RgMolecule (Marvin API documentation (c) 1998-2014 ChemAxon Ltd.)

java.lang.Object
- chemaxon.struc.MoleculeGraph
- - chemaxon.struc.Molecule
  - - chemaxon.struc.RgMolecule

All Implemented Interfaces:

chemaxon.core.calculations.valencecheck.MoleculeWithValence<MolAtom>, chemaxon.core.structure.MarkushStructureForBuilder, chemaxon.core.structure.MoleculeForBuilder, chemaxon.core.structure.RootStructureForBuilder, chemaxon.core.structure.StructureForBuilder, Incomplecule, chemaxon.struc.MObjectContainer, MTransformable, chemaxon.struc.RgMoleculeGraphIface, StereoConstants, Serializable
```
public class RgMolecule
extends Molecule
implements chemaxon.struc.RgMoleculeGraphIface, chemaxon.struc.MObjectContainer, chemaxon.core.structure.MarkushStructureForBuilder
```
A molecule or reaction containing R-groups.

Since:

Marvin 2.6

Version:

6.2

Author:

Peter Csizmadia, Szilveszter Juhos

See Also:
Serialized Form

Property Summary
- Properties inherited from class chemaxon.struc.MoleculeGraph
  hasSelfReferringProperty

Nested Class Summary
- Nested classes/interfaces inherited from class chemaxon.struc.MoleculeGraph
  MoleculeGraph.ValenceCheckState

Field Summary

Fields
Modifier and Type	Field and Description
`static String`	`DEFAULT_RLOGIC_RANGE` Default R-logic range.
`static int`	`RG_ID_MASK` R-group id mask in R-logic.
`static int`	`RG_ID2_FLAG` Other R-group ID's presence flag in R-logic.
`static int`	`RG_ID2_MASK` Mask of the other R-group's id in R-logic.
`static int`	`RG_ID2_OFF` Offset of the other R-group's id in R-logic.
`static int`	`RG_RESTH` The RestH flag in R-logic.

Fields inherited from class chemaxon.struc.Molecule
DEFAULT_UNGROUP, RECURSIVE_UNGROUP, RM_KEEP_LEAVINGGROUPS, RMCLEANUP_FROMSGROUPS, RMCLEANUP_SGROUPATOMS, RMSG_DEFAULT, RMSG_KEEP_CHILDREN, RMSG_KEEP_MULTICENTER, RMSG_KEEP_PARENT

Fields inherited from class chemaxon.struc.MoleculeGraph
AROM_AMBIGUOUS, AROM_BASIC, AROM_GENERAL, AROM_LOOSE, AROM_SUBSTRUCTURE, atomCount, AUTO_UNGROUP, bondCount, btab, CACHE_REMOVE_ALL, CACHE_REMOVE_AROMATAMODULE, CACHE_REMOVE_CACHEMEMORY, CACHE_REMOVE_GRINVMODULE, CACHE_REMOVE_PARITYMODULE, CACHE_REMOVE_SSSRMODULE, CACHE_REMOVE_TABS, cacheMemory, ctab, DEAROM_GENERAL, DEAROM_HUCKELCHECK, DEAROM_HUCKELCHECK_EX, DIM_MASK, FRAG_BASIC, FRAG_KEEPING_MULTICENTERS, FRAG_KEEPING_SGROUPS, FRAG_TYPE_COUNT, gearch, GRINV_DONT_STORE, GRINV_NOHYDROGEN, GRINV_OLDSTEREO, GRINV_STEREO, GRINV_USEMAPS, GRINV_VALUE_OPTIONS, grinvCC, INITIAL_CAPACITY, INVALID_LINKNODE_MESSAGE, MIN_RING_SIZE_FOR_TRANS_DB, OMIT_POSTCLEAN, orix, oriy, oriz, parentGraph, propertyContainer, RMCLEANUP_ALL, RMCLEANUP_EDGES, RMCLEANUP_FIXCOMPONENT, RMCLEANUP_MOBJECT, RMCLEANUP_NONE, RMCLEANUP_PARENTDOC, RMCLEANUP_STEREO, superGraph, theAtoms, theBonds, useOnlyFirstAtomInStereoCalculation, VALENCE_CHECK, VALENCE_CHECK_AMBIGUOUS

Fields inherited from interface chemaxon.struc.StereoConstants
ANTI, ATOMSTEREO_EITHER, ATOMSTEREO_MASK, ATOMSTEREO_NONE, ATOMSTEREO_SPECIFIC, CHIRALITY_M, CHIRALITY_MASK, CHIRALITY_P, CHIRALITY_r, CHIRALITY_R, CHIRALITY_s, CHIRALITY_S, CHIRALITYSUPPORT_ALL, CHIRALITYSUPPORT_NONE, CHIRALITYSUPPORT_SELECTED, CIS, CTUMASK, CTUNKNOWN, CTUNSPEC, DBS_ALL, DBS_MARKED, DBS_NONE, ENDO, EXO, PARITY_ALLENE, PARITY_EITHER, PARITY_EVEN, PARITY_MASK, PARITY_ODD, PARITY_TETRAHEDRAL, PARITY_UNSPEC, STGRP_ABS, STGRP_AND, STGRP_NONE, STGRP_OR, SYN, TRANS

Constructor Summary

Constructors
Constructor and Description

RgMolecule()
Creates a 2 dimensional RgMolecule.

Constructors
Constructor and Description
`RgMolecule()` Creates a 2 dimensional RgMolecule.

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`add(MolAtom node)` Adds an atom to the root structure.
`void`	`add(MolBond bond)` Adds a bond to the root structure.
`protected void`	`addAtomToFragment(MolAtom atom)` Adds an atom to a fragment.
`int`	`addRgroup(int rl, Molecule m)` Adds an R-group member.
`void`	`addRgroupBridge(int rgroupId1, int rgroupId2, Molecule m)` Adds an R-group bridge member.
`RgMolecule`	`addRgroupsTo(Molecule m)` Creates a read only RgMolecule from a simple molecule object.
`void`	`addSgroup(Sgroup sg, boolean setparent)` Adds an S-group to this object.
`void`	`aromatize(int method)` Aromatizes molecule.
`void`	`aromatize(int method, boolean checkAmbiguity)` Aromatizes molecule.
`boolean`	`canBeCT(int i2, int i3, boolean grcheck)` Determines whether the bond between the specified atoms can be a CIS/TRANS or not.
`boolean`	`canBeReactionComponent()` Tests whether an object of this class can be a reaction component.
`void`	`checkConsistency()` Deprecated. As of Marvin 5.7, no replacement. Not intended for public use, it was intended only for internal debugging.
`String`	`checkRlogicRange(int index, String range)` Checks an R-logic occurrence range string for syntax errors and returns a "normalized" string.
`protected void`	`checkSgroupConsistency()` Checks the consistency of S-groups.
`void`	`cleanupRemovedRgroupMember(MoleculeGraph m, int f)` Clean-up after R-group removal.
`void`	`clearForImport(String fmt)` Clear the edges vector and the properties.
`void`	`clearObjects()`
`RgMolecule`	`clone()` Clone the markush structure.
`void`	`clonecopy(int[] iatoms, MoleculeGraph g)` Copies the specified atoms of this graph to another one.
`void`	`clonecopy(MoleculeGraph g)` Make another molecule identical to this one.
`void`	`clonelesscopy(MoleculeGraph g)` Deprecated. as of Marvin 6.3. Not supported feature.
`RgMolecule`	`cloneMoleculeWithDocument()` Makes an identical copy of the molecule and its document.
`boolean`	`contains(MolAtom node)` Checks if the root structure or an R-group contains the specified node.
`boolean`	`contains(MolBond edge)` Checks if the root structure or an R-group contains the specified edge.
`protected chemaxon.struc.gearch.MoleculeGraphGearch`	`createGearch()`
`void`	`endReuse(int n)` End reusing atoms.
`protected void`	`fillSelectionMolecule(SelectionMolecule s)` Adds all atoms and bonds of the root structure and the R-groups to the specified molecule.
`int`	`findRgroupIndex(int rgid)` Finds R-group R#.
`protected boolean`	`fixSelfReferringProperty(MProp prop)` Fix a property containing reference to the molecule.
`void`	`fuse(MoleculeGraph g, boolean check)` Add the atoms and bonds of another molecule.
`protected void`	`fuse0(MoleculeGraph graph, boolean check)` Add those nodes and edges of a graph that are not already elements.
`List<MObject>`	`getAllObjects()`
`MolAtom`	`getAtom(int i)` Gets a node in the graph union.
`int`	`getAtomCount()` Gets the number of nodes in the root structure.
`int`	`getAtomCount(int atomicNumber)` Gets the number of atoms with the given atomic number in the root structure.
`IteratorFactory.AtomIterator`	`getAtomIterator()` Returns an iterator over the atoms in this molecule in proper sequence.
`MolBond`	`getBond(int i)` Gets an edge in the graph union.
`int`	`getBondCount()` Gets the number of edges in the root structure.
`IteratorFactory.BondIterator`	`getBondIterator()` Returns an iterator over the bonds in this molecule in proper sequence.
`chemaxon.core.util.BondTable`	`getBondTable()` Gets the bond table of the root structre.
`String`	`getComment()` Gets the comment of the root molecule.
`int[][]`	`getCtab()` Gets the connection table of the root structure.
`int`	`getDependentRgroupDefinition(int rGroupIndex)` Gets the R-group definition's index which depends on the referenced R-group definition.
`int`	`getFlags()` Gets the dimension and chiral flags.
`String`	`getFormula()` Gets the molecular formula in Hill order.
`MoleculeGraph`	`getGraphUnion()` Gets a graph containing all the atoms and bonds.
`int`	`getLocalParity(int i)` 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.
`int`	`getLonePairCount(int i)` Gets the number of lone pairs.
`double`	`getMass()` Calculates the molecular weight of the molecule.
`int`	`getMaxAttachmentPointOrder(int rgroupID)` Gets the maximal attachment point order of R-group definition molecules specified by an R-group ID.
`protected Molecule`	`getMostSimplifiedMolecule()` Gets the simplified molecule object even if there is a parent document with other objects.
`String`	`getName()` Gets the name of the root molecule.
`int`	`getObjectCount()`
`int`	`getParity(int i)` 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.
`Set<chemaxon.common.util.CommutativePair<Integer>>`	`getRgroupBridgeIds()` Returns the r-group bridge id pairs.
`List<Molecule>`	`getRgroupBridgeMembers(int rgroupId1, int rgroupId2)` Returns the corresponding r-group bridge members for the given r-group bridge id pair.
`Map<chemaxon.common.util.CommutativePair<Integer>,List<Molecule>>`	`getRgroupBridges()` Returns the r-group bridges, the id pairs and the corresponding r-group bridge members.
`int`	`getRgroupCount()` Gets the number of R-groups.
`int`	`getRgroupId(int i)` Gets the ID of an R-group.
`int`	`getRgroupIndex(long id)` Gets the R-group index from the R-group member ID.
`Molecule`	`getRgroupMember(int i, int j)` Gets an R-group member.
`int`	`getRgroupMemberCount(int i)` Gets the number of R-group members.
`MoleculeGraph`	`getRgroupMemberG(int i, int j)` Gets an R-group member.
`long`	`getRgroupMemberID(MolAtom node)` Gets the unique indentifier of the R-group member that contains the specified atom.
`int`	`getRgroupMemberIndex(long id)` Gets the R-group member index from the R-group member ID.
`int`	`getRlogic(int i)` Gets R-logic flags.
`String`	`getRlogicRange(int i)` Gets R-logic occurrence range.
`Molecule`	`getRoot()` Gets the root structure.
`MoleculeGraph`	`getRootG()` Gets the root structure.
`int`	`getStereo2(MolBond bond, MolAtom leftAtom, MolAtom rightAtom, boolean performGrinvCheck)` Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
`protected int`	`getSubGraphCount()` Gets the number of all "submolecules".
`protected void`	`getSubGraphs(MoleculeGraph[] arr, int off)` Gets all "submolecules".
`ValenceCheckOptions`	`getValenceCheckOptions()` Returns the options for valence checking.
`boolean`	`hasAtomSet()` Tests whether the molecule graph has atom sets.
`boolean`	`hasBondSet()` Tests whether the molecule graph has atom sets.
`boolean`	`hasRgroupContainedBy(Set<?> set)` Tests whether the molecule has an R-group that is a subset of the specified set of atoms.
`int`	`indexOf(MolAtom node)` Gets the index of the specified node in the graph union.
`int`	`indexOf(MolBond edge)` Gets the index of the specified edge in the graph union.
`protected void`	`insertNullAtoms(int i, int count)` Insert nulls into the atom array.
`protected void`	`insertNullBonds(int i, int count)` Insert nulls into the bond array.
`boolean`	`isAtom()` Deprecated. As of Marvin 14.7.7, no replacement. Not supported feature.
`boolean`	`isBond()` Deprecated. As of Marvin 14.7.7, no replacement. Not supported feature.
`boolean`	`isEmpty()` Ask if the molecule is empty or not.
`boolean`	`isIncompleteReaction()` Check whether the reaction is incomplete or not.
`boolean`	`isQuery()` Indicates if the molecule has query features.
`boolean`	`isReaction()` Checks if the structure represents a reaction or not.
`protected boolean`	`isRealAtomParent()` R-group molecule objects cannot be real node parents.
`boolean`	`isRestH(int rGroupIndex)` Informs whether the restH condition is set to the referenced R-group definition.
`boolean`	`isSelfReference(MProp p)` Tests whether the specified property is a self reference to the molecule.
`protected void`	`makeItSimilar(MoleculeGraph g)` Copies some properties of this molecule to the other one specified as argument.
`void`	`mergeAtoms(MolAtom that, MolAtom a)` Deprecated. As of Marvin 6.2, use `MergeUtil.mergeAtoms(MolAtom, MolAtom, boolean)` instead.
`MoleculeGraph`	`newInstance()` Creates a new RgMolecule object.
`SelectionMolecule`	`newSelectionMolecule()` Creates a new SelectionMolecule object appropriate for storing selection from this molecule.
`MPropertyContainer`	`properties()` Gets the property container.
`void`	`regenBonds()` Regenerate the edge vectors: remove their elements, then put the edge objects from the nodes into it.
`void`	`removeAll()` Remove all the atoms and bonds from the root structure, and from all the R-groups.
`void`	`removeAllBonds()` Remove all bonds from the root structure, and from all the R-groups.
`void`	`removeAtom(int i, int cleanupFlags)` Removes an atom and its bonds from the root structure.
`void`	`removeAtom(MolAtom node, int cleanupFlags)` Removes an atom and its bonds from the root structure and from all the R-groups.
`protected void`	`removeBond(int i, int cleanupFlags)` Remove a bond from the root structure.
`protected void`	`removeBond(MolBond edge, int cleanupFlags)` Remove a bond from the root structure, and from all the R-groups.
`void`	`removeDependentRgroupDefinition(int rGroupIndex)` Removes the dependent R-group definition of the referenced R-group definition.
`void`	`removeObject(MObject mo)`
`void`	`removeRestH(int rGroupIndex)` Removes the restH condition from an R-group definition.
`void`	`removeRgroup(int definition)` Removes an R-group.
`void`	`removeRgroupBridge(int rgroupId1, int rgroupId2)` Removes an r-group bridge.
`void`	`removeRgroupBridgeMember(int rgroupId1, int rgroupId2, int memberIndex)` Removes an r-group bridge.
`void`	`removeRgroupBridgeMembers(int rgroupId1, int rgroupId2, int[] memberIndexes)` Removes r-group members.
`void`	`removeRgroupMember(int definition, int member)` Removes an R-group member.
`void`	`removeRgroupMembers(int definition, int[] members)` Removes R-group members.
`void`	`replaceAtomsWithNewRgroup(SelectionMolecule sel, int rgid)` Replaces selected atoms with a new R-group.
`void`	`replaceBond(MolBond olde, MolBond newe)` Deprecated. as of Marvin 6.2, may constructs inconsistent `MoleculeGraph`. Use `MoleculeGraph.removeBond(MolBond)` for bond removal and `add(MolBond)` for adding a new bond to the molecule.
`MolAtom`	`reuseAtom(int z, int i)` Reuse an atom or create a new one.
`void`	`revalidateCoordDependentProps()` Revalidate coordinate dependent properties.
`int`	`rgroupIdOf(MolAtom node)` Finds the ID of the R-group (the number in R#) that contains the specified atom.
`int`	`rgroupIndexOf(MolAtom node)` Finds the index of the R-group (the number in R#) that contains the specified atom.
`void`	`selectAllObjects(boolean s)`
`void`	`setAbsStereo(boolean c)` Sets the absolute stereoconfiguration flag for the root structure and the R-groups.
`void`	`setAtom(int iu, MolAtom node)` Deprecated. as of Marvin 6.2, may constructs inconsistent `MoleculeGraph`. Use `MoleculeGraph.removeAtom(MolAtom)` and `add(MolAtom)` to modify the structure.
`void`	`setBond(int iu, MolBond edge)` Deprecated. as of Marvin 6.2, may constructs inconsistent `MoleculeGraph`. Use `MoleculeGraph.removeBond(MolBond)` for bond removal and `add(MolBond)` for adding a new bond to the molecule.
`void`	`setComment(String s)` Sets the comment of the root molecule.
`void`	`setDependentRgroupDefinition(int rGroupIndexIf, int rGroupIndexThen)` Sets the dependent R-group definition (`rGroupIndexThen`) for the referenced R-group definition (`rGroupIndexIf`).
`void`	`setDim(int d)` Sets the dimension of the root structure and the R-groups.
`protected void`	`setFlags(int f)` Sets the dimension and chiral flags.
`protected void`	`setFlags(int f, int mask)` Sets specified bits in the flags.
`void`	`setInputFormat(String format)` Sets the input file format.
`void`	`setLocation(DPoint3 p)` Set the origin of the molecule.
`void`	`setName(String s)` Sets the name of the root molecule.
`void`	`setRestH(int rGroupIndex)` Sets the restH condition on an R-group definition.
`void`	`setRlogic(int i, int f)` Sets R-logic flags.
`void`	`setRlogicRange(int index, String range)` Sets R-logic occurrence range.
`void`	`setRoot(Molecule mol)` Sets the root structure.
`void`	`setSgroupParent(MolAtom a, Sgroup sg, boolean set)` Sets or unsets an S-group as a parent of an atom in the root structure or an R-group.
`void`	`setValenceCheckOptions(ValenceCheckOptions options)` Sets the options for valence checking.
`void`	`sortBondsAccordingTo(MolBond[] order)` Sort edges in the same order as they appear in the specified array.
`boolean`	`stereoClean()` Reset the wedges of the molecule, based on the actual parity information in 2D remove wedges in 3D.
`protected void`	`sumConservedQuantities(MolAtom a, int[] atoms, int sign)` For internal use only.
`String`	`toString()` Overrides Object.toString() to ease debugging.
`void`	`transform(CTransform3D t, boolean incg)` Apply a transformation matrix to the atomic coordinates.
`int`	`unRgroupAtoms(Set<?> set)` Ungroup R-groups consisting of the specified atoms and make the be part of root.

Methods inherited from class chemaxon.struc.Molecule
addAtom0, addBond0, addSgroupClones, addSgroupsOf, bondlength, clear, clearExtraLabels, clearProperties, cloneAtoms, clonecopyWithoutSgroups, cloneMolecule, connectOriginalBondsToNewAtom, contractSgroups, contractSgroups, convertToFrags, countExpandableContractableSgroups, countOrderedComponentSgroups, dearomatize, expandSgroups, expandSgroups, exportToBinFormat, exportToFormat, exportToObject, findAllSgroupContaining, findContainingMulticenterSgroup, findContractableSgroup, findExpandableSgroup, findFrags, findFrags, findSgroupContaining, findSgroupOf, findSmallestSgroupContaining, getBonds, getEndPosition, getGraphUnionAsSelection, getInputFormat, getProperty, getPropertyCount, getPropertyKey, getPropertyKeys, getPropertyObject, getRootSgroups, getSgroup, getSgroupArray, getSgroupCount, getSgroupIterator, getSgroupLigands, getSimplifiedMolecule, getSortedSgroups, getStartPosition, getVisibleCoords, hasContractedSgroup, implicitizeHydrogens0, indexOf, isExpandable, isGUIContracted, isSgroup, rearrangeSgroups, removeAllSgroups, removeAtomFromChildren, removeSgroupFromList, removeSgroupsOf, removeSgroupsOf, reparentSgroups, replaceAtom, replaceSgroup, residueSymbolOf, residueTypeOf, setAtom0, setEndPosition, setGUIContracted, setGUIContracted, setProperty, setPropertyObject, setStartPosition, sortSgroupXBonds, toBinFormat, toFormat, toObject, ungroupSgroup, ungroupSgroup, ungroupSgroup, ungroupSgroup, ungroupSgroups, ungroupSgroups, ungroupSgroups

Methods inherited from class chemaxon.struc.MoleculeGraph
add, addAtomsAndBondsTo, addAtomWithoutChangingIt, addBondWithoutChangingIt, addExplicitHydrogens, addExplicitHydrogens, addExplicitLonePairs, addSimpleAtomWithoutChangingIt, adjustMultiChiralFlag, aromatize, aromatize, arrangeComponents, calcCenter, calcCenter, calcDehydrogenizedGrinv, calcHeight, calcHybridization, calcOutRect, calcOutRect, calcOutRectCenter, calcOutRectCenter, calcWidth, canBeCT, canBeCT, checkBondConsistency, clean, clean, clearCachedInfo, clonecopyMoleculeGraphWithoutSgroups, contains, createBHtab, createCHtab, createDehydrogenizedReadOnlyGraph, createSmolecule, dearomatize, findAtom, findAtomClone, findBasicFrags, findBond, findComponentIds, findComponentIds, findFrag, findFrag, findFragById, findFrags, findInArray, fuse, getAromaticAndAliphaticRings, getAtomArray, getAtomicNumber, getAtomReferenceList, getBondArray, getBtab, getCharge, getChirality, getCSSR, getDesiredLength, getDesiredLength, getDim, getDocument, getDocumentForChild, getEnclosingCube, getExactMass, getExplicitHcount, getExplicitLonePairCount, getEZStereo, getForefather, getFormalCharge, getFragCount, getFragCount, getFragIds, getFreeAttachmentPoints, getGrinv, getGrinv, getGrinv, getGrinv, getGrinvCC, getGrinvOptions, getImplicitHcount, getImplicitHCount, getLigand, getLigandAtno, getLigandBondType, getLigandCount, getLocation, getLock, getMaxRgroupAttachmentPointOrder, getParent, getParentDocument, getParityType, getPoints, getPossibleAttachmentPoints, getRadicalCount, getSmallestRingSizeForIdx, getSSSR, getSSSRBonds, getSSSRBondsAsBitSet, getSSSRBondSet, getSSSRBondSetInLong, getSSSRIdxesForAtoms, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getSubGraphs, getTotalCharge, getValenceCheckState, getValenceProperty, hasExplicitLonePairs, hasExtraLabelSet, hasImplicitH, hasSelfReferringProperty, hasValenceError, hydrogenize, implicitizeHydrogens, implicitizeHydrogens, implicitizeHydrogens, incGrinvCC, incGrinvCC, incGrinvCCOnly, insertAtom, insertBond, insertBondInOrder, isAbsStereo, isAcceptedSpecialLigand, isAtomInRing, isBondParallelWith, isGrinvCCValid, isLargeMolecule, isMolecule, isMultiChiral, isolate, isolate, isOnlyFirstAtomInStereoCalculation, isRing, isRingBond, isSimilarTo, isSymmetric, isValenceCheckEnabled, isValidLinkNode, mergeFrags, moveTo, pack, partialClean, partialClean, partialClean, qpropCheck, regenCtabs, regenGearch, removeAtom, removeAtom, removeBond, removeBond, removeExplicitLonePairs, removeIsolatedAtoms, removeIsolatedBonds, resetCtab, resetGrinvInParents, restoreCache, saveCache, setAtomSetSeqs, setBondSetSeqs, setChirality, setChirality, setGrinvCC, setGrinvOptions, setLinkNodeDefaultOuters, setLocalParity, setLocalParity, setParity, setParity, setParity, setSupergraph, setValenceCheckEnabled, setValenceCheckState, smol, transform, updateDim, useOnlyFirstAtomInStereoCalculation, valenceCheck, valenceCheck

Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - RG_ID_MASK
```
public static final int RG_ID_MASK
```
    R-group id mask in R-logic.
    
    See Also:
    getRlogic(int), setRlogic(int, int), Constant Field Values
  - RG_ID2_FLAG
```
public static final int RG_ID2_FLAG
```
    Other R-group ID's presence flag in R-logic.
    
    See Also:
    getRlogic(int), setRlogic(int, int), Constant Field Values
  - RG_ID2_OFF
```
public static final int RG_ID2_OFF
```
    Offset of the other R-group's id in R-logic.
    
    See Also:
    getRlogic(int), setRlogic(int, int), Constant Field Values
  - RG_ID2_MASK
```
public static final int RG_ID2_MASK
```
    Mask of the other R-group's id in R-logic.
    
    See Also:
    getRlogic(int), setRlogic(int, int), Constant Field Values
  - RG_RESTH
```
public static final int RG_RESTH
```
    The RestH flag in R-logic.
    
    See Also:
    getRlogic(int), setRlogic(int, int), Constant Field Values
  - DEFAULT_RLOGIC_RANGE
```
public static final String DEFAULT_RLOGIC_RANGE
```
    Default R-logic range. It is an empty string.
    
    See Also:
    Constant Field Values
- Constructor Detail
  - RgMolecule
```
public RgMolecule()
```
    Creates a 2 dimensional RgMolecule.
- Method Detail
  - setRoot
```
public void setRoot(Molecule mol)
```
    Sets the root structure.
    
    Parameters:
    mol - the root structure
  - getStereo2
```
public int getStereo2(MolBond bond,
             MolAtom leftAtom,
             MolAtom rightAtom,
             boolean performGrinvCheck)
```
    Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration. Calculates the stereo information if the molecule is 2D or 3D, reports previously set information if it is 0D. Atoms A2 and A3 are atom1 and atom2 of the specified bond. Both (A2, A3) = (atom1, atom2) and (A2, A3) = (atom2, atom1) works. If A1 or A4 is null 0 is returned. Not checking if the bond is in small ring (MoleculeGraph.MIN_RING_SIZE_FOR_TRANS_DB (so chemically the double bond with its ring ligand can be cis only), but due to the perspective depiction in two dimension the double bond ligand arrangement looks trans. In this case the chemically incorrect trans returned.
    
    Overrides:
    
    getStereo2 in class MoleculeGraph
    
    Parameters:
    bond - the bond
    leftAtom - atom A1
    rightAtom - atom A4
    performGrinvCheck - true if check atom equivalences using graph invariants
    
    Returns:
    the stereo flags
    See Also:
    StereoConstants.CTUMASK, MolBond.calcStereo2(), for detailed examples.
  - getRoot
```
public Molecule getRoot()
```
    Gets the root structure.
    
    Returns:
    the root
  - getRootG
```
public final MoleculeGraph getRootG()
```
    Gets the root structure.
    
    Specified by:
    
    getRootG in interface chemaxon.struc.RgMoleculeGraphIface
    
    Returns:
    the root
  - getRgroupCount
```
public int getRgroupCount()
```
    Gets the number of R-groups.
    
    Specified by:
    
    getRgroupCount in interface chemaxon.struc.RgMoleculeGraphIface
    
    Returns:
    number of R-groups
  - getRgroupMemberCount
```
public int getRgroupMemberCount(int i)
```
    Gets the number of R-group members.
    
    Specified by:
    
    getRgroupMemberCount in interface chemaxon.struc.RgMoleculeGraphIface
    
    Parameters:
    i - R-group index
    
    Returns:
    number of R-group members
  - getRgroupMember
```
public Molecule getRgroupMember(int i,
                       int j)
```
    Gets an R-group member.
    
    Parameters:
    i - R-group index
    j - member index
    
    Returns:
    the R-group member
  - getRgroupMemberG
```
public final MoleculeGraph getRgroupMemberG(int i,
                             int j)
```
    Gets an R-group member.
    
    Specified by:
    
    getRgroupMemberG in interface chemaxon.struc.RgMoleculeGraphIface
    
    Parameters:
    i - R-group index
    j - member index
    
    Returns:
    the R-group member
  - getRgroupId
```
public int getRgroupId(int i)
```
    Gets the ID of an R-group.
    
    Specified by:
    
    getRgroupId in interface chemaxon.struc.RgMoleculeGraphIface
    
    Parameters:
    i - R-group index
    
    Returns:
    number between 0 and MolAtom.RGROUP_MAX
  - findRgroupIndex
```
public int findRgroupIndex(int rgid)
```
    Finds R-group R#.
    
    Specified by:
    
    findRgroupIndex in interface chemaxon.struc.RgMoleculeGraphIface
    
    Parameters:
    rgid - number between 0 and MolAtom.RGROUP_MAX
    
    Returns:
    R-group index, or -1 if not found
  - addSgroup
```
public void addSgroup(Sgroup sg,
             boolean setparent)
```
    Adds an S-group to this object.
    
    Overrides:
    
    addSgroup in class Molecule
    
    Parameters:
    setparent - if true then the parent of the S-group is set to the root or that R-group member of this molecule which contains the S-group and the S-group is removed from the old parent molecule.
    sg - the S-group to add.
  - addRgroup
```
public int addRgroup(int rl,
            Molecule m)
```
    Adds an R-group member.
    
    Parameters:
    rl - R-logic flags or an R-group ID number between 0 and MolAtom.RGROUP_MAX
    m - the R-group
    
    Returns:
    the Rgroup index
  - addRgroupBridge
```
@Beta
public void addRgroupBridge(int rgroupId1,
                        int rgroupId2,
                        Molecule m)
```
    Adds an R-group bridge member.
    
    Parameters:
    rgroupId1 - the first R-group ID number between 0 and MolAtom.RGROUP_MAX for the bridge
    rgroupId2 - the second R-group ID number between 0 and MolAtom.RGROUP_MAX for the bridge
    m - the R-group
  - getRgroupBridgeIds
```
@Beta
public Set<chemaxon.common.util.CommutativePair<Integer>> getRgroupBridgeIds()
```
    Returns the r-group bridge id pairs.
    
    Returns:
    the r-group bridge id pairs
    Since:
    
    Marvin 14.8.4, Aug 4, 2014
  - getRgroupBridgeMembers
```
@Beta
public List<Molecule> getRgroupBridgeMembers(int rgroupId1,
                                         int rgroupId2)
```
    Returns the corresponding r-group bridge members for the given r-group bridge id pair.
    
    Parameters:
    rgroupId1 - the first id of the pair
    rgroupId2 - the second id of the pair
    
    Returns:
    the corresponding r-group bridge members for the given r-group bridge id pair
    Since:
    
    Marvin 14.8.4, Aug 4, 2014
  - getRgroupBridges
```
@Beta
public Map<chemaxon.common.util.CommutativePair<Integer>,List<Molecule>> getRgroupBridges()
```
    Returns the r-group bridges, the id pairs and the corresponding r-group bridge members.
    
    Returns:
    the r-group bridges
    Since:
    
    Marvin 14.8.4, Aug 4, 2014
  - removeRgroupMember
```
public void removeRgroupMember(int definition,
                      int member)
                        throws chemaxon.struc.IllegalRgroupDefinitionException,
                               chemaxon.struc.IllegalRgroupMemberException
```
    Removes an R-group member. If it is the last member to be removed then the whole R-group definition will be removed Note: the R-group members are always indexed continuously starting with 0
    
    Parameters:
    definition - the iteration number of the R-group definition
    member - the iteration number of the member
    
    Throws:
    
    IllegalRgroupDefinitionException - If the definition index is not valid
    
    IllegalRgroupMemberException - If the member index is not valid
    Since:
    
    5.10 2012.05.10
  - removeRgroupBridgeMember
```
@Beta
public void removeRgroupBridgeMember(int rgroupId1,
                                 int rgroupId2,
                                 int memberIndex)
                              throws chemaxon.struc.IllegalRgroupDefinitionException,
                                     chemaxon.struc.IllegalRgroupMemberException
```
    Removes an r-group bridge.
    
    Parameters:
    rgroupId1 - the first R-group ID number between 0 and MolAtom.RGROUP_MAX for the bridge
    rgroupId2 - the first R-group ID number between 0 and MolAtom.RGROUP_MAX for the bridge
    memberIndex - the index of the member
    
    Throws:
    
    IllegalRgroupDefinitionException - if the r-group id pair is not valid
    
    IllegalRgroupMemberException - If the member index is not valid
    Since:
    
    Marvin 14.8.11, Aug 5, 2014
  - removeRgroupMembers
```
public void removeRgroupMembers(int definition,
                       int[] members)
                         throws chemaxon.struc.IllegalRgroupDefinitionException,
                                chemaxon.struc.IllegalRgroupMemberException
```
    Removes R-group members. If the last member is removed then the whole R-group definition will be removed Note: the R-group members are always indexed continuously starting with 0
    
    Parameters:
    definition - the iteration number of the R-group definition
    members - the array of the iteration numbers of the members
    
    Throws:
    
    IllegalRgroupDefinitionException - If the definition index is not valid
    
    IllegalRgroupMemberException - If a member index is not valid
    Since:
    
    5.10 2012.05.10
  - removeRgroupBridgeMembers
```
@Beta
public void removeRgroupBridgeMembers(int rgroupId1,
                                  int rgroupId2,
                                  int[] memberIndexes)
                               throws chemaxon.struc.IllegalRgroupDefinitionException,
                                      chemaxon.struc.IllegalRgroupMemberException
```
    Removes r-group members. If the last member is removed then the whole R-group definition will be removed Note: the R-group members are always indexed continuously starting with 0
    
    Parameters:
    rgroupId1 - the first R-group ID number between 0 and MolAtom.RGROUP_MAX for the bridge
    rgroupId2 - the first R-group ID number between 0 and MolAtom.RGROUP_MAX for the bridge
    memberIndexes - the array of the indexes of the members
    
    Throws:
    
    IllegalRgroupDefinitionException - If the definition index is not valid
    
    IllegalRgroupMemberException - If a member index is not valid
  - removeRgroup
```
public void removeRgroup(int definition)
                  throws chemaxon.struc.IllegalRgroupDefinitionException
```
    Removes an R-group. Note: the R-group definitions are always indexed continuously starting with 0.
    
    Parameters:
    definition - the iteration number of the R-group definition
    
    Throws:
    
    IllegalRgroupDefinitionException - If the definition index is not valid
    Since:
    
    5.10 2012.05.10
  - removeRgroupBridge
```
@Beta
public void removeRgroupBridge(int rgroupId1,
                           int rgroupId2)
                        throws chemaxon.struc.IllegalRgroupDefinitionException
```
    Removes an r-group bridge.
    
    Parameters:
    rgroupId1 - the first R-group ID number between 0 and MolAtom.RGROUP_MAX for the bridge
    rgroupId2 - the first R-group ID number between 0 and MolAtom.RGROUP_MAX for the bridge
    
    Throws:
    
    IllegalRgroupDefinitionException - if the r-group id pair is not valid
    Since:
    
    Marvin 14.8.11, Aug 5, 2014
  - hasRgroupContainedBy
```
public boolean hasRgroupContainedBy(Set<?> set)
```
    Tests whether the molecule has an R-group that is a subset of the specified set of atoms.
    
    Parameters:
    set - set of atoms
    Since:
    
    5.0, 02/24/2007
  - unRgroupAtoms
```
public int unRgroupAtoms(Set<?> set)
```
    Ungroup R-groups consisting of the specified atoms and make the be part of root.
    
    Parameters:
    set - selected atoms
    
    Returns:
    the number of ungrouped R-group members
    Since:
    
    5.0, 02/24/2007
  - replaceAtomsWithNewRgroup
```
public void replaceAtomsWithNewRgroup(SelectionMolecule sel,
                             int rgid)
```
    Replaces selected atoms with a new R-group.
    
    Parameters:
    sel - selected atoms
    rgid - R-group ID
    Since:
    
    4.0, 06/30/2005
  - getRlogic
```
public int getRlogic(int i)
```
    Gets R-logic flags.
    
    Specified by:
    
    getRlogic in interface chemaxon.struc.RgMoleculeGraphIface
    
    Parameters:
    i - R-group index
    
    Returns:
    R-logic flags
    See Also:
    RG_ID_MASK, RG_ID2_FLAG, RG_ID2_OFF, RG_ID2_MASK, RG_RESTH
  - setRlogic
```
public void setRlogic(int i,
             int f)
```
    Sets R-logic flags.
    
    Parameters:
    i - R-group index
    f - R-logic flags
    See Also:
    RG_ID_MASK, RG_ID2_FLAG, RG_ID2_OFF, RG_ID2_MASK, RG_RESTH
  - getRlogicRange
```
public String getRlogicRange(int i)
```
    Gets R-logic occurrence range.
    
    Specified by:
    
    getRlogicRange in interface chemaxon.struc.RgMoleculeGraphIface
    
    Parameters:
    i - R-group index
    
    Returns:
    the occurrence range: By default it is an empty string which means "as drawn".
  - setRlogicRange
```
public void setRlogicRange(int index,
                  String range)
                    throws IllegalArgumentException
```
    Sets R-logic occurrence range. If null is given as range, de R-logic range is set to default empty string.
    
    Parameters:
    index - R-group index
    range - range of occurrance.
    
    Throws:
    
    IllegalArgumentException - bad occurrence range
  - checkRlogicRange
```
public String checkRlogicRange(int index,
                      String range)
                        throws IllegalArgumentException
```
    Checks an R-logic occurrence range string for syntax errors and returns a "normalized" string.
    
    Parameters:
    index - R-group index
    range - range of occurrence
    
    Returns:
    the normalized occurrence range string
    
    Throws:
    
    IllegalArgumentException - bad occurrence range
    Since:
    
    Marvin 3.4
  - clearForImport
```
public void clearForImport(String fmt)
```
    Clear the edges vector and the properties.
    
    Overrides:
    
    clearForImport in class Molecule
    
    Parameters:
    fmt - input file format. See the text formats on the File Formats in Marvin page.
    See Also:
    MoleculeGraph.theBonds, MoleculeGraph.orix, MoleculeGraph.oriy, MoleculeGraph.oriz, MoleculeGraph.setFlags(int)
  - setName
```
public void setName(String s)
```
    Sets the name of the root molecule.
    
    Overrides:
    
    setName in class Molecule
    
    Parameters:
    s - the molecule name, empty string or null (null is equivalent to empty string)
  - getName
```
public String getName()
```
    Gets the name of the root molecule.
    
    Specified by:
    
    getName in interface Incomplecule
    
    Overrides:
    
    getName in class Molecule
    
    Returns:
    the molecule name or an empty string
  - setComment
```
public void setComment(String s)
```
    Sets the comment of the root molecule.
    
    Overrides:
    
    setComment in class Molecule
    
    Parameters:
    s - the comment, empty string or null (null is equivalent to empty string)
  - getComment
```
public String getComment()
```
    Gets the comment of the root molecule.
    
    Overrides:
    
    getComment in class Molecule
    
    Returns:
    the comment or empty string
  - properties
```
public MPropertyContainer properties()
```
    Gets the property container.
    
    Specified by:
    
    properties in interface Incomplecule
    
    Overrides:
    
    properties in class MoleculeGraph
    
    Returns:
    the property container
    Since:
    
    Marvin 4.0, 06/20/2005
  - revalidateCoordDependentProps
```
public void revalidateCoordDependentProps()
```
    Revalidate coordinate dependent properties. This method should be called at molecule import, after all atomic coordinates and bonds are parsed.
    
    Overrides:
    
    revalidateCoordDependentProps in class MoleculeGraph
    
    Since:
    
    Marvin 4.1, 08/03/2006
  - setInputFormat
```
public void setInputFormat(String format)
```
    Sets the input file format.
    
    Overrides:
    
    setInputFormat in class Molecule
    
    Parameters:
    format - the input format
    See Also:
    Molecule.getInputFormat()
  - reuseAtom
```
public MolAtom reuseAtom(int z,
                int i)
```
    Reuse an atom or create a new one. If an atom is reused, all its properties except the corners are initialized.
    
    Overrides:
    
    reuseAtom in class Molecule
    
    Parameters:
    z - atomic number
    i - atom index
    
    Returns:
    the new or old atom
  - endReuse
```
public void endReuse(int n)
```
    End reusing atoms.
    
    Overrides:
    
    endReuse in class Molecule
    
    Parameters:
    n - number of atoms
    Since:
    
    Marvin 2.6
  - getCtab
```
public int[][] getCtab()
```
    Gets the connection table of the root structure. If there is no connection table for the molecule, then create it. ctab[i][j] will be the index of the jth neighbor of the ith atom.
    
    Overrides:
    
    getCtab in class MoleculeGraph
    
    Returns:
    the ctab array
  - getBondTable
```
public chemaxon.core.util.BondTable getBondTable()
```
    Gets the bond table of the root structre. If there is no bond table for the molecule, then create it. btab.elementAt(i, j) will be the index of the bond between atoms i and j, or -1 if there is no bond.
    
    Overrides:
    
    getBondTable in class MoleculeGraph
    
    Returns:
    the btab array
    Since:
    
    Marvin 5.4
  - rgroupIdOf
```
public int rgroupIdOf(MolAtom node)
```
    Finds the ID of the R-group (the number in R#) that contains the specified atom.
    
    Specified by:
    
    rgroupIdOf in interface chemaxon.struc.RgMoleculeGraphIface
    
    Parameters:
    node - the atom
    
    Returns:
    the R-group ID if found or -1 if not found
  - rgroupIndexOf
```
public int rgroupIndexOf(MolAtom node)
```
    Finds the index of the R-group (the number in R#) that contains the specified atom.
    
    Specified by:
    
    rgroupIndexOf in interface chemaxon.struc.RgMoleculeGraphIface
    
    Parameters:
    node - the atom
    
    Returns:
    the R-group index if found or -1 if not found
  - getRgroupMemberID
```
public long getRgroupMemberID(MolAtom node)
```
    Gets the unique indentifier of the R-group member that contains the specified atom.
    
    Specified by:
    
    getRgroupMemberID in interface chemaxon.struc.RgMoleculeGraphIface
    
    Parameters:
    node - the atom
    
    Returns:
    the ID or -1
    Since:
    
    Marvin 4.1, 11/23/2005
  - getRgroupIndex
```
public int getRgroupIndex(long id)
```
    Gets the R-group index from the R-group member ID.
    
    Specified by:
    
    getRgroupIndex in interface chemaxon.struc.RgMoleculeGraphIface
    
    Parameters:
    id - the R-group member ID or -1
    
    Returns:
    the R-group ID or -1
    Since:
    
    Marvin 4.1, 11/23/2005
  - getRgroupMemberIndex
```
public int getRgroupMemberIndex(long id)
```
    Gets the R-group member index from the R-group member ID.
    
    Specified by:
    
    getRgroupMemberIndex in interface chemaxon.struc.RgMoleculeGraphIface
    
    Parameters:
    id - the R-group member ID or -1
    
    Returns:
    the R-group member index or -1
    Since:
    
    Marvin 4.1, 11/23/2005
  - setDim
```
public void setDim(int d)
```
    Sets the dimension of the root structure and the R-groups.
    
    Overrides:
    
    setDim in class Molecule
    
    Parameters:
    d - 0, 2 or 3
    See Also:
    MoleculeGraph.getFlags()
  - getFlags
```
public int getFlags()
```
    Gets the dimension and chiral flags.
    
    Overrides:
    
    getFlags in class MoleculeGraph
    
    Returns:
    the flags
    Since:
    
    Marvin 5.0.1, 02/10/2008
  - setFlags
```
protected void setFlags(int f)
```
    Sets the dimension and chiral flags.
    
    Overrides:
    
    setFlags in class MoleculeGraph
    
    Parameters:
    f - the flags
    Since:
    
    Marvin 5.0.1, 02/10/2008
    
    See Also:
    MoleculeGraph.flags
  - setFlags
```
protected void setFlags(int f,
            int mask)
```
    Sets specified bits in the flags.
    
    Overrides:
    
    setFlags in class MoleculeGraph
    
    Parameters:
    f - new value of the specified bits
    mask - bits to set
  - setAbsStereo
```
public void setAbsStereo(boolean c)
```
    Sets the absolute stereoconfiguration flag for the root structure and the R-groups.
    
    Overrides:
    
    setAbsStereo in class MoleculeGraph
    
    Parameters:
    c - the absolute stereoconfiguration flag
    See Also:
    MoleculeGraph.setFlags(int)
  - getAtomCount
```
public int getAtomCount()
```
    Gets the number of nodes in the root structure.
    
    Specified by:
    
    getAtomCount in interface chemaxon.core.structure.StructureForBuilder
    
    Specified by:
    
    getAtomCount in interface Incomplecule
    
    Overrides:
    
    getAtomCount in class MoleculeGraph
    
    Returns:
    number of nodes
  - getAtomCount
```
public int getAtomCount(int atomicNumber)
```
    Gets the number of atoms with the given atomic number in the root structure. When atomicNumber is 1, sum includes only explicit Hydrogen atoms (but also D and T isotopes).
    
    Overrides:
    
    getAtomCount in class MoleculeGraph
    
    Parameters:
    atomicNumber - atomic number of atoms looked for
    
    Returns:
    number of atoms with the given atomic number
    Since:
    
    Marvin 5.5, 27/01/2011
  - getAtom
```
public MolAtom getAtom(int i)
```
    Gets a node in the graph union.
    
    Overrides:
    
    getAtom in class MoleculeGraph
    
    Parameters:
    i - node index
    
    Returns:
    the node object
  - setAtom
```
@Deprecated
public void setAtom(int iu,
                      MolAtom node)
```
    Deprecated. as of Marvin 6.2, may constructs inconsistent MoleculeGraph. Use MoleculeGraph.removeAtom(MolAtom) and add(MolAtom) to modify the structure.
    
    Sets the node at the specified index in the graph union.
    
    Overrides:
    
    setAtom in class MoleculeGraph
    
    Parameters:
    iu - the atom index
    node - the atom
  - clone
```
public RgMolecule clone()
```
    Clone the markush structure. Document is not cloned!
    
    Overrides:
    
    clone in class Molecule
    
    Returns:
    deep clone of the markush structure
  - cloneMoleculeWithDocument
```
public RgMolecule cloneMoleculeWithDocument()
```
    Description copied from class: Molecule
    
    Makes an identical copy of the molecule and its document. If the molecule does not have a parent, then copies non-molecular data: graphics objects, electron flows, text boxes, atom and bond sets (color, font and thickness). Otherwise (root, rgroup, component molecule) creates a new document.
    
    Overrides:
    
    cloneMoleculeWithDocument in class Molecule
    
    Returns:
    the copy
  - add
```
public void add(MolAtom node)
```
    Adds an atom to the root structure.
    
    Overrides:
    
    add in class MoleculeGraph
    
    Parameters:
    node - the atom
  - addAtomToFragment
```
protected void addAtomToFragment(MolAtom atom)
```
    Adds an atom to a fragment. S-groups are added only if all atoms are already in the molecule.
    
    Overrides:
    
    addAtomToFragment in class Molecule
    
    Parameters:
    atom - the atom reference
  - insertNullAtoms
```
protected void insertNullAtoms(int i,
                   int count)
```
    Insert nulls into the atom array.
    
    Overrides:
    
    insertNullAtoms in class MoleculeGraph
    
    Parameters:
    i - starting index
    count - number of new entries
    Since:
    
    Marvin 3.4
  - insertNullBonds
```
protected void insertNullBonds(int i,
                   int count)
```
    Insert nulls into the bond array.
    
    Overrides:
    
    insertNullBonds in class MoleculeGraph
    
    Parameters:
    i - starting index
    count - number of new entries
    Since:
    
    Marvin 3.5.5
  - getBondCount
```
public int getBondCount()
```
    Gets the number of edges in the root structure.
    
    Specified by:
    
    getBondCount in interface Incomplecule
    
    Overrides:
    
    getBondCount in class MoleculeGraph
    
    Returns:
    number of edges
  - getBond
```
public MolBond getBond(int i)
```
    Gets an edge in the graph union.
    
    Overrides:
    
    getBond in class MoleculeGraph
    
    Parameters:
    i - edge index
    
    Returns:
    the edge object
  - setBond
```
@Deprecated
public void setBond(int iu,
                      MolBond edge)
```
    Deprecated. as of Marvin 6.2, may constructs inconsistent MoleculeGraph. Use MoleculeGraph.removeBond(MolBond) for bond removal and add(MolBond) for adding a new bond to the molecule.
    
    Sets the edge at the specified index in the graph union.
    
    Overrides:
    
    setBond in class MoleculeGraph
    
    Parameters:
    iu - the bond index
    edge - the bond
  - replaceBond
```
@Deprecated
public void replaceBond(MolBond olde,
                          MolBond newe)
```
    Deprecated. as of Marvin 6.2, may constructs inconsistent MoleculeGraph. Use MoleculeGraph.removeBond(MolBond) for bond removal and add(MolBond) for adding a new bond to the molecule.
    
    Replaces an edge by another one.
    
    Overrides:
    
    replaceBond in class MoleculeGraph
    
    Parameters:
    olde - the old edge
    newe - the new edge
    Since:
    
    Marvin 4.1, 11/24/2005
  - add
```
public void add(MolBond bond)
```
    Adds a bond to the root structure.
    
    Overrides:
    
    add in class Molecule
    
    Parameters:
    bond - the bond to add
  - indexOf
```
public int indexOf(MolAtom node)
```
    Gets the index of the specified node in the graph union.
    
    Overrides:
    
    indexOf in class MoleculeGraph
    
    Parameters:
    node - the node
    
    Returns:
    the index, or -1 if not found
  - indexOf
```
public int indexOf(MolBond edge)
```
    Gets the index of the specified edge in the graph union.
    
    Overrides:
    
    indexOf in class MoleculeGraph
    
    Parameters:
    edge - the edge
    
    Returns:
    the index, or -1 if not found
    See Also:
    Object.equals(Object)
  - contains
```
public boolean contains(MolAtom node)
```
    Checks if the root structure or an R-group contains the specified node.
    
    Overrides:
    
    contains in class Molecule
    
    Parameters:
    node - the node object
    
    Returns:
    true if the graph contains the object, false otherwise
  - contains
```
public boolean contains(MolBond edge)
```
    Checks if the root structure or an R-group contains the specified edge.
    
    Overrides:
    
    contains in class MoleculeGraph
    
    Parameters:
    edge - the edge object
    
    Returns:
    true if the graph contains the object, false otherwise
    See Also:
    Object.equals(Object)
  - isEmpty
```
public boolean isEmpty()
```
    Ask if the molecule is empty or not.
    
    Overrides:
    
    isEmpty in class Molecule
    
    Returns:
    true if the graph does not contain any nodes or edges.
  - isQuery
```
public boolean isQuery()
```
    Indicates if the molecule has query features.
    
    Overrides:
    
    isQuery in class MoleculeGraph
    
    Returns:
    true if there are R-definitions for this molecule or the root has query features.
    Since:
    
    Marvin 4.1.2 08/30/2006
    
    See Also:
    MolAtom.isQuery(), MolBond.isQuery()
  - isAtom
```
@Deprecated
public boolean isAtom()
```
    Deprecated. As of Marvin 14.7.7, no replacement.
    Not supported feature.
    
    Determines whether the structure represents only one atom and an arbitrary number of bonds.
    
    Overrides:
    
    isAtom in class MoleculeGraph
    
    Returns:
    true the root structure represents an atom and there are no R-groups, false otherwise
  - isBond
```
@Deprecated
public boolean isBond()
```
    Deprecated. As of Marvin 14.7.7, no replacement.
    Not supported feature.
    
    Determines whether the structure represents only one bond and zero or two atoms. Determines whether the structure represents only one atom and an arbitrary number of bonds.
    
    Overrides:
    
    isBond in class MoleculeGraph
    
    Returns:
    true if the root structure represents a bond and there are no R-groups, false otherwise
  - isReaction
```
public boolean isReaction()
```
    Checks if the structure represents a reaction or not.
    
    Overrides:
    
    isReaction in class Molecule
    
    Returns:
    true if the root structure is a reaction
    Since:
    
    Marvin 3.0
  - canBeReactionComponent
```
public boolean canBeReactionComponent()
```
    Tests whether an object of this class can be a reaction component. This implementation returns false, an RgMolecule cannot be a reaction component.
    
    Overrides:
    
    canBeReactionComponent in class Molecule
    
    Returns:
    true if it can be a reactant, product or agent, false if adding it to an RxnMolecule is not supported
    Since:
    
    Marvin 4.1.13, 09/19/2007
  - hasAtomSet
```
public boolean hasAtomSet()
```
    Tests whether the molecule graph has atom sets.
    
    Overrides:
    
    hasAtomSet in class Molecule
    
    Returns:
    true if there are atom sets, false otherwise
    Since:
    
    Marvin 4.0, 03/02/2005
  - hasBondSet
```
public boolean hasBondSet()
```
    Tests whether the molecule graph has atom sets.
    
    Overrides:
    
    hasBondSet in class MoleculeGraph
    
    Returns:
    true if there are atom sets, false otherwise
    Since:
    
    Marvin 4.0, 03/02/2005
  - getMostSimplifiedMolecule
```
protected Molecule getMostSimplifiedMolecule()
```
    Gets the simplified molecule object even if there is a parent document with other objects.
    
    Overrides:
    
    getMostSimplifiedMolecule in class Molecule
    
    Returns:
    the root structure if there are no R-groups present, this otherwise
    Since:
    
    Marvin 4.1.13, 09/20/2007
  - addRgroupsTo
```
public RgMolecule addRgroupsTo(Molecule m)
```
    Creates a read only RgMolecule from a simple molecule object.
    
    Parameters:
    m - the simple molecule object
    
    Returns:
    RgMolecule containing R-groups from this object and the specified molecule as root
    Since:
    
    Marvin 3.1
  - removeAtom
```
public void removeAtom(MolAtom node,
              int cleanupFlags)
```
    Removes an atom and its bonds from the root structure and from all the R-groups. This method is for internal use only. Use MoleculeGraph.removeAtom(MolAtom) instead unless you are sure what you are doing.
    
    Overrides:
    
    removeAtom in class Molecule
    
    Parameters:
    node - the atom
    cleanupFlags - extra clean-up methods
    Since:
    
    Marvin 3.1
    
    See Also:
    MoleculeGraph.RMCLEANUP_NONE, MoleculeGraph.RMCLEANUP_ALL, MoleculeGraph.RMCLEANUP_EDGES, MoleculeGraph.RMCLEANUP_STEREO, Molecule.RMCLEANUP_SGROUPATOMS, Molecule.RMCLEANUP_FROMSGROUPS
  - removeAtom
```
public void removeAtom(int i,
              int cleanupFlags)
```
    Removes an atom and its bonds from the root structure. This method is for internal use only. Use MoleculeGraph.removeAtom(MolAtom) instead unless you are sure what you are doing.
    
    Overrides:
    
    removeAtom in class Molecule
    
    Parameters:
    i - the atom index
    cleanupFlags - extra clean-up methods
    Since:
    
    Marvin 3.1
    
    See Also:
    MoleculeGraph.RMCLEANUP_NONE, MoleculeGraph.RMCLEANUP_ALL, MoleculeGraph.RMCLEANUP_EDGES, MoleculeGraph.RMCLEANUP_STEREO, Molecule.RMCLEANUP_SGROUPATOMS, Molecule.RMCLEANUP_FROMSGROUPS
  - cleanupRemovedRgroupMember
```
public void cleanupRemovedRgroupMember(MoleculeGraph m,
                              int f)
```
    Clean-up after R-group removal.
    
    Specified by:
    
    cleanupRemovedRgroupMember in interface chemaxon.struc.RgMoleculeGraphIface
    
    Parameters:
    m - the removed R-group member
    f - clean-up flags
    Since:
    
    Marvin 4.1, 11/25/2005
  - removeBond
```
protected void removeBond(MolBond edge,
              int cleanupFlags)
```
    Remove a bond from the root structure, and from all the R-groups.
    
    Overrides:
    
    removeBond in class Molecule
    
    Parameters:
    edge - the bond
    cleanupFlags - extra clean-up methods
    Since:
    
    Marvin 3.1
    
    See Also:
    MoleculeGraph.RMCLEANUP_NONE, MoleculeGraph.RMCLEANUP_ALL, MoleculeGraph.RMCLEANUP_EDGES, MoleculeGraph.RMCLEANUP_STEREO, Molecule.RMCLEANUP_SGROUPATOMS, Molecule.RMCLEANUP_FROMSGROUPS
  - removeBond
```
protected void removeBond(int i,
              int cleanupFlags)
```
    Remove a bond from the root structure.
    
    Overrides:
    
    removeBond in class Molecule
    
    Parameters:
    i - the bond index
    cleanupFlags - extra clean-up methods
    Since:
    
    Marvin 3.1
    
    See Also:
    MoleculeGraph.RMCLEANUP_NONE, MoleculeGraph.RMCLEANUP_ALL, MoleculeGraph.RMCLEANUP_EDGES, MoleculeGraph.RMCLEANUP_STEREO, Molecule.RMCLEANUP_SGROUPATOMS, Molecule.RMCLEANUP_FROMSGROUPS
  - removeAllBonds
```
public void removeAllBonds()
```
    Remove all bonds from the root structure, and from all the R-groups.
    
    Overrides:
    
    removeAllBonds in class Molecule
  - removeAll
```
public void removeAll()
```
    Remove all the atoms and bonds from the root structure, and from all the R-groups.
    
    Overrides:
    
    removeAll in class Molecule
  - isRealAtomParent
```
protected boolean isRealAtomParent()
```
    R-group molecule objects cannot be real node parents.
    
    Overrides:
    
    isRealAtomParent in class MoleculeGraph
    
    Returns:
    false
    Since:
    
    Marvin 3.0
  - regenBonds
```
public void regenBonds()
```
    Regenerate the edge vectors: remove their elements, then put the edge objects from the nodes into it.
    
    Overrides:
    
    regenBonds in class MoleculeGraph
  - sortBondsAccordingTo
```
public void sortBondsAccordingTo(MolBond[] order)
```
    Sort edges in the same order as they appear in the specified array.
    
    Overrides:
    
    sortBondsAccordingTo in class MoleculeGraph
    
    Parameters:
    order - the array
    Since:
    
    Marvin 3.5, 09/02/2004
  - setLocation
```
public void setLocation(DPoint3 p)
```
    Set the origin of the molecule. The MolAtom coordinates are relative to this origin.
    
    Overrides:
    
    setLocation in class MoleculeGraph
    
    Parameters:
    p - the location
    See Also:
    MoleculeGraph.orix
  - fuse
```
public void fuse(MoleculeGraph g,
        boolean check)
```
    Add the atoms and bonds of another molecule.
    
    Overrides:
    
    fuse in class MoleculeGraph
    
    Parameters:
    g - the other molecule
    check - true if a containment check should be performed to ensure that only those nodes and edges are added that are not already elements - false if the graph is known to be disjoint from this graph and this check can be safely skipped
    Since:
    
    Marvin 5.0
  - checkConsistency
```
@Deprecated
public void checkConsistency()
```
    Deprecated. As of Marvin 5.7, no replacement.
    Not intended for public use, it was intended only for internal debugging.
    
    Checks the internal consistency of the structure. Use this method for debugging.
    
    Overrides:
    
    checkConsistency in class Molecule
    
    Throws:
    
    RuntimeException - if inconsistency found
    Since:
    
    Marvin 5.0, 11/06/2007
  - fuse0
```
protected void fuse0(MoleculeGraph graph,
         boolean check)
```
    Add those nodes and edges of a graph that are not already elements. If the graph is a reaction and the root structure is not a reaction then the root structure will become a reaction determined by the reaction arrow corresponding to the graph. For each connected component of the graph checks if it contains an atom connected to an RGgroup in this RgMolecule; if yes then also adds the component to that RGroup, otherwise adds it to the root structure.
    
    Overrides:
    
    fuse0 in class MoleculeGraph
    
    Parameters:
    graph - the graph that will be fused into this molecule
    check - true if a containment check should be performed to ensure that only those nodes and edges are added that are not already elements - false if the graph is known to be disjoint from this graph and this check can be safely skipped
    Since:
    
    Marvin 5.0
  - mergeAtoms
```
@Deprecated
public void mergeAtoms(MolAtom that,
                         MolAtom a)
```
    Deprecated. As of Marvin 6.2, use MergeUtil.mergeAtoms(MolAtom, MolAtom, boolean) instead.
    
    Merges bonds of an atom with another atom, then add the atom to the molecule.
    
    Overrides:
    
    mergeAtoms in class Molecule
    
    Parameters:
    that - the atom
    a - the other atom
  - setSgroupParent
```
public void setSgroupParent(MolAtom a,
                   Sgroup sg,
                   boolean set)
```
    Sets or unsets an S-group as a parent of an atom in the root structure or an R-group.
    
    Overrides:
    
    setSgroupParent in class Molecule
    
    Parameters:
    a - the atom
    sg - the S-group
    set - set (true) or unset (false)
    
    Throws:
    
    IllegalArgumentException - if neither root, nor any R-group contains the atom
    Since:
    
    Marvin 3.0
  - clonecopy
```
public void clonecopy(MoleculeGraph g)
```
    Make another molecule identical to this one. If the target molecule is not an RgMolecule, then only the root structure will be cloned.
    
    Overrides:
    
    clonecopy in class Molecule
    
    Parameters:
    g - the target molecule
  - clonecopy
```
public void clonecopy(int[] iatoms,
             MoleculeGraph g)
```
    Copies the specified atoms of this graph to another one. The RgMolecule implementation of this method is incomplete, R-groups are not handled.
    
    Overrides:
    
    clonecopy in class Molecule
    
    Parameters:
    iatoms - array of atom indices to copy
    g - the target graph
    Since:
    
    Marvin 5.0.2, 03/11/2008
  - isSelfReference
```
public boolean isSelfReference(MProp p)
```
    Tests whether the specified property is a self reference to the molecule.
    
    Overrides:
    
    isSelfReference in class MoleculeGraph
    
    Parameters:
    p - the property
    Since:
    
    Marvin 4.1.6, 02/11/2007
  - fixSelfReferringProperty
```
protected boolean fixSelfReferringProperty(MProp prop)
```
    Fix a property containing reference to the molecule. Called from clonelesscopy().
    
    Overrides:
    
    fixSelfReferringProperty in class Molecule
    
    Parameters:
    prop - the property
    Since:
    
    Marvin 4.1.6, 02/14/2007
    
    See Also:
    MoleculeGraph.clonecopy(MoleculeGraph)
  - clonelesscopy
```
@Deprecated
public void clonelesscopy(MoleculeGraph g)
```
    Deprecated. as of Marvin 6.3.
    Not supported feature.
    
    Copy to selection. Make another molecule identical to this one, but do not clone atoms, bonds, and the props.
    
    Overrides:
    
    clonelesscopy in class Molecule
    
    Parameters:
    g - the target molecule
  - getFormula
```
public String getFormula()
```
    Gets the molecular formula in Hill order.
    
    Overrides:
    
    getFormula in class MoleculeGraph
    
    Returns:
    the formula
  - getMass
```
public double getMass()
```
    Calculates the molecular weight of the molecule. Returns 0 if the molecule contains R-group or reaction
    
    Overrides:
    
    getMass in class MoleculeGraph
    
    Returns:
    the molecular weight
  - newInstance
```
public MoleculeGraph newInstance()
```
    Creates a new RgMolecule object. The dimension and the origin coordinates will be the same as in the original molecule.
    
    Overrides:
    
    newInstance in class Molecule
    
    Returns:
    an RgMolecule object
  - newSelectionMolecule
```
public SelectionMolecule newSelectionMolecule()
```
    Creates a new SelectionMolecule object appropriate for storing selection from this molecule.
    
    Overrides:
    
    newSelectionMolecule in class Molecule
    
    Returns:
    an empty selection molecule
    Since:
    
    Marvin 4.1, 11/24/2005
  - makeItSimilar
```
protected void makeItSimilar(MoleculeGraph g)
```
    Copies some properties of this molecule to the other one specified as argument. Copies properties in the root structures.
    
    Overrides:
    
    makeItSimilar in class Molecule
    
    Parameters:
    g - the molecule to change
  - isIncompleteReaction
```
public boolean isIncompleteReaction()
```
    Check whether the reaction is incomplete or not.
    
    Returns:
    true if something is missing, false if it seems to be okay
    Since:
    
    Marvin 2.9
  - transform
```
public void transform(CTransform3D t,
             boolean incg)
```
    Apply a transformation matrix to the atomic coordinates.
    
    Overrides:
    
    transform in class Molecule
    
    Parameters:
    t - the transformation matrix
    incg - increase grinvCC or not
  - getGraphUnion
```
public MoleculeGraph getGraphUnion()
```
    Gets a graph containing all the atoms and bonds.
    
    Overrides:
    
    getGraphUnion in class MoleculeGraph
    
    Returns:
    root.getGraphUnion() if there are no R-groups, getGraphUnionAsSelection() otherwise
    Since:
    
    Marvin 3.0, 11/11/2002
    
    See Also:
    Molecule.getGraphUnionAsSelection()
  - getSubGraphCount
```
protected final int getSubGraphCount()
```
    Gets the number of all "submolecules".
    
    Overrides:
    
    getSubGraphCount in class MoleculeGraph
    
    Returns:
    the number of submolecules
    Since:
    
    Marvin 4.1.2
    
    See Also:
    MoleculeGraph.getSubGraphs(MoleculeGraph[], int)
  - getSubGraphs
```
protected final void getSubGraphs(MoleculeGraph[] arr,
                int off)
```
    Gets all "submolecules".
    
    Overrides:
    
    getSubGraphs in class MoleculeGraph
    
    Parameters:
    arr - the output array
    off - offset
    Since:
    
    Marvin 4.1.2
    
    See Also:
    MoleculeGraph.getSubGraphs(), MoleculeGraph.getSubGraphCount()
  - fillSelectionMolecule
```
protected void fillSelectionMolecule(SelectionMolecule s)
```
    Adds all atoms and bonds of the root structure and the R-groups to the specified molecule.
    
    Overrides:
    
    fillSelectionMolecule in class Molecule
    
    Parameters:
    s - the selection molecule
    Since:
    
    Marvin 3.0, 11/05/2002
  - getLonePairCount
```
public int getLonePairCount(int i)
```
    Gets the number of lone pairs.
    
    Overrides:
    
    getLonePairCount in class MoleculeGraph
    
    Parameters:
    i - atom index
    
    Returns:
    the number of lone pairs
  - aromatize
```
public void aromatize(int method)
```
    Aromatizes molecule. Changes the bonds.
    Overrides:
    
    aromatize in class Molecule
    
    Parameters:
    method - Specifies the algorithm for aromatization. Possible values:
    
    AROM_BASIC - Basic aromatization
    
    AROM_GENERAL - General (Daylight compatible) aromatization
    
    Limits:
    
    AROM_BASIC: only up to 18 membered rings are checked
    
    AROM_GENERAL: no ring system limit
    Throws:
    
    SecurityException - cannot load module because of a security problem (firewall)
    Since:
    
    Marvin 3.4, Marvin 4.1
    
    See Also:
    MoleculeGraph.AROM_BASIC, MoleculeGraph.AROM_GENERAL, Document about aromatization
  - aromatize
```
public void aromatize(int method,
             boolean checkAmbiguity)
```
    Aromatizes molecule. Changes the bonds.
    Overrides:
    
    aromatize in class Molecule
    
    Parameters:
    method - Specifies the algorithm for aromatization. Possible values:
    
    AROM_BASIC - Basic aromatization
    
    AROM_GENERAL - General (Daylight compatible) aromatization
    
    Limits:
    
    AROM_BASIC: only up to 18 membered rings are checked
    
    AROM_GENERAL: no ring system limit
    checkAmbiguity - Specifies whether ANY bonds should be considered during aromatization.
    
    Throws:
    
    SecurityException - cannot load module because of a security problem (firewall)
    Since:
    
    Marvin 3.4, Marvin 4.1
    
    See Also:
    MoleculeGraph.AROM_BASIC, MoleculeGraph.AROM_GENERAL, Document about aromatization
  - checkSgroupConsistency
```
protected void checkSgroupConsistency()
```
    Checks the consistency of S-groups.
    
    Overrides:
    
    checkSgroupConsistency in class Molecule
    
    Throws:
    
    RuntimeException - if inconsistency found
    Since:
    
    Marvin 5.0, 11/06/2007
  - toString
```
public String toString()
```
    Overrides Object.toString() to ease debugging.
    
    Overrides:
    
    toString in class MoleculeGraph
    
    Returns:
    a string representation of the object
    Since:
    
    4.1, 11/28/2005
  - sumConservedQuantities
```
protected void sumConservedQuantities(MolAtom a,
                          int[] atoms,
                          int sign)
```
    For internal use only.
    
    Overrides:
    
    sumConservedQuantities in class MoleculeGraph
    
    Since:
    
    Marvin 4.1.13, 09/19/2007
    
    See Also:
    RxnMolecule.isIncompleteReaction()
  - createGearch
```
protected chemaxon.struc.gearch.MoleculeGraphGearch createGearch()
```
    Overrides:
    
    createGearch in class Molecule
  - getMaxAttachmentPointOrder
```
public int getMaxAttachmentPointOrder(int rgroupID)
```
    Gets the maximal attachment point order of R-group definition molecules specified by an R-group ID. The attachment point order of an R-gruop definition molecule is the maximal attachment point order of its atoms.
    
    Parameters:
    rgroupID - the rgroup identifier to specify the R-group definition molecules.
    
    Returns:
    the maximal attachment point order of the definition molecules.
    Since:
    
    Marvin 5.4
  - clearObjects
```
public void clearObjects()
```
    Specified by:
    
    clearObjects in interface chemaxon.struc.MObjectContainer
    
    Overrides:
    
    clearObjects in class Molecule
  - getObjectCount
```
public int getObjectCount()
```
    Specified by:
    
    getObjectCount in interface chemaxon.struc.MObjectContainer
    
    Overrides:
    
    getObjectCount in class Molecule
  - removeObject
```
public void removeObject(MObject mo)
```
    Specified by:
    
    removeObject in interface chemaxon.struc.MObjectContainer
    
    Overrides:
    
    removeObject in class Molecule
  - selectAllObjects
```
public void selectAllObjects(boolean s)
```
    Specified by:
    
    selectAllObjects in interface chemaxon.struc.MObjectContainer
    
    Overrides:
    
    selectAllObjects in class Molecule
  - getAllObjects
```
public List<MObject> getAllObjects()
```
    Specified by:
    
    getAllObjects in interface chemaxon.struc.MObjectContainer
    
    Overrides:
    
    getAllObjects in class Molecule
  - getParity
```
public int getParity(int i)
```
    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. Leaves the imported parity unchanged.
    
    Overrides:
    
    getParity in class MoleculeGraph
    
    Parameters:
    i - the index of the atom whose parity is to be determined
    
    Returns:
    0 for nonchiral, PARITY_ODD or PARITY_EVEN for atoms of odd or even parity, PARITY_ODD|PARITY_EVEN for atoms whose parity is unspecified or cannot be assigned -as they are defined in MolAtom
    
    Throws:
    
    SecurityException - the Parity module cannot be loaded because of security reasons (firewall)
    See Also:
    StereoConstants.PARITY_ODD, StereoConstants.PARITY_EVEN, MoleculeGraph.isAbsStereo(), setAbsStereo(boolean), MoleculeGraph.getParity(int)
  - getLocalParity
```
public int getLocalParity(int i)
```
    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. The molecule symmetry is not checked, so even an atom with same ligands can have parity. Leaves the imported parity unchanged. Contracted sgroups must be expanded to achieve consistent result.
    
    Overrides:
    
    getLocalParity in class MoleculeGraph
    
    Parameters:
    i - the index of the atom whose parity is to be determined
    
    Returns:
    PARITY_ODD or PARITY_EVEN for atoms of odd or even parity, PARITY_EITHER for atoms with wiggly bond 0 for atoms whose parity is unspecified or not known.
    
    Throws:
    
    SecurityException - the Parity module cannot be loaded because of security reasons (firewall)
    See Also:
    StereoConstants.PARITY_ODD, StereoConstants.PARITY_EVEN, StereoConstants.PARITY_EITHER, MoleculeGraph.isAbsStereo(), setAbsStereo(boolean), MoleculeGraph.getLocalParity(int)
  - stereoClean
```
public boolean stereoClean()
```
    Reset the wedges of the molecule, based on the actual parity information in 2D remove wedges in 3D. Take care of expanding the molecule if neccessary.
    
    Overrides:
    
    stereoClean in class MoleculeGraph
    
    Returns:
    true if succesful
    See Also:
    MoleculeGraph.stereoClean()
  - setValenceCheckOptions
```
public void setValenceCheckOptions(ValenceCheckOptions options)
```
    Sets the options for valence checking. To just enable/disable valence check in the molecule use MoleculeGraph.setValenceCheckEnabled(boolean). Calling this function with a not null parameter automatically enables the valence check.
    
    Overrides:
    
    setValenceCheckOptions in class MoleculeGraph
    
    Parameters:
    options - the new valence check options
    See Also:
    ValenceCheckOptions
  - getValenceCheckOptions
```
public ValenceCheckOptions getValenceCheckOptions()
```
    Returns the options for valence checking. To see if the valence check is enabled on the molecule use MoleculeGraph.isValenceCheckEnabled()
    
    Overrides:
    
    getValenceCheckOptions in class MoleculeGraph
    
    Returns:
    the valence check options
    See Also:
    ValenceCheckOptions
  - canBeCT
```
public boolean canBeCT(int i2,
              int i3,
              boolean grcheck)
```
    Determines whether the bond between the specified atoms can be a CIS/TRANS or not. In case of ring bonds the ring sizes of the ring for the existence of CIS/TRANS specific bond should be checked before calling this method as ring sizes are not checked in this method.
    
    Overrides:
    
    canBeCT in class MoleculeGraph
    
    Parameters:
    i2 - index of the first atom
    i3 - index of the second atom
    grcheck - true if check atom equivalences using graph invariants
    
    Returns:
    true if this is a double bond that can be either CIS, TRANS or EITHER, false otherwise.
    Since:
    
    Marvin 4.0 1/23/2005
  - getAtomIterator
```
public IteratorFactory.AtomIterator getAtomIterator()
```
    Returns an iterator over the atoms in this molecule in proper sequence.
    
    Overrides:
    
    getAtomIterator in class MoleculeGraph
    
    Returns:
    an iterator over the atoms in this molecule in proper sequencer
    Since:
    
    Marvin 6.2, 2013.09.09.
  - getBondIterator
```
public IteratorFactory.BondIterator getBondIterator()
```
    Returns an iterator over the bonds in this molecule in proper sequence.
    
    Overrides:
    
    getBondIterator in class MoleculeGraph
    
    Returns:
    an iterator over the bonds in this molecule in proper sequence
    Since:
    
    Marvin 6.2, 2013.09.09.
  - setRestH
```
public void setRestH(int rGroupIndex)
```
    Sets the restH condition on an R-group definition.
    
    Parameters:
    rGroupIndex - the index of the R-group definition
  - removeRestH
```
public void removeRestH(int rGroupIndex)
```
    Removes the restH condition from an R-group definition.
    
    Parameters:
    rGroupIndex - the index of the R-group definition
  - isRestH
```
public boolean isRestH(int rGroupIndex)
```
    Informs whether the restH condition is set to the referenced R-group definition.
    
    Parameters:
    rGroupIndex - the index of the R-group definition
    
    Returns:
    true if the restH condition is set false otherwise
  - setDependentRgroupDefinition
```
public void setDependentRgroupDefinition(int rGroupIndexIf,
                                int rGroupIndexThen)
```
    Sets the dependent R-group definition (rGroupIndexThen) for the referenced R-group definition (rGroupIndexIf).
    
    Parameters:
    rGroupIndexIf - the R-group definition on which the other one depends
    rGroupIndexThen - the R-group definition which depends on the other one
  - getDependentRgroupDefinition
```
public int getDependentRgroupDefinition(int rGroupIndex)
```
    Gets the R-group definition's index which depends on the referenced R-group definition.
    
    Parameters:
    rGroupIndex - the R-group definition index
    
    Returns:
    the index of the dependent R-group definition or -1 if none exists
  - removeDependentRgroupDefinition
```
public void removeDependentRgroupDefinition(int rGroupIndex)
```
    Removes the dependent R-group definition of the referenced R-group definition.
    
    Parameters:
    rGroupIndex - the R-group definition ID

Class RgMolecule

Property Summary

Properties inherited from class chemaxon.struc.MoleculeGraph

Nested Class Summary

Nested classes/interfaces inherited from class chemaxon.struc.MoleculeGraph

Field Summary

Fields inherited from class chemaxon.struc.Molecule

Fields inherited from class chemaxon.struc.MoleculeGraph

Fields inherited from interface chemaxon.struc.StereoConstants

Constructor Summary

Method Summary

Methods inherited from class chemaxon.struc.Molecule

Methods inherited from class chemaxon.struc.MoleculeGraph

Methods inherited from class java.lang.Object

Field Detail

RG_ID_MASK

RG_ID2_FLAG

RG_ID2_OFF

RG_ID2_MASK

RG_RESTH

DEFAULT_RLOGIC_RANGE

Constructor Detail

RgMolecule

Method Detail

setRoot

getStereo2

getRoot

getRootG

getRgroupCount

getRgroupMemberCount

getRgroupMember

getRgroupMemberG

getRgroupId

findRgroupIndex

addSgroup

addRgroup

addRgroupBridge

getRgroupBridgeIds

getRgroupBridgeMembers

getRgroupBridges

removeRgroupMember

removeRgroupBridgeMember

removeRgroupMembers

removeRgroupBridgeMembers

removeRgroup

removeRgroupBridge

hasRgroupContainedBy

unRgroupAtoms

replaceAtomsWithNewRgroup

getRlogic

setRlogic

getRlogicRange

setRlogicRange

checkRlogicRange

clearForImport

setName

getName

setComment

getComment

properties

revalidateCoordDependentProps

setInputFormat

reuseAtom

endReuse

getCtab

getBondTable

rgroupIdOf

rgroupIndexOf

getRgroupMemberID

getRgroupIndex

getRgroupMemberIndex

setDim

getFlags

setFlags

setFlags

setAbsStereo

getAtomCount

getAtomCount

getAtom

setAtom