.struc.MSelectionDocument
-
Removes an object from the document.
- removeObject(MObject) - Method in class chemaxon.struc.RgMolecule
-
- removeObject(MObject) - Method in class chemaxon.struc.RxnMolecule
-
Removes a graphical object from this.
- removeObject(MObject) - Method in class chemaxon.struc.Sgroup
-
Removes the specified MObject from this Sgroup.
- removeOLESupport() - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
-
Removing the support of OLE transfer format.
- removeOwner(PropertyChangeListener) - Method in class chemaxon.marvin.common.UserSettings
-
Removes an owner.
- removePharmacophorePoint(ComponentElement) - Method in class chemaxon.marvin.space.GraphicScene
-
- removeProperty(String) - Method in class chemaxon.struc.MolAtom
-
Removes the mapping for this property key from this atom if present.
- removeProperty(String) - Method in class chemaxon.struc.MolBond
-
Removes the mapping for this property key from this bond if present.
- removePropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.checkers.AbstractStructureChecker
-
- removePropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.checkers.AbstractStructureChecker
-
- removePropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.checkers.InvalidChecker
-
- removePropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.checkers.InvalidChecker
-
- removePropertyChangeListener(String, PropertyChangeListener) - Method in interface chemaxon.checkers.StructureChecker
-
Remove a PropertyChangeListener for a specific property.
- removePropertyChangeListener(PropertyChangeListener) - Method in interface chemaxon.checkers.StructureChecker
-
Remove a PropertyChangeListener from the listener list.
- removePropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.checkers.StructureCheckerDescriptor
-
Remove a PropertyChangeListener from the listener list.
- removePropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.checkers.StructureCheckerDescriptor
-
Remove a PropertyChangeListener for a specific property.
- removePropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.fixers.StructureFixerDescriptor
-
Remove a PropertyChangeListener from the listener list.
- removePropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.fixers.StructureFixerDescriptor
-
Remove a PropertyChangeListener for a specific property.
- removePropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.marvin.common.UserSettings
-
Remove a property change listener
- RemoveRadicalFixer - Class in chemaxon.fixers
-
- RemoveRadicalFixer() - Constructor for class chemaxon.fixers.RemoveRadicalFixer
-
- RemoveReactingCenterBondMarkFixer - Class in chemaxon.fixers
-
Fixer removes reactiong center bond marks from bonds.
- RemoveReactingCenterBondMarkFixer() - Constructor for class chemaxon.fixers.RemoveReactingCenterBondMarkFixer
-
- removeReactionArrow() - Method in class chemaxon.struc.RxnMolecule
-
Removes the reaction arrow of this reacion.
- removeRepeatingUnitAtom(MolAtom) - Method in class chemaxon.struc.sgroup.MultipleSgroup
-
Removes an atom from the list of paradigmatic repeating unit atoms.
- removeRestH(int) - Method in class chemaxon.struc.RgMolecule
-
Removes the restH condition from an R-group definition.
- removeRgroup(int) - Method in class chemaxon.struc.RgMolecule
-
Removes an R-group.
- removeRgroupBridge(int, int) - Method in class chemaxon.struc.RgMolecule
-
Removes an r-group bridge.
- removeRgroupBridgeMember(int, int, int) - Method in class chemaxon.struc.RgMolecule
-
Removes an r-group bridge.
- removeRgroupBridgeMembers(int, int, int[]) - Method in class chemaxon.struc.RgMolecule
-
Removes r-group members.
- removeRgroupMember(int, int) - Method in class chemaxon.struc.RgMolecule
-
Removes an R-group member.
- removeRgroupMembers(int, int[]) - Method in class chemaxon.struc.RgMolecule
-
Removes R-group members.
- removeSelectedComponents() - Method in class chemaxon.marvin.space.GraphicCell
-
Removes all selected components and all associated components from the cell.
- removeSelectedComponents() - Method in class chemaxon.marvin.space.GraphicScene
-
Removes all selected components from the active cell with all related components
(connected monitors, surface of a molecule).
- removeSgroupFromList(Sgroup) - Method in class chemaxon.struc.Molecule
-
Removes an S-group from the sgroupVector.
- removeSgroupsOf(Molecule, int) - Method in class chemaxon.struc.Molecule
-
Removes S-groups that are contained in a given molecule but
not contained in another molecule.
- removeSgroupsOf(Molecule) - Method in class chemaxon.struc.Molecule
-
Removes S-groups from this object and its parent.
- removeSketchRecentFile(File) - Method in class chemaxon.marvin.common.UserSettings
-
Remove a file from marvinsketch's recent file list
- removeStarAtoms() - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
-
Changes terminal star atoms (*) to carbon atoms (C).
- RemoveStereoCareBoxFixer - Class in chemaxon.fixers
-
Fixer for molecules containing Stereo Care Boxes.
- RemoveStereoCareBoxFixer() - Constructor for class chemaxon.fixers.RemoveStereoCareBoxFixer
-
- RemoveStereoInversionRetentionMarkFixer - Class in chemaxon.fixers
-
Removes stereo inversion retention marks.
- RemoveStereoInversionRetentionMarkFixer() - Constructor for class chemaxon.fixers.RemoveStereoInversionRetentionMarkFixer
-
- removeTransferable(TransferableDescriptor) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
-
- removeTransferable(String) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
-
- RemoveUnreferencedRgroupDefinitionsFixer - Class in chemaxon.fixers
-
- RemoveUnreferencedRgroupDefinitionsFixer() - Constructor for class chemaxon.fixers.RemoveUnreferencedRgroupDefinitionsFixer
-
- removeUnselectedComponents() - Method in class chemaxon.marvin.space.GraphicCell
-
Removes all unselected components and all associated components from the cell.
- removeUnselectedComponents() - Method in class chemaxon.marvin.space.GraphicScene
-
Removes all unselected components from the active cell with all related components
(connected monitors, surface of a molecule).
- removeUnselectedMonitors() - Method in class chemaxon.marvin.space.GraphicCell
-
Removes all unsselected monitor components from the cell.
- removeUnselectedMonitors() - Method in class chemaxon.marvin.space.GraphicScene
-
Removes all unselected monitor component from the scene.
- RemoveValencePropertyFixer - Class in chemaxon.fixers
-
- RemoveValencePropertyFixer() - Constructor for class chemaxon.fixers.RemoveValencePropertyFixer
-
- removeViewRecentFile(File) - Method in class chemaxon.marvin.common.UserSettings
-
Remove a file from marvinview's recent file list
- removeWhitespace(String) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Removes whitespace characters from the given string.
- RemoveZCoordinateFixer - Class in chemaxon.fixers
-
- RemoveZCoordinateFixer() - Constructor for class chemaxon.fixers.RemoveZCoordinateFixer
-
- RENDERING - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter: "rendering".
- RENDERING_MASK - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Rendering mode mask in display option flags.
- RENDERING_OFFSET - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Rendering mode offset in display option flags.
- RENDERING_QUALITY_HIGH - Static variable in class chemaxon.marvin.space.GraphicComponent
-
Highest though slowest drawing quality indicator.
- RENDERING_QUALITY_LOW - Static variable in class chemaxon.marvin.space.GraphicComponent
-
Lowest but fastest drawing quality indicator.
- RENDERING_QUALITY_MEDIUM - Static variable in class chemaxon.marvin.space.GraphicComponent
-
Medium drawing quality indicator.
- RENDERING_STYLES - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Array of rendering modes.
- renderingQuality - Variable in class chemaxon.marvin.space.GraphicComponent
-
The actual rendering quality.
- reparentSgroups(Molecule) - Method in class chemaxon.struc.Molecule
-
Change parents of all S-groups in this molecule.
- RepeatingUnitSgroup - Class in chemaxon.struc.sgroup
-
Source-based and structure-based representation of repeating unit groups (polymers and
repeating units with repetition ranges).
- RepeatingUnitSgroup(Molecule, int) - Constructor for class chemaxon.struc.sgroup.RepeatingUnitSgroup
-
Constructs an SRU S-group.
- RepeatingUnitSgroup(Molecule, String, int) - Constructor for class chemaxon.struc.sgroup.RepeatingUnitSgroup
-
Constructs an SRU S-group with connectivity.
- RepeatingUnitSgroup(RepeatingUnitSgroup, Molecule, Sgroup, int[]) - Constructor for class chemaxon.struc.sgroup.RepeatingUnitSgroup
-
Copy constructor.
- RepeatingUnitSgroup(RepeatingUnitSgroup, Molecule, Sgroup) - Constructor for class chemaxon.struc.sgroup.RepeatingUnitSgroup
-
Copy constructor.
- replace(int, int, String) - Method in class chemaxon.struc.graphics.MTextDocument
-
Replaces a substring in the document.
- replace(MProp, MProp) - Method in class chemaxon.struc.MPropertyContainer
-
Replaces or removes a property.
- replace(MProp, MProp) - Method in class chemaxon.struc.prop.MCollectionProp
-
Replaces or removes a property.
- replace(MProp, MProp) - Method in class chemaxon.struc.prop.MHashProp
-
Replaces or removes a property.
- replace(MProp, MProp) - Method in class chemaxon.struc.prop.MListProp
-
Replaces or removes a property.
- REPLACE_COORDINATE_BONDS - Static variable in class chemaxon.util.iterator.IteratorFactory
-
Replace coordinate bonds to multicenter atoms with coordinate bonds from
the metal to the represented atoms (in the MulticenterSgroup of the
multicenter).
- replaceAtom(MolAtom, MolAtom) - Method in class chemaxon.struc.graphics.MAtomSetPoint
-
Replaces a contained atom with another one.
- replaceAtom(MolAtom, MolAtom) - Method in class chemaxon.struc.graphics.MEFlowBasePoint
-
Replaces a contained atom with another one.
- replaceAtom(MolAtom, MolAtom) - Method in class chemaxon.struc.graphics.MPolyline
-
Replaces a contained atom with another one.
- replaceAtom(MolAtom, MolAtom) - Method in class chemaxon.struc.MObject
-
Replaces a contained atom with another one.
- replaceAtom(int, MolAtom) - Method in class chemaxon.struc.Molecule
-
Replaces the atom on the given index with the parameter atom and removes
the parameter atom from its original parent molecule if needed.
- replaceAtom(int, MolAtom) - Method in class chemaxon.struc.MoleculeGraph
-
Replaces the atom on the given index with the parameter atom and removes
the parameter atom from its original parent molecule if needed.
- replaceAtom(MolAtom, MolAtom, int) - Method in class chemaxon.struc.sgroup.MultipleSgroup
-
Replace an existing atom by a new one.
- replaceAtom(MolAtom, MolAtom) - Method in class chemaxon.struc.Sgroup
-
Replace an existing atom by a new one in this S-group and its parent
(recursively).
- replaceAtom(MolAtom, MolAtom, int) - Method in class chemaxon.struc.Sgroup
-
Replace an existing atom by a new one in this S-group and its parent
(recursively).
- replaceAtom(MolAtom, MolAtom, int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Replace an existing atom by a new one.
- replaceAtomsWithNewRgroup(SelectionMolecule, int) - Method in class chemaxon.struc.RgMolecule
-
Replaces selected atoms with a new R-group.
- replaceBond(MolBond, MolBond) - Method in class chemaxon.struc.MoleculeGraph
-
- replaceBond(MolBond, MolBond) - Method in class chemaxon.struc.RgMolecule
-
- replaceBond(MolBond, MolBond) - Method in class chemaxon.struc.RxnMolecule
-
- replaceMulticenterAtom(MolAtom, MolAtom) - Method in class chemaxon.struc.sgroup.MulticenterSgroup
-
- replaceSgroup(Sgroup, Sgroup) - Method in class chemaxon.struc.Molecule
-
Replaces an S-group with a new sgroup in the molecule.
- reportFormat - Variable in class chemaxon.checkers.StructureCheckOptions
-
The path of the report file
- reportPath - Variable in class chemaxon.checkers.StructureCheckOptions
-
The path of the report file
- reportPattern - Variable in class chemaxon.checkers.StructureCheckOptions
-
The path of the report file
- reportProperty - Variable in class chemaxon.checkers.StructureCheckOptions
-
The name of the report property, in the output structure file(s)
- reset() - Method in class chemaxon.marvin.io.PositionedInputStream
-
Repositions this stream to the position at the time the
mark method was last called on this input stream.
- reset() - Method in class chemaxon.marvin.space.SurfaceColoring
-
Resets all parameters to the default.
- reset(int) - Method in interface chemaxon.struc.WSmolecule
-
Clears the molecule and sets the array flags.
- resetAll() - Method in class chemaxon.marvin.space.GraphicScene
-
Resets view settings of all cells including rotation, zoom and shifting.
- resetAll() - Method in class chemaxon.marvin.space.MSpaceEasy
-
Resets view settings of all cells including rotation, zoom and shifting.
- resetBaseElectronContainer(MolAtom, MDocument) - Method in class chemaxon.struc.graphics.MEFlow
-
- resetCtab() - Method in class chemaxon.struc.MoleculeGraph
-
An operation performed that changed the connection table
and the graph invariants.
- resetFilePointer() - Method in class chemaxon.marvin.io.PositionedInputStream
-
Resets file pointer to zero.
- resetGrinvInParents() - Method in class chemaxon.struc.MoleculeGraph
-
Graph invariants must be recalculated for this graph and all parent
graphs.
- resetMap() - Method in class chemaxon.marvin.alignment.MinMaxDistance
-
- resetSettings() - Method in class chemaxon.marvin.space.GraphicScene
-
Sets all draw properties to the default value and resets view.
- resetView() - Method in class chemaxon.marvin.space.GraphicCell
-
- resetView() - Method in class chemaxon.marvin.space.GraphicScene
-
Resets view settings of the active cell including rotation, zoom and shifting.
- resetZoom() - Method in class chemaxon.marvin.space.GraphicCell
-
- reshape(GLAutoDrawable, int, int, int, int) - Method in class chemaxon.marvin.space.GraphicScene
-
Called by the drawable during the first repaint after the component has been resized.
- residueSymbolOf(int) - Static method in class chemaxon.struc.MolAtom
-
Gets the name of a residue.
- residueSymbolOf(int) - Static method in class chemaxon.struc.Molecule
-
Gets the name of a residue.
- residueTypeOf(String) - Static method in class chemaxon.struc.MolAtom
-
Gets the residue identifier for a residue name.
- residueTypeOf(String) - Static method in class chemaxon.struc.Molecule
-
Gets the residue identifier for a residue name.
- resize(double, double, double) - Method in class chemaxon.marvin.space.GraphicComponent
-
Resizes the component according to the given factors in each directions.
- resize(double, double, double) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
Resizes the component according to given factors.
- resize(double, double, double) - Method in class chemaxon.marvin.space.PharmacophoreArrow
-
Resizes the component according to the given factors in each direction.
- resize(double, double, double) - Method in class chemaxon.marvin.space.PharmacophorePoint
-
Resizes the component according to given factors.
- ResizeControl - Class in chemaxon.marvin.space.monitor
-
This control is to change the size of a GraphicComponent by changing the coordinates.
- ResizeControl(Monitor) - Constructor for class chemaxon.marvin.space.monitor.ResizeControl
-
Creates a new instance of ResizeControl
- RESONANCE - Static variable in class chemaxon.struc.RxnMolecule
-
Resonance arrow, the same as the two-headed single reaction arrow.
- ResonancePlugin - Class in chemaxon.marvin.calculations
-
Plugin class for finding resonant structures.
- ResonancePlugin() - Constructor for class chemaxon.marvin.calculations.ResonancePlugin
-
Constructor.
- RESSEQ_MAX - Static variable in class chemaxon.struc.MolAtom
-
Maximum residue sequence number is currently 8191.
- restoreCache(int) - Method in class chemaxon.struc.MoleculeGraph
-
Restores caches like connection table, bond table, etc.
- restoreCoords(MoleculeGraph, double[]) - Static method in class chemaxon.marvin.util.CleanUtil
-
Restores atomic coordinates.
- restoreDefaultParameters() - Method in class chemaxon.marvin.plugin.gui.ParameterPanel
-
Restores default parameters to parameter panel.
- restoreDefaultParameters() - Method in interface chemaxon.marvin.plugin.ParameterPanelHandler
-
Restores default parameters to parameter panel.
- restoreExplicitHydrogens(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
- RESTYPE_MAX - Static variable in class chemaxon.struc.MolAtom
-
Maximum residue type is currently 63.
- resultMolList - Variable in class chemaxon.marvin.plugin.CalculatorPluginDisplay
-
The result molecules to be displayed.
- resultValues - Variable in class chemaxon.marvin.plugin.CalculatorPluginDisplay
-
The result values to be displayed in MarvinSpace.
- RETROSYNTHETIC - Static variable in class chemaxon.struc.RxnMolecule
-
Retrosynthetic arrow, the same as the regular double reaction arrow.
- ReusableInputProducer - Class in chemaxon.util.concurrent.marvin
-
Input producer that provides reusable input.
- ReusableInputProducer(Object[]) - Constructor for class chemaxon.util.concurrent.marvin.ReusableInputProducer
-
Constructor.
- ReusablePluginWorkUnit - Class in chemaxon.marvin.plugin.concurrent
-
Work unit performing plugin calculation.
- ReusablePluginWorkUnit() - Constructor for class chemaxon.marvin.plugin.concurrent.ReusablePluginWorkUnit
-
Constructor.
- reuse(Object) - Method in class chemaxon.util.concurrent.marvin.ReusableInputProducer
-
Puts an input object into the input queue.
- reuseAtom(int, int) - Method in class chemaxon.struc.Molecule
-
Reuse an atom or create a new one.
- reuseAtom(int, int) - Method in class chemaxon.struc.RgMolecule
-
Reuse an atom or create a new one.
- reuseFont(String, int, double) - Method in class chemaxon.struc.graphics.MTextDocument
-
- revalidateCoordDependentProps() - Method in class chemaxon.struc.MoleculeGraph
-
Revalidate coordinate dependent properties.
- revalidateCoordDependentProps() - Method in class chemaxon.struc.RgMolecule
-
Revalidate coordinate dependent properties.
- revalidateCoordDependentProps() - Method in class chemaxon.struc.RxnMolecule
-
Revalidate coordinate dependent properties.
- reverse() - Method in class chemaxon.struc.graphics.MPolyline
-
Reverses the order of points.
- REVERSIBLE_EXPAND - Static variable in interface chemaxon.struc.sgroup.Expandable
-
- Rf - Static variable in class chemaxon.core.ChemConst
-
- Rg - Static variable in class chemaxon.core.ChemConst
-
- RG_ID2_FLAG - Static variable in class chemaxon.struc.RgMolecule
-
Other R-group ID's presence flag in R-logic.
- RG_ID2_MASK - Static variable in class chemaxon.struc.RgMolecule
-
Mask of the other R-group's id in R-logic.
- RG_ID2_OFF - Static variable in class chemaxon.struc.RgMolecule
-
Offset of the other R-group's id in R-logic.
- RG_ID_MASK - Static variable in class chemaxon.struc.RgMolecule
-
R-group id mask in R-logic.
- RG_RESTH - Static variable in class chemaxon.struc.RgMolecule
-
The RestH flag in R-logic.
- RgMolecule - Class in chemaxon.struc
-
A molecule or reaction containing R-groups.
- RgMolecule() - Constructor for class chemaxon.struc.RgMolecule
-
Creates a 2 dimensional RgMolecule.
- RGROUP - Static variable in class chemaxon.struc.MolAtom
-
"Atomic number" of the Rgroup query "atom".
- RGROUP_ATTACHMENT - Static variable in class chemaxon.struc.MolAtom
-
"Atomic number" of an ordered R-group attachment point.
- RGROUP_MAX - Static variable in class chemaxon.struc.MolAtom
-
Maximum R-group index (32767).
- RGROUP_MAX - Static variable in interface chemaxon.struc.Smolecule
-
Maximum R-group index (32767).
- RGROUP_RGROUP_MAP - Static variable in class chemaxon.checkers.result.ConvertConstants
-
This
String represents the key of cloned rgroup, original rgroup map
- RgroupAttachmentCountErrorChecker - Class in chemaxon.checkers
-
- RgroupAttachmentCountErrorChecker() - Constructor for class chemaxon.checkers.RgroupAttachmentCountErrorChecker
-
Creates a new RgroupAttachmentErrorChecker instance.
- RgroupAttachmentErrorChecker - Class in chemaxon.checkers
-
- RgroupAttachmentErrorChecker() - Constructor for class chemaxon.checkers.RgroupAttachmentErrorChecker
-
Creates a new RgroupAttachmentErrorChecker instance.
- RgroupAttachmentFixer - Class in chemaxon.fixers
-
A descendant of
AbstractStructureFixer that can fix R-group
attachment errors by adding missing attachment to R-group members having a
single attachment position available.
- RgroupAttachmentFixer() - Constructor for class chemaxon.fixers.RgroupAttachmentFixer
-
- RgroupCheckerResult - Class in chemaxon.checkers.result
-
- RgroupCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, List<RgroupInfo>, StructureCheckerErrorType, Molecule, String, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.RgroupCheckerResult
-
Deprecated.
use RgroupCheckerResult.RgroupCheckerResult(StructureChecker, List, List, List, StructureCheckerErrorType, Molecule, String, String, String, String, Icon, int) instead
- RgroupCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, List<RgroupInfo>, StructureCheckerErrorType, Molecule, String, String, String, String, Icon, int) - Constructor for class chemaxon.checkers.result.RgroupCheckerResult
-
Constructor which initialize all the properties.
- RGROUPED - Static variable in class chemaxon.struc.RxnMolecule
-
Add R-groups to component structure.
- rgroupIdOf(MolAtom) - Method in class chemaxon.struc.RgMolecule
-
Finds the ID of the R-group (the number in R#) that contains the
specified atom.
- rgroupIndexOf(MolAtom) - Method in class chemaxon.struc.RgMolecule
-
Finds the index of the R-group (the number in R#) that contains the
specified atom.
- RgroupOrphanAttachmentErrorChecker - Class in chemaxon.checkers
-
- RgroupOrphanAttachmentErrorChecker() - Constructor for class chemaxon.checkers.RgroupOrphanAttachmentErrorChecker
-
Creates a new RgroupAttachmentErrorChecker instance.
- RgroupReferenceErrorChecker - Class in chemaxon.checkers
-
Deprecated.
- RgroupReferenceErrorChecker() - Constructor for class chemaxon.checkers.RgroupReferenceErrorChecker
-
Deprecated.
Creates a new RgroupReferenceErrorChecker instance checking all R-group
errors by default.
- RgroupReferenceErrorChecker(Map<String, String>) - Constructor for class chemaxon.checkers.RgroupReferenceErrorChecker
-
Deprecated.
Creates a new RgroupRefereceErrorChecker instance reading checking
options from the params argument.
- RgroupReferenceFixer - Class in chemaxon.fixers
-
- RgroupReferenceFixer() - Constructor for class chemaxon.fixers.RgroupReferenceFixer
-
Deprecated.
- RGROUPS_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
R-group definitions visible flag.
- Rh - Static variable in class chemaxon.core.ChemConst
-
- Ring - Class in chemaxon.calculations
-
The ring class provides information of the ring types in a molecule.
- Ring() - Constructor for class chemaxon.calculations.Ring
-
- ringAtomCount() - Method in class chemaxon.calculations.Ring
-
Calculates the number of ring atoms in the molecule.
- ringAtomCount() - Method in class chemaxon.calculations.TopologyAnalyser
-
- ringBondCount() - Method in class chemaxon.calculations.Ring
-
Calculates the number of ring bonds in the molecule.
- ringBondCount() - Method in class chemaxon.calculations.TopologyAnalyser
-
- ringCount() - Method in class chemaxon.calculations.Ring
-
Calculates the number of rings (SSSR smallest set of smallest rings) in
the molecule.
- ringCount(int) - Method in class chemaxon.calculations.Ring
-
Calculates the number of rings (SSSR smallest set of smallest rings) of a
given size in the molecule.
- ringCount() - Method in class chemaxon.calculations.TopologyAnalyser
-
- ringCount(int) - Method in class chemaxon.calculations.TopologyAnalyser
-
- ringCountOfAtom(int) - Method in class chemaxon.calculations.Ring
-
Calculates the number of rings (SSSR smallest set of smallest rings) an
atom is part of.
- ringCountOfAtom(int) - Method in class chemaxon.calculations.TopologyAnalyser
-
- ringHasOnlyOneNeighbour(int[], Molecule, MolAtom) - Static method in class chemaxon.checkers.StructureCheckerHelper
-
This function determines if the ring (indexed with idx parameter) has
only one neighbour (and this neighbour is the the atom parameter) or not.
- rings() - Method in class chemaxon.calculations.Ring
-
Identifies the rings in the molecule.
- rings(int) - Method in class chemaxon.calculations.Ring
-
Identifies rings in the molecule having a given size.
- rings() - Method in class chemaxon.calculations.TopologyAnalyser
-
- rings(int) - Method in class chemaxon.calculations.TopologyAnalyser
-
- RingStrainErrorChecker - Class in chemaxon.checkers
-
RingStrainErrorChecker detects triple bonds, trans or cumulated double bonds small rings
containing less than 8 atoms.
- RingStrainErrorChecker() - Constructor for class chemaxon.checkers.RingStrainErrorChecker
-
Default constructor
- RingStrainErrorChecker(Map<String, String>) - Constructor for class chemaxon.checkers.RingStrainErrorChecker
-
Parameterized constructor.
If params contains "transDoubleBond"/"cumulatedDoubleBond"/"tripelBond" key with
value "true" then trans double bonds/cummulated double bonds/triple bonds will be
checked.
- ringSystemCount() - Method in class chemaxon.calculations.Ring
-
Calculates the number of ring systems.
- ringSystemCount(int) - Method in class chemaxon.calculations.Ring
-
Identifies ring systems having a given size (number of rings) in the
molecule.
- ringSystemCount() - Method in class chemaxon.calculations.TopologyAnalyser
-
- ringSystemCount(int) - Method in class chemaxon.calculations.TopologyAnalyser
-
- ringSystems() - Method in class chemaxon.calculations.Ring
-
Identifies the ring systems in the molecule.
- ringSystems(int) - Method in class chemaxon.calculations.Ring
-
Indentifies the ring systems in the molecule having a given size (number
of rings).
- ringSystems() - Method in class chemaxon.calculations.TopologyAnalyser
-
- ringSystems(int) - Method in class chemaxon.calculations.TopologyAnalyser
-
- RLOGIC_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
R-Logic visibility flag.
- RLOGIC_VISIBLE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter: "RLogicVisible" or "RLogic".
- rm - Variable in class chemaxon.marvin.space.GraphicComponent
-
Rotation matrix as a GeomCalc matrix.
- RM_KEEP_LEAVINGGROUPS - Static variable in class chemaxon.struc.Molecule
-
Deprecated.
As of Marvin 6.2, no replacement.
Not supported feature.
- RMCLEANUP_ALL - Static variable in class chemaxon.struc.MoleculeGraph
-
Perform all clean-up methods when removing an atom or a bond.
- RMCLEANUP_EDGES - Static variable in class chemaxon.struc.MoleculeGraph
-
When removing an atom or a bond, also remove the bond(s) from the atom
object(s).
- RMCLEANUP_FIXCOMPONENT - Static variable in class chemaxon.struc.MoleculeGraph
-
Remove called from RxnMolecule.fixComponent.
- RMCLEANUP_FROMSGROUPS - Static variable in class chemaxon.struc.Molecule
-
Remove atoms from S-groups.
- RMCLEANUP_MOBJECT - Static variable in class chemaxon.struc.MoleculeGraph
-
Remove graphics objects containing the removed atom.
- RMCLEANUP_NONE - Static variable in class chemaxon.struc.MoleculeGraph
-
Do not perform any clean-up methods when removing an atom or a bond.
- RMCLEANUP_PARENTDOC - Static variable in class chemaxon.struc.MoleculeGraph
-
Remove atom from parent document.
- RMCLEANUP_SGROUPATOMS - Static variable in class chemaxon.struc.Molecule
-
Remove S-groups of removed superatoms.
- RMCLEANUP_STEREO - Static variable in class chemaxon.struc.MoleculeGraph
-
When removing a H atom, keep stereo information unchanged.
- rmsd() - Method in class chemaxon.marvin.alignment.AlignRigidEasy
-
calculates the rmsd value
- RMSG_DEFAULT - Static variable in class chemaxon.struc.Molecule
-
Remove S-group's children and remove S-group from its parent.
- RMSG_KEEP_CHILDREN - Static variable in class chemaxon.struc.Molecule
-
Do not remove S-group's children.
- RMSG_KEEP_MULTICENTER - Static variable in class chemaxon.struc.Molecule
-
Do not remove central atom of multicenter S-groups.
- RMSG_KEEP_PARENT - Static variable in class chemaxon.struc.Molecule
-
Do not remove S-group from its parent.
- Rn - Static variable in class chemaxon.core.ChemConst
-
- RNA - Static variable in class chemaxon.formats.MFileFormat
-
RNA sequence.
- rotatableBondCount() - Method in class chemaxon.calculations.TopologyAnalyser
-
Calculates the number of rotatable bonds in the molecule.
- RotatableBondDetector - Class in chemaxon.marvin.alignment
-
- RotatableBondDetector(Molecule, boolean) - Constructor for class chemaxon.marvin.alignment.RotatableBondDetector
-
- rotate(double, double, double) - Method in class chemaxon.marvin.space.GraphicCell
-
- rotate(float[], float[]) - Method in class chemaxon.marvin.space.GraphicComponent
-
Rotates the component by changing its coordinates, and not just the view.
- rotate(float[], float[], float[]) - Method in class chemaxon.marvin.space.GraphicComponent
-
Rotates the given p point by changing its coordinates.
- rotate(int, float[], float[]) - Method in class chemaxon.marvin.space.GraphicComponent
-
Rotates the given p point by changing its coordinates.
- rotate(double, double, double) - Method in class chemaxon.marvin.space.GraphicScene
-
Sets the given rotation factor in the active cell or in every cells
in case of synchronous mode.
- rotate(float[], float[]) - Method in class chemaxon.marvin.space.MacroMoleculeComponent
-
Rotates its selected ligand by changing its coordinates, and not just the view.
- rotate(float[], float[]) - Method in class chemaxon.marvin.space.MoleculeComponent
-
Rotates the molecule with parameter center as an origin.
- rotate(float[], float[]) - Method in class chemaxon.marvin.space.PharmacophoreArrow
-
Rotates the component around the 3 axis, x, y, z, and given center.
- rotate(DPoint3, double, DPoint3) - Static method in class chemaxon.struc.graphics.MPolyline
-
- rotateBy(double, int, int, int, int) - Method in class chemaxon.marvin.alignment.DihedralRotator
-
Rotates the selected dihedral by the defined angle
- rotateTo(double, int, int, int, int) - Method in class chemaxon.marvin.alignment.DihedralRotator
-
Sets the dihedral defined by the atoms a1-a4 to the angle
- rotateTo(float[]) - Method in class chemaxon.marvin.space.GraphicScene
-
Sets the matrix of rotation explicitly in the active cell or in every cells
in case of synchronous mode.
- ROWS - Static variable in class chemaxon.marvin.view.ViewParameterConstants
-
Identifier of parameter: "rows".
- RS_ALL - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
R/S shown always.
- RS_ALL_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
R/S shown always.
- RS_MASK - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Chirality support mask in display option flags.
- RS_OFF - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
R/S not shown.
- RS_OFF_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
R/S not shown.
- RS_OFFSET - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Chirality support offset in display option flags.
- RS_OPTIONS - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Array of chirality support levels.
- RS_SELECTED - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
R/S shown only if chiral flag is set in molecule or the atom's enhanced stereo type is
absolute.
- RS_SELECTED_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
R/S shown only if chiral flag is set in molecule or the atom's enhanced stereo type is
absolute.
- Ru - Static variable in class chemaxon.core.ChemConst
-
- run(String[]) - Method in class chemaxon.checkers.StructureCheck
-
This method runs the command line parameterized by the args array of
String
- run() - Method in class chemaxon.marvin.calculations.AlignmentPlugin
-
- run() - Method in class chemaxon.marvin.calculations.ChargePlugin
-
Runs the charge calculation.
- run() - Method in class chemaxon.marvin.calculations.ConformerPlugin
-
Runs the conformer calculation.
- run() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
-
Runs the tool.
- run() - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
Runs the tool.
- run() - Method in class chemaxon.marvin.calculations.HBDAPlugin
-
Runs the charge calculation.
- run() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
-
Runs the Huckel analysis calculation.
- run() - Method in class chemaxon.marvin.calculations.IonChargePlugin
-
Runs the charge calculation on the microspecies with sufficiently large distribution
on the given pH.
- run() - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
-
Runs the isoelectric point and charge distribution calculations.
- run() - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
-
Runs the tool.
- run() - Method in class chemaxon.marvin.calculations.logDPlugin
-
Runs the logD calculation.
- run() - Method in class chemaxon.marvin.calculations.logPPlugin
-
Runs the logP calculation.
- run() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
-
Stores the input molecule with ungrouped sgroups.
- run() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Creates enumerated structures.
- run() - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
-
Runs the tool.
- run() - Method in class chemaxon.marvin.calculations.MSAPlugin
-
Runs the surface area calculation.
- run() - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
-
Runs the orbital electornegativity calculation.
- run() - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Runs the macro pKa calculation.
- run() - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
-
Runs the charge calculation.
- run() - Method in class chemaxon.marvin.calculations.RefractivityPlugin
-
Runs the refractivity calculation.
- run() - Method in class chemaxon.marvin.calculations.ResonancePlugin
-
Calculates the resonant structures.
- run() - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
-
Runs the plugin.
- run() - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
-
Run calculation
- run() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Calculates the tautomers.
- run() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Runs the tool.
- run() - Method in class chemaxon.marvin.calculations.TPSAPlugin
-
Runs the surface area calculation.
- run() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Runs the tool.
- runScript(String) - Method in class chemaxon.jep.Evaluator
-
Runs a script, variables will be added to the base variable table
and can be referenced by chemical expressions.
- RXN - Static variable in class chemaxon.formats.MFileFormat
-
MDL Rxnfiles.
- RXN_V3_OUT - Static variable in class chemaxon.formats.MFileFormat
-
MDL Extended Rxnfiles.
- RxnMolecule - Class in chemaxon.struc
-
Reaction.
- RxnMolecule() - Constructor for class chemaxon.struc.RxnMolecule
-
Create a reaction.
- RXNSTEREO_INVERSION - Static variable in class chemaxon.struc.MolAtom
-
The stereo configuration of the atom is inverted during the reaction.
- RXNSTEREO_NONE - Static variable in class chemaxon.struc.MolAtom
-
The stereo configuration of the atom is not considered during the
reaction.
- RXNSTEREO_RETENTION - Static variable in class chemaxon.struc.MolAtom
-
The stereo configuration of the atom is retained during the reaction.
- S - Static variable in class chemaxon.core.ChemConst
-
- save(String) - Method in class chemaxon.marvin.common.UserSettings
-
Save the persistent properties to the config file set by the constructor.
- save(String, String) - Method in class chemaxon.marvin.common.UserSettings
-
Save the persistent properties to the file given as the first parameter.
- SAVE_PROPERTIES - Static variable in class chemaxon.marvin.common.ParameterConstants
-
- saveAsMacro() - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Shows the modal macro manager dialog, setting current selection as new macro
- saveCache(int) - Method in class chemaxon.struc.MoleculeGraph
-
Saves caches like connection table, bond table, etc.
- saveCoords(MoleculeGraph, double[]) - Static method in class chemaxon.marvin.util.CleanUtil
-
Saves atomic coordinates.
- saveParameters() - Method in class chemaxon.marvin.plugin.gui.ParameterPanel
-
Saves parameters from parameter panel.
- saveParameters() - Method in interface chemaxon.marvin.plugin.ParameterPanelHandler
-
Saves parameters from parameter panel.
- saveParameterSettings() - Method in class chemaxon.marvin.plugin.PluginFactory.PluginRecord
-
- saveParameterSettings() - Method in class chemaxon.marvin.plugin.PluginFactory
-
Saves plugin parameter settings to file
$HOME/chemaxon/<plugin class name>Parameters.properties (Windows), or
$HOME/.chemaxon/<plugin class name>Parameters.properties (UNIX / Linux).
- Sb - Static variable in class chemaxon.core.ChemConst
-
- Sc - Static variable in class chemaxon.core.ChemConst
-
- scalar(DPoint3, DPoint3) - Static method in class chemaxon.struc.DPoint3
-
Calculates the scalar product of the two vectors
- SCALE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter: "scale".
- scale - Variable in class chemaxon.marvin.util.MolImageSize
-
Deprecated.
- scale(double) - Method in class chemaxon.struc.DPoint3
-
Scales the vector with the given factor.
- SCALED_BALLS - Static variable in class chemaxon.marvin.space.MoleculeComponent
-
- scaledBalls - Variable in class chemaxon.marvin.space.MoleculeComponent
-
- SCENE_RANGE - Static variable in class chemaxon.marvin.space.GraphicScene
-
- scheduler - Variable in class chemaxon.marvin.view.swing.TableSupport
-
Record access task scheduler.
- SCN_EITHER_UNKNOWN - Static variable in class chemaxon.struc.Sgroup
-
Either unknown S-group connectivity.
- SCN_HEAD_TO_HEAD - Static variable in class chemaxon.struc.Sgroup
-
Head-to-head S-group connectivity.
- SCN_HEAD_TO_TAIL - Static variable in class chemaxon.struc.Sgroup
-
Head-to-tail S-group connectivity.
- SCREEN - Static variable in class chemaxon.license.LicenseManager
-
Identifier of product: Screen
- SCREEN3D - Static variable in class chemaxon.license.LicenseManager
-
Identifier of product: 3D Screen
- SCRIPT - Static variable in class chemaxon.marvin.view.ViewParameterConstants
-
Identifier of parameter: "script".
- SDF - Static variable in class chemaxon.formats.MdlCompressor
-
- SDF - Static variable in class chemaxon.formats.MFileFormat
-
MDL SDfiles.
- Se - Static variable in class chemaxon.core.ChemConst
-
- secondaryAtomIndexes() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AtomSelection
-
Deprecated.
- secondaryBonds - Variable in class chemaxon.util.iterator.IteratorFactory.BondIterator
-
Secondary bonds that replace a coordinate bond to the multicenter
with coordinate bonds from the metal to the represented atoms (in the
MulticenterSgroup of the multicenter).
- secondaryBonds - Variable in class chemaxon.util.iterator.IteratorFactory.NeighbourIterator
-
Secondary bonds that replace a coordinate bond to the multicenter
with coordinate bonds from the metal to the represented atoms (in the
MulticenterSgroup of the multicenter).
- SECTION - Static variable in class chemaxon.naming.DocumentToStructure
-
The section of the document where the structure was found.
- seek(long, int, int) - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
-
Sets the file-pointer offset, measured from the beginning of this
file, at which the next read or write occurs.
- seek(long, int, int) - Method in class chemaxon.marvin.io.MRecordImporter
-
Sets the file-pointer offset, measured from the beginning of this
file, at which the next read or write occurs.
- seek(long, int, int) - Method in interface chemaxon.marvin.io.MRecordReader
-
Sets the file-pointer offset, measured from the beginning of this
file, at which the next read or write occurs.
- seek(long, int) - Method in class chemaxon.marvin.io.PositionedInputStream
-
Sets the file-pointer offset, measured from the beginning of this
file, at which the next read or write occurs.
- seekForward(int, MProgressMonitor, int, Runnable) - Method in class chemaxon.marvin.io.MDocSource
-
Seeks in forward direction.
- seekRecord(int, MProgressMonitor) - Method in class chemaxon.formats.MolImporter
-
Seek the specified record.
- seekRecord(int, MProgressMonitor) - Method in class chemaxon.marvin.io.ArrayMDocSource
-
Seeks the specified record.
- seekRecord(int, MProgressMonitor) - Method in class chemaxon.marvin.io.MDocSource
-
Seeks the specified record.
- seekRecordAtFraction(double, int, int, int, MProgressMonitor) - Method in class chemaxon.marvin.io.MDocSource
-
Seeks an approximate file position.
- seekVisitedRecord(int) - Method in class chemaxon.formats.MolImporter
-
Seeks an already visited position in case of rewindable input.
- seekVisitedRecord(int) - Method in class chemaxon.marvin.io.ArrayMDocSource
-
Seeks an already visited position in case of rewindable input.
- seekVisitedRecord(int) - Method in class chemaxon.marvin.io.MDocSource
-
Seeks an already visited position in case of rewindable input.
- select() - Method in class chemaxon.marvin.space.GraphicComponent
-
Sets the component to be selected.
- select(ComponentElement) - Method in class chemaxon.marvin.space.GraphicComponent
-
Sets the specific part of the component to be selected.
- select() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- select() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
-
Sets all visualizers to be selected.
- select() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- select() - Method in class chemaxon.marvin.space.MoleculeComponent
-
Sets the whole component to be selected.
- select() - Method in class chemaxon.marvin.space.monitor.DihedralMonitor
-
When the monitor is selected, a DihedralControl is created or changes
its direction if it was alredy created.
- select() - Method in class chemaxon.marvin.space.monitor.Label
-
The color of the label changes by selection.
- select() - Method in class chemaxon.marvin.space.PharmacophoreArrow
-
Sets the component to be selected.
- select() - Method in class chemaxon.marvin.space.PharmacophorePoint
-
Sets the component to be selected.
- SELECTABLE - Static variable in class chemaxon.marvin.view.ViewParameterConstants
-
Identifier of parameter: "selectable".
- selectAllAtoms() - Method in class chemaxon.marvin.space.MoleculeComponent
-
Sets all atoms to be selected.
- selectAllConnectedObjects(boolean) - Method in class chemaxon.struc.MDocument
-
Selects or unselects all objects in this document and objects that belong to the
chemical structure of this document.
- selectAllObjects(boolean) - Method in class chemaxon.struc.MDocument
-
Selects or unselects all objects.
- selectAllObjects(boolean) - Method in class chemaxon.struc.Molecule
-
- selectAllObjects(boolean) - Method in class chemaxon.struc.RgMolecule
-
- selectAllObjects(boolean) - Method in class chemaxon.struc.RxnMolecule
-
- selectAllObjects(boolean) - Method in class chemaxon.struc.Sgroup
-
Sets the selection state of the MObject-s that belong to this Sgroup.
- selectAtom(int) - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- selectAtom(int) - Method in class chemaxon.marvin.space.MoleculeComponent
-
Sets the atom with the given index to be selected.
- selectComponentElementsInside(BoundingBox) - Method in class chemaxon.marvin.space.GraphicCell
-
Sets all components lying inside the given box to be selected.
- selectComponentElementsInside(BoundingBox) - Method in class chemaxon.marvin.space.GraphicComponent
-
The component will be selected if it is inside the given box.
- selectComponentElementsInside(BoundingBox) - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- selectComponentElementsInside(BoundingBox) - Method in class chemaxon.marvin.space.MacroMoleculeComponent
-
Visualizers lying in the given box will be selected.
- selectComponentElementsInside(BoundingBox) - Method in class chemaxon.marvin.space.MoleculeComponent
-
Atoms lying in the given box will be selected.
- SELECTED_INDEX - Static variable in class chemaxon.marvin.view.ViewParameterConstants
-
Identifier of parameter: "selectedIndex".
- selectedAtomCount() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- selectedAtomCount() - Method in class chemaxon.marvin.space.MoleculeComponent
-
Returns the number of atoms being selected.
- selectedAtoms - Variable in class chemaxon.marvin.space.MoleculeComponent
-
- selectedItemCoordinates - Variable in class chemaxon.marvin.space.monitor.Monitor
-
- selectedItems - Variable in class chemaxon.marvin.space.monitor.Monitor
-
Storage of the items of monitoring.
- SELECTION - Static variable in class chemaxon.marvin.view.ViewParameterConstants
-
Identifier of parameter: "selection".
- selectionBar - Variable in class chemaxon.marvin.space.MSpaceEasy
-
- selectionBeforeInit - Variable in class chemaxon.marvin.space.MoleculeComponent
-
- SelectionMolecule - Class in chemaxon.struc
-
A selection object which can contain atoms and bonds without real parent relationship
(the real parent of atoms and bonds is another MoleculeGraph ancestor).
- SelectionMolecule() - Constructor for class chemaxon.struc.SelectionMolecule
-
- selectionPointer - Variable in class chemaxon.marvin.space.monitor.Monitor
-
Points to the next empty space in selectedItems.
- selectItem(ComponentElement) - Method in class chemaxon.marvin.space.monitor.Label
-
Parameter item will be the selected item of the monitor.
- selectItem(GraphicComponent) - Method in class chemaxon.marvin.space.monitor.Label
-
The given component will be the selected item of the Label.
- selectItem(ComponentElement) - Method in class chemaxon.marvin.space.monitor.MeasurementMonitor
-
Puts the item to the selection and clears its description.
- selectItem(ComponentElement) - Method in class chemaxon.marvin.space.monitor.Monitor
-
Puts item to the selection.
- selectItem(ComponentElement) - Method in class chemaxon.marvin.space.monitor.PositionMonitor
-
Parameter item will be the selected item of the monitor.
- selectItem(GraphicComponent) - Method in class chemaxon.marvin.space.monitor.PositionMonitor
-
The given component will be the selected item of the monitor.
- separator - Variable in class chemaxon.marvin.plugin.CalculatorPluginOutput
-
The separator string separating the results for different result types.
- SEPARATOR - Static variable in class chemaxon.marvin.plugin.PluginFactory
-
Menuitem separator in Tools menu:
if present then separator will be added to the Tools menu after the plugin menuitem.
- SERVICE - Static variable in class chemaxon.marvin.services.soap.SoapServiceDescriptor
-
Property key for service name as
String
- SERVICE_CONFIGURATION_PATH_PROPERTY_KEY - Static variable in class chemaxon.marvin.services.ServiceDescriptorTools
-
Java System Property key to globally override default configuration path.
- SERVICE_DIALOG_PROVIDER_CLASS_NAME_PROPERTY_KEY - Static variable in class chemaxon.marvin.services.ServiceDescriptorTools
-
Java System Property key to globally override default Service Dialog Provider class with custom implementation.
- ServiceArgument<T> - Class in chemaxon.marvin.services
-
Describes an argument passed to services
- ServiceArgument(Class<T>, T) - Constructor for class chemaxon.marvin.services.ServiceArgument
-
Constructs a service argument with specified type and value
- ServiceArgument(Class<T>, T, boolean) - Constructor for class chemaxon.marvin.services.ServiceArgument
-
Constructs a service argument with specified type and value
- ServiceDescriptorEditor<T extends chemaxon.marvin.services.ServiceDescriptor> - Interface in chemaxon.marvin.services
-
Provides editor suport for ServiceDescriptor
- ServiceDescriptorEditorProvider - Interface in chemaxon.marvin.services
-
- ServiceDescriptorReader - Interface in chemaxon.marvin.services
-
Reader for ServiceDescriptors
- ServiceDescriptorTools - Class in chemaxon.marvin.services
-
- ServiceDescriptorTools() - Constructor for class chemaxon.marvin.services.ServiceDescriptorTools
-
- ServiceDescriptorWriter - Interface in chemaxon.marvin.services
-
Writer for ServiceDescriptors
- ServiceDialogProvider - Interface in chemaxon.marvin.services
-
Provides
Dialog instances to provide argument editor and result view for
ServiceDescriptor
- ServiceException - Exception in chemaxon.marvin.services
-
Exception for failure indication for services.
- ServiceException(String, Throwable) - Constructor for exception chemaxon.marvin.services.ServiceException
-
- ServiceException(String) - Constructor for exception chemaxon.marvin.services.ServiceException
-
- ServiceException(Throwable) - Constructor for exception chemaxon.marvin.services.ServiceException
-
- ServiceHandler<DT extends chemaxon.marvin.services.ServiceDescriptor> - Class in chemaxon.marvin.services
-
Manages service calls.
- ServiceHandler() - Constructor for class chemaxon.marvin.services.ServiceHandler
-
- set(float, float, float, float, float, float) - Method in class chemaxon.marvin.space.BoundingBox
-
Sets the minimum and maximum coordinates of the box.
- set(CTransform3D) - Method in class chemaxon.struc.CTransform3D
-
Copy.
- set(DPoint3) - Method in class chemaxon.struc.DPoint3
-
Set coordinates.
- set(MolAtom) - Method in class chemaxon.struc.MolAtom
-
Set all atom properties except the coordinates.
- set(String, MProp) - Method in class chemaxon.struc.MPropertyContainer
-
Sets a property object.
- set(String, MProp, int) - Method in class chemaxon.struc.MPropertyContainer
-
Sets a property object.
- set(int, MProp) - Method in class chemaxon.struc.prop.MListProp
-
Sets an element.
- set(MolAtom) - Method in class chemaxon.struc.sgroup.SgroupAtom
-
Set properties of this S-group superatom.
- SET_COLORING_ENABLED - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter: "setColoringEnabled".
- SET_SCHEME_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Set coloring flag in display options.
- setAbsoluteLabelsVisible(boolean) - Method in class chemaxon.marvin.MolPrinter
-
Set 'Absolute' label visibility.
- setAbsoluteLabelVisible(String) - Method in class chemaxon.marvin.common.UserSettings
-
Show or hide Abolute labels
- setAbsolutePlacement(boolean) - Method in class chemaxon.struc.sgroup.DataSgroup
-
Sets whether the placement of this attached data is absolute or relative
to the objects it is attached.
- setAbsoluteXY(DPoint3) - Method in class chemaxon.struc.sgroup.DataSgroup
-
Sets the X and Y coordinates of the data label in the molecule's
coordinate system, considering absolute/relative placement.
- setAbsoluteXY(double, double) - Method in class chemaxon.struc.sgroup.DataSgroup
-
Sets the X and Y coordinates of the data label in the molecule's
coordinate system, considering absolute/relative placement.
- setAbsStereo(boolean) - Method in class chemaxon.struc.MoleculeGraph
-
Sets the absolute stereoconfiguration flag.
- setAbsStereo(boolean) - Method in class chemaxon.struc.RgMolecule
-
Sets the absolute stereoconfiguration flag for the root structure and
the R-groups.
- setAbsStereo(boolean) - Method in class chemaxon.struc.RxnMolecule
-
Sets the absolute stereoconfiguration flag for all the structures.
- setAcceptor(boolean) - Method in class chemaxon.marvin.space.PharmacophorePoint
-
Sets or clears the acceptor property of the PharmacophorePoint.
- setAccuracyMode(AlignmentAccuracyMode) - Method in class chemaxon.marvin.calculations.AlignmentPlugin
-
- setAcidicpKaUpperLimit(double) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Sets the maximum acidic pKa (default: 20).
- setActionB(int, String) - Method in class chemaxon.marvin.beans.MViewPane
-
Sets the action string (URL or JavaScript expression) of a button in a GridBagView table.
- setActionC(int, String) - Method in class chemaxon.marvin.beans.MViewPane
-
Sets one of the two action strings (JavaScript expressions) of a checkbox in a GridBagView
table.
- setActionMap(ActionMap) - Method in class chemaxon.struc.graphics.MTextBox
-
Sets the ActionMap to map.
- setActionsEnabled(boolean) - Method in class chemaxon.marvin.plugin.gui.OptionsPane
-
Enables / disables action buttons.
- setActionStringTokens(String[]) - Method in class chemaxon.checkers.StructureCheckerDescriptor
-
Sets the action string token of the checker
- setActionStringTokens(String[]) - Method in class chemaxon.fixers.StructureFixerDescriptor
-
Sets the action string token of the fixer
- setActive() - Method in class chemaxon.marvin.space.GraphicCell
-
Sets this cell to the active cell of the scene.
- setActiveCell(int) - Method in class chemaxon.marvin.space.GraphicScene
-
Sets the ith cell to be the active cell of the scene.
- setAddServices(boolean) - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
-
Sets the services display
- setAdvancedSave(boolean) - Method in class chemaxon.marvin.common.UserSettings
-
Sets wether the user prefers advanced svae or not.
- setAlias(String) - Method in class chemaxon.marvin.services.ServiceArgument
-
Sets the argument alias.
- setAliasstr(String) - Method in class chemaxon.struc.MolAtom
-
Sets the alias string or pseudo atom type string for pseudo atoms.
- setAlignmentMode(int) - Method in class chemaxon.util.HitColoringAndAlignmentOptions
-
Sets the alignment mode.
- setAlignScaffold(boolean) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Sets the scaffold aligning mode.
- setAllowTraditionalNitrogen(boolean) - Method in class chemaxon.checkers.ValenceErrorChecker
-
Sets if the checker should allow traditional N representation
- setAminoAcidBondColoringEnabled(boolean) - Method in class chemaxon.marvin.common.UserSettings
-
Sets wether the user uses peptide bridge coloring or not.
- setAminoAcidBondColoringEnabled(boolean) - Method in class chemaxon.marvin.MolPrinter
-
Sets peptide bridge coloring enabled.
- setAnimated(boolean) - Method in class chemaxon.marvin.beans.MViewPane
-
Starts or stops animation in each cells of the table or in the simple viewer.
- setAnimated(int, boolean) - Method in class chemaxon.marvin.beans.MViewPane
-
Sets animation of a cell of the table.
- setAnimDelay(double) - Method in class chemaxon.marvin.beans.MViewPane
-
Sets the repeat delay for animations.
- setAnimFPS(double) - Method in class chemaxon.marvin.beans.MViewPane
-
Sets the frames per second for animations.
- setAnimSync(boolean) - Method in class chemaxon.marvin.beans.MViewPane
-
Sets the animation synchronization.
- setAnionic(boolean) - Method in class chemaxon.marvin.space.PharmacophorePoint
-
Sets or clears the anionic property of the PharmacophorePoint.
- setAntialias(boolean) - Method in class chemaxon.marvin.space.GraphicCell
-
Switches the full scene anti-aliasing on/off.
- setAntialias(boolean) - Method in class chemaxon.marvin.space.GraphicScene
-
Enables/disables full scene anti-aliasing.
- setAnyBondStyles(String) - Method in class chemaxon.marvin.MolPrinter
-
Sets the any bond style.
- setArcAngle(double) - Method in class chemaxon.struc.graphics.MPolyline
-
Sets the central angle of the arc.
- setArcHeight(double) - Method in class chemaxon.struc.graphics.MRoundedRectangle
-
- setArcWidth(double) - Method in class chemaxon.struc.graphics.MRoundedRectangle
-
- setAromatic(boolean) - Method in class chemaxon.marvin.space.PharmacophorePoint
-
Sets or clears the aromatic property of the PharmacophorePoint.
- setAromaticityChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker
-
Sets the option determining if the checker detects aromaticity atom query
properties or not.
- setAromatizationMethod(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Sets the aromatization method.
- setAromatize(boolean) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
-
Deprecated.
The original input structure is not aromatized. No need to
use.
- setAromatizeMethod(int) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the aromatize method.
- setArrow(boolean) - Method in class chemaxon.struc.graphics.MPolyline
-
Sets or unsets arrow mode.
- setArrowFlags(int, int) - Method in class chemaxon.struc.graphics.MPolyline
-
Sets the flags.
- setArrowLength(int, double) - Method in class chemaxon.struc.graphics.MPolyline
-
Sets the arrow head length.
- setArrowWidth(int, double) - Method in class chemaxon.struc.graphics.MPolyline
-
Sets the arrow head width.
- setAssigned(int, boolean) - Method in class chemaxon.marvin.alignment.AlignmentMolecule
-
- setAtno(int) - Method in class chemaxon.struc.MolAtom
-
Sets the atomic number.
- setAtom(int) - Method in class chemaxon.jep.context.AtomContext
-
Sets the input atom.
- setAtom(int, MolAtom) - Method in class chemaxon.struc.MoleculeGraph
-
- setAtom(int, MolAtom) - Method in class chemaxon.struc.RgMolecule
-
- setAtom(int, MolAtom) - Method in class chemaxon.struc.RxnMolecule
-
- setAtom(int, MolAtom) - Method in class chemaxon.struc.sgroup.MultipleSgroup
-
Sets the specified atom in the S-group graph.
- setAtom(int, MolAtom) - Method in class chemaxon.struc.Sgroup
-
Sets the specified atom in the S-group graph.
- setAtom(int, MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Sets the specified atom in the S-group graph.
- setAtom0(int, MolAtom) - Method in class chemaxon.struc.Molecule
-
Sets the atom at the specified index.
- setAtom0(int, MolAtom) - Method in class chemaxon.struc.MoleculeGraph
-
Sets the atom at the specified index.
- setAtom0(int, MolAtom) - Method in class chemaxon.struc.SelectionMolecule
-
Sets the atom at the specified index.
- setAtom1(int) - Method in class chemaxon.marvin.alignment.MinMaxDistance
-
- setAtom1(MolBond, MolAtom) - Static method in class chemaxon.struc.MolAtom
-
Sets the first atom of a bond.
- setAtom1(MolBond, MolAtom) - Static method in class chemaxon.struc.sgroup.SgroupAtom
-
Sets the first node of an edge.
- setAtom2(int) - Method in class chemaxon.marvin.alignment.MinMaxDistance
-
- setAtom2(MolBond, MolAtom) - Static method in class chemaxon.struc.MolAtom
-
Sets the second atom of a bond.
- setAtom2(MolBond, MolAtom) - Static method in class chemaxon.struc.sgroup.SgroupAtom
-
Sets the second node of an edge.
- setAtomFont(Font) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the atom symbol font name.
- setAtomIndexMap(int[]) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
- setAtomMap(int) - Method in class chemaxon.struc.MolAtom
-
Sets the atom-atom mapping number.
- setAtomMap(int, int) - Method in interface chemaxon.struc.WSmolecule
-
Sets the atom-atom mapping number.
- setAtomMappingMethod(int) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the atom mapping method.
- setAtomMappingVisible(boolean) - Method in class chemaxon.marvin.beans.MarvinPane
-
Shows or hides the atom mapping.
- setAtomMappingVisible(boolean) - Method in class chemaxon.marvin.MolPrinter
-
Sets the atom mapping visibility.
- setAtomNumberingType(int) - Method in class chemaxon.marvin.beans.MarvinPane
-
Sets the atom numbering.
- setAtomNumberingType(int) - Method in class chemaxon.marvin.MolPrinter
-
sets atom numbering type.
- setAtomNumbersVisible(boolean) - Method in class chemaxon.marvin.beans.MarvinPane
-
Deprecated.
in 6.2.0. Use setAtomNumberingType() instead
- setAtomNumbersVisible(boolean) - Method in class chemaxon.marvin.MolPrinter
-
Deprecated.
in 6.2.0. Use setAtomNumberingType() instead.
- setAtomPropertiesVisible(boolean) - Method in class chemaxon.marvin.common.UserSettings
-
Sets atom properties visibility.
- setAtomPropertiesVisible(boolean) - Method in class chemaxon.marvin.MolPrinter
-
Set the atom properties visibility
- setAtomPropertyList(ArrayList) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
Sets a list of atomic properties that can be mapped as coloring on the surface.
- setAtomRadiusExtension(float) - Method in class chemaxon.marvin.space.SurfaceColoring
-
In case of {#RADIUS_VDW_EXTENDED} mode the extension can be set.
- setAtoms(List<MolAtom>) - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
-
- setAtoms(List<MolAtom>) - Method in interface chemaxon.checkers.result.StructureCheckerResult
-
This method sets the atoms property
- setAtoms(int, int) - Method in class chemaxon.marvin.space.monitor.DihedralControl
-
Sets 2 atoms as the 2 end of the torsion bond.
- setAtoms(MolAtom[]) - Method in class chemaxon.struc.graphics.MAtomSetPoint
-
Sets the atoms.
- setAtomSetColor(int, Color) - Method in class chemaxon.marvin.beans.MarvinPane
-
Sets the color of an atom set.
- setAtomSetColorMode(int, int) - Method in class chemaxon.struc.MDocument
-
Sets the atom set coloring mode.
- setAtomSetFont(int, MFont) - Method in class chemaxon.struc.MDocument
-
Sets the font of an atom set.
- setAtomSetRGB(int, int) - Method in class chemaxon.struc.MDocument
-
Sets the color of an atom set.
- setAtomSetSeq(int, int, int) - Method in class chemaxon.marvin.beans.MViewPane
-
Sets the set sequence number of the atom.
- setAtomSetSeq(int, String, String, int) - Method in class chemaxon.marvin.view.MDocStorage
-
Sets atom set sequence numbers.
- setAtomSetSeq(int, String, int, int) - Method in class chemaxon.marvin.view.MDocStorage
-
Sets the atom set sequence number of an atom.
- setAtomSetSeqs(int, String, int[]) - Method in class chemaxon.marvin.view.MDocStorage
-
Sets atom set sequence numbers.
- setAtomSetSeqs(int) - Method in class chemaxon.struc.MoleculeGraph
-
Sets the set sequence number of all atoms.
- setAtomsize(double) - Method in class chemaxon.marvin.beans.MarvinPane
-
Sets the atom size.
- setAtomSize(double) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the atom size in C-C bond length units.
- setAtomsize(double) - Method in class chemaxon.marvin.MolPrinter
-
- setAtomSize(double) - Method in class chemaxon.marvin.MolPrinter
-
Sets the size of displayed atoms in units of regular bond length.
- setAtomStereo(int, int) - Method in interface chemaxon.struc.WSmolecule
-
Sets atom stereo properties.
- setAtomSymbolsVisible(boolean) - Method in class chemaxon.marvin.beans.MarvinPane
-
Shows or hides the atom symbols in 3D.
- setAtomSymbolsVisible(boolean) - Method in class chemaxon.marvin.MolPrinter
-
Sets atom symbol visibility in 3D mode.
- setAttach(int) - Method in class chemaxon.struc.MolAtom
-
- setAttach(int, Sgroup) - Method in class chemaxon.struc.MolAtom
-
- setAttachmentPointOrder(MolAtom, int, int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Sets a new order for the given attachment point.
- setAttachParentSgroup(Sgroup) - Method in class chemaxon.struc.MolAtom
-
Sets the attach parent s-group information to the extra atom properties
- setAttribute(String, String) - Method in class chemaxon.struc.graphics.MBracket
-
Sets the value of an attribute.
- setAttribute(String, String) - Method in class chemaxon.struc.graphics.MEFlow
-
- setAttribute(String, String) - Method in class chemaxon.struc.graphics.MPolyline
-
Sets the value of an attribute.
- setAttribute(String, String) - Method in class chemaxon.struc.graphics.MRectangle
-
Sets the value of an attribute.
- setAttribute(String, String) - Method in class chemaxon.struc.graphics.MRoundedRectangle
-
Sets the value of an attribute.
- setAttribute(String, String) - Method in class chemaxon.struc.graphics.MTextBox
-
Sets the value of an attribute.
- setAttribute(String, String) - Method in class chemaxon.struc.MObject
-
Sets the value of an attribute.
- setAttributes(int, int, MTextAttributes) - Method in class chemaxon.struc.graphics.MTextDocument
-
Sets attributes of selected text.
- setAutoCheckStructure(boolean) - Method in class chemaxon.marvin.common.UserSettings
-
Turn on automatic Structure checking
- setAutoHeight(boolean) - Method in class chemaxon.struc.graphics.MTextBox
-
Turns on/off automatic height calculation.
- setAutomaticFogEnabled(boolean) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the fog to automatic calculation mode.
- setAutoPopup(boolean) - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
-
Sets the auto popup behaviour
- setAutoScale(boolean) - Method in class chemaxon.marvin.beans.MSketchPane
-
Sets the autoscale property.
- setAutoSize(boolean) - Method in class chemaxon.struc.graphics.MTextBox
-
Turns on/off automatic size calculation.
- setAutoTabScale(boolean) - Method in class chemaxon.marvin.beans.MViewPane
-
Allows or disallows automatic changing of tab scale.
- setBackground(Color) - Method in class chemaxon.struc.MObject
-
Sets the background color of the object.
- setBackgroundColor(JTable, boolean, boolean, int, int) - Method in class chemaxon.marvin.beans.MolRenderer
-
Sets the background color for the current cell based on selection.
- setBackgroundColor(JTable, MViewPane, boolean, int, int) - Method in class chemaxon.marvin.beans.MViewEditor
-
Sets the background color for the current cell based on selection.
- setBackgroundColor(JTable, boolean, boolean, int, int) - Method in class chemaxon.marvin.beans.MViewRenderer
-
Sets the background color for the current cell based on selection.
- setBackgroundColor(Color) - Method in class chemaxon.marvin.MolPrinter
-
Sets the background color.
- setBackgroundColor(Color) - Method in class chemaxon.marvin.space.GraphicCell
-
Sets the background color of the cell used by drawing smooth background.
- setBackgroundColor(float[]) - Method in class chemaxon.marvin.space.GraphicCell
-
Sets the background color of the cell used by drawing smooth background.
- setBackgroundColor(Color) - Method in class chemaxon.marvin.space.GraphicScene
-
Sets the background color of the scene and an alpha value of 0
(transparent background).
- setBackgroundColor(float[]) - Method in class chemaxon.marvin.space.GraphicScene
-
- setBackgroundColor(Color) - Method in class chemaxon.marvin.space.monitor.Label
-
Sets the background color of the label.
- setBackgroundColorMode(int) - Method in class chemaxon.marvin.space.monitor.Label
-
Sets the coloring mode of the background.
- setBallRadius(double) - Method in class chemaxon.marvin.beans.MarvinPane
-
Sets the ball radius in units of covalent radius.
- setBallRadius(double) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the ball radius for ball and stick mode.
- setBallRadius(double) - Method in class chemaxon.marvin.MolPrinter
-
Sets the ball radius for "ball and stick" mode.
- setBarrierLimit(double) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
-
Set the energy barrier limit.
- setBaseElectronContainer(MolAtom, MDocument) - Method in class chemaxon.struc.graphics.MEFlow
-
- setBaseElectronContainerIndex(int) - Method in class chemaxon.struc.graphics.MEFlow
-
- setBaseElectronContainerIndex(int) - Method in class chemaxon.struc.graphics.MEFlowBasePoint
-
- setBaseElectronIndexInContainer(int) - Method in class chemaxon.struc.graphics.MEFlow
-
- setBaseElectronIndexInContainer(int) - Method in class chemaxon.struc.graphics.MEFlowBasePoint
-
- setBaseFontFamily(String) - Method in class chemaxon.struc.graphics.MTextBox
-
Sets the base font family.
- setBaseFontStyle(int) - Method in class chemaxon.struc.graphics.MTextBox
-
Sets the base font style.
- setBasicpKaLowerLimit(double) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Sets the minimum basic pKa (default: -10).
- setBestLigandPosition(MolAtom, MolAtom) - Static method in class chemaxon.marvin.util.CleanUtil
-
Calculates and sets an optimal position for a ligand atom.
- setBestLigandPosition(MolAtom, MolAtom, double) - Static method in class chemaxon.marvin.util.CleanUtil
-
Calculates and sets an optimal position for a ligand atom.
- setBicycloStereo(BicycloStereoDescriptor[]) - Method in class chemaxon.struc.MolAtom
-
Registers the bicyclo stereo information for this atom.
- setBond(int, MolBond) - Method in class chemaxon.struc.MoleculeGraph
-
- setBond(int, MolBond) - Method in class chemaxon.struc.RgMolecule
-
- setBond(int, MolBond) - Method in class chemaxon.struc.RxnMolecule
-
- setBond(int, MolBond) - Method in class chemaxon.struc.SelectionMolecule
-
- setBondCorrespondence(MolBond[]) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
-
Sets the crossing bonds (head and tail) of a ladder-type
polymer.
- setBondDraggedAlong(boolean) - Method in class chemaxon.marvin.beans.MSketchPane
-
Sets the visibility of the currently used bond at the mouse cursor.
- setBondDraggedAlong(boolean) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the visibility of the currently used bond at the mouse cursor.
- setBondLengthVisible(boolean) - Method in class chemaxon.marvin.beans.MarvinPane
-
Sets the bond length display option.
- setBondLengthVisible(boolean) - Method in class chemaxon.marvin.MolPrinter
-
Sets the bond length visibility
- setBonds(List<MolBond>) - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
-
- setBonds(List<MolBond>) - Method in interface chemaxon.checkers.result.StructureCheckerResult
-
This method sets the bonds property
- setBondSetColor(int, Color) - Method in class chemaxon.marvin.beans.MarvinPane
-
Sets the color of a bond set.
- setBondSetColorMode(int, int) - Method in class chemaxon.struc.MDocument
-
Sets the bond set coloring mode.
- setBondSetRGB(int, int) - Method in class chemaxon.struc.MDocument
-
Sets the color of a bond set.
- setBondSetSeq(int, String, String, int) - Method in class chemaxon.marvin.view.MDocStorage
-
Sets bond set sequence numbers.
- setBondSetSeq(int, String, int, int, int) - Method in class chemaxon.marvin.view.MDocStorage
-
Sets bond set sequence numbers.
- setBondSetSeqAll(int, String, int) - Method in class chemaxon.marvin.view.MDocStorage
-
Sets all bond set sequence numbers.
- setBondSetSeqs(int, String, List<int[]>) - Method in class chemaxon.marvin.view.MDocStorage
-
Sets bond set sequence numbers.
- setBondSetSeqs(int) - Method in class chemaxon.struc.MoleculeGraph
-
Sets the set sequence number of all bonds.
- setBondSetThickness(int, double) - Method in class chemaxon.struc.MDocument
-
Sets the thickness of a bond set.
- setBondSpacing(double) - Method in class chemaxon.marvin.beans.MarvinPane
-
Sets the double bond spacing.
- setBondSpacing(double) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the double bond spacing.
- setBondSpacing(double) - Method in class chemaxon.marvin.MolPrinter
-
Sets the double bond spacing that is the distance of the two lines representing a double
bond.
- setBondWidth(double) - Method in class chemaxon.marvin.beans.MarvinPane
-
- setBondWidth(double) - Method in class chemaxon.marvin.MolPrinter
-
- setBorder(JTable, boolean, boolean, int, int) - Method in class chemaxon.marvin.beans.MolRenderer
-
Sets the border for the current cell based on selection.
- setBorder(JTable, MViewPane, boolean, int, int) - Method in class chemaxon.marvin.beans.MViewEditor
-
Sets the border for the current cell based on selection.
- setBorder(JTable, boolean, boolean, int, int) - Method in class chemaxon.marvin.beans.MViewRenderer
-
Sets the border for the current cell based on selection.
- setBorderColor(Color) - Method in class chemaxon.marvin.space.monitor.Label
-
Sets the border color of the label.
- setBorderColorMode(int) - Method in class chemaxon.marvin.space.monitor.Label
-
Sets the coloring mode of the border.
- setBorderWidth(int) - Method in class chemaxon.marvin.beans.MViewPane
-
Sets the width of the border between cells.
- setBoundingBox() - Method in class chemaxon.marvin.space.MoleculeComponent
-
Computes the bounding box of the visible atoms of the molecule, and adds
2 angstroms to each side.
- setBounds(int, int, int, int) - Method in class chemaxon.marvin.space.GraphicScene
-
Moves and resizes this component.
- setBracketOrientation(int) - Method in class chemaxon.struc.graphics.MBracket
-
Sets the orientation of the bracket.
- setBuiltInColorMapperMethod(int) - Method in class chemaxon.marvin.space.SurfaceColoring
-
Selection of built-in color palettes through their identifier.
- setBuiltInColorMapperMethod(int, boolean) - Method in class chemaxon.marvin.space.SurfaceColoring
-
Selection of built-in color palettes through their identifier.
- setByteOrder(ByteBuffer) - Method in class chemaxon.marvin.io.PositionedInputStream
-
- setC(int, boolean) - Method in class chemaxon.marvin.beans.MViewPane
-
Sets the state of a checkbox in a GridBagView table.
- setCacheCapacity(int) - Method in class chemaxon.marvin.view.MDocStorage
-
Sets the maximum number of cached documents.
- setCalcAlways(boolean) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Deprecated.
replaced by setModel(int)
- setCalculateEnergy(boolean) - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
Sets the calculation of dreiding energy.
- setCalculateForLEConformer(String) - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
Sets the condition for lowest energy conformer calculation before geometry
calculations are processed.
- setCalculateMMFF94Energy(boolean) - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
Sets the calculation of MMFF94 energy.
- setCalculateMoleculeProjections(boolean) - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
Sets the calculation of molecule projections.
- setCalculateVolume(boolean) - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
- setCanceled(boolean) - Method in class chemaxon.checkers.runner.BasicCheckerRunner
-
Sets the canceled
- setCarbonVisibility(String) - Method in class chemaxon.marvin.MolPrinter
-
Sets the visibility style of the C labels on Carbon atoms.
- setCasNumberLookup(boolean) - Method in class chemaxon.naming.DocumentExtractor
-
Deprecated.
Enable or disable the lookup of CAS numbers (requires network access).
- setCationic(boolean) - Method in class chemaxon.marvin.space.PharmacophorePoint
-
Sets or clears the cationic property of the PharmacophorePoint.
- setCellDrawProperties(Properties) - Method in class chemaxon.marvin.space.GraphicCell
-
Sets the drawing properties of all components of the cell.
- setCellDrawProperty(int, String, String) - Method in class chemaxon.marvin.space.GraphicScene
-
Sets the given draw property to the given cell.
- setCellIndex(int) - Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
-
Sets the viewer cell index.
- setCellIndex(int) - Method in class chemaxon.marvin.space.CellOrComponentId
-
Sets the internal index of the cell.
- setCellProperty(String, String) - Method in class chemaxon.marvin.space.MSpaceEasy
-
Sets a draw property of MarvinSpace that will affect the active cell only.
- setCellSize(Dimension) - Method in class chemaxon.marvin.view.swing.TableSupport
-
Sets the molecule cell size for GridBagView.
- setCellStyle(String, CellStyle) - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
Sets the cell style of the property column with the given name
- setCenter(float[]) - Method in class chemaxon.marvin.space.monitor.Control
-
Sets the center of the transformation.
- setCenterMolecule(boolean) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
-
Center the molecule before MD calculation
(It is not set by default.)
- setCentralAtom(MolAtom) - Method in class chemaxon.struc.sgroup.MulticenterSgroup
-
Sets the central atom of this sgroup.
- setChangeSupport(PropertyChangeSupport) - Method in class chemaxon.checkers.runner.BasicCheckerRunner
-
Sets the changeSupport
- setCharge(int) - Method in class chemaxon.struc.MolAtom
-
Sets the charge.
- setCharge(int, int) - Method in interface chemaxon.struc.WSmolecule
-
Sets the charge of an ion.
- setChargeFont(Font) - Method in class chemaxon.marvin.MolPrinter
-
Sets the circled charge's font.
- setChargeFontSize(double) - Method in class chemaxon.marvin.MolPrinter
-
Sets the circled charge's font's size.
- setChargeLocation(int) - Method in class chemaxon.struc.Sgroup
-
Sets the charge location attribute of the S-group.
- setChargeWithCircle(boolean) - Method in class chemaxon.marvin.MolPrinter
-
Sets the visibility of Charge with Circle
- setCheck3DStereo(boolean) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
-
Sets the 3D stereo conformation checking of the structure.
- setCheckerConfigFileName(String) - Method in class chemaxon.marvin.common.UserSettings
-
- setCheckerConfigURL(String) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the URL of the configuration for Checkers in marvin sketch.
- setCheckerList(List<StructureChecker>) - Method in class chemaxon.checkers.runner.BasicCheckerRunner
-
Sets the checkerList
- setChirality(Map<Integer, Integer>) - Method in class chemaxon.struc.MoleculeGraph
-
Sets the chiralities of atoms.
- setChirality(int, int) - Method in class chemaxon.struc.MoleculeGraph
-
Set chirality of an atom of the Molecule instance based on both
the coordinates of the neighboring atoms and the stereo information
of the bonds to those.
- setChiralitySupport(int) - Method in class chemaxon.marvin.beans.MarvinPane
-
Sets chirality support to show or hide the R/S labels.
- setChiralitySupport(String) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the chirality support parameter.
- setChiralitySupport(int) - Method in class chemaxon.marvin.MolPrinter
-
Sets the chirality display mode.
- setCircledChargeFont(Font) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the circled charge symbol font name.
- setCircledChargeSize(double) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the circled charge font size in C-C bond length units.
- setClassName(String) - Method in class chemaxon.marvin.services.localservice.LocalServiceDescriptor
-
Sets the full class name of the service
- setClean(int, String) - Method in class chemaxon.formats.MolExporter
-
Sets molecule cleaning in exporter.
- setClean(int, String, MolFilter) - Method in class chemaxon.formats.MolExporter
-
Sets molecule cleaning in exporter.
- setClean2dOpts(String) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the 2D cleaning options.
- setClean3dOpts(String) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the 3D cleaning options.
- setCleanDim(int) - Method in class chemaxon.marvin.beans.MarvinPane
-
Sets the space dimensions for cleaning.
- setCleanHOption(boolean) - Method in class chemaxon.marvin.common.UserSettings
-
- setCleanHOptionEnabled(boolean) - Method in class chemaxon.marvin.common.UserSettings
-
Sets to add an explicit hydrogen atom to chiral centers having no terminal atoms when 2D
cleaning is performed.
- setCleanResultStructures(boolean) - Method in class chemaxon.marvin.calculations.ResonancePlugin
-
- setCleanResultStructures(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Deprecated.
obsolate method
- setClearClipboardBeforeExport(boolean) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
-
Sets whether the subsystem should clear the clipboard before a copy operation.
- setCloridIonConcentration(double) - Method in class chemaxon.marvin.calculations.logDPlugin
-
Sets the Cl- concentration (default: 0.1).
- setCloridIonConcentration(double) - Method in class chemaxon.marvin.calculations.logPPlugin
-
Sets the Cl- concentration (default: 0.1).
- setCloseEnabled(boolean) - Method in class chemaxon.marvin.beans.MSketchPane
-
Set the accessibility of the Close menu item in the File menu.
- setColor(AlignmentProperties.ColoringScheme) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
-
sets which atomtypes to use.
- setColor(Color) - Method in class chemaxon.marvin.space.ComponentElement
-
Assignes a color to the CompnentElement.
- setColor(Color) - Method in class chemaxon.marvin.space.GraphicComponent
-
Sets the constant color of the component.
- setColor(float[]) - Method in class chemaxon.marvin.space.GraphicComponent
-
Sets the constant color of the component.
- setColor(int, int, int) - Method in class chemaxon.marvin.space.GraphicComponent
-
Sets the constant color of the component.
- setColor(float, float, float) - Method in class chemaxon.marvin.space.GraphicComponent
-
Sets the constant color of the component.
- setColor(Color) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- setColor(Color) - Method in class chemaxon.marvin.space.MoleculeComponent
-
Sets the constant color of the component.
- setColor(float[]) - Method in class chemaxon.marvin.space.MoleculeComponent
-
Sets the constant color of the component.
- setColor(float, float, float) - Method in class chemaxon.marvin.space.MoleculeComponent
-
Sets the constant color of the component.
- setColor(float[]) - Method in class chemaxon.marvin.space.SurfaceComponent
-
Sets the constant color of the surface.
- setColor(Color) - Method in class chemaxon.marvin.space.SurfaceComponent
-
Sets the constant color of the surface.
- setColor(Color) - Method in class chemaxon.struc.MObject
-
Sets the color of the object.
- SETCOLOR_COLORLESS - Static variable in class chemaxon.struc.MDocument
-
The atom/bond set is colorless, normal (CPK, Monochrome etc.) colors
are used.
- SETCOLOR_DEFAULT - Static variable in class chemaxon.struc.MDocument
-
Default set colors are used for coloring the atom/bond set.
- SETCOLOR_SPECIFIED - Static variable in class chemaxon.struc.MDocument
-
The user specified set colors are used for coloring the atom/bond set.
- setColoring(int) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Sets hit coloring options.
- setColoringEnabled(boolean) - Method in class chemaxon.util.HitColoringAndAlignmentOptions
-
Sets whether substructure hit coloring should be used.
- setColoringScheme(AlignmentProperties.ColoringScheme) - Method in class chemaxon.marvin.alignment.Alignment
-
- setColorScheme(String) - Method in class chemaxon.marvin.beans.MarvinPane
-
Sets the color scheme.
- setColorScheme(String) - Method in class chemaxon.marvin.MolPrinter
-
Sets the color scheme.
- setColumnCount(int) - Method in class chemaxon.marvin.beans.MViewParams
-
Sets the nuber of columns.
- setColumnWidth(String, int) - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
Sets the column width of property column with the given name
- setColumnWidth(int) - Method in class chemaxon.marvin.view.swing.TableOptions
-
Sets the default column width.
- setColumnWidth(int, int) - Method in class chemaxon.marvin.view.swing.TableOptions
-
Sets the default width of a specified column.
- setComment(String) - Method in class chemaxon.struc.Molecule
-
Sets the comment.
- setComment(String) - Method in class chemaxon.struc.RgMolecule
-
Sets the comment of the root molecule.
- setComponent(GraphicComponent) - Method in class chemaxon.marvin.space.monitor.Control
-
Sets the component to the transformation.
- setComponent(GraphicComponent) - Method in class chemaxon.marvin.space.monitor.DihedralControl
-
Sets the affecting component of the DihedralControl which has to be a MoleculeComponent.
- setComponentIndex(int) - Method in class chemaxon.marvin.space.CellOrComponentId
-
Warning: for internal use only.
- setComponentProperty(Object, String, String) - Method in class chemaxon.marvin.space.MSpaceEasy
-
Sets a draw property of MarvinSpace that will affect only the given component.
- setConfigurationReader(ConfigurationReader) - Method in class chemaxon.checkers.runner.BasicCheckerRunner
-
- setConfigurationReader(ConfigurationReader) - Method in interface chemaxon.checkers.runner.CheckerRunner
-
Sets a new configuration for the Runner.
- setConfirmExit(boolean) - Method in class chemaxon.marvin.beans.MSketchPane
-
Sets to drop confirmation dialog about exit or not.
- setConformerCount(int) - Method in class chemaxon.marvin.alignment.Alignment
-
The the dihedral angles of every flexible molecule should be randomized
before alignment.
- setConformerCount(int) - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
-
- setConnectionCountChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker
-
Sets the option determining if the checker detects connection count atom
query properties or not.
- setConnectivity(int) - Method in class chemaxon.struc.Sgroup
-
Sets S-group connectivity.
- setConsiderTautomerization(boolean) - Method in class chemaxon.marvin.calculations.logDPlugin
-
Sets to consider tautomerization in calculation.
- setConsiderTautomerization(boolean) - Method in class chemaxon.marvin.calculations.logPPlugin
-
Sets to consider tautomerization.
- setConsiderTautomerization(boolean) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Sets to consider tautomerization.
- setConstantAtomRadius(float) - Method in class chemaxon.marvin.space.SurfaceColoring
-
In case of {#RADIUS_CONSTANT} mode the constant radius can be set.
- setConstantDistanceRadius(float) - Method in class chemaxon.marvin.space.SurfaceColoring
-
In case of distance weighted property values constant radius can be set.
- setContext(CodeAssistDataProvider.Context) - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
-
Sets the evaluation context
- setContext(String) - Method in class chemaxon.struc.sgroup.DataSgroup
-
Sets the context of this data sgroup.
- setContext(int) - Method in class chemaxon.struc.sgroup.DataSgroup
-
Sets the context of this data sgroup.
- setContexts(int, int, int, int, int, GL2, GLU) - Method in class chemaxon.marvin.space.GraphicCell
-
Sets the indices of row and column of the scene in which this cell is in,
and sets the GL2 related variables to be able to draw.
- setControl(DihedralControl) - Method in class chemaxon.marvin.space.monitor.DihedralMonitor
-
Sets a DihedralControl to the monitor.
- setControl(Control) - Method in class chemaxon.marvin.space.monitor.PositionMonitor
-
Sets the control of the monitor, and the center of the control to the center of the monitor.
- setConvergenceLimit(double) - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
-
- setCoordDependent(long) - Method in class chemaxon.struc.MProp
-
Sets the property as coordinate dependent.
- setCoordinateBondStyle(String) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the "coordinative" bond line style when both atoms are single.
- setCoordinateBondStyle(String) - Method in class chemaxon.marvin.MolPrinter
-
Set the coordinate bond line style when both atoms are single.
- setCoordinateBondStyleAtMulticenter(String) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the "coordinative" bond line style when one of the atoms is multicenter.
- setCoordinateBondStyleAtMulticenter(String) - Method in class chemaxon.marvin.MolPrinter
-
Set the coordinate bond line style.
- setCoordinates(Object, int) - Method in class chemaxon.marvin.space.AtomProperty.SmoleculeAtomProperty
-
- setCoordinates(float[]) - Method in class chemaxon.marvin.space.ComponentElement
-
Sets the coordinates of the ComponentElement.
- setCopyAsFormat(String) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the selected format in the Copy As dialog.
- setCorners(MPoint, MPoint) - Method in class chemaxon.struc.graphics.MRectangle
-
Sets the corners.
- setCorners(double, double, double, double) - Method in class chemaxon.struc.MolAtom
-
Used internally by MolPainter.
- setCornersRadius(double, double) - Method in class chemaxon.struc.graphics.MRoundedRectangle
-
- setCorrectionData(PKaTrainingResult) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Sets correction data for calculation
- setCorrectionLibrary(String) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Sets the correction library.
- setCorrectionLibraryPath(String) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Sets the correction library file directly.
- setCount(int) - Method in class chemaxon.marvin.alignment.PairwiseAlignment
-
- setCount(int) - Method in interface chemaxon.marvin.alignment.PairwiseComparison
-
- setCount(int) - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D
-
- setCoupled(boolean) - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder
-
Coupled/decoupled spectrum.
- setCouplingConstants(double[][]) - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
Sets coupling constants.
- setCouplingNeeded(boolean) - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
Sets whether spin-spin couplings are taken into account.
- setCrossingBond(int, MolBond) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Change the crossing bond of an attachment point.
- setCrossingBondType(int, BondType) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Deprecated.
As of Marvin 6.2, no replacement.
Not supported feature.
- setCTCrossedBond(MoleculeGraph) - Static method in class chemaxon.marvin.util.CleanUtil
-
Convert wiggly type double bonds to crossed.
- setCTWigglyBond(MoleculeGraph) - Static method in class chemaxon.marvin.util.CleanUtil
-
Convert crossed double bonds to wiggly type.
- setCTWigglyBond(MoleculeGraph, int) - Static method in class chemaxon.marvin.util.CleanUtil
-
Convert crossed double bond to wiggly type.
- setCurrentDefaultFontMetrics(FontMetrics) - Method in class chemaxon.struc.graphics.MTextBox
-
Sets the current height of the text..
- setCurrentFont(MFont, int) - Method in class chemaxon.struc.graphics.MTextBox
-
Sets font for selected text or the next character to be typed.
- setCurrentForeground(Color) - Method in class chemaxon.struc.graphics.MTextBox
-
Sets color for selected text or the next character to be typed.
- setCurrentHeight(double) - Method in class chemaxon.struc.graphics.MTextBox
-
Sets the current height of the text..
- setCurrentTextAttributes(MTextAttributes) - Method in class chemaxon.struc.graphics.MTextBox
-
Sets the attributes for the selected text or the next character
to be typed.
- setCurrentWidth(double) - Method in class chemaxon.struc.graphics.MTextBox
-
Sets the current height of the text..
- setCursorPos(int, boolean) - Method in class chemaxon.struc.graphics.MTextBox
-
Sets the cursor position.
- setCursorRow(int) - Method in class chemaxon.struc.graphics.MTextBox
-
Sets the cursor row number.
- setCustomName(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor
-
Sets the customName
- setData(String) - Method in class chemaxon.struc.sgroup.DataSgroup
-
Sets the data value to be set.
- setDataDetached(boolean) - Method in class chemaxon.struc.sgroup.DataSgroup
-
Sets whether the data should be displayed close to the objects or
separately (detached).
- setDataLine(int, String) - Method in class chemaxon.struc.sgroup.DataSgroup
-
Sets a line of data.
- setDebug(int) - Method in class chemaxon.marvin.beans.MarvinPane
-
Switches on the debug messages.
- setDefaultFont(JEditorPane) - Static method in class chemaxon.marvin.util.SwingUtil
-
Sets the SWING default font in the JEditorPane.
- setDefaultFont(MFont) - Method in class chemaxon.struc.graphics.MTextDocument
-
Sets the default font.
- setDefaultNodeWeightBehavior(AlignmentProperties.ColorNotSpecifiedCase) - Method in class chemaxon.marvin.alignment.Alignment
-
- setDefaultSaveFormat(String) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the default molecule format in the "Save As" dialog.
- setDefaultStyle(CellStyle) - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
Sets the cell style applied for the value cells of the columns
having no explicit formatting.
- setDehidrogenize(boolean) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
-
Deprecated.
The explicit Hydrogens are not removed from the original
input structure. No need to use.
- setDehydrogenize(boolean) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
-
Set dehydrogenize parameter
- setDependentRgroupDefinition(int, int) - Method in class chemaxon.struc.RgMolecule
-
Sets the dependent R-group definition (rGroupIndexThen) for
the referenced R-group definition (rGroupIndexIf).
- setDescription(String) - Method in class chemaxon.checkers.AbstractStructureChecker
-
- setDescription(String) - Method in class chemaxon.checkers.InvalidChecker
-
- setDescription(String) - Method in interface chemaxon.checkers.StructureChecker
-
Deprecated.
This method isn't needed anymore and will be removed in 6.0
- setDescription(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor
-
Sets the description of the concerning checker
- setDescription(String) - Method in class chemaxon.fixers.AbstractStructureFixer
-
- setDescription(String) - Method in interface chemaxon.fixers.StructureFixer
-
Deprecated.
- setDescription(String) - Method in class chemaxon.fixers.StructureFixerDescriptor
-
Sets the description of the concerning fixer
- setDescription(String) - Method in class chemaxon.marvin.space.ComponentElement
-
Sets a brief description to the ComponentElement that will
be returned by {#getDescription()}.
- setDescriptor(T) - Method in interface chemaxon.marvin.services.ServiceDescriptorEditor
-
- setDescriptorURI(String) - Method in class chemaxon.marvin.services.json.JsonServiceDescriptor
-
Sets the URI of the JSON RPC descriptor file
- setDesiredBufferSize(int) - Method in class chemaxon.marvin.io.PositionedInputStream
-
Sets desired buffer size.
- setDetachable(boolean) - Method in class chemaxon.marvin.beans.MViewPane
-
Sets the detachable property.
- setDetectCumulatedDoubleBonds(boolean) - Method in class chemaxon.checkers.RingStrainErrorChecker
-
Sets the detectCumulatedDoubleBonds property
- setDetectTransDoubleBonds(boolean) - Method in class chemaxon.checkers.RingStrainErrorChecker
-
Sets the detectTransDoubleBonds
- setDetectTripleBonds(boolean) - Method in class chemaxon.checkers.RingStrainErrorChecker
-
Sets the detectTripleBonds property
- setDim(int) - Method in class chemaxon.struc.Molecule
-
Sets the dimension.
- setDim(int) - Method in class chemaxon.struc.MoleculeGraph
-
Sets the dimension.
- setDim(int) - Method in class chemaxon.struc.RgMolecule
-
Sets the dimension of the root structure and the R-groups.
- setDim(int) - Method in class chemaxon.struc.RxnMolecule
-
Sets the dimension for all the structures.
- setDirectory(File) - Method in class chemaxon.marvin.beans.MarvinPane
-
Sets the working directory, if the Load/Save is in Last Opened Mode.
- setDisabledGroupTypes(List<String>) - Method in class chemaxon.marvin.beans.MSketchPane
-
- setDisplayChargeWithCircle(boolean) - Method in class chemaxon.marvin.common.UserSettings
-
- setDisplayedChars(int) - Method in class chemaxon.struc.sgroup.DataSgroup
-
Sets the number of characters to be displayed (1...999 or 0 for no
restriction)
- setDisplayedLines(int) - Method in class chemaxon.struc.sgroup.DataSgroup
-
Sets the number of lines to be displayed (0: show all)
- setDisplayLabelsAndBoxes(boolean) - Method in class chemaxon.util.HitColoringAndAlignmentOptions
-
Set the option to show labels and bounding boxes for the parts of
the result: target, query, score.
- setDisplayLonePairsAsLine(boolean) - Method in class chemaxon.marvin.common.UserSettings
-
- setDisplayQuality(int) - Method in class chemaxon.marvin.MolPrinter
-
Deprecated.
since Marvin 6.4 only high quality exists
- setDispopts(int) - Method in class chemaxon.marvin.beans.MarvinPane
-
Sets display options.
- setDispopts(int) - Method in class chemaxon.marvin.MolPrinter
-
Modifies the display options in the advanced way of handling display options.
- setDispopts(int, int) - Method in class chemaxon.marvin.MolPrinter
-
- setDispoptsExt(int) - Method in class chemaxon.marvin.MolPrinter
-
Modifies the extended display options in the advanced way of handling display options.
- setDispoptsExt(int, int) - Method in class chemaxon.marvin.MolPrinter
-
- setDispQuality(int) - Method in class chemaxon.marvin.beans.MarvinPane
-
Deprecated.
Does nothing. Deprecated since Marvin 6.4.
- setDistanceRadiusExtension(float) - Method in class chemaxon.marvin.space.SurfaceColoring
-
In case of distance weighted property values radius extension can be set.
- setDistanceRadiusMode(int) - Method in class chemaxon.marvin.space.SurfaceColoring
-
In case of distance weighted property values the distance computation can
be set differently from the property radius but in the same way.
- setDiversity(double) - Method in class chemaxon.marvin.calculations.ConformerPlugin
-
Sets the diversity limit for the calculation.
- setDoc(MDocument) - Method in class chemaxon.marvin.MolPrinter
-
Sets the current document and calculates its bounds.
- setDocSource(MDocSource, int, int) - Method in class chemaxon.marvin.view.MDocStorage
-
Sets the document source.
- setDocument(MDocument) - Method in class chemaxon.marvin.beans.MSketchPane
-
Sets the document.
- setDocument(int, MDocument) - Method in class chemaxon.marvin.beans.MViewPane
-
Sets the document
- setDocument(int, MDocument) - Method in class chemaxon.marvin.view.swing.TableSupport
-
Sets the k-th record directly.
- setDomainMax(double) - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
Sets the upper end of the spectrum.
- setDomainMin(double) - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
Sets the lower end of the spectrum.
- setDominantTautomerDistributionCalculation(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Sets dominant tautomer distribution calculation: if true then dominant tautomer
distribution is calculated.
- setDonor(boolean) - Method in class chemaxon.marvin.space.PharmacophorePoint
-
Sets or clears the donor property of the PharmacophorePoint.
- setDoodle(boolean) - Method in class chemaxon.checkers.runner.BasicCheckerRunner
-
Sets the isDoodle
- setDotDirName(String) - Static method in class chemaxon.util.DotfileUtil
-
Sets the subdirectory name for the configuration files.
- setDoublePrecision(String) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Sets the precision in the decimal format.
- setDoublePrecision(int) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Sets the double -> string conversion precision
(maximal number of fraction digits)
with zero-padding (12.56 -> 12.5600 if precision=4).
- setDoublePrecision(int, boolean) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Sets the double -> string conversion precision
(maximal number of fraction digits).
- setDownWedge(String) - Method in class chemaxon.marvin.beans.MarvinPane
-
Sets the wedge bond display convention.
- setDownWedge(String) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the convention to use for displaying a down wedge.
- setDownWedge(String) - Method in class chemaxon.marvin.MolPrinter
-
Set the down wedge orientation.
- setDraggable(boolean) - Method in class chemaxon.marvin.beans.MViewPane
-
Allows or denies mouse dragged events in cells.
- setDraggedObject(MObject) - Method in class chemaxon.struc.MDocument
-
Sets the dragged object.
- setDrawing(boolean) - Method in class chemaxon.marvin.space.SurfaceComponent
-
- setDrawingPrimitiveType(int) - Method in class chemaxon.marvin.space.SurfaceComponent
-
Sets the type of drawn primitives.
- setDrawingPrimitiveType(int, int) - Method in class chemaxon.marvin.space.SurfaceComponent
-
Sets the type of drawn primitives.
- setDrawProperties(Properties) - Method in class chemaxon.marvin.space.GraphicComponent
-
Forces the component to set all drawing property stored in drawProperties,
and loose every old setting.
- setDrawProperty(String, String) - Method in class chemaxon.marvin.space.GraphicCell
-
Sets the drawing properties of all components of the cell.
- setDrawProperty(String, String) - Method in class chemaxon.marvin.space.GraphicComponent
-
This is the gate of draw properties from outside to the component.
- setDrawProperty(Properties) - Method in class chemaxon.marvin.space.GraphicScene
-
Sets the given draw properties to the entire scene.
- setDrawProperty(String, String) - Method in class chemaxon.marvin.space.GraphicScene
-
Sets the draw property for all cells.
- setDrawProperty(String, String, int) - Method in class chemaxon.marvin.space.GraphicScene
-
Sets the draw property either to the entire scene or to the active cell.
- setDrawProperty(String, String) - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- setDrawProperty(String, String) - Method in class chemaxon.marvin.space.MacroMoleculeComponent
-
- setDrawProperty(String, String, MacroMoleculeComponent.MoleculeVisualizer) - Method in class chemaxon.marvin.space.MacroMoleculeComponent
-
Sets the given draw property to the given visualizer.
- setDrawProperty(String, String) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
This is the gate of draw properties from outside to the component.
- setDrawProperty(String, String) - Method in class chemaxon.marvin.space.MoleculeComponent
-
- setDrawProperty(String, String) - Method in class chemaxon.marvin.space.monitor.Label
-
- setDrawProperty(String, String) - Method in class chemaxon.marvin.space.PharmacophoreArrow
-
- setDrawProperty(String, String) - Method in class chemaxon.marvin.space.PharmacophorePoint
-
Sets drawing properties specific to PharmacophoreSphere.
- setDrawProperty(String, String) - Method in class chemaxon.marvin.space.SurfaceComponent
-
This is the gate of draw properties from outside to the component.
- setDrawSphere(boolean) - Method in class chemaxon.marvin.space.GraphicCell
-
Enables/disables drawing of the rotation sphere.
- setDrawType(String) - Method in class chemaxon.marvin.space.PharmacophoreArrow
-
Sets current drawing type.
- setDrawType(String) - Method in class chemaxon.marvin.space.PharmacophorePoint
-
Sets current drawing type.
- setDrawType(String) - Method in class chemaxon.marvin.space.SurfaceComponent
-
Sets the drawing type of the surface.
- setDropTarget(DropTargetListener) - Method in class chemaxon.marvin.space.GraphicScene
-
Sets the DropTarget of the graphic canvas.
- setEditable(int) - Method in class chemaxon.marvin.beans.MViewEditor
-
Sets the mode that determines if the structure is editable.
- setEditable(int) - Method in class chemaxon.marvin.beans.MViewPane
-
Sets the mode that determines if the structure is editable.
- setEditorClassName(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor
-
Sets the editorClassName
- setElectronIndex(String, int) - Method in class chemaxon.struc.graphics.MEFlowBasePoint
-
- setElectronProp(int) - Method in class chemaxon.struc.MolAtom
-
Sets the number of lone pairs.
- setElectronToAtomMapping(MolAtom, MElectronContainer) - Method in class chemaxon.struc.graphics.MChemicalStruct
-
- setEnabled(boolean) - Method in class chemaxon.marvin.beans.MarvinPane
-
Enables or disables this component, depending on the value of the parameter b.
- setEnabled(boolean) - Method in class chemaxon.marvin.beans.MViewPane
-
Enables or disables this component, depending on the value of the parameter b.
- setEnabledT(int, int, boolean) - Method in class chemaxon.marvin.view.MDocStorage
-
Set the enabled state of a text field in a record.
- setEnableTranslateAndRotate(boolean) - Method in class chemaxon.marvin.alignment.AlignmentMolecule
-
- setEncoding(String, String) - Method in class chemaxon.marvin.io.MolExportModule
-
Sets the output encoding using the export options.
- setEncoding(Encoding) - Method in class chemaxon.marvin.io.PositionedInputStream
-
Sets the encoding.
- setEncoding(String) - Method in class chemaxon.marvin.io.PositionedInputStream
-
Sets the encoding.
- setEncodings(String) - Method in class chemaxon.formats.MolConverter.Builder
-
Sets the input and/or output encoding.
- setEncodings(String) - Method in class chemaxon.formats.MolConverter.Options
-
Deprecated.
- setEndPosition(long) - Method in class chemaxon.struc.MDocument
-
Sets the end position of this document in the input file.
- setEndPosition(long) - Method in class chemaxon.struc.Molecule
-
Sets the end position of this molecule in the input file.
- setEnrtyRadiusMode(int) - Method in class chemaxon.marvin.space.SurfaceColoring
-
Atom properties will effect surface vertices being closer than a certain radius.
- setEnumCodeNeeded(boolean) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Indicates whether unique Markush enumeration code
should be generated.
- setEnumerateHomology(boolean) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Sets if homology groups should be enumerated or not.
- setEnumerateMarkush(boolean) - Method in class chemaxon.util.HitColoringAndAlignmentOptions
-
Sets whether markush structures should be hit enumerated according
to the query structure.
- setErrorProcessor(ErrorProcessor) - Method in class chemaxon.formats.MolExporter
-
Sets the error handler interface for concurrent mode.
- setEuler(double, double, double) - Method in class chemaxon.struc.CTransform3D
-
Sets the rotational component using the Euler angles provided.
- setExcludeAntiAromaticCompounds(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Sets whether antiaromatic compounds should be generated.
- setExcluded(AbbreviatedGroupChecker.Abbreviations) - Method in class chemaxon.checkers.AbbreviatedGroupChecker
-
Sets the abbreviations to be excluded
- setExcluded(boolean) - Method in class chemaxon.marvin.space.PharmacophorePoint
-
Sets or clears the excluded property of the PharmacophorePoint.
- setExcludeHalogens(boolean) - Method in class chemaxon.marvin.calculations.HBDAPlugin
-
Sets if halogens should be excluded from hydrogen bond acceptors.
- setExcludePhosphorus(boolean) - Method in class chemaxon.marvin.calculations.TPSAPlugin
-
Sets to exclude phosphorus from PSA calculation.
Default: true, phosphorus i excluded.
- setExcludeSulfur(boolean) - Method in class chemaxon.marvin.calculations.HBDAPlugin
-
Sets if sulfur atom should be excluded from hydrogen bond acceptors.
- setExcludeSulfur(boolean) - Method in class chemaxon.marvin.calculations.TPSAPlugin
-
Sets to exclude sulfur from PSA calculation.
Default: true, sulfur i excluded.
- setExclusiveColor(byte[]) - Method in class chemaxon.marvin.space.SurfaceComponent
-
Vertices having the given color will not be drawn and also their neighbouring
vertices belonging to the same primitive.
- setExclusiveDrawing(boolean) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- setExclusiveDrawing(boolean) - Method in class chemaxon.marvin.space.SurfaceComponent
-
- setExperimentalEnabled(boolean) - Method in class chemaxon.marvin.beans.MarvinPane
-
Enable or disable experimental features.
- setExpertMode(boolean) - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
-
Sets the expert mode
- setExplicitConnectionCountChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker
-
Sets the option determining if the checker detects explicit connection
count atom query properties or not.
- setExplicitH(boolean) - Method in class chemaxon.marvin.MolPrinter
-
Deprecated.
As of Marvin 5.5.1 this method does nothing. This method will be removed in a
future release.
- setExplicitHVisible(boolean) - Method in class chemaxon.marvin.MolPrinter
-
Deprecated.
As of Marvin 5.5.1 this method does nothing. This method will be removed in a
future release.
- setExpression(String) - Method in class chemaxon.marvin.services.DynamicArgument
-
Sets the expression
- setExternalCheckerConfigURL(String) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the URL of the configuration file containing the list of external Checkers in marvin
sketch.
- setExtraLabel(String) - Method in class chemaxon.struc.MolAtom
-
Sets the extra atom label (also called atom value):
"label" or "label1|label2".
- setExtraLabelColor(long) - Method in class chemaxon.struc.MolAtom
-
Sets the extra label color(s):
lower 32 bits and upper 32 bits as
(alpha<<24 + red<<16 + green<<8 + blue).
- setExtraLabelColor(int, int) - Method in class chemaxon.struc.MolAtom
-
Sets the extra label colors:
lower 32 bits and upper 32 bits as
(alpha<<24 + red<<16 + green<<8 + blue).
- setExtraLabelColorsForDocument(Molecule) - Method in class chemaxon.struc.MDocument
-
Sets the coloring mode sets and colors of extra labels
- setExtraLabelSetColorMode(int, int) - Method in class chemaxon.struc.MDocument
-
- setExtraLabelSetRGBs(int, int) - Method in class chemaxon.struc.MDocument
-
- setExtraLabelSetRGBs(int, int, int) - Method in class chemaxon.struc.MDocument
-
- setExtraLabelSetSeq(int) - Method in class chemaxon.struc.MolAtom
-
- setEZLabelsVisible(boolean) - Method in class chemaxon.marvin.MolPrinter
-
Sets the visibility state of absolute double bond stereo configuration labels.
- setEzVisible(boolean) - Method in class chemaxon.marvin.beans.MarvinPane
-
Sets the E/Z display option.
- setEZVisible(boolean) - Method in class chemaxon.marvin.common.UserSettings
-
Show or hide E/Z labels
- setEzVisible(boolean) - Method in class chemaxon.marvin.MolPrinter
-
- setField(int, Molecule, String, MProp) - Method in class chemaxon.marvin.io.MFieldAccessor
-
Sets a property.
- setFieldAccessor(MFieldAccessor) - Method in class chemaxon.marvin.view.MDocStorage
-
Sets the field accessor.
- setFieldFont(String, Font) - Method in class chemaxon.marvin.beans.MViewPane
-
Sets the font for a named field in a table.
- setFieldFontSize(int) - Method in class chemaxon.marvin.view.swing.TableOptions
-
Sets the field font size.
- setFieldName(String) - Method in class chemaxon.struc.sgroup.DataSgroup
-
Sets the data field name.
- setFields(String[]) - Method in class chemaxon.formats.MolConverter.Builder
-
Sets the included fields to be shown in a table.
- setFields(String[]) - Method in class chemaxon.formats.MolConverter.Options
-
Deprecated.
- setFields(int, Molecule, String[], MProp[]) - Method in class chemaxon.marvin.io.MFieldAccessor
-
Sets properties.
- setFieldsShown(boolean) - Method in class chemaxon.marvin.view.swing.TableOptions
-
Show or hide SDfile fields in the table
- setFieldType(int) - Method in class chemaxon.struc.sgroup.DataSgroup
-
Sets the field type.
- setFieldType(String) - Method in class chemaxon.struc.sgroup.DataSgroup
-
Sets the field type from string representation.
- setFile(File) - Method in class chemaxon.marvin.beans.MarvinPane
-
Sets the current molecule file but does not load it.
- setFilter(MolFilter) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Sets the molecule filter.
- setFilter(MolFilter) - Method in class chemaxon.marvin.util.MolFragLoader
-
Sets the fragment filter.
- setFingerprint(int[]) - Method in class chemaxon.jep.context.MolContext
-
Sets the fingerprint of the input molecule.
- setFingerprintGenerator(FingerprintGenerator) - Method in class chemaxon.jep.Evaluator
-
Sets the fingerprint generator object (needed for query strings).
- setFiveLongRings(List<List<MolAtom>>) - Method in class chemaxon.checkers.result.MetalloceneCheckerResult
-
This method sets the fiveLongRings property.
- setFixed(int) - Method in class chemaxon.marvin.view.MDocStorage
-
Sets a document as fixed.
- setFixerClassName(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor
-
Sets the fixerClassName
- setFixMode(FixMode) - Method in class chemaxon.checkers.StructureCheckerDescriptor
-
Sets the fixMode
- setFlags(int) - Method in class chemaxon.struc.graphics.MPolyline
-
Sets the flags.
- setFlags(int) - Method in class chemaxon.struc.MolAtom
-
Sets the flags.
- setFlags(int, int) - Method in class chemaxon.struc.MolAtom
-
Sets the flags.
- setFlags(int) - Method in class chemaxon.struc.MolBond
-
Sets bond type (4 bit), stereo (2+2+1 bit), topology (2 bit)
bond set (5 bit) and reacting center (7 bits) information.
- setFlags(int, int) - Method in class chemaxon.struc.MolBond
-
Sets bond type (3 bit), stereo (2+2+1 bit), and topology (2 bit)
information.
- setFlags(int) - Method in class chemaxon.struc.MoleculeGraph
-
Sets the flags of the molecule.
- setFlags(int, int) - Method in class chemaxon.struc.MoleculeGraph
-
Sets specified bits in the flags.
- setFlags(int) - Method in class chemaxon.struc.RgMolecule
-
Sets the dimension and chiral flags.
- setFlags(int, int) - Method in class chemaxon.struc.RgMolecule
-
Sets specified bits in the flags.
- setFlexibleRingRotatableBondCount(int) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
-
- setFlexibleRingRotatableBondCount(int) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
-
- setFlexibleRingSize(int) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
-
- setFlexibleRingSize(int) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
-
- setFlexibleRingSize(int) - Method in class chemaxon.marvin.alignment.PairwiseAlignment
-
- setFlipped(boolean) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
-
Sets the flip property of this sgroup.
- setFocus(MObject) - Method in class chemaxon.struc.MDocument
-
Focus to the specified object.
- setFogFactor(int) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the fog factor.
- setFontScale(double) - Method in class chemaxon.struc.graphics.MTextBox
-
Sets the font scaling factor.
- setForcedFlexible(boolean) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
-
- setForceField(String) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
-
Sets the force field type.
- setForegroundColor(Color) - Method in class chemaxon.marvin.space.monitor.Label
-
Sets the color of the characters on the label.
- setFormat(String) - Method in class chemaxon.calculations.dipole.DipoleCalculator.Builder
-
Sets the dipole export format.
- setFormat(String) - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder
-
Sets the spectrum export format.
- setFormat(String) - Method in class chemaxon.formats.MolInputStream
-
Sets the molecule file format.
- setFormat(String) - Method in class chemaxon.marvin.beans.MarvinPane
-
Sets the default molecule file format.
- setFormat(String) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
-
- setForSpecIsotopeSymbol(String) - Method in class chemaxon.struc.MolAtom
-
- setFrequency(double) - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder
-
Sets NMR measurement frequency.
- setFrequency(double) - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
Sets the NMR measurement frequency.
- setFromSgroupCopy(SgroupAtom) - Method in class chemaxon.struc.sgroup.SgroupAtom
-
Make a copy of this S-group superatom.
- setGenerateDistanceRanges(boolean) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
-
Generate intermolecular atomic distance ranges by tweaking conformation.
- setGeneratePreferredIUPACName(boolean) - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
-
Sets preferred IUPAC name generation.
- setGenerateTraditionalIUPACName(boolean) - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
-
Sets traditional IUPAC name generation.
- setGenNameFontSize(int) - Method in class chemaxon.marvin.view.swing.TableOptions
-
Sets the IUPAC name font size.
- setGenNameShown(boolean) - Method in class chemaxon.marvin.view.swing.TableOptions
-
Set visibility of IUPAC names.
- setGeom3D(boolean) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
-
Sets 3D geometry consideration.
- setGL(GL2, GLU) - Method in class chemaxon.marvin.space.GraphicComponent
-
Sets the GL2 rendering environment.
- setGL(GL2, GLU) - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- setGL(GL2, GLU) - Method in class chemaxon.marvin.space.MacroMoleculeComponent
-
Sets GL2 in all of its visualizers.
- setGL(GL2, GLU) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- setGL(GL2, GLU) - Method in class chemaxon.marvin.space.MoleculeComponent
-
Sets drawing related variable.
- setGlobalGUIProperties(MPropertyContainer) - Method in class chemaxon.marvin.beans.MarvinPane
-
- setGlobalGUIProperties(MPropertyContainer) - Method in class chemaxon.marvin.io.MolExportModule
-
Pass and set the global GUI properties container.
- setGrabbingEnabled(boolean) - Method in class chemaxon.formats.MolImporter
-
Deprecated.
as of Marvin 6.2. It has no effect on the code.
- setGraphInvariantVisible(boolean) - Method in class chemaxon.marvin.MolPrinter
-
Sets the graph invariant visibility
- setGrinv(boolean) - Method in class chemaxon.marvin.beans.MarvinPane
-
Deprecated.
as of Marvin 3.5, use setGrinvVisible(boolean) instead
- setGrinvCC(long) - Method in class chemaxon.struc.MoleculeGraph
-
Sets the graph invariant change count.
- setGrinvOptions(int) - Method in class chemaxon.struc.MoleculeGraph
-
Sets graph invariant calculation options passed to the module.
- setGrinvVisible(boolean) - Method in class chemaxon.marvin.beans.MarvinPane
-
Shows or hides the graph invariants.
- setGUIContracted(boolean) - Method in class chemaxon.struc.Molecule
-
- setGUIContracted(boolean, int) - Method in class chemaxon.struc.Molecule
-
- setGUIMode(boolean) - Method in class chemaxon.marvin.calculations.HBDAPlugin
-
Deprecated.
- setGUIPropertyContainer(MPropertyContainer) - Method in class chemaxon.struc.MDocument
-
Sets the property container storing MarvinPane settings
- setGUIProperyContainer(MPropertyContainer) - Method in class chemaxon.struc.MDocument
-
- setGUIStateRecursively(boolean) - Method in class chemaxon.struc.Sgroup
-
- setGUIStateRecursively(boolean, int) - Method in class chemaxon.struc.Sgroup
-
- setGUIStateRecursively(boolean) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Sets the expanded/contracted state recursively.
- setHalfWidth(double) - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
Sets NMR half-width.
- setHeadCrossingBonds(MolBond[]) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
-
Sets the head crossing bonds.
- setHeaderCellSize(int, int) - Method in class chemaxon.marvin.beans.MViewParams
-
Sets a logical cell extent by interpreting rows and columns as part of a sub-table.
- setHeaderStyle(CellStyle) - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
Sets the cell style for the header row
- setHelpText(String) - Method in class chemaxon.checkers.AbstractStructureChecker
-
- setHelpText(String) - Method in class chemaxon.checkers.InvalidChecker
-
- setHelpText(String) - Method in interface chemaxon.checkers.StructureChecker
-
Deprecated.
This method isn't needed anymore and will be removed in 6.0
- setHelpText(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor
-
Sets the help text of the concerning checker
- setHelpText(String) - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
-
Sets the help text displayed on empty component
- setHighlighted(boolean) - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- setHighlighted(boolean) - Method in class chemaxon.marvin.space.MoleculeComponent
-
This functionality is currently unavailable.
- setHighlighted(boolean) - Method in class chemaxon.marvin.space.PharmacophoreArrow
-
Sets the component to be highlighted.
- setHighlighted(boolean) - Method in class chemaxon.marvin.space.PharmacophorePoint
-
Sets the highlighted state of the pharmacophore point.
- setHitColor(Color) - Method in class chemaxon.util.HitColoringAndAlignmentOptions
-
Sets the color to be used when coloring the substructure hit.
- setHitHomologyColor(Color) - Method in class chemaxon.util.HitColoringAndAlignmentOptions
-
Set the color of user defined homologies in a substructure hit.
- setHomogeneousPaletteColors(byte[][]) - Method in class chemaxon.marvin.space.SurfaceColoring
-
This is an easy way to create a homogenous palette and use it as a color mapper.
- setHorizontalAlignment(int) - Method in class chemaxon.struc.graphics.MTextBox
-
Sets the horizontal alignment.
- setHybridizationState(int) - Method in class chemaxon.struc.MolAtom
-
Sets the hybridization state.
- setHybridizationState(int, int) - Method in interface chemaxon.struc.WSmolecule
-
Sets the hybridization state of an atom.
- setHydrogenCountChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker
-
Sets the option determining if the checker detects hydrogen count atom
query properties or not.
- setHydrogenize(boolean) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
-
Set hydrogenize parameter
- setHydrophobic(boolean) - Method in class chemaxon.marvin.space.PharmacophorePoint
-
Sets or clears the hydrophobic property of the PharmacophorePoint.
- setHyperfine(boolean) - Method in class chemaxon.marvin.calculations.ConformerPlugin
-
Sets the hyperfine option for calculation.
- setIcon(Icon) - Method in class chemaxon.checkers.AbstractStructureChecker
-
- setIcon(Icon) - Method in class chemaxon.checkers.InvalidChecker
-
- setIcon(Icon) - Method in interface chemaxon.checkers.StructureChecker
-
Deprecated.
This method isn't needed anymore and will be removed in 6.0
- setIconImage(JFrame) - Static method in class chemaxon.marvin.space.MSpaceEasy
-
Sets the MarvinSpace icon to the frame.
- setIconPath(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor
-
Sets the icon path
- setIDBackgroundRGBA(int, int) - Method in class chemaxon.marvin.view.MDocStorage
-
Sets the background color's RGBA value in a record.
- setIdentity() - Method in class chemaxon.struc.CTransform3D
-
Makes identity transformation.
- setIDForegroundRGBA(int, int) - Method in class chemaxon.marvin.view.MDocStorage
-
Sets the foreground color's RGBA value in a record.
- setIgnoreConfigurationErrors(boolean) - Method in class chemaxon.checkers.runner.BasicCheckerRunner
-
- setIgnoreConfigurationErrors(boolean) - Method in interface chemaxon.checkers.runner.CheckerRunner
-
Sets whether configuration errors should be ignored on execution.
- setIgnoreError(boolean) - Method in class chemaxon.formats.MolConverter
-
Sets the 'ignoreError' option.
- setImageImportServiceURL(String) - Method in class chemaxon.marvin.common.UserSettings
-
- setImplicitH(String) - Method in class chemaxon.marvin.beans.MarvinPane
-
Sets the display method of implicit hydrogens.
- setImplicitH(String) - Method in class chemaxon.marvin.MolPrinter
-
Sets the display method of implicit hydrogens.
- setImplicitHBasedOnValence(Valence) - Method in class chemaxon.struc.MolAtom
-
Deprecated.
as of Marvin 6.0.1, exists only for internal usage
Usage: Internal usage only.
- setImplicitHcount(int) - Method in class chemaxon.struc.MolAtom
-
Sets the number of implicit hydrogens.
- setImplicitHcount(int, int) - Method in interface chemaxon.struc.WSmolecule
-
Sets the number of implicit Hydrogens.
- setImplicitHydrogenCountChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker
-
Sets the option determining if the checker detects implicit hydrogen
count atom query properties or not.
- setImplicitHydrogenMode(boolean) - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
Sets implicit hydrogen mode.
- setImporter(MolImporter) - Method in class chemaxon.marvin.util.MolFragLoader
-
Sets the fragment iterator from the specified importer.
- setIn3D(boolean) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
-
Sets to display the molecule in 3D.
- setInactive() - Method in class chemaxon.marvin.space.GraphicCell
-
Deactivates this cell, so it is no longer the active cell of the scene.
- setIndex(int) - Method in class chemaxon.checkers.runner.BasicCheckerRunner
-
Sets the index
- setIndex(int) - Method in class chemaxon.marvin.space.GraphicCell
-
Sets the internal index of the cell.
- setIndexOfOriginalLigand(int) - Method in class chemaxon.marvin.plugin.CalculatorPlugin.HydrogenData
-
- setIndices(int, int) - Method in class chemaxon.marvin.space.GraphicCell
-
Sets which row and column of the scene is this cell in.
- setInitialTemperature(double) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
-
Sets the initial temperature.
- setInput(Object) - Method in class chemaxon.marvin.plugin.concurrent.PluginWorkUnit
-
Sets the input molecule.
- setInput(Object) - Method in class chemaxon.marvin.plugin.concurrent.ReusablePluginWorkUnit
-
Sets the plugin object and the input molecule.
- setInput(Object) - Method in class chemaxon.util.concurrent.marvin.CompositeWorkUnit
-
Sets the input in each work unit.
- setInput(Object) - Method in interface chemaxon.util.concurrent.WorkUnit
-
- setInputFormat(String) - Method in class chemaxon.struc.MDocument
-
Sets the input file format.
- setInputFormat(String) - Method in class chemaxon.struc.Molecule
-
Sets the input file format.
- setInputFormat(String) - Method in class chemaxon.struc.RgMolecule
-
Sets the input file format.
- setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.AlignmentPlugin
-
- setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ChargePlugin
-
Sets the input molecule.
- setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ConformerPlugin
-
Sets the input molecule.
- setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
-
Sets the input molecule.
- setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
Sets the input molecule.
- setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.HBDAPlugin
-
Sets the input molecule.
- setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
-
Sets the input molecule.
- setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.IonChargePlugin
-
Sets the input molecule.
- setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
-
Sets the input molecule.
- setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
-
Sets the input molecule.
- setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.logDPlugin
-
Sets the input molecule.
- setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.logPPlugin
-
Sets the input molecule.
- setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
-
Sets the input molecule.
- setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Sets the input molecule.
- setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
-
Sets the input molecule.
- setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MSAPlugin
-
Sets the input molecule.
- setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
-
Sets the input molecule.
- setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Sets the input molecule.
- setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
-
Sets the input molecule.
- setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.RefractivityPlugin
-
Sets the input molecule.
- setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ResonancePlugin
-
Sets the input molecule.
- setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
-
Sets the input molecule.
- setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
-
Set input molecule to process
- setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Sets the input molecule.
- setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Sets the input molecule.
- setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.TPSAPlugin
-
Sets the input molecule.
- setInputMolecule(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Sets the input molecule.
- setInputMoleculeModified(boolean) - Method in class chemaxon.marvin.calculations.ResonancePlugin
-
- setInputMoleculeModified(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
- setInputProducers(InputProducer[]) - Method in class chemaxon.util.concurrent.marvin.CompositeInputProducer
-
Sets the input producers.
- setIntegrator(String) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
-
Sets the integrator used for calculations.
- setInvisibleSets(long) - Method in class chemaxon.marvin.beans.MarvinPane
-
Sets the visibility of the specified atom sets.
- setIsValenceCheckNeeded(boolean) - Method in class chemaxon.struc.MolAtom
-
- setIterator(MoleculeIterator) - Method in class chemaxon.marvin.util.MolFragLoader
-
Sets the fragment iterator.
- setKeepExplicitHydrogens(boolean) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
-
Sets if result molecule keeps explicit hydrogens or not
- setKeepExplicitHydrogens(boolean) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
-
Sets if result molecule keeps explicit hydrogens or not
- setKeepExplicitHydrogens(boolean) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Sets if result molecule keeps explicit hydrogens or not
- setKeepHydrogens(Properties) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
- setKeepMapping(boolean) - Method in class com.chemaxon.mapper.AutoMapper.Options
-
Default value true
- setKeepMapping(boolean) - Method in class com.chemaxon.mapper.AutoMapper
-
- setKeepMapping(boolean) - Method in interface com.chemaxon.mapper.Mapper
-
Sets if the initial mapping of the given object should be kept or not.
- setKeepSingleAtom(boolean) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
-
Set behavior on acyclic input
- setL(int, String) - Method in class chemaxon.marvin.beans.MViewPane
-
Sets a label in a GridBagView table.
- setL(int, int, String) - Method in class chemaxon.marvin.view.MDocStorage
-
Sets a text label in a record.
- setLabel(Label) - Method in class chemaxon.marvin.space.monitor.MeasurementMonitor
-
Sets the Label of the monitor that is to display the measurement.
- setLabel2DDrawing(boolean) - Method in class chemaxon.marvin.space.monitor.Label
-
Sets the drawing mode of the label that can be drawing in plane
or in exact depth.
- setLabelCenter(int) - Method in class chemaxon.struc.sgroup.SgroupAtom
-
Sets the index of the character in the label the bonds should point to.
- setLabelProperty(int, boolean, boolean) - Method in class chemaxon.marvin.beans.MViewParams
-
Defines properties for cells containing label components.
- setLabels(boolean) - Method in class chemaxon.marvin.beans.MarvinPane
-
Deprecated.
use setAtomSymbolsVisible(v) instead
- setLabelSize(String) - Method in class chemaxon.marvin.space.monitor.Label
-
Sets the size of the label font.
- setLastSketchFrameSize(Dimension) - Method in class chemaxon.marvin.common.UserSettings
-
- setLayout(int, int) - Method in class chemaxon.marvin.space.MSpaceEasy
-
Sets the number of rows and columns of cells the viewport is sepearted to.
- setLeavingGroup(int, int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Deprecated.
As of Marvin 6.2, no replacement.
Not supported feature.
- setLeavingGroup(int, int, String) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Deprecated.
As of Marvin 6.2, no replacement.
Not supported feature.
- setLeavingGroup(int, int, String, BondType) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Deprecated.
As of Marvin 6.2, no replacement.
Not supported feature.
- setLeavingGroupAlternativeName(int, String) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Deprecated.
As of Marvin 6.2, no replacement.
Not supported feature.
- setLeftName(String) - Method in class chemaxon.struc.sgroup.SgroupAtom
-
Set the string that will be shown at the left side of the molecule.
- setLfin(boolean) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
-
Set handling option for multi fragment (disconnected) inputs
- setLfout(boolean) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
-
Set handling option for multi fragment (disconnected) results.
- setLicense(String) - Static method in class chemaxon.license.LicenseManager
-
Sets a pre-read license file to the license manager to read and validate licenses from.
- setLicenseEnvironment(String) - Method in class chemaxon.calculations.Ring
-
This method is for internal use only.
- setLicenseEnvironment(String) - Method in class chemaxon.calculations.TopologyAnalyser
-
- setLicenseEnvironment(String) - Method in class chemaxon.checkers.AbstractStructureChecker
-
- setLicenseEnvironment(String) - Method in class chemaxon.jep.Evaluator
-
For internal usage only.
- setLicenseEnvironment(String) - Method in class chemaxon.marvin.alignment.AlignRigidEasy
-
- setLicenseEnvironment(String) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
-
- setLicenseEnvironment(String) - Method in class chemaxon.marvin.alignment.PairwiseAlignment
-
- setLicenseEnvironment(String) - Method in interface chemaxon.marvin.alignment.PairwiseComparison
-
- setLicenseEnvironment(String) - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D
-
- setLicenseEnvironment(String) - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
- setLicenseEnvironment(String) - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
-
- setLicenseEnvironment(String) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
- setLicenseEnvironment(String) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
- setLicenseEnvironment(String) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Sets license environment to be stored.
- setLicenseFile(String) - Static method in class chemaxon.license.LicenseManager
-
Sets the license file location to the license manager to read and validate
licenses from.
- setLigandErrorVisible(boolean) - Method in class chemaxon.marvin.common.UserSettings
-
Show or hide ligand errors
- setLigandErrorVisible(boolean) - Method in class chemaxon.marvin.MolPrinter
-
Sets the bond's ligand error visibility
- setLigandOrder(int, MolAtom) - Method in class chemaxon.struc.MolAtom
-
Sets the order of a specified ligand.
- setLigandOrderVisibility(String) - Method in class chemaxon.marvin.MolPrinter
-
Sets the ligand order visibility.
- setLineColor(Color) - Method in class chemaxon.struc.MObject
-
Sets the color of the object.
- setLineNumberInFile(int) - Method in exception chemaxon.formats.MolFormatException
-
Sets the line number relative to the first line of the file.
- setLineNumberInRecord(int) - Method in exception chemaxon.formats.MolFormatException
-
Sets the line number relative to the first line of the record.
- setLinkNodeDefaultOuters() - Method in class chemaxon.struc.MolAtom
-
Sets link node outer atoms to default values, if they are not set yet.
- setLinkNodeDefaultOuters(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
-
Sets link node outer atoms to default values, if they are not set yet;
making sure that the resulting link node configuration is valid.
- setLinkNodeOuterAtom(int, int) - Method in class chemaxon.struc.MolAtom
-
Sets one of the link node's outer neighbor atoms.
- setList(int[], int) - Method in class chemaxon.struc.MolAtom
-
Sets the list elements.
- setList(int[]) - Method in class chemaxon.struc.MolAtom
-
Sets the list elements.
- setListeners(MDocStorage.Listener[]) - Method in class chemaxon.marvin.view.MDocStorage
-
- setListFont(Font) - Method in class chemaxon.marvin.view.swing.TableOptions
-
- setLoadSaveLocation(String) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the load/save filechooser working directory selection method names, based on the
preferences dialog.
- setLoadWorkingDir(String) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the filechooser's default working directory, if the filechooser working directory
selection method is saveCustomLocation.
- setLocalAromaticChecking(boolean) - Method in class chemaxon.core.calculations.valencecheck.ValenceCheckOptions.Builder
-
- setLocalAromatiChecking(boolean) - Method in class chemaxon.core.calculations.valencecheck.ValenceCheckOptions.Builder
-
- setLocalMenuName(String) - Method in class chemaxon.checkers.AbstractStructureChecker
-
- setLocalMenuName(String) - Method in class chemaxon.checkers.InvalidChecker
-
- setLocalMenuName(String) - Method in interface chemaxon.checkers.StructureChecker
-
Deprecated.
This method isn't needed anymore and will be removed in 6.0
- setLocalMenuName(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor
-
Sets the local menu name of the concerning checker
- setLocalParity(int[], boolean) - Method in class chemaxon.struc.MoleculeGraph
-
In case of 2D molecule change the bonds flag (UP/DOWN),
in case of 0D molecule set the atom flags
to achieve the specified parity array.
- setLocalParity(int[], int[], boolean) - Method in class chemaxon.struc.MoleculeGraph
-
Set given local parity for the given atomic indexes.
- setLocation(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MAtomSetPoint
-
Sets the atom coordinates.
- setLocation(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MEFlowBasePoint
-
Sets the atom coordinates.
- setLocation(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MMidPoint
-
Sets the location
- setLocation(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MRectanglePoint
-
Sets the coordinates.
- setLocation(DPoint3) - Method in class chemaxon.struc.MolAtom
-
Sets the coordinates.
- setLocation(DPoint3) - Method in class chemaxon.struc.MoleculeGraph
-
Set the origin of the molecule.
- setLocation(DPoint3, CTransform3D) - Method in class chemaxon.struc.MPoint
-
Sets the point's location.
- setLocation(DPoint3) - Method in class chemaxon.struc.RgMolecule
-
Set the origin of the molecule.
- setLocation(DPoint3) - Method in class chemaxon.struc.RxnMolecule
-
Set the origin of the molecule.
- setLogger(CalculatorLogger) - Method in class chemaxon.calculations.dipole.DipoleCalculator.Builder
-
- setLogger(CalculatorLogger) - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder
-
- setLogger(StructureCheckerLogger) - Method in class chemaxon.checkers.runner.AdvancedCheckerRunner
-
Sets the logger.
- setlogPMethod(int) - Method in class chemaxon.marvin.calculations.logDPlugin
-
Sets the logP calculation method.
- setlogPMethod(int) - Method in class chemaxon.marvin.calculations.logPPlugin
-
Sets the logP calculation method.
- setLogPTrainingId(String) - Method in class chemaxon.marvin.calculations.logDPlugin
-
Sets the user defined logP training.
- setLonePairAsLine(boolean) - Method in class chemaxon.marvin.MolPrinter
-
Sets the visibility of Lone Pairs
- setLonePairAutoCalc(boolean) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the state of the automatic lone pair calculation.
- setLonePairsAutoCalculated(boolean) - Method in class chemaxon.marvin.MolPrinter
-
Sets the state of the automatic calculation of lone pairs.
- setLonePairsVisible(boolean) - Method in class chemaxon.marvin.beans.MarvinPane
-
Shows or hides (implicit) lone pairs.
- setLonePairsVisible(boolean) - Method in class chemaxon.marvin.MolPrinter
-
Sets the visibility state of lone pairs.
- setLowerCutoffValue(double) - Method in class chemaxon.marvin.space.SurfaceColoring
-
Cutoff values can be set to the built-in two pole palettes.
- setLowestEnergyConformerCalculation(boolean) - Method in class chemaxon.marvin.calculations.ConformerPlugin
-
Switchs the lowest energy conformer calculation on/off.
- setM(int, Molecule...) - Method in class chemaxon.marvin.beans.MViewPane
-
Sets the nth animation or structure.
- setM(int, String) - Method in class chemaxon.marvin.beans.MViewPane
-
Deprecated.
As of Marvin 5.2.5, it is recommended to import the molecule in advance, e.g. by
using MolImporter, then set the cell synchronously using
MViewPane.setM(int, Molecule...). The reason is to simplify the public API and
minimize the risk of related concurrency problems in user codes.
- setM(int, String, String) - Method in class chemaxon.marvin.beans.MViewPane
-
Deprecated.
As of Marvin 5.2.5, it is recommended to import the molecule in advance, e.g. by
using MolImporter, then set the cell synchronously using
MViewPane.setM(int, Molecule...). The reason is to simplify the public API and
minimize the risk of related concurrency problems in user codes.
- setM(int, File, String) - Method in class chemaxon.marvin.beans.MViewPane
-
Deprecated.
As of Marvin 5.2.5, it is recommended to import the molecule in advance, e.g. by
using MolImporter, then set the cell synchronously using
MViewPane.setM(int, Molecule...). The reason is to simplify the public API and
minimize the risk of related concurrency problems in user codes.
- setMacroMoleculeComponent(MacroMoleculeComponent) - Method in class chemaxon.marvin.space.MoleculeComponent
-
A MacroMoleculeComponent can be set and in this case this will be a
visualizer of a ligand in the macromolecule.
- setMag(double) - Method in class chemaxon.marvin.beans.MSketchPane
-
Deprecated.
As of Marvin 2.8.1, replaced by setScale()
- setMainMoleculeGraph(MoleculeGraph) - Method in class chemaxon.struc.MDocument
-
Sets the main molecule graph.
- setMappingStyle(Mapper.MappingStyle) - Method in class com.chemaxon.mapper.AutoMapper.Options
-
- setMappingStyle(Mapper.MappingStyle) - Method in class com.chemaxon.mapper.AutoMapper
-
Sets the mapping style
- setMappingStyle(Mapper.MappingStyle) - Method in interface com.chemaxon.mapper.Mapper
-
Sets the mapping style
- setMarkBonds(boolean) - Method in class com.chemaxon.mapper.AutoMapper.Options
-
Default value false
- setMarkBonds(boolean) - Method in class com.chemaxon.mapper.AutoMapper
-
- setMarkBonds(boolean) - Method in interface com.chemaxon.mapper.Mapper
-
Sets if the changing bonds should be marked or not.
- setMarkushDisplayMode(int) - Method in class chemaxon.util.HitColoringAndAlignmentOptions
-
Sets the Markush display mode.
- setMarvinCompMode(boolean) - Method in class chemaxon.marvin.io.formats.smiles.SmartsAtomQuerifier
-
Marvin compatibility mode.
- setMassno(int) - Method in class chemaxon.struc.MolAtom
-
Sets the mass number.
- setMassno(int, int) - Method in interface chemaxon.struc.WSmolecule
-
Sets the mass number.
- setMax(float, float, float) - Method in class chemaxon.marvin.space.BoundingBox
-
Sets the maximum coordinates of the box.
- setMaxCols(int) - Method in class chemaxon.marvin.view.swing.TableOptions
-
Set maximum value of columns in the table
- setMaximum(int) - Method in interface chemaxon.common.util.MProgressMonitor
-
Gets the maximum value.
- setMaximum(int) - Method in interface chemaxon.marvin.alignment.AlignmentMoleculeFactory.ProgressBarInterface
-
- setMaximumTautomerizationPathLength(int) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Sets the maximum allowed length of the tautomerization path in chemical bonds.
- setMaximumValue(double) - Method in class chemaxon.marvin.space.SurfaceColoring
-
Sets the greatest property value of the surface vertices considered.
- setMaxIons(int) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
In case of
pKaPlugin.MODEL_SMALL model, it
sets the maximum number of ionizable atoms to be considered
and uses simple calculation method to compute pKa values.
- setMaxNumberOfConformers(int) - Method in class chemaxon.marvin.calculations.ConformerPlugin
-
Sets the maximum number of conformers to be calculated.
- setMaxNumberOfStereoisomers(int) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
-
Sets the maxinum number of stereoisomers to be generated.
- setMaxOutputQueueSize(int) - Method in interface chemaxon.util.concurrent.ConcurrentProcessor
-
Sets the maximum size of the output queue.
- setMaxRepetitions(int) - Method in class chemaxon.struc.MolAtom
-
Sets the maximum number of repetitions for a link atom.
- setMaxRows(int) - Method in class chemaxon.marvin.view.swing.TableOptions
-
Set maximum value of rows in the table
- setMaxSize(int) - Method in class chemaxon.marvin.view.swing.TableOptions
-
Set the maximum number of molecules displayed in the table.
- setMaxStructureCount(long) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Sets the maximum number of structures to be generated.
- setMaxStructureCount(int) - Method in class chemaxon.marvin.calculations.ResonancePlugin
-
Sets the maximum number of structures to be generated.
- setMaxStructureCount(int) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Sets the maximum number of structures to be generated.
- setMaxThreadCount(int) - Method in class com.chemaxon.mapper.AutoMapper.Options
-
Default value
Integer.MAX_VALUE
The number of threads used for mapping will be the minimum of maxThreadCount and the number of available
processors.
- setMaxX(float) - Method in class chemaxon.marvin.space.BoundingBox
-
Sets the maximum x coordinate of the box.
- setMaxY(float) - Method in class chemaxon.marvin.space.BoundingBox
-
Sets the maximum y coordinate of the box.
- setMaxZ(float) - Method in class chemaxon.marvin.space.BoundingBox
-
Sets the maximum z coordinate of the box.
- setMergedst(double) - Method in class chemaxon.marvin.beans.MSketchPane
-
Sets the merge distance.
- setMessage(String) - Method in interface chemaxon.marvin.alignment.AlignmentMoleculeFactory.ProgressBarInterface
-
- setMetalAtoms(List<MolAtom>) - Method in class chemaxon.checkers.result.MetalloceneCheckerResult
-
This method sets the metalAtoms property
- setMethylsRotatable(boolean) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
-
This is a speedup heuristics.
- setMicropKaCalc(boolean) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Sets micro pKa calculation.
- setMin(float, float, float) - Method in class chemaxon.marvin.space.BoundingBox
-
Sets the minimum coordinates of the box.
- setMinDistTryCount(int) - Method in class chemaxon.marvin.alignment.MinMaxDistance
-
- setMinimum(int) - Method in interface chemaxon.marvin.alignment.AlignmentMoleculeFactory.ProgressBarInterface
-
- setMinimumCommonSize(int) - Method in class chemaxon.marvin.alignment.Alignment
-
Deprecated.
- setMinimumCommonSize(int) - Method in class chemaxon.marvin.alignment.PairwiseAlignment
-
- setMinimumCommonSize(int) - Method in class chemaxon.marvin.calculations.AlignmentPlugin
-
Deprecated.
- setMinimumHeight(double) - Method in class chemaxon.struc.graphics.MTextBox
-
Sets the minimum height of the text..
- setMinimumHeightSet(boolean) - Method in class chemaxon.struc.graphics.MTextBox
-
Turns on/off minimum height calculation.
- setMinimumValue(double) - Method in class chemaxon.marvin.space.SurfaceColoring
-
Sets the lowest property value of the surface vertices considered.
- setMinRepetitions(int) - Method in class chemaxon.struc.MolAtom
-
Sets the minimum number of repetitions for a link node.
- setMinX(float) - Method in class chemaxon.marvin.space.BoundingBox
-
Sets the minimum x coordinate of the box.
- setMinY(float) - Method in class chemaxon.marvin.space.BoundingBox
-
Sets the minimum y coordinate of the box.
- setMinZ(float) - Method in class chemaxon.marvin.space.BoundingBox
-
Sets the minimum z coordinate of the box.
- setMMFF94(boolean) - Method in class chemaxon.marvin.calculations.ConformerPlugin
-
Sets the forcefield to MMFF94.
- setMMFF94Optimization(boolean) - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
Sets MMFF94 optimization.
- setMode(AlignmentAccuracyMode) - Method in class chemaxon.marvin.alignment.Alignment
-
- setMode(AlignmentAccuracyMode) - Method in class chemaxon.marvin.alignment.PairwiseAlignment
-
- setModel(int) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Sets the calculation model.
- setMol(Molecule) - Method in class chemaxon.marvin.beans.MSketchPane
-
Sets the molecule.
- setMol(Molecule, boolean) - Method in class chemaxon.marvin.beans.MSketchPane
-
- setMol(String) - Method in class chemaxon.marvin.beans.MSketchPane
-
Starts loading a molecule into the sketcher.
- setMol(String, String) - Method in class chemaxon.marvin.beans.MSketchPane
-
Starts loading a molecule into the sketcher.
- setMol(File, String) - Method in class chemaxon.marvin.beans.MSketchPane
-
Sets the molecule.
- setMol(Molecule) - Method in class chemaxon.marvin.MolPrinter
-
Sets the current molecule and calculate its bounds.
- setMol(String) - Method in class chemaxon.marvin.MolPrinter
-
Sets the current molecule and calculate its bounds.
- setMolbg(Color) - Method in class chemaxon.marvin.beans.MarvinPane
-
Sets the molecule background color.
- setMolBytes(byte[]) - Method in class chemaxon.marvin.io.MRecord
-
Sets the molecule bytes.
- setMolCenter(int, String, DPoint3) - Method in class chemaxon.marvin.view.MDocStorage
-
Sets a molecule center.
- setMolecule(String) - Method in class chemaxon.calculations.ElementalAnalyser
-
Specifies a molecule to calculate with.
- setMolecule(MoleculeGraph) - Method in class chemaxon.calculations.ElementalAnalyser
-
Specifies a molecule to calculate with.
- setMolecule(Smolecule) - Method in class chemaxon.calculations.ElementalAnalyser
-
- setMolecule(MoleculeGraph) - Method in class chemaxon.calculations.Ring
-
Specifies a molecule to calculate with.
- setMolecule(MoleculeGraph, int) - Method in class chemaxon.calculations.Ring
-
Specifies a molecule to calculate with.
- setMolecule(MoleculeGraph) - Method in class chemaxon.calculations.stereo.Stereochemistry
-
Specifies a molecule to calculate with.
- setMolecule(MoleculeGraph) - Method in class chemaxon.calculations.TopologyAnalyser
-
Specifies a molecule to calculate with.
- setMolecule(MoleculeGraph, int) - Method in class chemaxon.calculations.TopologyAnalyser
-
Specifies a molecule to calculate with.
- setMolecule(Molecule) - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
-
- setMolecule(Molecule) - Method in interface chemaxon.checkers.result.StructureCheckerResult
-
This method sets the molecule
- setMolecule(Molecule) - Method in class chemaxon.checkers.runner.AdvancedCheckerRunner
-
- setMolecule(Molecule) - Method in class chemaxon.checkers.runner.BasicCheckerRunner
-
- setMolecule(Molecule) - Method in interface chemaxon.checkers.runner.CheckerRunner
-
Sets the molecule to be checked by the checkers
- setMolecule(Molecule) - Method in class chemaxon.checkers.runner.SketchCheckerRunner
-
- setMolecule(Molecule) - Method in class chemaxon.jep.context.MolContext
-
Sets the input molecule.
- setMolecule(Molecule) - Method in class chemaxon.marvin.alignment.MinMaxDistance
-
- setMolecule(Molecule, boolean, boolean) - Method in class chemaxon.marvin.calculations.ChargePlugin
-
- setMolecule(String) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
-
Specifies a molecule to calculate with.
- setMolecule(Molecule, boolean, boolean) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
-
- setMolecule(Molecule) - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
-
Sets the Molecule which will be represented by the MTransferable.
- setMolecule(Molecule) - Method in interface chemaxon.marvin.modules.datatransfer.MTransferable
-
Sets the Molecule which will be represented by the transferable.
- setMolecule(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Sets the input molecule after standardization.
- setMolecule(Molecule, boolean) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Sets the input molecule after an optional standardization.
- setMolecule(Molecule, boolean, boolean) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Sets the input molecule after an optional standardization and/or modification.
- setMolecule(Molecule, boolean, boolean, boolean) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
- setMolecule(Object) - Method in class chemaxon.marvin.space.AtomProperty.MoleculeAtomProperty
-
- setMolecule(Object) - Method in class chemaxon.marvin.space.AtomProperty.SmoleculeAtomProperty
-
- setMolecule(Molecule) - Method in class chemaxon.marvin.space.MoleculeComponent
-
Sets the Molecule of the MoleculeComponent to mol,
sets proper atomIterators, and computes the bounding box.
- setMoleculeCellSize(int, int) - Method in class chemaxon.marvin.beans.MViewParams
-
Sets the preferred size of the cells containing molecules.
- setMoleculeMovie(MMoleculeMovie) - Method in class chemaxon.struc.MDocument
-
Sets the molecule movie.
- setMolecules(AlignmentMolecule, AlignmentMolecule) - Method in class chemaxon.marvin.alignment.Alignment
-
- setMolecules(AlignmentMolecule, AlignmentMolecule) - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
-
- setMolecules(ArrayList) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
The surface will be the molecular surface of the given molecules.
- setMoleculeToAlign(Molecule, boolean) - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
-
Sets the molecule to align to the reference.
- setMolID(int) - Method in class chemaxon.marvin.alignment.AlignmentMolecule
-
- setMolIndex(int) - Method in exception chemaxon.marvin.io.MolExportException
-
Sets the molecule index.
- setMolNameFontSize(int) - Method in class chemaxon.marvin.view.swing.TableOptions
-
Sets the molecule name font size.
- setMolNameShown(boolean) - Method in class chemaxon.marvin.view.swing.TableOptions
-
Sets visibility of molecule names.
- setMolPainter(int, String, MolPainter) - Method in class chemaxon.marvin.view.MDocStorage
-
Sets a molecule painter.
- setMolTemplate(Molecule) - Method in class chemaxon.marvin.MolPrinter
-
- setMoreErrorMessage(String) - Method in class chemaxon.checkers.AbstractStructureChecker
-
- setMoreErrorMessage(String) - Method in class chemaxon.checkers.InvalidChecker
-
- setMoreErrorMessage(String) - Method in interface chemaxon.checkers.StructureChecker
-
Deprecated.
This method isn't needed anymore and will be removed in 6.0
- setMoreErrorMessage(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor
-
Sets the more error message of the concerning checker
- setMotionMode(int) - Method in class chemaxon.marvin.space.GraphicCell
-
Notifies every component of moving and standing modes.
- setMotionMode(int) - Method in class chemaxon.marvin.space.GraphicComponent
-
Sets the motion state of the component.
- setMotionMode(int) - Method in class chemaxon.marvin.space.GraphicScene
-
Notifies every cell of moving and standing modes.
- setMPLabelsVisible(boolean) - Method in class chemaxon.marvin.MolPrinter
-
Sets the visibility state of M/P labels.
- setMPVisible(boolean) - Method in class chemaxon.marvin.beans.MarvinPane
-
Sets the M/P display option.
- setMPVisible(boolean) - Method in class chemaxon.marvin.common.UserSettings
-
- setMrvWithSettings(String) - Method in class chemaxon.marvin.beans.MSketchPane
-
Sets the molecule and its display settings.
- setMsCalc(boolean) - Method in class chemaxon.marvin.calculations.HBDAPlugin
-
Sets microspecies calculation.
- setMsCalc(boolean) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Sets calculation of microspecies distributions.
- setMSLogic(Map<MRArrow, RxnMolecule>) - Method in class chemaxon.struc.RxnMolecule
-
Sets the hash that stores arrow - reaction mapping.
- setMultiplets(Multiplet[]) - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
Sets Multiplet array of the spectrum.
- setMultiplier(int) - Method in class chemaxon.struc.sgroup.MultipleSgroup
-
Sets the multiplier.
- setNaKIonConcentration(double) - Method in class chemaxon.marvin.calculations.logDPlugin
-
Sets the Na+, K+ concentration (default: 0.1).
- setNaKIonConcentration(double) - Method in class chemaxon.marvin.calculations.logPPlugin
-
Sets the Na+, K+ concentration (default: 0.1).
- setName(String) - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
Sets the name of the NMR spectrum
- setName(String) - Method in class chemaxon.checkers.AbstractStructureChecker
-
- setName(String) - Method in class chemaxon.checkers.InvalidChecker
-
- setName(String) - Method in interface chemaxon.checkers.StructureChecker
-
Deprecated.
This method isn't needed anymore and will be removed in 6.0
- setName(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor
-
Sets the checker name
- setName(String) - Method in class chemaxon.fixers.AbstractStructureFixer
-
- setName(String) - Method in interface chemaxon.fixers.StructureFixer
-
Deprecated.
- setName(String) - Method in class chemaxon.fixers.StructureFixerDescriptor
-
Sets the fixer name
- setName(String) - Method in class chemaxon.marvin.services.ServiceArgument
-
Sets the name of the argument
- setName(String) - Method in class chemaxon.marvin.space.GraphicComponent
-
Sets the name of the component.
- setName(String) - Method in class chemaxon.struc.Molecule
-
Sets the molecule name.
- setName(String) - Method in class chemaxon.struc.RgMolecule
-
Sets the name of the root molecule.
- setNameIOServiceURL(String) - Method in class chemaxon.marvin.common.UserSettings
-
- setNameSpace(String) - Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor
-
Sets the namespace
- setNavmode(String) - Method in class chemaxon.marvin.beans.MViewPane
-
Sets the mouse drag action.
- setNearEdgeTolerance(int) - Method in class chemaxon.marvin.space.GraphicCell
-
Sets the tolerance we consider to be near the edge of the cell.
- setNearEdgeTolerance(int) - Method in class chemaxon.marvin.space.GraphicScene
-
Sets a border near the boundary of the cells in which mouse handling can
work other way.
- setNegativeCriterium(double) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
Sets the lowest negative value colored.
- setNodeType(AlignmentProperties.NodeType) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
-
- setNoErrorMessage(String) - Method in class chemaxon.checkers.AbstractStructureChecker
-
- setNoErrorMessage(String) - Method in class chemaxon.checkers.InvalidChecker
-
- setNoErrorMessage(String) - Method in interface chemaxon.checkers.StructureChecker
-
Deprecated.
This method isn't needed anymore and will be removed in 6.0
- setNoErrorMessage(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor
-
Sets the no error message of the concerning checker
- setNonHitColor(Color) - Method in class chemaxon.util.HitColoringAndAlignmentOptions
-
Sets the color to be used when coloring the part of the
target which is not matching to the query.
- setNonHitColor3D(Color) - Method in class chemaxon.util.HitColoringAndAlignmentOptions
-
Sets the color to be used when coloring the part of the
3D target which is not matching to the query.
- setNonQueryImplicitHcount(int) - Method in class chemaxon.struc.MolAtom
-
Sets the number of non-query implicit hydrogens attached.
- setNotSpecCase(AlignmentProperties.ColorNotSpecifiedCase) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
-
- setNucleus(NMRSpectrum.Nucleus) - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder
-
Sets the NMR active nucleus.
- setNumberOfAtomsAcceptToRotate(int) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
-
If only a given number of atoms (or less) can be found at one of the side
of the dihedral skip this.
- setNumberOfNMRActiveNuclei(int) - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
Sets number of the NMR active nuclei.
- setObject(MObject, int) - Method in class chemaxon.struc.MDocument
-
Sets an object
- setObject(String, Object) - Method in class chemaxon.struc.MPropertyContainer
-
Sets a property object.
- setObject(MObject, int) - Method in class chemaxon.struc.MSelectionDocument
-
Sets an object
- setObjectContainingSelection(MObject) - Method in class chemaxon.struc.MDocument
-
Sets the object that contains the selection.
- setOeqcheck(boolean) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
-
Set oeqcheck parameter
- setOKActionListener(ActionListener) - Method in class chemaxon.marvin.plugin.PluginFactory
-
Sets the "OK" button pressed action listener.
- setOneErrorMessage(String) - Method in class chemaxon.checkers.AbstractStructureChecker
-
- setOneErrorMessage(String) - Method in class chemaxon.checkers.InvalidChecker
-
- setOneErrorMessage(String) - Method in interface chemaxon.checkers.StructureChecker
-
Deprecated.
This method isn't needed anymore and will be removed in 6.0
- setOneErrorMessage(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor
-
Sets the one error message of the concerning checker
- setOptimization(int) - Method in class chemaxon.marvin.calculations.ConformerPlugin
-
Sets the optimization criteria for the calculation.
- setOptimization(int) - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
Sets the optimization criteria for lowest energy conformer calculation.
- setOptimizeProjection(boolean) - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
- setOptions(String) - Method in class chemaxon.marvin.io.formats.mdl.MolImport
-
Sets the import options.
- setOptions(String) - Method in class chemaxon.marvin.io.MolImportModule
-
Sets the import options.
- setOptions(String) - Method in class chemaxon.marvin.io.MRecordImporter
-
Sets the options for the import module.
- setOptions(HitColoringAndAlignmentOptions, String) - Static method in class chemaxon.util.HitColoringAndAlignmentOptions
-
Parses the option list given while updating a HitColoringAndAlignmentOptions
object.
- setOrientationType(AlignmentProperties.OrientationType) - Method in class chemaxon.marvin.alignment.Alignment
-
- setOrigin(int, int) - Method in class chemaxon.marvin.space.GraphicCell
-
Sets the leftmost and bottomost coordinate of the cell.
- setOutput(OutputStream, String) - Method in class chemaxon.formats.MolConverter.Builder
-
Sets the output stream.
- setOutput(File, String) - Method in class chemaxon.formats.MolConverter.Builder
-
Sets the output file.
- setOutput(String, String) - Method in class chemaxon.formats.MolConverter.Builder
-
Sets the output file.
- setOutput(File, String) - Method in class chemaxon.formats.MolConverter.Options
-
Deprecated.
- setOutput(OutputStream, String) - Method in class chemaxon.formats.MolConverter.Options
-
Deprecated.
- setOutput(String, String) - Method in class chemaxon.formats.MolConverter.Options
-
Deprecated.
- setOutputFlags(int) - Method in class chemaxon.formats.MolConverter.Builder
-
Sets output flags.
- setOutputFlags(int) - Method in class chemaxon.formats.MolConverter.Options
-
Deprecated.
- setOutputParameters(Object[]) - Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
-
Prepares the output based on the result type string.
- setOutputStream(OutputStream) - Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
-
Sets the output stream.
- setPageFormat(PageFormat, String) - Method in class chemaxon.marvin.common.UserSettings
-
- setPageSettings(PageSettings) - Method in class chemaxon.struc.MDocument
-
Sets the page settings of multipage molecular document.
- setPalette(int) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
Sets a built-in palette used during coloring the molecular surface.
- setPalette(byte[][]) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
Sets colors to be used by the color palette.
- setPaletteMaximum(double) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
Sets the largest positive value colored.
- setPaletteMinimum(double) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
Sets the largest negative value colored.
- setParameters(String) - Method in interface chemaxon.jep.MolCondition
-
Deprecated.
Sets condition parameters.
- setParameters(Properties) - Method in class chemaxon.marvin.calculations.AlignmentPlugin
-
Sets the input parameters for the plugin.
- setParameters(Properties) - Method in class chemaxon.marvin.calculations.ChargePlugin
-
Sets the input parameters for the plugin.
- setParameters(Properties) - Method in class chemaxon.marvin.calculations.ConformerPlugin
-
Sets the input parameters for the plugin.
- setParameters(Properties) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
-
Sets the input parameters for the plugin.
- setParameters(Properties) - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
Sets the input parameters for the plugin.
- setParameters(Properties) - Method in class chemaxon.marvin.calculations.HBDAPlugin
-
Sets the input parameters for the plugin.
- setParameters(Properties) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
-
Sets the input parameters for the plugin.
- setParameters(Properties) - Method in class chemaxon.marvin.calculations.IonChargePlugin
-
Sets the input parameters for the plugin.
- setParameters(Properties) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
-
Sets the input parameters for the plugin.
- setParameters(Properties) - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
-
Sets the input parameters for the plugin.
- setParameters(Properties) - Method in class chemaxon.marvin.calculations.logDPlugin
-
Sets the input parameters for the plugin.
- setParameters(Properties) - Method in class chemaxon.marvin.calculations.logPPlugin
-
Sets the input parameters for the plugin.
- setParameters(Properties) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
-
Sets the input parameters for the plugin.
- setParameters(Properties) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
-
Sets the input parameters for the plugin.
- setParameters(Properties) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Sets the input parameters for the plugin.
- setParameters(Properties) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
-
Sets the input parameters for the plugin.
- setParameters(Properties) - Method in class chemaxon.marvin.calculations.MSAPlugin
-
Sets the input parameters for the plugin.
- setParameters(Properties) - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
-
Sets the input parameters for the plugin.
- setParameters(Properties) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Sets the input parameters for the plugin.
- setParameters(Properties) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
-
Sets the input parameters for the plugin.
- setParameters(Properties) - Method in class chemaxon.marvin.calculations.RefractivityPlugin
-
Sets the input parameters for the plugin.
- setParameters(Properties) - Method in class chemaxon.marvin.calculations.ResonancePlugin
-
Sets the input parameters for the plugin.
- setParameters(Properties) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
-
Sets the input parameters for the plugin.
- setParameters(Properties) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
-
Sets the input parameters for the plugin
Accepted parameters:
type: [bmf|mcs|sssr|cssr|allringsystems|largestringsystem|
largestring|keep] Framework calculation type
bmf: Bemis-Murcko framework
bmfl: Bemis-Murcko loose framework
mcs: Pairwise Maximum Common Substructure
sssr: SSSR
cssr: CSSR
allringsystems: all fused ring systems
largestringsystem: largest fused ring system
largestring: largest ring
keep: no framework reduction; useful for testing pre/post process
keepsingleatom: [true|false] If set true then a single atom
will be assigned to acyclic fragments.
- setParameters(Properties) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Sets the input parameters for the plugin.
- setParameters(Properties) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Sets the input parameters for the plugin.
- setParameters(Properties) - Method in class chemaxon.marvin.calculations.TPSAPlugin
-
Sets the input parameters for the plugin.
- setParameters(Properties) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Sets the input parameters for the plugin.
- setParameters(Properties) - Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
-
Sets parameters.
- setParameters(Properties) - Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
-
Sets the parameter table.
- setParams(String) - Method in class chemaxon.marvin.beans.MarvinPane
-
Sets the parameter string.
- setParent(Component) - Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
-
Sets the parent component.
- setParentComponent(Component) - Method in class chemaxon.marvin.plugin.PluginFactory
-
Sets the parent component - this is used to set options panes positions.
- setParentMolecule(Molecule) - Method in class chemaxon.struc.Sgroup
-
Sets the parent molecule.
- setParity(int, int) - Method in class chemaxon.struc.MoleculeGraph
-
Change the bonds flag (UP/DOWN) connected to the given atom to achieve
the specified parity.
- setParity(int[]) - Method in class chemaxon.struc.MoleculeGraph
-
Change the bonds flag (UP/DOWN) connected to the whole molecule
to achieve the specified parity array.
- setParity(int[], boolean) - Method in class chemaxon.struc.MoleculeGraph
-
Change the bonds flag (UP/DOWN) connected to the whole molecule
to achieve the specified parity array.
- setPatternMolecule(Molecule) - Method in class chemaxon.util.MolAligner
-
Sets pattern molecule and calculates its dimension
- setPeptideDisplay(String) - Method in class chemaxon.marvin.MolPrinter
-
Sets the Peptide display settings.
- setPeptideDisplayType(String) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the peptide displaying tpye.
- setpH(double) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
-
Sets a single pH value for the calculation of charge distribution.
- setpH(double) - Method in class chemaxon.marvin.calculations.logDPlugin
-
Sets a single pH value for the logD calculation.
- setpH(double) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
-
Sets the pH: major microspecies on given pH is taken as input molecule
if set to
Double.NaN then the input molecule is taken as it is.
- setpH(double) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
-
Sets the pH: major microspecies on given pH is taken as input molecule
if set to
Double.NaN then the input molecule is taken as it is.
- setpH(double) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Sets the pH value for the calculation of microspecies distributions.
- setpH(double) - Method in class chemaxon.marvin.calculations.ResonancePlugin
-
Deprecated.
As of Marvin 5.0 pH effect is not considered
- setpH(double) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Sets the pH to be considered in dominant tautomer generation.
- setpHLower(double) - Method in class chemaxon.marvin.calculations.HBDAPlugin
-
Sets pH lower limit for the calculation of microspecies distributions.
- setpHLower(double) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
-
Sets pH lower limit for the calculation of charge distribution
(default: 0.0).
- setpHLower(double) - Method in class chemaxon.marvin.calculations.logDPlugin
-
Sets pH lower limit (default: 0.0).
- setpHLower(double) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Sets pH lower limit for the calculation of microspecies distributions.
- setpHStep(double) - Method in class chemaxon.marvin.calculations.HBDAPlugin
-
Sets pH step for the calculation of microspecies distributions.
- setpHStep(double) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
-
Sets pH step for the calculation of charge distribution.
- setpHStep(double) - Method in class chemaxon.marvin.calculations.logDPlugin
-
Sets pH step to be taken between the pH lower and upper limits
(default: 1.0).
- setpHStep(double) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Sets pH step for the calculation of microspecies distributions.
- setpHUpper(double) - Method in class chemaxon.marvin.calculations.HBDAPlugin
-
Sets pH upper limit for the calculation of microspecies distributions.
- setpHUpper(double) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
-
Sets pH upper limit for the calculation of charge distribution
(default: 14.0).
- setpHUpper(double) - Method in class chemaxon.marvin.calculations.logDPlugin
-
Sets pH upper limit (default: 14.0).
- setpHUpper(double) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Sets pH upper limit for the calculation of microspecies distributions.
- setPickMatrix() - Method in class chemaxon.marvin.space.GraphicCell
-
- setPiece(String) - Method in class chemaxon.marvin.beans.MSketchPane
-
Sets the molecule piece.
- setpKaCorrectionLibrary(String) - Method in class chemaxon.marvin.calculations.logDPlugin
-
Sets the pKa correction library.
- setpKaPrefixType(int) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Sets pKa prefix type (default:
pKaPlugin.STATICpKaPREFIX)
STATIC pKa prefix: pKa's prefix does not depend on the submitted micro state
DYNAMIC pKa prefix: pKa's prefix does depend on the submitted micro state
- setPlainText(String) - Method in class chemaxon.struc.graphics.MTextDocument
-
Sets the document as plain text.
- setPlugin(CalculatorPlugin) - Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
-
Sets the plugin.
- setPlugin(CalculatorPlugin) - Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
-
Sets the calculator plugin object.
- setPlugin(CalculatorPlugin) - Method in class chemaxon.marvin.plugin.concurrent.PluginWorkUnit
-
Sets the plugin object.
- setPoints(MPoint[]) - Method in class chemaxon.struc.graphics.MPolyline
-
Sets the points.
- setPoints(MPoint[]) - Method in class chemaxon.struc.graphics.MTextBox
-
Sets the points.
- setPopupMenusEnabled(boolean) - Method in class chemaxon.marvin.beans.MarvinPane
-
Allows popup menus.
- setPortName(String) - Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor
-
Sets the port name
- setPos(int) - Method in class chemaxon.struc.sgroup.DataSgroup
-
Sets the data display DASP position (0...9).
- setPosition(float, float, float) - Method in class chemaxon.marvin.space.monitor.Label
-
Sets the monitor's position defined by 3 coordinates.
- setPosition(float[]) - Method in class chemaxon.marvin.space.monitor.Label
-
Sets the monitor's position defined by 3 coordinates.
- setPosition(float, float) - Method in class chemaxon.marvin.space.monitor.Label
-
Sets the monitor's position defined by 2 coordinates.
- setPosition(float, float, float) - Method in class chemaxon.marvin.space.monitor.PositionMonitor
-
Sets the monitor's position
- setPosition(float[]) - Method in class chemaxon.marvin.space.monitor.PositionMonitor
-
Sets the monitor's position
- setPosition(double, double, double) - Method in class chemaxon.marvin.space.PharmacophoreArrow
-
Sets the position of the PharmacophoreArrow.
- setPosition(double, double, double) - Method in class chemaxon.marvin.space.PharmacophorePoint
-
Sets the position of the PharmacophorePoint.
- setPositiveCriterium(double) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
Sets the lowest positive value colored.
- setPreferredSize(Dimension) - Method in class chemaxon.marvin.beans.MViewPane
-
Sets the preferred size of the component.
- setPrefix(String) - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
-
Sets the code assist invoke prefix
- setPrefixMode(boolean) - Method in interface chemaxon.naming.NameConverter
-
Set the prefix mode flag.
- setPrehydrogenize(boolean) - Method in class chemaxon.marvin.calculations.ConformerPlugin
-
Turns the prehydrogenization on/off.
- setPrintEnabled(boolean) - Method in class chemaxon.marvin.beans.MarvinPane
-
Set the accessibility of the Print menu item in the File menu.
- setPriority(int) - Method in class chemaxon.fixers.StructureFixerDescriptor
-
Sets the fixer priority.
- setProbeRadius(double) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
Sets thwe probe radius that is the radius of a water molecule used in computing surfaces.
- setProductAtomsByMap(MolAtom[]) - Method in class chemaxon.jep.context.ReactionContext
-
- setProducts(Molecule[]) - Method in class chemaxon.jep.context.ReactionContext
-
- setProgress(int) - Method in interface chemaxon.marvin.alignment.AlignmentMoleculeFactory.ProgressBarInterface
-
- setProgressBar(AlignmentMoleculeFactory.ProgressBarInterface) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
-
- setProgressBar(AlignmentMoleculeFactory.ProgressBarInterface) - Method in class chemaxon.marvin.alignment.PairwiseAlignment
-
- setProgressBar(AlignmentMoleculeFactory.ProgressBarInterface) - Method in interface chemaxon.marvin.alignment.PairwiseComparison
-
- setProgressBar(AlignmentMoleculeFactory.ProgressBarInterface) - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D
-
- setProgressBar(ProgressBarInterface) - Method in class chemaxon.marvin.space.GraphicComponent
-
- setProgressBar(JMSpaceProgressBar) - Method in class chemaxon.marvin.space.GraphicScene
-
- setProgressBar(ProgressBarInterface) - Method in class chemaxon.marvin.space.MacroMoleculeComponent
-
- setProgressBar(ProgressBarInterface) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- setProgressBar(ProgressBarInterface) - Method in class chemaxon.marvin.space.SurfaceColoring
-
- setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.alignment.PairwiseAlignment
-
- setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.calculations.AlignmentPlugin
-
- setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.calculations.ConformerPlugin
-
- setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
Sets a progress observer to be used to display progress status.
- setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
-
- setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
-
- setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Sets a progress observer to be used in
pKaPlugin.run() to display progress status.
- setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.calculations.ResonancePlugin
-
- setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
-
- setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
- setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
-
Sets the progress monitor.
- setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.io.MRecordImporter
-
Sets the progress monitor.
- setProgressMonitor(MProgressMonitor) - Method in interface chemaxon.marvin.io.MRecordReader
-
Sets the progress monitor.
- setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
- setProgressValue(int) - Method in interface chemaxon.common.util.MProgressMonitor
-
Set progress.
- setProperties(Properties) - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
-
Sets display properties of the Molecule.
- setProperties(Properties) - Method in interface chemaxon.marvin.modules.datatransfer.MTransferable
-
Sets display properties of the Molecule.
- setProperty(AlignmentProperties) - Method in class chemaxon.marvin.alignment.Alignment
-
- setProperty(String, String) - Method in class chemaxon.marvin.common.UserSettings
-
Sets a property for the given key with the given value.
- setProperty(String, String, boolean) - Method in class chemaxon.marvin.common.UserSettings
-
Sets a property for the given key with the given value.
- setProperty(String, String) - Method in class chemaxon.marvin.space.MSpaceEasy
-
Sets a draw property of MarvinSpace.
- setProperty(String, String) - Method in class chemaxon.struc.Molecule
-
Sets an RDfile/SDfile property.
- setPropertyColorMapperMethod(Method) - Method in class chemaxon.marvin.space.SurfaceColoring
-
Colors will be got by this method.
- setPropertyColorMapperRange(double, double) - Method in class chemaxon.marvin.space.SurfaceColoring
-
Sets the range of the built-in palette.
- setPropertyColorObject(Object) - Method in class chemaxon.marvin.space.SurfaceColoring
-
Colors will be got from this object.
- setPropertyMethod(Method) - Method in class chemaxon.marvin.space.SurfaceColoring
-
Atom properties will be got by this method.
- setPropertyObject(Object, int) - Method in class chemaxon.marvin.space.SurfaceColoring
-
Atom properties will be get from this object.
- setPropertyObject(String, Object) - Method in class chemaxon.struc.Molecule
-
Sets an RDfile/SDfile property object.
- setPropertyValueDecreasement(int) - Method in class chemaxon.marvin.space.SurfaceColoring
-
Atom property values can decrease when getting farhter from the atom center.
- setProtectAllTetrahedralStereoCenters(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Sets the protection of all tetrahedral stereo centers: if true then all tetrahedral stereo
information is preserved by the tautomer generator.
- setProtectAromaticity(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Sets aromaticity protection: if true then aromatic bonds are not modified by the tautomer
generator.
- setProtectCharge(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Sets charge protection: if true then the charge of charged atoms are not modified by the tautomer
generator.
- setProtectDoubleBondStereo(boolean) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
-
Sets double bond stereo protection: if true then the stereo configuration of double bonds
with preset stereo information will not be changed.
- setProtectDoubleBondStereo(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Sets double bond stereo protection: if true then double bonds stereo information is preserved by
the tautomer generator.
- setProtectEsterGroups(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Sets the protection of ester groups: if true then ester groups are excluded from the tautomerization.
- setProtectLabeledTetrahedralStereoCenters(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Sets the protection of labeled tetrahedral stereo centers: if true then labeled tetrahedral stereo
centers are protected by the tautomer generator.
- setProtectTetrahedralStereo(boolean) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
-
Sets the protection of tetrahedral stereo centers: if true then stereo configuration of
tetrahedral stereo centers with preset stereo information will not be changed.
- setPruneIn(boolean) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
-
Set prunein parameter
- setPruneOut(boolean) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
-
Set pruneout parameter
- setQProp(String, Object) - Method in class chemaxon.struc.MolAtom
-
Sets a query property.
- setQProp(String, int) - Method in class chemaxon.struc.MolAtom
-
Sets a query property as an integer.
- setQuery(Molecule) - Method in class chemaxon.marvin.alignment.PairwiseAlignment
-
- setQuery(AlignmentMolecule) - Method in class chemaxon.marvin.alignment.PairwiseAlignment
-
- setQuery(Molecule) - Method in interface chemaxon.marvin.alignment.PairwiseComparison
-
- setQuery(AlignmentMolecule) - Method in interface chemaxon.marvin.alignment.PairwiseComparison
-
- setQuery(Molecule) - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D
-
- setQuery(AlignmentMolecule) - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D
-
- setQueryAromaticity(int) - Method in class chemaxon.struc.MolAtom
-
Sets the aromatic/aliphatic query property.
- setQueryCode(String) - Method in class chemaxon.struc.sgroup.DataSgroup
-
Sets the program code for the query option.
- setQueryDisplay(boolean) - Method in class chemaxon.util.HitColoringAndAlignmentOptions
-
Set query display option
- setQueryMode(boolean) - Method in class chemaxon.formats.MolImporter
-
Sets query mode.
- setQueryMode(boolean) - Method in class chemaxon.marvin.io.MRecordImporter
-
Sets the query mode.
- setQueryOp(String) - Method in class chemaxon.struc.sgroup.DataSgroup
-
Sets the data query operator.
- setQueryRigidForced(boolean) - Method in class chemaxon.marvin.alignment.PairwiseAlignment
-
- setQueryRigidForced(boolean) - Method in interface chemaxon.marvin.alignment.PairwiseComparison
-
Set this molecule to be rigid in the input conformation even if it
contains rotatable bonds
- setQueryRigidForced(boolean) - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D
-
- setQuerystr(MolAtom, String, int) - Static method in class chemaxon.marvin.io.formats.smiles.SmartsAtomQuerifier
-
Assigns the query properties string to this atom while setting all
necessary atom and query properties.
- setQuerystr(MolAtom, String) - Static method in class chemaxon.marvin.io.formats.smiles.SmartsAtomQuerifier
-
Assigns the query properties string to this atom while setting all
necessary atom and query properties.
- setQuerystr(String) - Method in class chemaxon.struc.MolAtom
-
- setQuerystr(String, int) - Method in class chemaxon.struc.MolAtom
-
- setQuerystr(String) - Method in class chemaxon.struc.QueryBond
-
Sets the query string.
- setQueryString(String) - Method in class chemaxon.struc.MolAtom
-
Assigns the query string to this atom.
- setRadical(int) - Method in class chemaxon.struc.MolAtom
-
- setRadical(int, int) - Method in interface chemaxon.struc.WSmolecule
-
Sets the radical value of an atom.
- setRadicalValue(AtomProperty.Radical) - Method in class chemaxon.struc.MolAtom
-
Sets the radical value.
- setRadius(double) - Method in class chemaxon.marvin.space.PharmacophoreArrow
-
Sets the radius of the arrow.
- setRadius(float) - Method in class chemaxon.marvin.space.PharmacophorePoint
-
Sets the radius of the PharmaCophorePoint.
- setRandomEnumeration() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Sets random enumeration.
- setRange(IntRange) - Method in class chemaxon.marvin.util.MolFragLoader
-
Sets the (1-based) fragment index range to be loaded.
- setRationalTautomerGenerationMode(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Generates only rational tautomers
- setReactantAtomsByMap(MolAtom[]) - Method in class chemaxon.jep.context.ReactionContext
-
- setReactants(Molecule[]) - Method in class chemaxon.jep.context.ReactionContext
-
- setReaction(RxnMolecule) - Method in class chemaxon.jep.context.ReactionContext
-
Sets the reaction.
- setReactionArrow(DPoint3[]) - Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
-
Sets the reaction arrow.
- setReactionArrow(DPoint3[]) - Method in class chemaxon.struc.RxnMolecule
-
Sets the endpoint coordinates of the reaction arrow.
- setReactionArrow() - Method in class chemaxon.struc.RxnMolecule
-
Sets the stored reaction arrow to its calculated value.
- setReactionArrow(MRArrow) - Method in class chemaxon.struc.RxnMolecule
-
Sets the reaction arrow.
- setReactionArrow0() - Method in class chemaxon.struc.RxnMolecule
-
Sets the stored reaction arrow 'arrowPoints' to its calculated value.
- setReactionArrowEndPoints(DPoint3[]) - Method in class chemaxon.struc.RxnMolecule
-
Sets the endpoints of the reaction arrow in this reaction.
- setReactionArrowType(int) - Method in class chemaxon.struc.RxnMolecule
-
Sets the reaction arrow type.
- setReactionArrowType(String) - Method in class chemaxon.struc.RxnMolecule
-
Sets the reaction arrow type from type name.
- setReactionSmarts(String) - Method in class chemaxon.checkers.SubstructureChecker
-
Sets the reactionSmarts
- setReactionStereo(int) - Method in class chemaxon.struc.MolAtom
-
Sets the reaction stereo property describing how the stereo configuration
of the atom changes during the reaction.
- setReactionSupport(boolean) - Method in class chemaxon.marvin.beans.MSketchPane
-
Allows or disallows reaction drawing.
- setReciprocalConstant(double) - Method in class chemaxon.marvin.space.SurfaceColoring
-
Atom property values will decrease by (1.0/(4*PI*c)) * (v/(d*d)).
- setRecordIDBackground(int, Color) - Method in class chemaxon.marvin.beans.MViewPane
-
Highlights a record by setting the background of its identifier field.
- setRecordIDForeground(int, Color) - Method in class chemaxon.marvin.beans.MViewPane
-
Highlights a record by setting the foreground of its identifier field.
- setReference(Molecule) - Method in class chemaxon.marvin.alignment.AlignRigidEasy
-
sets the reference molecule which remains intact
- setReference(double[][]) - Method in class chemaxon.marvin.alignment.AlignRigidEasy
-
- setReferenceMolecule(Molecule, boolean) - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
-
Sets the reference molecule to align to.
- setRelativeXCoordinate(float) - Method in class chemaxon.marvin.space.monitor.Label
-
Sets the coordinate considered as the x coordinate of the origin in window coordinates.
- setRelativeYCoordinate(float) - Method in class chemaxon.marvin.space.monitor.Label
-
Sets the coordinate considered as the y coordinate of the origin in window coordinates.
- setRemoveUnusedDefinitions(boolean) - Method in class chemaxon.util.HitColoringAndAlignmentOptions
-
Sets the remove unused definitions option.
- setRendering(String) - Method in class chemaxon.marvin.beans.MarvinPane
-
Sets the rendering style.
- setRendering(String) - Method in class chemaxon.marvin.MolPrinter
-
Sets the rendering style of atoms and bonds.
- setRenderingQuality(int) - Method in class chemaxon.marvin.space.GraphicComponent
-
Sets the rendering quality.
- setRenderingQuality(String) - Method in class chemaxon.marvin.space.PharmacophoreArrow
-
- setRenderingQuality(int) - Method in class chemaxon.marvin.space.PharmacophoreArrow
-
Sets the rendering quality, see RENDERING_* constants.
- setRenderingQuality(String) - Method in class chemaxon.marvin.space.PharmacophorePoint
-
- setRenderingQuality(int) - Method in class chemaxon.marvin.space.PharmacophorePoint
-
- setRepeatingUnitAtom(MolAtom, boolean) - Method in class chemaxon.struc.sgroup.MultipleSgroup
-
Adds or removes an atom to/from the list of paradigmatic repeating
unit atoms.
- setRequestMethod(JsonServiceDescriptor.Method) - Method in class chemaxon.marvin.services.json.JsonServiceDescriptor
-
Sets the HTTP method of the request.
- setResidueAtomId(int) - Method in class chemaxon.struc.MolAtom
-
Sets the residue atom identifier.
- setResidueSeq(int) - Method in class chemaxon.struc.MolAtom
-
Sets the residue sequence number.
- setResidueType(int) - Method in class chemaxon.struc.MolAtom
-
Sets the residue type.
- setRestH(int) - Method in class chemaxon.struc.RgMolecule
-
Sets the restH condition on an R-group definition.
- setResultList(List<StructureCheckerResult>) - Method in class chemaxon.checkers.runner.BasicCheckerRunner
-
Sets the resultList
- setReturnTypes(Class<?>[]) - Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor
-
Sets the array of return types
- setRgroup(int) - Method in class chemaxon.struc.MolAtom
-
Sets the R-group ID.
- setRgroupAttachmentPointOrder(int) - Method in class chemaxon.struc.MolAtom
-
Sets the attachment point order of an R-group attachment point.
- setRgroupId(int, int) - Method in interface chemaxon.struc.WSmolecule
-
Sets the R-group identifier of an atom.
- setRgroupsVisible(boolean) - Method in class chemaxon.marvin.beans.MarvinPane
-
Shows or hides R-group definitions.
- setRgroupsVisible(boolean) - Method in class chemaxon.marvin.MolPrinter
-
Sets whether the R-group definitions are visible.
- setRightName(String) - Method in class chemaxon.struc.sgroup.SgroupAtom
-
Set the string that will be shown at the right side of the molecule.
- setRingBondCountChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker
-
Sets the option determining if the checker detects ring bond count atom
query properties or not.
- setRingChainTautomerizationAllowed(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Sets if ring tautomers are allowed or not.
Default true
- setRingCountChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker
-
Sets the option determining if the checker detects ring count atom query
properties or not.
- setRingFlexibility(int, int) - Method in class chemaxon.marvin.calculations.AlignmentPlugin
-
If BOTH the two parameters is true for the ring then the ring is treated flexible.
- setRlogic(int, int) - Method in class chemaxon.struc.RgMolecule
-
Sets R-logic flags.
- setRlogicRange(int, String) - Method in class chemaxon.struc.RgMolecule
-
Sets R-logic occurrence range.
- setRLogicVisible(String) - Method in class chemaxon.marvin.common.UserSettings
-
Sets R-logic visibility
- setRLogicVisible(boolean) - Method in class chemaxon.marvin.MolPrinter
-
Set R-logic visibility.
- setRoot(Molecule) - Method in class chemaxon.struc.RgMolecule
-
Sets the root structure.
- setRotatable(Molecule) - Method in class chemaxon.marvin.alignment.AlignRigidEasy
-
sets the molecule to translate and rotate during the alignment
- setRotatable(double[][]) - Method in class chemaxon.marvin.alignment.AlignRigidEasy
-
- setRotateMatrix(float[]) - Method in class chemaxon.marvin.space.GraphicCell
-
Sets the matrix of rotation explicitly.
- setRotateMatrix(float[]) - Method in class chemaxon.marvin.space.GraphicComponent
-
Sets the rotation matrix in order to get the proper mapping of a vector to the viewing plane.
- setRotateMatrix(float[]) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- setRotation(double, double, double, double) - Method in class chemaxon.struc.CTransform3D
-
Sets the rotation components.
- setRotationCenter(DPoint3) - Method in class chemaxon.struc.CTransform3D
-
Sets the rotation center.
- setRowAndColumn0(int) - Method in class chemaxon.struc.graphics.MTextBox
-
- setRowCount(int) - Method in class chemaxon.marvin.beans.MViewParams
-
Sets the total nuber of rows.
- setRowHeight(int) - Method in class chemaxon.marvin.view.swing.TableOptions
-
Sets the row height.
- setSamplingAccuracy(int) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
-
- setSamplingAccuracy(AtropIsomerDetector.Accuracy) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
-
- setSamplingInterval(double) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
-
Number of trajectory frames to be stored from the sampling start time to
the end of calculation.
- setSamplingStart(double) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
-
Sets the beginning of trajectory sampling.
- setSaveGUIPropertiesInMRV(boolean) - Method in class chemaxon.marvin.common.UserSettings
-
Sets whether the GUI properties should be saved when saving as a Marvin file
- setSaveIniEnabled(boolean) - Method in class chemaxon.marvin.beans.MarvinPane
-
Enables or disables automatic preference saving.
- setSaveLoadZoomFactorToMRV(boolean) - Method in class chemaxon.marvin.common.UserSettings
-
Tells wether to save the zoom factor information to mrv files or not.
- setScale(double) - Method in class chemaxon.marvin.beans.MSketchPane
-
Sets the scale factor and changes magnification of the canvas.
- setScale(double) - Method in class chemaxon.marvin.MolPrinter
-
Sets the scale factor in units of regular bond length.
- setScale(double) - Method in class chemaxon.struc.CTransform3D
-
Sets the scale factor.
- setSceneSize(int, int) - Method in class chemaxon.marvin.space.GraphicScene
-
Sets the number of rows and columns.
- setSDFColoring(String, Properties) - Method in class chemaxon.marvin.view.swing.TableSupport
-
Sets SDF coloring.
- setSearchAll(boolean) - Method in class chemaxon.checkers.RatomChecker
-
Sets the option determining if the checker detects all R-atoms or not.
- setSearchBridgehead(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker
-
Sets whether the checker search for bridgehead explicit hydrogens
- setSearchCharged(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker
-
Sets whether the checker search for charged explicit hydrogens
- setSearchCircularReference(boolean) - Method in class chemaxon.checkers.RgroupReferenceErrorChecker
-
Deprecated.
Sets the option determining if the checker detects nested R-atoms
referencing to their own R-groups directly or in circularly or not.
- setSearchContracted(boolean) - Method in class chemaxon.checkers.AbbreviatedGroupChecker
-
Sets the checker should search for contracted abbreviated groups or not
- setSearchDefaultValence(boolean) - Method in class chemaxon.checkers.ValencePropertyChecker
-
Sets checker to detect valence properties with the default valence of
the current atom type.
- setSearchDisconnected(boolean) - Method in class chemaxon.checkers.RatomChecker
-
Sets the option determining if the checker detects R-atoms not connected
to any other atoms or not.
- setSearchExpanded(boolean) - Method in class chemaxon.checkers.AbbreviatedGroupChecker
-
Sets the checker should search for expanded abbreviated groups or not
- setSearchGeneric(boolean) - Method in class chemaxon.checkers.RatomChecker
-
Sets the option determining if the checker detects R-atoms without
identifier numbers or not.
- setSearchHConnected(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker
-
Sets whether the checker search for H connected explicit hydrogens
- setSearchIsotopic(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker
-
Sets whether the checker search for isotopic explicit hydrogens
- setSearchLinker(boolean) - Method in class chemaxon.checkers.RatomChecker
-
Sets the option determining if the checker detects R-atoms with more than
one connection or not.
- setSearchLonely(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker
-
Sets whether the checker search for lonely explicit hydrogens
- setSearchMapped(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker
-
Sets whether the checker search for mapped explicit hydrogens
- setSearchMissingRatom(boolean) - Method in class chemaxon.checkers.RgroupReferenceErrorChecker
-
Deprecated.
- setSearchMissingRgroup(boolean) - Method in class chemaxon.checkers.RgroupReferenceErrorChecker
-
Deprecated.
Sets the option determining if the checker detects missing R-groups or
not.
- setSearchNested(boolean) - Method in class chemaxon.checkers.RatomChecker
-
Sets the option determining if the checker detects R-atoms within
R-groups or not.
- setSearchNonDefaultValence(boolean) - Method in class chemaxon.checkers.ValencePropertyChecker
-
Sets checker to detect valence properties with non-default valence of
the current atom type.
- setSearchPolymerEndGroup(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker
-
Sets whether the checker search for polymer end group explicit hydrogens
- setSearchRadical(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker
-
Sets whether the checker search for radical explicit hydrogens
- setSearchSelfReference(boolean) - Method in class chemaxon.checkers.RgroupReferenceErrorChecker
-
Deprecated.
- setSearchSgroup(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker
-
Sets whether the checker search for S-group explicit hydrogens
- setSearchSgroupEnd(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker
-
Sets whether the checker search for S-group end explicit hydrogens
- setSearchUnusedRgroup(boolean) - Method in class chemaxon.checkers.RgroupReferenceErrorChecker
-
Deprecated.
Sets the option determining if the checker detects missing R-atoms or
not.
- setSearchValenceError(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker
-
Sets whether the checker search for valence errored explicit hydrogens
- setSearchWedged(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker
-
Sets whether the checker search for wedged explicit hydrogens
- setSelectable(boolean) - Method in class chemaxon.marvin.beans.MViewPane
-
Enables the user to select a cell by clicking on it or using the cursor movement keys.
- setSelected(boolean) - Method in class chemaxon.struc.graphics.MChemicalStruct
-
Selects or unselects the object.
- setSelected(MoleculeGraph, boolean) - Static method in class chemaxon.struc.graphics.MChemicalStruct
-
Selects or unselects atoms in a molecule graph.
- setSelected(boolean) - Method in class chemaxon.struc.graphics.MTextBox
-
Selects or unselects the text box.
- setSelected(boolean) - Method in class chemaxon.struc.MObject
-
Selects or unselects the object.
- setSelected(boolean) - Method in class chemaxon.struc.MolAtom
-
Selects or unselects this atom.
- setSelectedAtoms(int, String, int[]) - Method in class chemaxon.marvin.view.MDocStorage
-
Sets the selected atom indices.
- setSelectedAtoms(int, String, String) - Method in class chemaxon.marvin.view.MDocStorage
-
Sets the selected atom indices.
- setSelectedFields(String[]) - Method in class chemaxon.marvin.view.swing.TableOptions
-
Set selected fields array in Table Options dialog box
- setSelectedIndex(int) - Method in class chemaxon.marvin.beans.MViewPane
-
Selects a molecule.
- setSeparator(String) - Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
-
Sets the separator string.
- SETSEQ_MAX - Static variable in class chemaxon.struc.MolAtom
-
Maximum atom set sequence number is currently 63.
- SETSEQ_MAX - Static variable in class chemaxon.struc.MolBond
-
Maximum bond set sequence number.
- SETSEQ_OFF - Static variable in class chemaxon.struc.MolBond
-
Bond set sequence number offset in flags.
- setServicesConfigurationPath(String) - Method in class chemaxon.jep.Evaluator
-
Sets the custom services configuration path.
- setServicesConfigURL(String) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the URL of the configuration for Services in marvin
- setSetColor(int, Color) - Method in class chemaxon.marvin.beans.MarvinPane
-
Deprecated.
as of Marvin 3.3, replaced by setAtomSetColor
- setSetColoringEnabled(boolean) - Method in class chemaxon.marvin.beans.MarvinPane
-
Enable or disable atom/bond set coloring.
- setSetColoringEnabled(boolean) - Method in class chemaxon.marvin.MolPrinter
-
Colors atoms and bonds according to the color of the pre-defined set they belong to.
- setSetSeq(int, int, int) - Method in class chemaxon.marvin.beans.MViewPane
-
Deprecated.
as of Marvin 3.3, replaced by setAtomSetSeq
- setSetSeq(int) - Method in class chemaxon.struc.MolAtom
-
Sets the atom set sequence number.
- setSetSeq(int) - Method in class chemaxon.struc.MolBond
-
Sets the bond set.
- setSeverity(CheckerSeverity) - Method in class chemaxon.checkers.StructureCheckerDescriptor
-
Sets the severity of the concerning checker
- setSgroupGraph(SelectionMolecule) - Method in class chemaxon.struc.Sgroup
-
Sets the molecule graph.
- setSgroupGraph(SelectionMolecule) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Sets the molecule graph.
- setSgroupParent(MolAtom, Sgroup, boolean) - Method in class chemaxon.struc.Molecule
-
Sets or unsets an S-group as a parent of an atom.
- setSgroupParent(MolAtom, Sgroup, boolean) - Method in class chemaxon.struc.RgMolecule
-
Sets or unsets an S-group as a parent of an atom in the root structure
or an R-group.
- setSgroupParent(MolAtom, Sgroup, boolean) - Method in class chemaxon.struc.RxnMolecule
-
Sets or unsets an S-group as a parent of an atom in reactants, products
or agents.
- setSheetName(String) - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
Sets the sheet name the structures/molecules added to.
- setShifts(Shift[]) - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
Sets chemical shifts.
- setShowMultiMoleculeOnEditSource(boolean) - Method in class chemaxon.marvin.common.UserSettings
-
- setSimilarityScoreDisplay(int) - Method in class chemaxon.util.HitColoringAndAlignmentOptions
-
Sets the mode of similarity score display.
- setSimpView(int) - Method in class chemaxon.marvin.beans.MSketchPane
-
- setSingleCellLabelShown(boolean) - Method in class chemaxon.marvin.view.swing.TableOptions
-
Tests whether label should be shown for a single cell.
- setSize(int, int) - Method in class chemaxon.marvin.space.GraphicCell
-
Sets the size of the viewport of this cell in pixels.
- setSize(int, int) - Method in class chemaxon.marvin.space.GraphicScene
-
Sets the physical size of the scene.
- setSize(int, int) - Method in class chemaxon.marvin.space.MSpaceEasy
-
Sets the physical size of the graphic canvas.
- setSize(int) - Method in class chemaxon.marvin.view.MDocStorage
-
Sets the total number of entries.
- setSketchAnyBond(String) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the default any bond drawing style in the sketcher.
- setSketchArrowHeadLength(double) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the arrow head length.
- setSketchArrowHeadWidth(double) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the arrow head width.
- setSketchArrowTailLength(double) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the arrow tail length.
- setSketchArrowTailWidth(double) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the arrow tail width.
- setSketchCarbonVisibility(String) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the default carbon visibility style in the sketcher.
- setSketchColorScheme(String) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the sketcher's default color scheme.
- setSketchImplicitH(String) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the display method of implicit hydrogens for the sketcher.
- setSketchLigandOrderVisibility(String) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the default ligand order visibility style in the sketcher.
- setSketchLoadWorkingDir(String) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the load working directory for MarvinSketch load filechooser.
- setSketchMode(int) - Method in class chemaxon.marvin.beans.MSketchPane
-
Sets the sketching mode.
- setSketchMolbg2d(Color) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the sketcher's default 2D molecule background color.
- setSketchMolbg3d(Color) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the sketcher's default 3D molecule background color.
- setSketchRecentFileListSize(int) - Method in class chemaxon.marvin.common.UserSettings
-
- setSketchRendering2d(String) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the rendering style for the 2D sketcher.
- setSketchRendering3d(String) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the rendering style for the 3D sketcher.
- setSketchSaveWorkingDir(String) - Method in class chemaxon.marvin.common.UserSettings
-
Not implemented yet, don't use it.
- setSkip(int, double) - Method in class chemaxon.struc.graphics.MPolyline
-
Sets the distance of the (visible) head or tail from the corresponding
line end point.
- setSkipsToEndPoints() - Method in class chemaxon.struc.graphics.MEFlow
-
- setSmallestRingSizeChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker
-
Sets the option determining if the checker detects smallest ring size
atom query properties or not.
- setSMARTS(MolAtom, String) - Static method in class chemaxon.marvin.io.formats.smiles.SmartsAtomQuerifier
-
Sets SMARTS query string data.
- setSMARTS(String) - Method in class chemaxon.struc.MolAtom
-
- setSMILESFontSize(int) - Method in class chemaxon.marvin.view.swing.TableOptions
-
Sets the SMILES font size.
- setSMILESShown(boolean) - Method in class chemaxon.marvin.view.swing.TableOptions
-
Set visibility of SMILES strings.
- setSmoothBackgroud(boolean) - Method in class chemaxon.marvin.space.GraphicCell
-
Enables/disables shaded background coloring.
- setSmoothBackground(boolean) - Method in class chemaxon.marvin.space.GraphicScene
-
Enables/disables shaded background.
- setSmoothColoringToCutoffValues(boolean) - Method in class chemaxon.marvin.space.SurfaceColoring
-
See Palette.smoothColorToCutoffValues(boolean).
- setSolventRadius(double) - Method in class chemaxon.marvin.calculations.MSAPlugin
-
Sets solvent radius.
- setSpecIsotopeSymbolPreferred(boolean) - Method in class chemaxon.struc.MolAtom
-
Sets special isotope symbol usage preference.
- setSrgoups(List<Sgroup>) - Method in class chemaxon.checkers.result.SgroupCheckerResult
-
This method sets the groups property
- setStartAt(int) - Method in class chemaxon.marvin.view.swing.TableOptions
-
Set the index number of the molecule that is the first to be displayed.
- setStartColumn(int) - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
- setStartEnd(MolAtom, MPoint) - Method in class chemaxon.struc.graphics.MEFlowBasePoint
-
Sets the atoms.
- setStartPosition(long) - Method in class chemaxon.struc.MDocument
-
Sets the starting position of this document in the input file.
- setStartPosition(long) - Method in class chemaxon.struc.Molecule
-
Sets the starting position of this molecule in the input file.
- setStartRow(int) - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
- setStartupSelectorShown(boolean) - Method in class chemaxon.marvin.common.UserSettings
-
- setStepNumber(int) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
-
Sets the number of simulation steps.
- setStepTime(double) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
-
Sets the simulation timestep.
- setStereo2Flags(MolAtom, MolAtom, int) - Method in class chemaxon.struc.MolBond
-
Sets double bond stereo information.
- setStereoGroupNumber(int) - Method in class chemaxon.struc.MolAtom
-
Sets the stereochemical group number for AND and OR groups of the
enhanced stereo representation.
- setStereoGroupType(int) - Method in class chemaxon.struc.MolAtom
-
Sets the stereochemical group type for enhanced stereo representation.
- setStereoisomerismType(int) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
-
Sets which type of stereoiseomers should be generated.
- setStickdst(double) - Method in class chemaxon.marvin.beans.MSketchPane
-
Sets the sticking distance.
- setStickThickness(double) - Method in class chemaxon.marvin.beans.MarvinPane
-
Sets the stick thickness.
- setStickThickness(double) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the stick diameter for ball and stick mode.
- setStickThickness(double) - Method in class chemaxon.marvin.MolPrinter
-
Sets the 3D stick's diameter.
- setString(String, String) - Method in class chemaxon.struc.MPropertyContainer
-
Sets a property.
- setStructureCellHeight(int) - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
Sets the height of the structure cell.
- setStructureCellWidth(int) - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
Sets the width of the structure cell in 1/256 of normal character width.
- setStructureColumnIndex(int) - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
- setStructureColumnName(String) - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
- setStructureID(String) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Sets structure ID to be used in Markush code generation.
- setSubscript(String) - Method in class chemaxon.struc.sgroup.MultipleSgroup
-
Sets the subscript.
- setSubscript(String) - Method in class chemaxon.struc.Sgroup
-
Sets the subscript for non-superatom S-groups.
- setSubsetChangable(boolean) - Method in class chemaxon.marvin.view.swing.TableOptions
-
Sets whether startAt and maxSize can be changed.
- setSubstitutionCountChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker
-
Sets the option determining if the checker detects substitution count
atom query properties or not.
- setSubType(int) - Method in class chemaxon.struc.Sgroup
-
Sets polymer S-group subtype.
- setSupergraph(MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
-
Sets the given molecule as the supergraph of this graph.
- setSupergraph(MoleculeGraph) - Method in class chemaxon.struc.RxnMolecule
-
Sets the given molecule as the supergraph of this graph and its
components.
- setSurface(SurfaceComponent) - Method in class chemaxon.marvin.space.SurfaceColoring
-
Sets the surface for coloring.
- setSurfaceAreaType(int) - Method in class chemaxon.marvin.calculations.MSAPlugin
-
- setSurfacePrecision(String) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
Sets the surface precision by setting a quality.
- setSurfacePrecision(float) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
Explicitly sets the grid resolution from which the surface is computed.
- setSurfacePrecision() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
Resolution will be set automatically according to the number of atoms
and the rendering quality.
- setSurfaceSimplificationEnabled(boolean) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
The number of surface polygons can be reduced by the following algorithm:
Paul Bourke: Surface (polygonal) Simplification
http://astronomy.swin.edu.au/~pbourke/modelling/surfsimp/
This method enables/disables simplification.
- setSurfaceType(String) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
Sets the type of the surface and computes the surface with the necessary method.
- setSymbolTable(SymbolTable) - Method in class chemaxon.jep.ChemJEP
-
Sets the SymbolTable object.
- setSymmetryFiltering(boolean) - Method in class chemaxon.marvin.calculations.ResonancePlugin
-
Sets symmetry fitlering: if true then symmetrical structures
are filtered out, otherwise symmetrical structures are returned as duplicates.
- setSymmetryFiltering(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Sets symmetry fitlering: if true then symmetrical structures
are filtered out, otherwise symmetrical structures are returned as duplicates.
- setSynchronousMode(boolean) - Method in class chemaxon.marvin.space.GraphicScene
-
Sets handling of cells to synchronous/asynchronous.
- setT(int, String) - Method in class chemaxon.marvin.beans.MViewPane
-
Sets a text field in a GridBagView table.
- setT(int, int, String) - Method in class chemaxon.marvin.view.MDocStorage
-
Sets a text field in a record.
- setTabScale(double) - Method in class chemaxon.marvin.beans.MViewPane
-
Sets the magnification in the molecule cells.
- setTag(char) - Method in class chemaxon.struc.sgroup.DataSgroup
-
Sets the tag character for the footnote display.
- setTailCrossingBonds(MolBond[]) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
-
Sets the tail crossing bonds.
- setTakeCanonicalForm(boolean) - Method in class chemaxon.marvin.calculations.ResonancePlugin
-
Sets whether canonical form should be taken.
- setTakeCanonicalForm(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Sets whether canonical form should be generated.
- setTakeDominantTautomers(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Sets whether dominant tautomers should be generated.
- setTakeGenericTautomer(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Sets whether generic tautomer should be generated.
- setTakeMajorContributors(boolean) - Method in class chemaxon.marvin.calculations.ResonancePlugin
-
Sets whether major contributors should be taken.
- setTakeMajorTatomericForm(boolean) - Method in class chemaxon.marvin.calculations.logPPlugin
-
- setTakeMajorTatomericForm(boolean) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
-
Sets to use major tautomeric form in calculation.
- setTakeMajorTatomericForm(boolean) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
- setTakeMajorTautomer(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Sets whether major tautomer should be generated.
- setTakeMostStableTautomer(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
- setTakePartialNeutralization(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Sets if partial neutralization prior to canonical tauotmer generation is allowed or not.
- setTakeResonantStructures(boolean) - Method in class chemaxon.marvin.calculations.ChargePlugin
-
Sets calculation with resonant structures.
- setTakeResonantStructures(boolean) - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
-
Sets calculation with resonant structures.
- setTakeStandardForm(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
For internal use only.
- setTargetMolecule(Molecule) - Method in class chemaxon.util.MolAligner
-
Sets target molecule and calculates its dimension
- setTargetRigidForced(boolean) - Method in class chemaxon.marvin.alignment.PairwiseAlignment
-
- setTargetRigidForced(boolean) - Method in interface chemaxon.marvin.alignment.PairwiseComparison
-
Set this molecule to be rigid in the input conformation even if it
contains rotatable bonds
- setTargetRigidForced(boolean) - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D
-
- setTCenter(int) - Method in class chemaxon.struc.graphics.MRectangle
-
Sets the transformed point.
- setTemperature(double) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Sets the temperature (default: 298 Kelvin).
- setTerminalBondDeletionStyle(String) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the bond deletion style.
- setText(String) - Method in class chemaxon.marvin.space.monitor.Label
-
Sets an explicit text to the label, that has priority to the description of the selected component.
- setText(String) - Method in class chemaxon.struc.graphics.MTextBox
-
Sets the text.
- setThickness(double) - Method in class chemaxon.struc.graphics.MPolyline
-
Sets the line thickness.
- setThreadCount(int) - Method in class chemaxon.formats.MolConverter
-
Sets the number of threads for concurrent processing.
- setThreadCount(int) - Method in class chemaxon.formats.MolExporter
-
Sets the number of threads for concurrent processing.
- setThreadCount(int) - Method in class chemaxon.formats.MolImporter
-
Sets the number of threads for concurrent processing.
- setThreadCount(int) - Method in class chemaxon.marvin.io.MRecordImporter
-
Sets the number of threads for concurrent processing.
- setThrowable(Throwable) - Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
-
Sets the throwable object.
- setTimelimit(int) - Method in class chemaxon.marvin.calculations.ConformerPlugin
-
Sets the timelimit for the calculation.
- setTimeLimit(double) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Sets an upper time limit for the canonical tautomer generation.
- setTitle(String) - Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
-
Sets the frame title.
- setToolbarConfigPath(String) - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
-
Sets the toolbar configuration path
- setTopLeftIndex(int) - Method in class chemaxon.marvin.beans.MViewPane
-
Scrolls to the specified cell.
- setTopLevelContainer(Container) - Method in class chemaxon.marvin.beans.MarvinPane
-
Sets the top level container (JFrame, JDialog, etc) of the pane.
- setTOption(int) - Method in class chemaxon.struc.graphics.MRectangle
-
Sets the transformation options.
- setTraditionalNitrogenAllowed(boolean) - Method in class chemaxon.core.calculations.valencecheck.ValenceCheckOptions.Builder
-
- setTraining(String) - Method in class chemaxon.marvin.calculations.logPPlugin
-
Sets the user defined training.
- setTransfer(Transferable) - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
-
Sets the Transferable which contains the Molecule that should be retrieved.
- setTransfer(Transferable) - Method in interface chemaxon.marvin.modules.datatransfer.MTransferable
-
Sets the Transferable for importing Molecule from that.
- setTransformationCenter(UOID) - Method in class chemaxon.marvin.space.GraphicCell
-
Sets the transformation center to the center of the component
with the given id and resets shifting values.
- setTransformationCenter(float, float, float) - Method in class chemaxon.marvin.space.GraphicCell
-
Sets the transformation center and resets shifting values.
- setTransformationCenter(UOID) - Method in class chemaxon.marvin.space.GraphicScene
-
Sets the center of transformation of the active cell to the
coordinates of the named component.
- setTransformationCenter(float[]) - Method in class chemaxon.marvin.space.GraphicScene
-
Sets the transformation center explicitly to the given value.
- setTransformationCenterX(float) - Method in class chemaxon.marvin.space.GraphicCell
-
Sets the x coordinate of the transformation center.
- setTransformationCenterY(float) - Method in class chemaxon.marvin.space.GraphicCell
-
Sets the y coordinate of the transformation center.
- setTransformationCenterZ(float) - Method in class chemaxon.marvin.space.GraphicCell
-
Sets the z coordinate of the transformation center.
- setTransformationEnabled(boolean) - Method in class chemaxon.marvin.common.UserSettings
-
Enable/disable transformation
- setTranslation(DPoint3) - Method in class chemaxon.struc.CTransform3D
-
- setTranslation(double, double, double) - Method in class chemaxon.struc.CTransform3D
-
- setTransparent(boolean) - Method in class chemaxon.marvin.MolPrinter
-
Sets the transparency state of the painting.
- setTransparentBackground(boolean) - Method in class chemaxon.marvin.space.GraphicScene
-
Enables/disables transparent background color.
- setType(int) - Method in class chemaxon.checkers.AromaticityErrorChecker
-
- setType(StructuralFrameworksPlugin.FrameworkTypes) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
-
Set framework type to calculate.
- setType(Class<T>) - Method in class chemaxon.marvin.services.ServiceArgument
-
Sets the class of the argument
- setType(int) - Method in class chemaxon.struc.graphics.MBracket
-
Sets the bracket type.
- setType(int) - Method in class chemaxon.struc.MolBond
-
Sets bond type and does valence checking for the endpoints.
- setTypes(List<String>) - Method in class chemaxon.checkers.AtomTypeChecker
-
Sets the checked atom types
- setUndo(int) - Method in class chemaxon.marvin.beans.MSketchPane
-
Sets the maximum undo depth.
- setUnit(DipoleResult.Unit) - Method in class chemaxon.calculations.dipole.DipoleResult
-
- setUnit(NMRSpectrum.Unit) - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder
-
Sets NMR spectrum unit.
- setUnit(NMRSpectrum.Unit) - Method in class chemaxon.calculations.nmr.NMRSpectrum
-
Sets the unit type.
- setUnitDisplayed(boolean) - Method in class chemaxon.struc.sgroup.DataSgroup
-
Sets whether the units string should be displayed.
- setUnits(String) - Method in class chemaxon.struc.sgroup.DataSgroup
-
Sets the unit of this data field.
- setUnsaturationChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker
-
Sets the option determining if the checker detects unsaturation atom
query properties or not.
- setUpperCutoffValue(double) - Method in class chemaxon.marvin.space.SurfaceColoring
-
Cutoff values can be set to the built-in two pole palettes.
- setUseAllAtoms(boolean) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
-
- setUseOriginal(boolean) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
-
Deprecated.
always false: Molecule is always converted before alignment, but coordinates are written
back to the original one.
- setUserSettings(UserSettings) - Method in class chemaxon.marvin.beans.MarvinPane
-
Sets the user settings object.
- setUserTypes(String) - Method in class chemaxon.marvin.calculations.logPPlugin
-
Sets user types.
- setValence(int, int) - Method in interface chemaxon.struc.WSmolecule
-
Sets the valence.
- setValenceCheckEnabled(boolean) - Method in class chemaxon.struc.MoleculeGraph
-
Enables or disables valence check on this molecule graph,
depending on the value of the parameter b.
- setValenceCheckOptions(ValenceCheckOptions) - Method in class chemaxon.struc.MoleculeGraph
-
Sets the options for valence checking.
- setValenceCheckOptions(ValenceCheckOptions) - Method in class chemaxon.struc.RgMolecule
-
Sets the options for valence checking.
- setValenceCheckState(MoleculeGraph.ValenceCheckState) - Method in class chemaxon.struc.MoleculeGraph
-
- setValenceError(boolean) - Method in class chemaxon.struc.MolAtom
-
Sets or clears the valence error flag.
- setValenceErrorVisible(boolean) - Method in class chemaxon.marvin.beans.MSketchPane
-
Shows or hides valence errors
- setValenceErrorVisible(boolean) - Method in class chemaxon.marvin.common.UserSettings
-
Show or hide valence errors
- setValenceErrorVisible(boolean) - Method in class chemaxon.marvin.MolPrinter
-
Sets the visibility state of valence errors.
- setValenceErrorVisibleInView(boolean) - Method in class chemaxon.marvin.beans.MViewPane
-
Shows or hides valence errors
- setValenceErrorVisibleInView(boolean) - Method in class chemaxon.marvin.common.UserSettings
-
Show or hide valence errors in MarvinView
- setValenceProp(int) - Method in class chemaxon.struc.MolAtom
-
Sets the valence property.
- setValencePropertyVisible(boolean) - Method in class chemaxon.marvin.common.UserSettings
-
Sets atom valence property visibility.
- setValencePropertyVisible(boolean) - Method in class chemaxon.marvin.MolPrinter
-
Sets the atom valence propertiy visibility
- setvalidateSgroupsAtCreation(boolean) - Method in class chemaxon.marvin.common.UserSettings
-
Set the validation of the possible sgroups and allow only the chemically correct ones on
sgroups creation and edit dialog.
- setValue(T) - Method in class chemaxon.marvin.services.ServiceArgument
-
Sets the service argument value
- setVerbose(boolean) - Method in class chemaxon.jep.Evaluator
-
Sets verbose mode.
- setVerbose(boolean) - Method in class chemaxon.marvin.space.GraphicCell
-
Sets the verbose level on/off.
- setVerbose(int) - Method in class chemaxon.marvin.space.GraphicCell
-
Sets the verbose level to the given level.
- setVerbose(boolean) - Method in class chemaxon.marvin.space.GraphicScene
-
Sets the verbose level on/off.
- setVerbose(int) - Method in class chemaxon.marvin.space.GraphicScene
-
Sets the verbose level to the given level.
- setVerbose(boolean) - Method in class chemaxon.marvin.space.MSpaceEasy
-
Sets whether writing technical details to console is enabled or not.
- setVerbosePrinter(StructuralFrameworksPlugin.VerbosePrinter) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
-
Set or clear verbose printer
Verbose messages will be sent to the verbose printer to ease debugging
- setVerticalAlignment(int) - Method in class chemaxon.struc.graphics.MTextBox
-
Sets the vertical alignment.
- setViewAnyBond(String) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the default any bond drawing style in the viewer.
- setViewAtomMarkEnabled(boolean) - Method in class chemaxon.marvin.common.UserSettings
-
Sets atom mark and highlight visibility in Marvin View.
- setViewCarbonVisibility(String) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the default carbon visibility style in the viewer.
- setViewColorScheme(String) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the viewer's default color scheme.
- setViewHandlerType(int) - Method in class chemaxon.marvin.view.swing.TableOptions
-
Sets the view handler type.
- setViewImplicitH(String) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the display method of implicit hydrogens for the viewer.
- setViewLayout(int) - Method in class chemaxon.marvin.common.UserSettings
-
Set the layout of MarvinView.
- setViewLigandOrderVisibility(String) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the default ligand order visibility style in the viewer.
- setViewLoadWorkingDir(String) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the load working directory for MarvinView load filechooser.
- setViewMolbg2d(Color) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the default molecule background color for the 2D viewer.
- setViewMolbg3d(Color) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the default molecule background color for the 3D viewer.
- setViewNavmode2d(String) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the navigation mode for the 2D viewer.
- setViewNavmode3d(String) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the navigation mode for the 3D viewer.
- setViewRecentFileListSize(int) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the recent file list requested size, if it is smaller than zero, then the size will be
zero, if it is more than 10 then the size will be 10.
- setViewRendering2d(String) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the rendering style for the 2D viewer.
- setViewRendering3d(String) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the rendering style for the 3D viewer.
- setViewSaveWorkingDir(String) - Method in class chemaxon.marvin.common.UserSettings
-
Not implemented, don't use it.
- setVisible(boolean) - Method in class chemaxon.marvin.space.GraphicComponent
-
Indicates whether the component will appear on the graphic scene
at the next draw or not.
- setVisible(boolean) - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- setVisible(boolean) - Method in class chemaxon.marvin.space.MacroMoleculeComponent
-
Sets all of the visualizers to visible/invisible.
- setVisible(boolean) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
Sets the surface to be visible/invisible.
- setVisible(boolean) - Method in class chemaxon.marvin.space.MoleculeComponent
-
Sets the component to be visible/invisible.
- setVisibleRows(int) - Method in class chemaxon.marvin.beans.MViewParams
-
Sets the nuber of visible rows.
- setWebServiceName(String) - Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor
-
Sets the webservice name
- setWeightMode(int) - Method in class chemaxon.marvin.space.SurfaceColoring
-
Way of handling values when multiple atoms have effect on one surface vertex.
- setWeightOfMethods(double, double, double, double) - Method in class chemaxon.marvin.calculations.logDPlugin
-
Sets the weight of logP calculation methods.
- setWeightOfMethods(double, double, double, double) - Method in class chemaxon.marvin.calculations.logPPlugin
-
Sets the weight of logP calculation methods.
- setWeights(double[]) - Method in class chemaxon.struc.graphics.MAtomSetPoint
-
Sets the atom weights for location calculation.
- setWigglyBondVisibility(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Sets how wiggly bonds connected to double bonds are displayed.
For internal use only.
- setWinScale(double) - Method in class chemaxon.marvin.beans.MViewPane
-
Sets the magnification in the zoom windows.
- setWireThickness(double) - Method in class chemaxon.marvin.beans.MarvinPane
-
Sets the line thickness for wireframe mode.
- setWireThickness(double) - Method in class chemaxon.marvin.common.UserSettings
-
Sets the bond thickness in wireframe mode.
- setWireThickness(double) - Method in class chemaxon.marvin.MolPrinter
-
Sets the line thickness for wireframe mode.
- setWithCondition(float, float, float) - Method in class chemaxon.marvin.space.BoundingBox
-
This is the best way of passing coordinates to the box.
- setWithCondition(BoundingBox) - Method in class chemaxon.marvin.space.BoundingBox
-
Extends the box with the given box, say gives the bounding box of the two boxes.
- setWord(ByteBuffer, int, int) - Method in class chemaxon.marvin.io.PositionedInputStream
-
- setWorkerThreadCount(int) - Method in interface chemaxon.util.concurrent.ConcurrentProcessor
-
Sets the number of worker threads used by this processor.
- setWorkOnBackground(boolean) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
-
Starts or stops the background worker thread and ensures the required state for the type of
work.
- setWorkUnits(WorkUnit[]) - Method in class chemaxon.util.concurrent.marvin.CompositeWorkUnit
-
Sets the work units.
- setWsdlURI(String) - Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor
-
Sets the WSDL URI
- setX(double) - Method in class chemaxon.struc.MolAtom
-
Sets the X coordinate.
- setX(double) - Method in class chemaxon.struc.sgroup.DataSgroup
-
Sets the X coordinate.
- setXState(int) - Method in class chemaxon.struc.Sgroup
-
Sets the expanded/contracted state.
- setXState(int, int) - Method in class chemaxon.struc.Sgroup
-
- setXState0(int) - Method in class chemaxon.struc.Sgroup
-
- setXY(double, double) - Method in class chemaxon.struc.MolAtom
-
Sets the x and y coordinates.
- setXYZ(double, double, double) - Method in class chemaxon.struc.MolAtom
-
Sets the coordinates.
- setY(double) - Method in class chemaxon.struc.MolAtom
-
Sets the Y coordinate.
- setY(double) - Method in class chemaxon.struc.sgroup.DataSgroup
-
Sets the Y coordinate.
- setZ(double) - Method in class chemaxon.struc.MolAtom
-
Sets the Z coordinate.
- setZero() - Method in class chemaxon.struc.CTransform3D
-
Sets all components to zero.
- setZoomToScaffoldOnLoad(boolean) - Method in class chemaxon.marvin.common.UserSettings
-
- SEVERITY - Static variable in class chemaxon.checkers.StructureCheckerDescriptor
-
severity of checker
- Sg - Static variable in class chemaxon.core.ChemConst
-
- SGROUP - Static variable in class chemaxon.struc.MolAtom
-
"Atomic number" of an Sgroup.
- Sgroup - Class in chemaxon.struc
-
Structural group representation in the molecule.
- Sgroup(Molecule, int) - Constructor for class chemaxon.struc.Sgroup
-
Deprecated.
As of Marvin 5.12, replaced by
SgroupFactory.createSgroup(Molecule, SgroupType).
- Sgroup(Molecule, int, int) - Constructor for class chemaxon.struc.Sgroup
-
Deprecated.
As of Marvin 5.12, replaced by
SgroupFactory.createSgroup(Molecule, SgroupType) and
Sgroup.setXState(int).
- Sgroup(Molecule, SgroupType) - Constructor for class chemaxon.struc.Sgroup
-
- Sgroup(Molecule, SgroupType, int) - Constructor for class chemaxon.struc.Sgroup
-
- Sgroup(Sgroup, Molecule, Sgroup) - Constructor for class chemaxon.struc.Sgroup
-
Copy constructor.
- Sgroup(Sgroup, Molecule, Sgroup, int[]) - Constructor for class chemaxon.struc.Sgroup
-
Copy constructor.
- SGROUP_H - Static variable in class chemaxon.struc.MolAtom
-
Hydrogen atom which is the only atom in an Sgroup.
- SGROUP_SGROUP_MAP - Static variable in class chemaxon.checkers.result.ConvertConstants
-
This
String represents the key of cloned sgroup, original sgroup map
- SGROUP_TYPE_COUNT - Static variable in class chemaxon.struc.Sgroup
-
Number of S-group types.
- SGROUP_TYPENAMES - Static variable in class chemaxon.marvin.io.formats.mdl.MolfileUtil
-
Array of S-group type names.
- SgroupAtom - Class in chemaxon.struc.sgroup
-
S-group superatom.
- SgroupAtom(SuperatomSgroup) - Constructor for class chemaxon.struc.sgroup.SgroupAtom
-
Constructs a superatom for a superatom type S-group.
- SgroupCheckerResult - Class in chemaxon.checkers.result
-
- SgroupCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, StructureCheckerErrorType, Molecule, String, List<Sgroup>, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.SgroupCheckerResult
-
Constructor which initialize all the properties.
- SGROUPEND_H - Static variable in class chemaxon.struc.MolAtom
-
Hydrogen atom which have a neighbor that is in a SuperatomSgroup.
- sgroupGraph - Variable in class chemaxon.struc.Sgroup
-
The S-group's internal structure.
- sgroupList - Variable in class chemaxon.marvin.io.formats.mdl.MolImport
-
- sgroupType - Variable in class chemaxon.struc.Sgroup
-
The S-group type.
- SgroupType - Enum in chemaxon.struc
-
Enum of possible sgroup types.
- SHAPELY_SCHEME - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Shapely color scheme in display option flags.
- SHAPELY_SCHEME_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Shapely color scheme.
- shift(double, double) - Method in class chemaxon.marvin.space.GraphicCell
-
- shift(double, double) - Method in class chemaxon.marvin.space.GraphicScene
-
Sets the given shift factor in the active cell or in every cells
in case of synchronous mode.
- shift(int, int) - Method in class chemaxon.marvin.space.monitor.Label
-
A label can be shifted in x,y direction.
- shiftAnimated(double, double, int) - Method in class chemaxon.marvin.space.GraphicScene
-
Sets the given shift factor dividing by n parts.
- shiftx - Variable in class chemaxon.marvin.space.monitor.Label
-
Relative position of the label of the component with respect to the reference
point of the labeled component.
- shifty - Variable in class chemaxon.marvin.space.monitor.Label
-
Relative position of the label of the component with respect to the reference
point of the labeled component.
- shininess - Static variable in class chemaxon.marvin.space.monitor.Control
-
- SHORTCUTS - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter: "shortcuts".
- shortestPath(int, int) - Method in class chemaxon.calculations.TopologyAnalyser
-
Calculates the shortest topological path (number of bonds) between two
atoms.
- shortName() - Method in enum com.chemaxon.calculations.solubility.DefaultSolubilityCategory
-
- shortName() - Method in class com.chemaxon.calculations.solubility.SolubilityCategories.UndefinedSolubilityCategory
-
- shortName() - Method in interface com.chemaxon.calculations.solubility.SolubilityCategory
-
Returns the name of category.
- SHOW_SETS - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter: "showSets".
- showAllComponents() - Method in class chemaxon.marvin.space.GraphicCell
-
Sets all components to visible.
- showAllComponents(Class) - Method in class chemaxon.marvin.space.GraphicCell
-
Sets all components of the given class to visible.
- showAllComponents() - Method in class chemaxon.marvin.space.GraphicScene
-
Sets all invisible component of the active cell to visible.
- showAllComponents(Class) - Method in class chemaxon.marvin.space.GraphicScene
-
Sets all components of the given class in the active cell to be visible.
- showAllMonitors() - Method in class chemaxon.marvin.space.GraphicCell
-
Sets all monitor type components (labels as well) to visible.
- showAllMonitors() - Method in class chemaxon.marvin.space.GraphicScene
-
Sets all monitor component of the active cell to visible.
- showDialog() - Method in class chemaxon.marvin.view.swing.TableOptions
-
Bring up Table Options dialog box
- showErrorDialog(String, Throwable) - Method in class chemaxon.marvin.beans.MarvinPane
-
Show error dialog.
- showFaded() - Method in class chemaxon.marvin.space.GraphicCell
-
Sets all faded components to visible.
- showFaded() - Method in class chemaxon.marvin.space.GraphicComponent
-
A descendant should overwrite this method to have its faded part become visible.
- showFaded() - Method in class chemaxon.marvin.space.GraphicScene
-
Sets the drawing mode of all faded elements back to the original drawing mode.
- showFaded() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- showFaded() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
-
The faded visualizers will be fully visible again.
- showFaded() - Method in class chemaxon.marvin.space.MoleculeComponent
-
Faded atoms will be fully visible again.
- showFileDialog(String, Molecule) - Method in class chemaxon.marvin.beans.MarvinPane
-
Shows an Open or Save file dialog.
- showFileOpenDialog() - Method in class chemaxon.marvin.beans.MarvinPane
-
Shows file open dialog.
- showHeader(boolean) - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
- showInsertFunctionDialog() - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Shows the modal insert function dialog
- showManageFavoritesDialog() - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Shows the modal favourite manager dialog
- showManageMacrosDialog() - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Shows the modal macro manager dialog
- showSelectedNodes() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
-
- showStartupSelector() - Method in class chemaxon.marvin.beans.MSketchPane
-
This method is used in startup time to throw up a skin selector dialog.
- showVolume(boolean) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
For Gaussian Cube surfaces it can be enabled to visualize the volumetric data
from which the surface is generated.
- Si - Static variable in class chemaxon.core.ChemConst
-
- similarity(Molecule) - Method in class chemaxon.marvin.alignment.PairwiseAlignment
-
- similarity(AlignmentMolecule) - Method in class chemaxon.marvin.alignment.PairwiseAlignment
-
- similarity(Molecule) - Method in interface chemaxon.marvin.alignment.PairwiseComparison
-
Calculates the 3D similarity between the previously set query and the
target.
- similarity(AlignmentMolecule) - Method in interface chemaxon.marvin.alignment.PairwiseComparison
-
- similarity(Molecule) - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D
-
- similarity(AlignmentMolecule) - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D
-
- SIMILARITY - Static variable in class chemaxon.util.HitColoringAndAlignmentOptions
-
The similarity score is shown and stored in the MPropertyContainer of the
Molecule.
- SIMILARITY_LABEL - Static variable in class chemaxon.util.HitColoringAndAlignmentOptions
-
Label for the similarity score part of the hit.
- SIMILARITY_OFF - Static variable in class chemaxon.util.HitColoringAndAlignmentOptions
-
The similarity score is neither shown nor stored in the
MPropertyContainer of the Molecule.
- similarityScoreDisplay - Variable in class chemaxon.util.HitColoringAndAlignmentOptions
-
- SIMPLE_VIEW - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter: "simpView".
- simplifyIncompleteReactionToMolecule() - Method in class chemaxon.struc.RxnMolecule
-
Simplify a reaction to a molecule if possible.
- simplifyMolecule() - Method in class chemaxon.struc.MDocument
-
Simplifies the main molecule object if possible.
- simplifyToMolecule() - Method in class chemaxon.struc.RxnMolecule
-
Simplifies this RxnMolecule by moving the atoms and bonds from the
reactants, products, and agents to a Molecule.
- SINGLE_OR_AROMATIC - Static variable in class chemaxon.struc.MolBond
-
Single or aromatic query bond type.
- SINGLE_OR_DOUBLE - Static variable in class chemaxon.struc.MolBond
-
Single or double query bond type.
- SINGLE_THREADED - Static variable in class chemaxon.util.concurrent.processors.ConcurrentProcessors
-
- sinkIsAtom() - Method in class chemaxon.struc.graphics.MEFlow
-
Gets whether this arrow's sink is an atom.
- sinkIsBond() - Method in class chemaxon.struc.graphics.MEFlow
-
Gets whether this arrow's sink is a bond.
- sinkIsIncipBond() - Method in class chemaxon.struc.graphics.MEFlow
-
Gets whether this arrow's sink is an incipient bond.
- size() - Method in class chemaxon.formats.recognizer.RecognizerList
-
Deprecated.
Gets the total number of elements.
- size(int) - Method in class chemaxon.formats.recognizer.RecognizerList
-
Deprecated.
Gets the size of list at the specified level.
- size - Variable in class chemaxon.marvin.space.monitor.Control
-
- size() - Method in class chemaxon.struc.MPropertyContainer
-
Gets the total number of properties.
- size() - Method in class chemaxon.struc.prop.MHashProp
-
Gets the table size.,
- size() - Method in class chemaxon.struc.prop.MListProp
-
Gets the array size.
- sizeToString(double) - Static method in class chemaxon.struc.graphics.MFont
-
Converts an integer or fractional size to a string.
- sizeX - Variable in class chemaxon.marvin.space.monitor.Label
-
- sizeY - Variable in class chemaxon.marvin.space.monitor.Label
-
- SKC - Static variable in class chemaxon.formats.MFileFormat
-
SKC file format
- SKETCH_ANY_BOND - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter: "sketchAnyBond".
- SKETCH_ARROW_HEAD_LENGTH - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter: "sketchArrowHeadLength".
- SKETCH_ARROW_HEAD_WIDTH - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter: "sketchArrowHeadWidth".
- SKETCH_ARROW_TAIL_LENGTH - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter: "sketchArrowTailLength".
- SKETCH_ARROW_TAIL_WIDTH - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter: "sketchArrowTailWidth".
- SKETCH_CARBON_VISIBILITY - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter: "sketchCarbonVisibility".
- SKETCH_HELP - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter: "sketchHelp".
- SKETCH_LIGAND_ORDER_VISIBILITY - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter: "sketchLigandOrderVisibility".
- SKETCH_QUICK_HELP - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter: "sketchQuickHelp".
- SKETCH_STARTUP_SHOWN - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
- SKETCHABLE - Static variable in class chemaxon.marvin.beans.MViewPane
-
Editing mode identifier meaning the structures can be edited with the Edit > Structure menu
or double click and launches MarvinSketch in a new window.
- SketchCheckerRunner - Class in chemaxon.checkers.runner
-
WARNING!
THIS IS AN INTERNAL CLASS.
- SketchCheckerRunner(ConfigurationReader) - Constructor for class chemaxon.checkers.runner.SketchCheckerRunner
-
- SKETCHPANEL_LAST_HEIGHT - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
- SKETCHPANEL_LAST_WIDTH - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
- SketchParameterConstants - Class in chemaxon.marvin.sketch
-
Parameters of MarvinSketch Applet and Bean.
The parameters of the JMSketch applet can be set using the <param> HTML tag.
- SKIN - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter: "skin".
- skip(long) - Method in class chemaxon.marvin.io.PositionedInputStream
-
Skips over and discards n bytes of data.
- SKIP_COORDINATE_BONDS - Static variable in class chemaxon.util.iterator.IteratorFactory
-
Exclude coordinate bonds from bond iteration.
- SKIP_COVALENT_BONDS - Static variable in class chemaxon.util.iterator.IteratorFactory
-
Exclude covalent bonds from bond iteration.
- SKIP_EXPLICIT_H - Static variable in class chemaxon.util.iterator.IteratorFactory
-
Exclude explicit hydrogens from atom iteration.
- SKIP_LONE_PAIR - Static variable in class chemaxon.util.iterator.IteratorFactory
-
Exclude lone pairs from atom iteration.
- SKIP_MULTICENTER - Static variable in class chemaxon.util.iterator.IteratorFactory
-
Exclude multicenters from atom iteration.
- SKIP_PSEUDO_ATOM - Static variable in class chemaxon.util.iterator.IteratorFactory
-
Exclude pseudo atoms from atom iteration.
- skipLine() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
-
Skips the next line.
- skipLine() - Method in class chemaxon.marvin.io.PositionedInputStream
-
Skips the next line.
- skipRecord() - Method in class chemaxon.formats.MolImporter
-
Skips the next molecule or document instead of reading it into memory.
- skipRecord() - Method in class chemaxon.marvin.io.ArrayMDocSource
-
Skips the next document.
- skipRecord() - Method in class chemaxon.marvin.io.MDocSource
-
Skips the next document.
- skipRecord() - Method in class chemaxon.marvin.io.MRecordImporter
-
Skips the next document.
- skipRecord() - Method in interface chemaxon.marvin.io.MRecordReader
-
Skips the next record.
- skipRecords(int, int, MProgressMonitor, int, Runnable) - Method in class chemaxon.marvin.io.MDocSource
-
- Sm - Static variable in class chemaxon.core.ChemConst
-
- SM_ATOM - Static variable in class chemaxon.marvin.beans.MSketchPane
-
Atom mode.
- SM_BOND - Static variable in class chemaxon.marvin.beans.MSketchPane
-
Bond mode.
- SM_DELETE - Static variable in class chemaxon.marvin.beans.MSketchPane
-
Delete mode.
- SM_FLAGS_OFF - Static variable in class chemaxon.marvin.beans.MSketchPane
-
Offset of flags in sketch mode.
- SM_MASK - Static variable in class chemaxon.marvin.beans.MSketchPane
-
Sketch mode mask.
- SM_SELECT - Static variable in class chemaxon.marvin.beans.MSketchPane
-
Select mode.
- SM_SELECT_LASSO - Static variable in class chemaxon.marvin.beans.MSketchPane
-
Lasso select mode.
- SMALL_FONT_SIZE - Static variable in class chemaxon.marvin.space.monitor.Label
-
- smallestRing() - Method in class chemaxon.calculations.Ring
-
Identifies the smallest ring (number of atoms) in the molecule.
- smallestRing() - Method in class chemaxon.calculations.TopologyAnalyser
-
- smallestRingSize() - Method in class chemaxon.calculations.Ring
-
Calculates the size of the smallest ring in the molecule.
- smallestRingSize() - Method in class chemaxon.calculations.TopologyAnalyser
-
- smallestRingSizeOfAtom(int) - Method in class chemaxon.calculations.Ring
-
Calculates the size of the smallest ring an atom is a member of.
- smallestRingSizeOfAtom(int) - Method in class chemaxon.calculations.TopologyAnalyser
-
- smallestRingSystem() - Method in class chemaxon.calculations.Ring
-
Identifies the smallest ring system (number of rings) in the molecule.
- smallestRingSystem() - Method in class chemaxon.calculations.TopologyAnalyser
-
- smallestRingSystemSize() - Method in class chemaxon.calculations.Ring
-
Calculates the size of the smallest ring system (number of rings) in the
molecule.
- smallestRingSystemSize() - Method in class chemaxon.calculations.TopologyAnalyser
-
- SMARTS - Static variable in class chemaxon.formats.MFileFormat
-
SMARTS.
- SMARTS_H_DAYLIGHT_COMP_MODE - Static variable in class chemaxon.struc.MolAtom
-
Option flag to express daylight-type smarts atom parsing of H.
- SMARTS_H_MARVIN_COMP_MODE - Static variable in class chemaxon.struc.MolAtom
-
Option flag to express marvin-pre-3.5-type smarts atom parsing of H.
- SmartsAtomQuerifier - Class in chemaxon.marvin.io.formats.smiles
-
Class for partial interpretation of smarts atoms.
- SmartsAtomQuerifier() - Constructor for class chemaxon.marvin.io.formats.smiles.SmartsAtomQuerifier
-
Creates a new SmartsAtomQuerifier object.
- SMILES - Static variable in class chemaxon.formats.MFileFormat
-
SMILES.
- SMILESRecognizer - Class in chemaxon.formats.recognizer
-
Deprecated.
as of Marvin 2014.07.21.0 intended for internal use only
- SMILESRecognizer() - Constructor for class chemaxon.formats.recognizer.SMILESRecognizer
-
Deprecated.
- smol() - Method in class chemaxon.struc.MoleculeGraph
-
Gets a
Smolecule representation of this molecule.
- Smolecule - Interface in chemaxon.struc
-
Array-based abstract molecule class.
- SMOOTH_STICKS - Static variable in class chemaxon.marvin.space.MoleculeComponent
-
- smoothStickColoring - Variable in class chemaxon.marvin.space.MoleculeComponent
-
- Sn - Static variable in class chemaxon.core.ChemConst
-
- SoapServiceDescriptor - Class in chemaxon.marvin.services.soap
-
Service descriptor of SOAP type requests.
- SoapServiceDescriptor() - Constructor for class chemaxon.marvin.services.soap.SoapServiceDescriptor
-
- SolubilityCalculator - Class in com.chemaxon.calculations.solubility
-
Solubility calculator.
API usage example:
- SolubilityCalculator() - Constructor for class com.chemaxon.calculations.solubility.SolubilityCalculator
-
Constructor.
- SolubilityCategories - Class in com.chemaxon.calculations.solubility
-
Array of solubility categories.
- SolubilityCategories(SolubilityCategory[], SolubilityUnit) - Constructor for class com.chemaxon.calculations.solubility.SolubilityCategories
-
Constructor.
- SolubilityCategories.UndefinedSolubilityCategory - Class in com.chemaxon.calculations.solubility
-
Undefined category.
- SolubilityCategories.UndefinedSolubilityCategory() - Constructor for class com.chemaxon.calculations.solubility.SolubilityCategories.UndefinedSolubilityCategory
-
- SolubilityCategory - Interface in com.chemaxon.calculations.solubility
-
Interface for solubility categories.
- SolubilityResult - Interface in com.chemaxon.calculations.solubility
-
Solubility prediction result.
- SolubilityUnit - Enum in com.chemaxon.calculations.solubility
-
Solubility unit.
- SOLVENT - Static variable in class chemaxon.marvin.calculations.MSAPlugin
-
Surface area type: 3D solvent accessible surface area.
- SolventChecker - Class in chemaxon.checkers
-
SolventChecker detects common solvents in multicomponent structures.
- SolventChecker() - Constructor for class chemaxon.checkers.SolventChecker
-
Default constructor
- sort(Sgroup[], int) - Static method in class chemaxon.struc.Sgroup
-
Sorts S-groups in parent-child or child-parent order.
- SORT_CHILD_PARENT - Static variable in class chemaxon.struc.Sgroup
-
Parent-child sort order.
- SORT_PARENT_CHILD - Static variable in class chemaxon.struc.Sgroup
-
Parent-child sort order.
- sortBondsAccordingTo(MolBond[]) - Method in class chemaxon.struc.MoleculeGraph
-
Sorts bonds in the same order as they appear in another chemical graph.
- sortBondsAccordingTo(MolBond[]) - Method in class chemaxon.struc.RgMolecule
-
Sort edges in the same order as they appear in the specified array.
- sortBondsAccordingTo(MolBond[]) - Method in class chemaxon.struc.RxnMolecule
-
Sort edges in the same order as they appear in the specified array.
- sortSgroupXBonds() - Method in class chemaxon.struc.Molecule
-
Deprecated.
As of Marvin 5.12, no replacement.
Crossing bonds of a SuperatomSgroup do not need to be sorted
any more. It is not advised to sort them anyway because then the indexes of
bonds change in the parent molecule.
- sortXBonds() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Deprecated.
As of Marvin 5.12, no replacement.
Crossing bonds of a SuperatomSgroup do not need to be sorted
any more. It is not advised to sort them anyway because then the indexes of
bonds change in the parent molecule.
- SOURCE_TEXT - Static variable in class chemaxon.naming.DocumentToStructure
-
The source text, as it appears in the original document.
- sourceIsAtom() - Method in class chemaxon.struc.graphics.MEFlow
-
Gets whether this arrow's source is an atom.
- sourceIsBond() - Method in class chemaxon.struc.graphics.MEFlow
-
Gets whether this arrow's source is a bond.
- SPACEFILL - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Spacefill rendering mode.
- SPACEFILL_RENDERING_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Spacefill rendering mode.
- spacefillPrecision - Variable in class chemaxon.marvin.space.MoleculeComponent
-
- specular - Static variable in class chemaxon.marvin.space.monitor.Control
-
- SPIN - Static variable in class chemaxon.marvin.view.ViewParameterConstants
-
Identifier of parameter: "spin".
- SPLASH_SCREEN_IMAGE - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter: "splashScreenImage".
- splitAllDisconnectedComponents() - Method in class chemaxon.struc.RxnMolecule
-
Replaces all disconnected reaction components by its connected fragments
in the structure array.
- splitComponentParts(MoleculeGraph, int) - Method in class chemaxon.struc.RxnMolecule
-
Finds those component parts that are contained in the molecule graph m and
creates separate components from the fragments contained in m, splitting them from the previous merges.
- splitDisconnectedComponent(long) - Method in class chemaxon.struc.RxnMolecule
-
Replaces a disconnected reaction component by its connected fragments
in the structure array.
- splitDisconnectedComponent(int, int) - Method in class chemaxon.struc.RxnMolecule
-
Replaces a disconnected reaction component by its connected fragments
in the structure array.
- splitFileAndOptions(String) - Static method in class chemaxon.formats.MFileFormatUtil
-
Parses "file{options}" strings used in molecule file import.
- splitFormatAndOptions(String) - Static method in class chemaxon.formats.MFileFormatUtil
-
Parses "format:options" strings used in molecule file import and export.
- Sr - Static variable in class chemaxon.core.ChemConst
-
- sringsize() - Method in class chemaxon.struc.MolAtom
-
Calculate the size of smallest ring containing this atom.
- SST_ALTERNATING - Static variable in class chemaxon.struc.Sgroup
-
Alternating polymer S-group subtype.
- SST_BLOCK - Static variable in class chemaxon.struc.Sgroup
-
Block polymer S-group subtype.
- SST_RANDOM - Static variable in class chemaxon.struc.Sgroup
-
Random polymer S-group subtype.
- ST_AMINOACID - Static variable in class chemaxon.struc.Sgroup
-
Amino acid s-group type.
- ST_ANY - Static variable in class chemaxon.struc.Sgroup
-
Any polymer S-group type.
- ST_COMPONENT - Static variable in class chemaxon.struc.Sgroup
-
Component S-group type.
- ST_COPOLYMER - Static variable in class chemaxon.struc.Sgroup
-
Copolymer S-group type.
- ST_CROSSLINK - Static variable in class chemaxon.struc.Sgroup
-
Crosslink S-group type.
- ST_DATA - Static variable in class chemaxon.struc.Sgroup
-
Data S-group type.
- ST_FORMULATION - Static variable in class chemaxon.struc.Sgroup
-
Formulation S-group type.
- ST_GENERIC - Static variable in class chemaxon.struc.Sgroup
-
Generic S-group type.
- ST_GRAFT - Static variable in class chemaxon.struc.Sgroup
-
Graft S-group type.
- ST_MER - Static variable in class chemaxon.struc.Sgroup
-
Mer S-group type.
- ST_MIXTURE - Static variable in class chemaxon.struc.Sgroup
-
Mixture S-group type.
- ST_MODIFICATION - Static variable in class chemaxon.struc.Sgroup
-
Modification S-group type.
- ST_MONOMER - Static variable in class chemaxon.struc.Sgroup
-
Monomer S-group type.
- ST_MULTICENTER - Static variable in class chemaxon.struc.Sgroup
-
Multicenter S-group type.
- ST_MULTIPLE - Static variable in class chemaxon.struc.Sgroup
-
Multiple group S-group type.
- ST_SRU - Static variable in class chemaxon.struc.Sgroup
-
SRU (Structural Repeating Unit: polymers and repeating units with
repetition ranges) S-group type.
- ST_SUPERATOM - Static variable in class chemaxon.struc.Sgroup
-
Superatom S-group type.
- standardize(Molecule) - Method in interface chemaxon.jep.Standardizer
-
- standardize(Molecule) - Method in class chemaxon.marvin.calculations.AlignmentPlugin
-
- standardize(Molecule) - Method in class chemaxon.marvin.calculations.ConformerPlugin
-
Expands sgroups.
- standardize(Molecule) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
-
Prevents default standardization: does nothing.
- standardize(Molecule) - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
Expands sgroups.
- standardize(Molecule) - Method in class chemaxon.marvin.calculations.IonChargePlugin
-
Standardizes the molecule.
- standardize(Molecule) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
-
Standardizes the molecule.
- standardize(Molecule) - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
-
Standardizes the molecule.
- standardize(Molecule) - Method in class chemaxon.marvin.calculations.logDPlugin
-
Standardizes the molecule.
- standardize(Molecule) - Method in class chemaxon.marvin.calculations.logPPlugin
-
Standardizes the molecule.
- standardize(Molecule) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
-
Standardizes the molecule.
- standardize(Molecule) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
-
Standardizes the molecule.
- standardize(Molecule) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Prevents default standardization: does nothing.
- standardize(Molecule) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
-
Expands sgroups.
- standardize(Molecule) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Standardizes the molecule.
- standardize(Molecule) - Method in class chemaxon.marvin.calculations.RefractivityPlugin
-
Standardizes the molecule.
- standardize(Molecule) - Method in class chemaxon.marvin.calculations.ResonancePlugin
-
Standardizes the molecule.
- standardize(Molecule) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
-
Clears enhanced stereo information.
- standardize(Molecule) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
-
Standardize input molecule
Standardization currently ungroups SGroups
- standardize(Molecule) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Standardizes the molecule.
- standardize(Molecule) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Expands sgroups.
- standardize(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Standardizes the molecule by performing the transformations necessary
to run the plugin (aromatize, dehydrogenize, bring nitro groups to
common form, ...).
- standardizeIonicGroups(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Default standardization:
nitro groups:
[O-:1][N+:2] >> [O:1]=[N:2], [NH1+:1][O-:2] >> [H:3][O:2][N:1]
sulphynil groups: [#6][S+:1]([#6])[#8-:2]>>[#6][S:1]([#6])=[O:2]
- standardizeNeutralGroups(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Neutral -> ionic standardization:
[O:1]=[N:2] >> [O-:1][N+:2], [H:3][O:2][N:1] >> [NH1+:1][O-:2]
sulphynil group transformation: [#6][S:1]([#6])=[O:2] >> [#6][S+:1]([#6])[#8-:2]
- Standardizer - Interface in chemaxon.jep
-
Wrapper interface for chemaxon.reaction.Standardzier class.
- STANDARDIZER - Static variable in class chemaxon.license.LicenseManager
-
Identifier of product: Standardizer
- STAR - Static variable in class chemaxon.struc.MolAtom
-
"Atomic number" of the star atom.
- StarAtomChecker - Class in chemaxon.checkers
-
A descendant of
AtomChecker detecting so called star atoms having "*" as atomic symbol.
- StarAtomChecker() - Constructor for class chemaxon.checkers.StarAtomChecker
-
Default constructor
- start() - Method in interface chemaxon.marvin.alignment.AlignmentMoleculeFactory.ProgressBarInterface
-
- start(MDocSource, String) - Method in class chemaxon.marvin.view.swing.TableSupport
-
Starts loading molecules.
- start() - Method in interface chemaxon.util.concurrent.ConcurrentProcessor
-
- startEMFGenerator() - Static method in class chemaxon.util.ImageExportUtil
-
Starts the initialization of the .NET based EMF generator on a background thread.
- startGrabLines() - Method in class chemaxon.marvin.io.PositionedInputStream
-
Starts grabbing lines.
- startNow(MDocSource, String) - Method in class chemaxon.marvin.view.swing.TableSupport
-
Starts loading molecules immediately.
- startPermanentResources() - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
-
Starts all the permanent native resources that have to be started to do fast and reliable
copy in Marvin.
- STATICpKaPREFIX - Static variable in class chemaxon.marvin.calculations.pKaPlugin
-
pKa's prefix (acidic/basic) does not depend on the submitted micro state (default)
- STATUS_BAR - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter: "statusBar".
- STEP_DEFAULT - Static variable in class chemaxon.marvin.calculations.AlignmentPlugin
-
- stepWedge() - Method in class chemaxon.struc.MolBond
-
- stepWedge(MolBond[]) - Static method in class chemaxon.struc.MolBond
-
Flip the given bonds to the next state
ONLY 1 bond is set to chiral
starting from the last bond
- stereo(int) - Method in class chemaxon.calculations.stereo.Stereochemistry
-
Calculates absolute stereo configuration of the given atom.
- stereo(int, int) - Method in class chemaxon.calculations.stereo.Stereochemistry
-
Calculates absolute stereo configuration of the given double bond.
- stereo(int) - Method in class chemaxon.calculations.TopologyAnalyser
-
- stereo(int, int) - Method in class chemaxon.calculations.TopologyAnalyser
-
- STEREO1_MASK - Static variable in class chemaxon.struc.MolBond
-
Single bond stereo mask.
- STEREO2_CARE - Static variable in class chemaxon.struc.MolBond
-
Cis/trans info of this bond is taken care of during
the SSS process if this flag is set - used only for query bonds.
- STEREO_MASK - Static variable in class chemaxon.struc.MolBond
-
Single and double bond stereo mask.
- StereoAnalysis - Class in com.chemaxon.calculations.stereoanal
-
The stereo analysis module is able to calculate stereochemical descriptors for a molecule,
giving an analysis in terms of the stereochemical properties.
API usage example:
- StereoAnalysis(Molecule) - Constructor for class com.chemaxon.calculations.stereoanal.StereoAnalysis
-
Creates an analysis.
- StereoCareBoxChecker - Class in chemaxon.checkers
-
Checker to find molecules containing Stereo Care Boxes.
- StereoCareBoxChecker() - Constructor for class chemaxon.checkers.StereoCareBoxChecker
-
Creates a stereo care box checker.
- StereoCenter - Interface in com.chemaxon.calculations.stereoanal.stereocenters
-
Interface for stereo centers.
- StereoCenterVisitor - Interface in com.chemaxon.calculations.stereoanal.filters
-
Visitor interface for stereo centers.
- StereoCheckUtility - Class in chemaxon.checkers
-
Utility class for stereo chemistry checkers
- StereoCheckUtility() - Constructor for class chemaxon.checkers.StereoCheckUtility
-
- Stereochemistry - Class in chemaxon.calculations.stereo
-
Central class for accessing functions analyzing the topology of a molecule.
- Stereochemistry() - Constructor for class chemaxon.calculations.stereo.Stereochemistry
-
- stereoClean() - Method in class chemaxon.struc.MoleculeGraph
-
Reset the wedges of the molecule, based on the actual
parity information in 2D, remove wedges in 3D.
- stereoClean() - Method in class chemaxon.struc.RgMolecule
-
Reset the wedges of the molecule, based on the actual
parity information in 2D remove wedges in 3D.
- stereoClean() - Method in class chemaxon.struc.RxnMolecule
-
Reset the wedges of the molecule, based on the actual
parity information in 2D remove wedges in 3D.
- StereoConstants - Interface in chemaxon.struc
-
Constants for atom parity and double bond stereo.
- StereoConstants - Interface in com.chemaxon.calculations.stereoanal
-
Wrapper interface for stereo constants.
- StereoConstants.EnhancedStereoType - Enum in com.chemaxon.calculations.stereoanal
-
Enhanced stereo flags.
- StereoConstants.StereoValue - Interface in com.chemaxon.calculations.stereoanal
-
Deprecated.
- StereoConstants.StereoValue.AtropStereo - Enum in com.chemaxon.calculations.stereoanal
-
Deprecated.
As of Marvin 14.9.15, replaced by
AtropStereoIUPACDescriptor.
- StereoConstants.StereoValue.AxialStereo - Enum in com.chemaxon.calculations.stereoanal
-
Deprecated.
As of Marvin 14.9.15, replaced by
AxialStereoIUPACDescriptor.
- StereoConstants.StereoValue.CisTransStereo - Enum in com.chemaxon.calculations.stereoanal
-
Deprecated.
As of Marvin 14.9.15, replaced by
CisTransStereoIUPACDescriptor.
- StereoConstants.StereoValue.TetrahedralStereo - Enum in com.chemaxon.calculations.stereoanal
-
Deprecated.
As of Marvin 14.9.15, replaced by
TetrahedralStereoIUPACDescriptor.
- StereoConstants.Type - Enum in com.chemaxon.calculations.stereoanal
-
Stereo center type.
- stereoDoubleBondCount() - Method in class chemaxon.calculations.stereo.Stereochemistry
-
Calculates the number of stereo double bonds.
- stereoDoubleBondCount() - Method in class chemaxon.calculations.TopologyAnalyser
-
- StereoInversionRetentionMarkChecker - Class in chemaxon.checkers
-
Detects reaction inversion/retention marks on atoms.
- StereoInversionRetentionMarkChecker() - Constructor for class chemaxon.checkers.StereoInversionRetentionMarkChecker
-
Default constructor
- StereoisomerPlugin - Class in chemaxon.marvin.calculations
-
Plugin class for stereoisomer calculation.
- StereoisomerPlugin() - Constructor for class chemaxon.marvin.calculations.StereoisomerPlugin
-
- stericEffectIndex(int) - Method in class chemaxon.calculations.TopologyAnalyser
-
Calculates topological steric effect index (TSEI) of an atom from
covalent radii values and topological distances.
- STGRP_ABS - Static variable in interface chemaxon.struc.StereoConstants
-
Absolute stereo group type for enhanced stereo representation.
- STGRP_AND - Static variable in interface chemaxon.struc.StereoConstants
-
AND stereo group type for enhanced stereo representation.
- STGRP_NONE - Static variable in interface chemaxon.struc.StereoConstants
-
Empty stereo group type setting meaning no enhanced stereo label.
- STGRP_OR - Static variable in interface chemaxon.struc.StereoConstants
-
OR stereo group type for enhanced stereo representation.
- STICK_DISTANCE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter: "stickdst".
- STICK_THICKNESS - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter: "stickThickness".
- stickRadius - Variable in class chemaxon.marvin.space.MoleculeComponent
-
- STICKS - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Sticks rendering mode.
- STICKS_RENDERING_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Sticks rendering mode.
- stickSlicePrecision - Variable in class chemaxon.marvin.space.MoleculeComponent
-
- stop() - Method in interface chemaxon.marvin.alignment.AlignmentMoleculeFactory.ProgressBarInterface
-
- storageSizeChanged(MDocStorage, int, int) - Method in interface chemaxon.marvin.view.MDocStorage.Listener
-
Storage size changed.
- storageSizeFinalized(MDocStorage) - Method in interface chemaxon.marvin.view.MDocStorage.Listener
-
Final storage size determined.
- store() - Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
-
Stores a new result item.
- storeDoc(MDocument, int, String) - Method in class chemaxon.marvin.view.MDocStorage
-
Store new document and free the oldest accessed if the number of documents is too much to fit
in memory.
- storeDrawProperty(String, String) - Method in class chemaxon.marvin.space.GraphicComponent
-
Stores the given property.
- storeMainDoc(MDocument, int) - Method in class chemaxon.marvin.view.MDocStorage
-
Store new document and free the oldest accessed if the number of documents is too much to fit
in memory.
- storeTemporaryObject(String, Object) - Method in class chemaxon.struc.MolAtom
-
Stores an object temporarily.
- StraightDoubleBondChecker - Class in chemaxon.checkers
-
- StraightDoubleBondChecker() - Constructor for class chemaxon.checkers.StraightDoubleBondChecker
-
Constructs EitherDoubleBondChecker instance
- stringBuffer - Variable in class chemaxon.marvin.io.MolExportModule
-
This buffer can contain the molecule file contents, in case of a
text format.
- stringToArray(String, String, int, int) - Static method in class chemaxon.marvin.io.MPropHandler
-
- stringToScalar(String, String) - Static method in class chemaxon.marvin.io.MPropHandler
-
- stringValue() - Method in class chemaxon.struc.prop.MStringProp
-
Gets the string value.
- STRUCTURAL_FRAMEWORKS_PLUGIN - Static variable in class chemaxon.license.LicenseManager
-
Identifier of product: Structural Frameworks Plugin
- StructuralFrameworksPlugin - Class in chemaxon.marvin.calculations
-
Plugin class to calculate Bemis-Murcko and other structural scaffolds of input
molecules.
- StructuralFrameworksPlugin() - Constructor for class chemaxon.marvin.calculations.StructuralFrameworksPlugin
-
- StructuralFrameworksPlugin.FrameworkTypes - Enum in chemaxon.marvin.calculations
-
FrameworkTypes represents the available calculations
- StructuralFrameworksPlugin.VerbosePrinter - Interface in chemaxon.marvin.calculations
-
Verbose printer specification
- structure - Variable in class chemaxon.naming.DocumentExtractor.Hit
-
Deprecated.
The chemical structure corresponding to the name.
- STRUCTURE_CHECKER - Static variable in class chemaxon.license.LicenseManager
-
Identifier of product: Structure Checker
- STRUCTURE_TO_NAME - Static variable in class chemaxon.license.LicenseManager
-
Identifier of product: Structure to Name
- StructureCheck - Class in chemaxon.checkers
-
- StructureCheck() - Constructor for class chemaxon.checkers.StructureCheck
-
Creates a new structures checker console, sets the logging on null
stream.
- StructureChecker - Interface in chemaxon.checkers
-
General interface describing functions that are available for a chemical structure checker.
- StructureCheckerDescriptor - Class in chemaxon.checkers
-
- StructureCheckerDescriptor(Class<? extends StructureChecker>) - Constructor for class chemaxon.checkers.StructureCheckerDescriptor
-
Constructs a descriptor based on checker class.
- StructureCheckerErrorType - Enum in chemaxon.checkers
-
Enum containing possible error types for structure checkers.
- StructureCheckerFactory - Class in chemaxon.checkers
-
Deprecated.
use CheckerFixerFactory instead
- StructureCheckerFactory() - Constructor for class chemaxon.checkers.StructureCheckerFactory
-
- StructureCheckerFactory(String, String) - Constructor for class chemaxon.checkers.StructureCheckerFactory
-
- StructureCheckerFactory(InputStream, InputStream) - Constructor for class chemaxon.checkers.StructureCheckerFactory
-
- StructureCheckerHelper - Class in chemaxon.checkers
-
This helper class contains utility functions used by
StructureChecker
instances providing constants and utility functions.
- StructureCheckerHelper() - Constructor for class chemaxon.checkers.StructureCheckerHelper
-
- StructureCheckerResult - Interface in chemaxon.checkers.result
-
- StructureCheckerUtility - Class in chemaxon.checkers
-
Utility to handle core features
- StructureCheckerUtility() - Constructor for class chemaxon.checkers.StructureCheckerUtility
-
- StructureCheckOptions - Class in chemaxon.checkers
-
Options descriptor for structure checker command line interface
- StructureCheckOptions() - Constructor for class chemaxon.checkers.StructureCheckOptions
-
- StructureCheckOptions.Mode - Enum in chemaxon.checkers
-
The mode of the structure check
- StructureCheckOptions.ModeConverter - Class in chemaxon.checkers
-
Converter for Mode enumeration.
- StructureCheckOptions.ModeConverter() - Constructor for class chemaxon.checkers.StructureCheckOptions.ModeConverter
-
- StructureCheckOptions.Type - Enum in chemaxon.checkers
-
The output type of the structure check
- StructureCheckOptions.TypeConverter - Class in chemaxon.checkers
-
Converter for Type enumeration.
- StructureCheckOptions.TypeConverter() - Constructor for class chemaxon.checkers.StructureCheckOptions.TypeConverter
-
- StructureFixer - Interface in chemaxon.fixers
-
- StructureFixerDescriptor - Class in chemaxon.fixers
-
- StructureFixerDescriptor(Class<? extends StructureFixer>) - Constructor for class chemaxon.fixers.StructureFixerDescriptor
-
Constructs a descriptor based on fixer class.
- StructureFixerFactory - Class in chemaxon.fixers
-
Deprecated.
use CheckerFixerFactory instead
- StructureFixerFactory() - Constructor for class chemaxon.fixers.StructureFixerFactory
-
Deprecated.
Default constructor.
- StructureFixerFactory(String) - Constructor for class chemaxon.fixers.StructureFixerFactory
-
Deprecated.
Parameterized constructor.
- StructureFixerFactory(String, String) - Constructor for class chemaxon.fixers.StructureFixerFactory
-
Deprecated.
Parameterized constructor.
- StructureFixerFactory(InputStream, InputStream) - Constructor for class chemaxon.fixers.StructureFixerFactory
-
Deprecated.
Parameterized constructor.
- StructureToJC4XL - Class in chemaxon.formats.documents.jchemexcel
-
Adds molecule/structure data to a JChemExcel workbook.
- StructureToJC4XL(Workbook, OutputStream) - Constructor for class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
- StructureToJC4XL(OutputStream) - Constructor for class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
Constructor for adding molecule/structure data one-by-one
to store them in a JChemExcel workbook.
- SubjectToRemoval - Annotation Type in com.chemaxon.common.annotations
-
The entity denoted by this annotation is deprecated and will be removed
in the first major release following the specified date.
- substring(int) - Method in class chemaxon.struc.graphics.MTextDocument.Section
-
Gets a substring.
- substring(int, int) - Method in class chemaxon.struc.graphics.MTextDocument.Section
-
Gets a substring.
- substring(int) - Method in class chemaxon.struc.graphics.MTextDocument
-
Gets a substring of the document.
- substring(int, int) - Method in class chemaxon.struc.graphics.MTextDocument
-
Gets a substring of the document.
- SubstructureChecker - Class in chemaxon.checkers
-
- SubstructureChecker() - Constructor for class chemaxon.checkers.SubstructureChecker
-
Default constructor.
- SubstructureChecker(Map<String, String>) - Constructor for class chemaxon.checkers.SubstructureChecker
-
Parameterized constructor.
- SubstructureChecker(String) - Constructor for class chemaxon.checkers.SubstructureChecker
-
Parameterized constructor.
- SubstructureCheckerResult - Class in chemaxon.checkers.result
-
- SubstructureCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, StructureCheckerErrorType, Molecule, String, String, String, String, Icon, List<int[]>, String) - Constructor for class chemaxon.checkers.result.SubstructureCheckerResult
-
Constructor which initialize all the properties.
- SubstructureFixer - Class in chemaxon.fixers
-
Fixer to fix substructure issues.
- SubstructureFixer() - Constructor for class chemaxon.fixers.SubstructureFixer
-
- subtract(DPoint3) - Method in class chemaxon.struc.DPoint3
-
Subtract the given v2 vector from this one.
- subtract(DPoint3, DPoint3) - Static method in class chemaxon.struc.DPoint3
-
Calculates the difference of the two vectors
- SUM_OF_VALUES - Static variable in class chemaxon.marvin.space.SurfaceColoring
-
Will the sum of the affecting properties be mapped onto the surface.
- sumConservedQuantities(MolAtom, int[], int) - Method in class chemaxon.struc.MoleculeGraph
-
For internal use only.
- sumConservedQuantities(MolAtom, int[], int) - Method in class chemaxon.struc.RgMolecule
-
For internal use only.
- sumDistanceSquare(MoleculeGraph, DPoint3) - Static method in class chemaxon.marvin.util.CleanUtil
-
Calculates the sum of the distance square for each atom from a point.
- SuperatomSgroup - Class in chemaxon.struc.sgroup
-
Superatom S-group.
- SuperatomSgroup(Molecule) - Constructor for class chemaxon.struc.sgroup.SuperatomSgroup
-
Constructs a superatom S-group in expanded state.
- SuperatomSgroup(Molecule, boolean) - Constructor for class chemaxon.struc.sgroup.SuperatomSgroup
-
Constructs a superatom S-group.
- SuperatomSgroup(SuperatomSgroup, Molecule, Sgroup, int[]) - Constructor for class chemaxon.struc.sgroup.SuperatomSgroup
-
Copy constructor.
- superGraph - Variable in class chemaxon.struc.MoleculeGraph
-
Parent of all parents.
- SURE - Static variable in class chemaxon.formats.recognizer.AbbrevGroupRecognizer
-
Deprecated.
Line is surely in the given format.
- SURE - Static variable in class chemaxon.formats.recognizer.PDBRecognizer
-
Deprecated.
Line is surely in the given format.
- SURFACE_COLOR_GRID_MAPPING - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- SURFACE_COLOR_PROPERTY_MAPPING - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- SURFACE_COLOR_TYPE_ATOMTYPE - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- SURFACE_COLOR_TYPE_B_FACTOR - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- SURFACE_COLOR_TYPE_CHAIN - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- SURFACE_COLOR_TYPE_CONSTANT - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- SURFACE_COLOR_TYPE_EP - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- SURFACE_COLOR_TYPE_RAINBOW - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- SURFACE_COLOR_TYPE_RESIDUE - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- SURFACE_COLOR_TYPE_SS - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- SURFACE_SIMPLIFICATION_ENABLED - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- SURFACE_SMOOTHNESS - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
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- SURFACE_TYPE_BLOBBY - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
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- SURFACE_TYPE_CONNOLLY - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
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- SURFACE_TYPE_GAUSSIAN - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
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- SURFACE_TYPE_SAS - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
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- SURFACE_TYPE_VDW - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
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- SurfaceColoring - Class in chemaxon.marvin.space
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SurfaceColoring is an easy-to-use tool to map different properties as colors
onto surfaces.
- SurfaceColoring(SurfaceComponent) - Constructor for class chemaxon.marvin.space.SurfaceColoring
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The given surface is to be colored after the parametrization.
- SurfaceColoring(ArrayList, SurfaceComponent) - Constructor for class chemaxon.marvin.space.SurfaceColoring
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The given surface of the given molecules is to be colored after the parametrization.
- SurfaceColoring(ArrayList, SurfaceComponent, float) - Constructor for class chemaxon.marvin.space.SurfaceColoring
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The given surface of the given molecules is to be colored after the parametrization.
- surfaceColorType - Variable in class chemaxon.marvin.space.MolecularSurfaceComponent
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- SurfaceComponent - Class in chemaxon.marvin.space
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Class that represents a surface defined by its vertices, normal vectors and
polygons.
- SurfaceComponent(int) - Constructor for class chemaxon.marvin.space.SurfaceComponent
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Creates a new instance of SurfaceComponent, sets its draw type to FILLED_TYPE.
- SurfaceComponent(int, int) - Constructor for class chemaxon.marvin.space.SurfaceComponent
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Creates a new SurfaceComponent, sets its draw type to FILLED_TYPE.
- SurfaceComponent(int, int, int, int) - Constructor for class chemaxon.marvin.space.SurfaceComponent
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Creates a new SurfaceComponent, sets its draw type to FILLED_TYPE.
- surfaceGridPrecision - Variable in class chemaxon.marvin.space.MolecularSurfaceComponent
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- surfaceOf(GraphicComponent) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
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Tells whether it is the molecular surface of the given component (molecule).
- surfaceSimplification() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
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Runs the (might be time-consuming) algorithm thst reduces the number of triangles
of the surface.
- surfaceSimplificationEnabled - Variable in class chemaxon.marvin.space.MolecularSurfaceComponent
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- surfaceSimplificationTolerance - Variable in class chemaxon.marvin.space.MolecularSurfaceComponent
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- surfaceSmoothnessFactor - Variable in class chemaxon.marvin.space.MolecularSurfaceComponent
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- surfaceType - Variable in class chemaxon.marvin.space.MolecularSurfaceComponent
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- SVG - Static variable in class chemaxon.formats.MFileFormat
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Scalable Vector Graphics.
- swap() - Method in class chemaxon.struc.MolBond
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Change orientation.
- swapAtoms(int, int) - Method in class chemaxon.struc.SelectionMolecule
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Swap two atoms.
- swapHeadTail() - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
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Swaps the head and tail bonds of this sru if both are set.
- SwingUtil - Class in chemaxon.marvin.util
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Swing utility functions.
- SwingUtil() - Constructor for class chemaxon.marvin.util.SwingUtil
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- SYBYLMOL - Static variable in class chemaxon.formats.MFileFormat
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Tripos SYBYL molfiles.
- SYM_CX - Static variable in class chemaxon.struc.MolAtom
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Atom symbol string for CxSMILES export.
- SYM_EXPLH - Static variable in class chemaxon.struc.MolAtom
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Atom symbol string contains explicit H count if this flag is set.
- SYM_IMPLH - Static variable in class chemaxon.struc.MolAtom
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Atom symbol string contains implicit H count is shown flag is set.
- SYM_MOLEX - Static variable in class chemaxon.struc.MolAtom
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Atom symbol string for Molfile export.
- SYM_NEUTRAL - Static variable in class chemaxon.struc.MolAtom
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Atom symbol string does not contain the charge if this flag is set.
- SYM_SMARTS - Static variable in class chemaxon.struc.MolAtom
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Atom symbol string for SMILES export.
- SYM_SQBRACKETS - Static variable in class chemaxon.struc.MolAtom
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Atom symbol is shown in square brackets if this flag is set.
- symbolOf(int) - Static method in class chemaxon.struc.MolAtom
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Gets the element symbol for the specified atomic number.
- symbolOf(int, int) - Static method in class chemaxon.struc.MolAtom
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Gets the special element symbol for the specified atomic and mass
numbers.
- SYN - Static variable in interface chemaxon.struc.StereoConstants
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Non-CIP stereodescriptor, syn (relative configuration).
- szegedIndex() - Method in class chemaxon.calculations.TopologyAnalyser
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Calculates the Szeged index of the molecule.