Deprecated API

Contents

• Deprecated Interfaces
• Deprecated Classes
• Deprecated Enums
• Deprecated Fields
• Deprecated Methods
• Deprecated Constructors
• Deprecated Enum Constants

Deprecated Interfaces

Interface and Description
chemaxon.marvin.util.CopyOptConstants 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.
chemaxon.jep.MolCondition Will be removed soon.
com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue

Deprecated Classes

Class and Description
chemaxon.formats.recognizer.AbbrevGroupRecognizer as of Marvin 2014.07.21.0 intended for internal use only
chemaxon.fixers.AbsentChiralFlagFixer use AddChiralFlagFixer
chemaxon.fixers.AbsoluteStereoFixer use RemoveInvalidChiralFlagFixer
chemaxon.formats.recognizer.Base64Recognizer as of Marvin 2014.07.21.0 intended for internal use only
chemaxon.fixers.CovalentCounterionFixer use ConvertToIonicFormFixer
chemaxon.fixers.CrossedDoubleBondFixer use ConvertToWigglyDoubleBondFixer
chemaxon.formats.recognizer.CubeRecognizer as of Marvin 2014.07.21.0 intended for internal use only
chemaxon.naming.DocumentExtractor use chemaxon.formats.MolImporter or chemaxon.naming.DocumentToStructure instead.
chemaxon.marvin.calculations.EnumerationPlugin Use MarkushEnumerationPlugin
chemaxon.fixers.ExplicitHydrogenFixer use RemoveExplicitHydrogenFixer
chemaxon.fixers.IsotopeFixer use ConvertToElementalFormFixer
chemaxon.formats.MolConverter.Options as of Marvin 5.2.3, use MolConverter.Builder instead.
chemaxon.marvin.util.MoleculeUtil as of Marvin 5.11.1
chemaxon.marvin.util.MolImageSize since 5.5 use ImageExport methods to get this data if you need it. this class will be deleted in a future release.
chemaxon.formats.recognizer.PDBRecognizer as of Marvin 2014.07.21.0 intended for internal use only
chemaxon.formats.recognizer.PeptideRecognizer as of Marvin 2014.07.21.0 intended for internal use only
chemaxon.checkers.result.ReactionCheckerResult
chemaxon.formats.recognizer.RecognizerList as of Marvin 2014.07.21.0 not used
chemaxon.checkers.RgroupReferenceErrorChecker
chemaxon.fixers.RgroupReferenceFixer use RemoveUnreferencedRgroupDefinitionsFixer
chemaxon.formats.recognizer.SMILESRecognizer as of Marvin 2014.07.21.0 intended for internal use only
chemaxon.checkers.StructureCheckerFactory use CheckerFixerFactory instead
chemaxon.fixers.StructureFixerFactory use CheckerFixerFactory instead
chemaxon.fixers.WigglyDoubleBondFixer use ConvertToCrossedDoubleBondFixer

Deprecated Enums

Enum and Description
chemaxon.struc.MoleculeGraph.ValenceCheckState As of Marvin 6.0, replaced by MoleculeGraph.setValenceCheckOptions(ValenceCheckOptions) and ValenceCheckOptions.
com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.AtropStereo As of Marvin 14.9.15, replaced by AtropStereoIUPACDescriptor.
com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.AxialStereo As of Marvin 14.9.15, replaced by AxialStereoIUPACDescriptor.
com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.CisTransStereo As of Marvin 14.9.15, replaced by CisTransStereoIUPACDescriptor.
com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.TetrahedralStereo As of Marvin 14.9.15, replaced by TetrahedralStereoIUPACDescriptor.

Deprecated Fields

Field and Description
chemaxon.util.HitColoringAndAlignmentOptions.alignmentMode as of JChem 5.10, use HitColoringAndAlignmentOptions.setAlignmentMode(int) and HitColoringAndAlignmentOptions.getAlignmentMode() to access this field.
chemaxon.marvin.paint.DispOptConsts.APPLY_DEPTH_CUE As of Marvin 5.4.1, replaced by DispOptConsts.AUTOMATIC_FOG
chemaxon.marvin.common.ParameterConstants.ATOM_NUMBERS_VISIBLE in 6.2.0 use atomNumberingType parameter instead.
chemaxon.marvin.paint.DispOptConsts.AUTOMATIC_FOG
chemaxon.struc.MoleculeGraph.CACHE_REMOVE_SSSRMODULE As of Marvin 5.12, no replacement. SSSR module is not cached any more.
chemaxon.util.HitColoringAndAlignmentOptions.coloring as of JChem 5.10, use HitColoringAndAlignmentOptions.setColoringEnabled(boolean) and HitColoringAndAlignmentOptions.isColoringEnabled() to access this field.
chemaxon.struc.sgroup.Expandable.COORDS_UPDATE As of Marvin 6.2, no replacement. Not supported feature.
chemaxon.marvin.util.CopyOptConstants.COPY_AS_IMAGE_BITMAP
chemaxon.marvin.util.CopyOptConstants.COPY_AS_IMAGE_EMF
chemaxon.marvin.util.CopyOptConstants.COPY_AS_OLE
chemaxon.marvin.util.CopyOptConstants.COPY_AS_TEXT
chemaxon.marvin.common.ParameterConstants.COPY_OPTIONS since 5.3.3 has no sense
chemaxon.struc.MolAtom.CTSPECIFIC_H As of Marvin 5.11 Graph invariants are checked by default when calculating CIS/TRANS stereo, so this option is out of use.
chemaxon.struc.StereoConstants.CTUNKNOWN As of Marvin 6.1, Usage: In the specified methods the CIS|TRANS or CIS|TRANS|CTUNSPEC values are used instead.
chemaxon.marvin.common.ParameterConstants.DISPLAY_QUALITY Deprecated since Marvin 6.4. No settings is used intead of this, only High Quality exists from now on.
chemaxon.util.HitColoringAndAlignmentOptions.enumerateMarkush as of JChem 5.12, use HitColoringAndAlignmentOptions.setEnumerateMarkush(boolean) and HitColoringAndAlignmentOptions.getEnumerateMarkush() to access this field.
chemaxon.marvin.common.ParameterConstants.EXPLICIT_H since 5.3
chemaxon.marvin.util.CopyOptConstants.FMT_EMF will be deleted, no need to this constant
chemaxon.marvin.util.CopyOptConstants.FMT_IMAGE will be deleted, no need to this constant
chemaxon.marvin.util.CopyOptConstants.FMT_MOL will be deleted, no need to this constant
chemaxon.marvin.util.CopyOptConstants.FMT_MRV will be deleted, no need to this constant
chemaxon.marvin.util.CopyOptConstants.FMT_OLE will be deleted, no need to this constant
chemaxon.marvin.util.CopyOptConstants.FMT_PLAINTEXT will be deleted, no need to this constant
chemaxon.marvin.util.CopyOptConstants.FMT_RXN will be deleted, no need to this constant
chemaxon.marvin.util.CopyOptConstants.FMT_SMILES will be deleted, no need to this constant
chemaxon.marvin.util.CopyOptConstants.FMT_STRING will be deleted, no need to this constant
chemaxon.marvin.util.CopyOptConstants.FMT_STRUCTURE
chemaxon.marvin.util.MolImageSize.height
chemaxon.util.HitColoringAndAlignmentOptions.hitColor as of JChem 5.10, use HitColoringAndAlignmentOptions.setHitColor(Color) and HitColoringAndAlignmentOptions.getHitColor() to access this field.
chemaxon.util.HitColoringAndAlignmentOptions.hitHomologyColor as of JChem 5.10, use HitColoringAndAlignmentOptions.setHitHomologyColor(Color) and HitColoringAndAlignmentOptions.getHitHomologyColor() to access this field.
chemaxon.util.iterator.IteratorFactory.INCLUDE_CHEMICAL_ATOMS As of Marvin 6.2, Use IteratorFactory.INCLUDE_CHEMICAL_ATOMS_ONLY instead.
chemaxon.util.HitColoringAndAlignmentOptions.markushDisplayMode as of JChem 5.10, use HitColoringAndAlignmentOptions.setMarkushDisplayMode(int) and HitColoringAndAlignmentOptions.getMarkushDisplayMode() to access this field.
chemaxon.util.HitColoringAndAlignmentOptions.nonHitColor as of JChem 5.10, use HitColoringAndAlignmentOptions.setNonHitColor(Color) and HitColoringAndAlignmentOptions.getNonHitColor() to access this field.
chemaxon.util.HitColoringAndAlignmentOptions.nonHitColor3D as of JChem 5.10, use HitColoringAndAlignmentOptions.setNonHitColor3D(Color) and HitColoringAndAlignmentOptions.getNonHitColor3D() to access this field.
chemaxon.marvin.plugin.PluginFactory.PRELOAD Not used.
chemaxon.checkers.RgroupReferenceErrorChecker.PROPERTY_KEY_SEARCH_MISSING_RATOM
chemaxon.checkers.RgroupReferenceErrorChecker.PROPERTY_KEY_SEARCH_SELF_REFERENCE
chemaxon.marvin.paint.DispOptConsts.QUALITY_MASK since Marvin 6.4 only high quality exists
chemaxon.marvin.paint.DispOptConsts.QUALITY_OFFSET Since Marvin 6.4 only high quality exists
chemaxon.marvin.sketch.SketchParameterConstants.REACTION_ERROR_VISIBLE As of Version 5.3.2, this method is deprecated and has no replacement. It will be removed in a future version of Marvin.
chemaxon.struc.sgroup.Expandable.REVERSIBLE_EXPAND as of Marvin 6.2, use Expandable.LEAVE_COORDS_UNCHANGED instead
chemaxon.struc.Molecule.RM_KEEP_LEAVINGGROUPS As of Marvin 6.2, no replacement. Not supported feature.
chemaxon.marvin.util.MolImageSize.scale
chemaxon.util.HitColoringAndAlignmentOptions.similarityScoreDisplay as of JChem 5.10, use HitColoringAndAlignmentOptions.setSimilarityScoreDisplay(int) and HitColoringAndAlignmentOptions.getSimilarityScoreDisplay() to access this field.
chemaxon.formats.MdlCompressor.TEXTMODE as of Marvin 3.1, there is no possibility to do that
chemaxon.checkers.runner.configuration.reader.ConfigurationReader.USER_CHECKERS_CONFIG_PATH Configuration file URL can be set in MarvinSketch preferences, and stored in UserSettings.
chemaxon.struc.MoleculeGraph.VALENCE_CHECK_AMBIGUOUS As of Marvin 6.0, replaced by ValenceCheckOptions.
chemaxon.marvin.common.ParameterConstants.VIEW_EXPLICIT_H @deprecated As of release 5.3, this method is deprecated and has no replacement. It will be removed in a future version of Marvin.
chemaxon.marvin.util.MolImageSize.width

Deprecated Methods

Method and Description
chemaxon.struc.MoleculeGraph.addExplicitHydrogens(int) As of Marvin 5.7, replaced by Hydrogenize.convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int). Usage: Hydrogenize.convertImplicitHToExplicit(molecule, null, f);
chemaxon.struc.MoleculeGraph.addExplicitHydrogens(int, MolAtom[]) As of Marvin 5.7, replaced by Hydrogenize.convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int). Usage: Hydrogenize.convertImplicitHToExplicit(molecule, atoms, f);
chemaxon.struc.MoleculeGraph.addExplicitLonePairs() As of Marvin 5.7, replaced by Hydrogenize.convertImplicitLonePairsToExplicit(MoleculeGraph, MolAtom[]). Usage: Hydrogenize.convertImplicitLonePairsToExplicit(molecule, null);
chemaxon.calculations.hydrogenize.Hydrogenize.addHAtoms(MoleculeGraph) since Marvin 5.11 use convertImplicitHToExplicit(MoleculeGraph) instead
chemaxon.calculations.hydrogenize.Hydrogenize.addHAtoms(MoleculeGraph, MolAtom[]) since Marvin 5.11 use convertImplicitHToExplicit(MoleculeGraph, MolAtom[]) instead
chemaxon.calculations.hydrogenize.Hydrogenize.addHAtoms(MoleculeGraph, MolAtom[], int) since Marvin 5.11 use convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int) instead
chemaxon.formats.MolConverter.Options.addInput(File, String)
chemaxon.formats.MolConverter.Options.addInput(InputStream, String)
chemaxon.formats.MolConverter.Options.addInput(String, String)
chemaxon.calculations.hydrogenize.Hydrogenize.addLonePairs(MoleculeGraph, MolAtom[]) since Marvin 5.11 use convertImplicitLonePairsToExplicit(MoleculeGraph, MolAtom[]) isntead
chemaxon.struc.MObject.addNotify() As of Marvin 6.1, replaced by MObject.addNotify(MDocument).
chemaxon.marvin.beans.MarvinPane.addToolsMenu(Container) Not used.
chemaxon.marvin.modules.datatransfer.ClipboardHandler.addTransferable(String, String, Integer, Integer, boolean, boolean) use ClipboardHandler.addTransferable(String, String, Integer, Integer, boolean, boolean, boolean) instead.
chemaxon.calculations.TopologyAnalyser.aliphaticAtomCount() as of release 5.5, replaced by Ring.aliphaticAtomCount()
chemaxon.calculations.TopologyAnalyser.aliphaticBondCount() as of release 5.5, replaced by Ring.aliphaticBondCount()
chemaxon.calculations.TopologyAnalyser.aliphaticRingCount() as of release 5.5, replaced by Ring.aliphaticRingCount()
chemaxon.calculations.TopologyAnalyser.aliphaticRingCount(int) as of release 5.5, replaced by Ring.aliphaticRingCount(int)
chemaxon.calculations.TopologyAnalyser.aliphaticRings() as of release 5.5, replaced by Ring.aliphaticRings()
chemaxon.calculations.TopologyAnalyser.aliphaticRings(int) as of release 5.5, replaced by Ring.aliphaticRings(int)
chemaxon.calculations.TopologyAnalyser.aromaticAtomCount() as of release 5.5, replaced by Ring.aromaticAtomCount()
chemaxon.calculations.TopologyAnalyser.aromaticBondCount() as of release 5.5, replaced by Ring.aromaticBondCount()
chemaxon.calculations.TopologyAnalyser.aromaticRingCount() as of release 5.5, replaced by Ring.aromaticRingCount()
chemaxon.calculations.TopologyAnalyser.aromaticRingCount(int) as of release 5.5, replaced by Ring.aromaticRingCount(int)
chemaxon.calculations.TopologyAnalyser.aromaticRings() as of release 5.5, replaced by Ring.aromaticRings()
chemaxon.calculations.TopologyAnalyser.aromaticRings(int) as of release 5.5, replaced by Ring.aromaticRings(int)
chemaxon.struc.MoleculeGraph.arrangeComponents() As of Marvin 5.7, replaced by CleanUtil.arrangeComponents(MoleculeGraph, boolean, boolean). Usage: CleanUtil.arrangeComponents(molecule, true, true);
chemaxon.marvin.util.MoleculeUtil.arrangeCrossingBonds(MolBond, Molecule, boolean) as of Marvin 5.11.1 use MoleculeGraph.setBond(int, MolBond)
chemaxon.calculations.TopologyAnalyser.asymmetricAtomCount() as of release 5.5, replaced by Stereochemistry.asymmetricAtomCount()
chemaxon.calculations.TopologyAnalyser.asymmetricAtoms() as of release 5.5, replaced by Stereochemistry.asymmetricAtoms()
chemaxon.formats.MolConverter.Options.build()
chemaxon.calculations.TopologyAnalyser.carboaliphaticRingCount() as of release 5.5, replaced by Ring.carboaliphaticRingCount()
chemaxon.calculations.TopologyAnalyser.carboaromaticRingCount() as of release 5.5, replaced by Ring.carboaromaticRingCount()
chemaxon.calculations.TopologyAnalyser.carboRingCount() as of release 5.5, replaced by Ring.carboRingCount()
chemaxon.calculations.TopologyAnalyser.carboRingCount(int) as of release 5.5, replaced by Ring.carboRingCount(int)
chemaxon.calculations.TopologyAnalyser.carboRings() as of release 5.5, replaced by Ring.carboRings()
chemaxon.calculations.TopologyAnalyser.carboRings(int) as of release 5.5, replaced by Ring.carboRings(int)
chemaxon.calculations.TopologyAnalyser.chainAtomCount() as of release 5.5, replaced by Ring.chainAtomCount()
chemaxon.calculations.TopologyAnalyser.chainBondCount() as of release 5.5, replaced by Ring.chainBondCount()
chemaxon.struc.MoleculeGraph.checkConsistency() As of Marvin 5.7, no replacement. Not intended for public use, it was intended only for internal debugging.
chemaxon.struc.RgMolecule.checkConsistency() As of Marvin 5.7, no replacement. Not intended for public use, it was intended only for internal debugging.
chemaxon.struc.Molecule.checkConsistency() As of Marvin 5.7, no replacement. Not intended for public use, it was intended only for internal debugging.
chemaxon.calculations.TopologyAnalyser.chiralCenterCount() as of release 5.5, replaced by Stereochemistry.chiralCenterCount()
chemaxon.calculations.TopologyAnalyser.chiralCenters() as of release 5.5, replaced by Stereochemistry.chiralCenters()
chemaxon.formats.MolConverter.Options.clean(int)
chemaxon.struc.MoleculeGraph.clean(int, String) As of Marvin 5.7, replaced by Cleaner.clean(MoleculeGraph, int, String).
chemaxon.formats.MolConverter.Options.clean(int, String)
chemaxon.struc.MoleculeGraph.clean(int, String, MProgressMonitor) As of Marvin 5.7, replaced by Cleaner.clean(MoleculeGraph, int, String, MProgressMonitor).
chemaxon.formats.MolConverter.Options.clear()
chemaxon.formats.MolConverter.Options.clone()
chemaxon.marvin.util.MolImageSize.clone()
chemaxon.struc.sgroup.SuperatomSgroup.cloneLeavingGroups(SuperatomSgroup) As of Marvin 6.2, no replacement. Not supported feature.
chemaxon.struc.RxnMolecule.clonelesscopy(MoleculeGraph) as of Marvin 6.3. Not supported feature.
chemaxon.struc.MoleculeGraph.clonelesscopy(MoleculeGraph) as of Marvin 6.3. Not supported feature.
chemaxon.struc.RgMolecule.clonelesscopy(MoleculeGraph) as of Marvin 6.3. Not supported feature.
chemaxon.struc.Molecule.clonelesscopy(MoleculeGraph) as of Marvin 6.3. Not supported feature.
chemaxon.struc.Molecule.cloneMolecule() as of Marvin 2014.09.01.0 use Molecule.clone() instead
chemaxon.marvin.io.formats.mdl.MolExport.convertMultiCenterSgroupsToData(Molecule) as of Marvin 6.1. we only export Multicenter s-groups in MOL V3000 format
chemaxon.struc.MProp.convertToString(String) As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
chemaxon.struc.MProp.convertToString(String, int) As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String).
chemaxon.struc.MDocument.Prop.convertToString(String, int) As of release 5.7, replaced by MolExporter.convertToString(MDocument, String, int)
chemaxon.struc.prop.MDoubleProp.convertToString(String, int) As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
chemaxon.struc.prop.MDoubleArrayProp.convertToString(String, int) As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
chemaxon.struc.prop.MBooleanProp.convertToString(String, int) As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String).
chemaxon.struc.prop.MHCoords3DProp.convertToString(String, int) As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
chemaxon.struc.prop.MMoleculeProp.convertToString(String, int) As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String).
chemaxon.struc.prop.MHashProp.convertToString(String, int) As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
chemaxon.struc.prop.MIntegerArrayProp.convertToString(String, int) As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
chemaxon.struc.prop.MStringProp.convertToString(String, int) As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
chemaxon.struc.prop.MIntegerProp.convertToString(String, int) As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
chemaxon.struc.prop.MObjectProp.convertToString(String, int) As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
chemaxon.struc.prop.MListProp.convertToString(String, int) As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
chemaxon.marvin.view.MDocStorage.countRecordsInFraction(double, int, MProgressMonitor)
chemaxon.marvin.alignment.AlignmentMolecule.create(byte[])
chemaxon.struc.MoleculeGraph.createBHtab() As of Marvin 6.2, no replacement. No replacement.
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(boolean, boolean) use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities. Default toolbar configuration will be used for toolbars.
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(boolean, boolean, boolean) use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities. Default toolbar configuration will be used for toolbars.
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(boolean, boolean, CodeAssistDataProvider.Context) use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities. Default toolbar configuration will be used for toolbars.
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(boolean, CodeAssistDataProvider.Context) use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) 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.
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(CodeAssistDataProvider.Context) use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) 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.
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String) use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) 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.
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, boolean) use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) 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
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, boolean, boolean) use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities. Default toolbar configuration will be used for toolbars.
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, boolean, boolean, boolean) use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities. Default toolbar configuration will be used for toolbars.
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, boolean, boolean, CodeAssistDataProvider.Context) use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities. Default toolbar configuration will be used for toolbars.
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, boolean, CodeAssistDataProvider.Context) use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) 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
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, CodeAssistDataProvider.Context) use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) 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.
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, String) use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) 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
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, String, boolean) use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities. Default toolbar configuration will be used for toolbars.
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, String, boolean, boolean) use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities. Default toolbar configuration will be used for toolbars.
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, String, boolean, CodeAssistDataProvider.Context) use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities. Default toolbar configuration will be used for toolbars.
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, String, boolean, String) use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, String, boolean, String, boolean) use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, String, boolean, String, boolean, CodeAssistDataProvider.Context) use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, String, boolean, String, CodeAssistDataProvider.Context) use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
chemaxon.marvin.beans.MarvinPane.createMenu(ResourceBundle, String) as of Marvin 3.3.1, replaced by SwingUtil.createMenu
chemaxon.formats.MFileFormat.createRecognizer(String) as of Marvin 2014.07.21.0 use MFileFormat.createRecognizer() instead
chemaxon.marvin.calculations.ResonancePlugin.createStandardizedMolecule(Molecule, boolean) Use ResonancePlugin.createStandardizedMolecule(Molecule) instead
chemaxon.marvin.calculations.TautomerizationPlugin.createStandardizedMolecule(Molecule, boolean)
chemaxon.marvin.plugin.CalculatorPlugin.createStandardizedMolecule(Molecule, boolean) Use CalculatorPlugin.createStandardizedMolecule(Molecule) instead
chemaxon.marvin.plugin.CalculatorPlugin.dehydrogenize(Molecule) MoleculeGraph.implicitizeHydrogens(int) with parameter MolAtom.ALL_H does the same.
chemaxon.struc.sgroup.SuperatomSgroup.expandOther(int, Molecule) as of Marvin 6.2. use SuperatomSgroup.expand(int) instead on the s-groups desired to be expanded
chemaxon.struc.Molecule.exportToBinFormat(String) As of Marvin 5.7, replaced by MolExporter.exportToBinFormat(Molecule, String).
chemaxon.struc.MDocument.exportToBinFormat(String) As of release 5.7, replaced by MolExporter.exportToBinFormat(MDocument, String).
chemaxon.struc.Molecule.exportToFormat(String) As of Marvin 5.7, replaced by MolExporter.exportToFormat(Molecule, String).
chemaxon.struc.MDocument.exportToFormat(String) As of release 5.7, replaced by MolExporter.exportToFormat(MDocument, String)
chemaxon.struc.Molecule.exportToObject(String) As of Marvin 5.7, replaced by MolExporter.exportToObject(Molecule, String).
chemaxon.struc.MDocument.exportToObject(String) As of release 5.7, replaced by MolExporter.exportToObject(MDocument, String)
chemaxon.struc.MoleculeGraph.findComponentIds() As of Marvin 6.0, replaced by MoleculeGraph.getFragIds(int) and MoleculeGraph.FRAG_BASIC. Usage: mol.getFragIds(MoleculeGraph.FRAG_BASIC);
chemaxon.struc.MoleculeGraph.findFrag(int, MoleculeGraph) As of Marvin 5.6, replaced by MoleculeGraph.findFrag(int, int, MoleculeGraph) and MoleculeGraph.FRAG_KEEPING_MULTICENTERS. Usage: mol.findFrag(i, MoleculeGraph.FRAG_KEEPING_MULTICENTERS, frag);
chemaxon.struc.MoleculeGraph.findFrags(Class) As of Marvin 5.6, replaced by MoleculeGraph.findFrags(Class, int) and MoleculeGraph.FRAG_KEEPING_MULTICENTERS. Usage: mol.findFrags(cl, MoleculeGraph.FRAG_KEEPING_MULTICENTERS);
chemaxon.calculations.TopologyAnalyser.fusedAliphaticRingCount() as of release 5.5, replaced by Ring.fusedAliphaticRingCount()
chemaxon.calculations.TopologyAnalyser.fusedAliphaticRingCount(int) as of release 5.5, replaced by Ring.fusedAliphaticRingCount(int)
chemaxon.calculations.TopologyAnalyser.fusedAliphaticRings() as of release 5.5, replaced by Ring.fusedAliphaticRings()
chemaxon.calculations.TopologyAnalyser.fusedAliphaticRings(int) as of release 5.5, replaced by Ring.fusedAliphaticRings(int)
chemaxon.calculations.TopologyAnalyser.fusedAromaticRingCount() as of release 5.5, replaced by Ring.fusedAromaticRingCount()
chemaxon.calculations.TopologyAnalyser.fusedAromaticRingCount(int) as of release 5.5, replaced by Ring.fusedAromaticRingCount(int)
chemaxon.calculations.TopologyAnalyser.fusedAromaticRings() as of release 5.5, replaced by Ring.fusedAromaticRings()
chemaxon.calculations.TopologyAnalyser.fusedAromaticRings(int) as of release 5.5, replaced by Ring.fusedAromaticRings(int)
chemaxon.calculations.TopologyAnalyser.fusedRingCount() as of release 5.5, replaced by Ring.fusedRingCount()
chemaxon.marvin.alignment.AlignmentMoleculeFactory.generate(int, int, Molecule, boolean, boolean) Use AlignmentMoleculeFactory.create(Molecule, AlignmentProperties.DegreeOfFreedomType) instead.
chemaxon.marvin.alignment.AlignmentMoleculeFactory.generate(int, Molecule, boolean, boolean) Use AlignmentMoleculeFactory.create(Molecule, AlignmentProperties.DegreeOfFreedomType) instead. Molecule based on the values of the setters.
chemaxon.marvin.alignment.AlignmentMoleculeFactory.generateData(int, Molecule, boolean, boolean)
chemaxon.marvin.calculations.TopologyAnalyserPlugin.getAliphaticRingCountOfSize(int) Use TopologyAnalyserPlugin.getAliphaticRingCount(int)
chemaxon.marvin.calculations.TopologyAnalyserPlugin.getAromaticRingCountOfSize(int) Use TopologyAnalyserPlugin.getAromaticRingCount(int)
chemaxon.struc.MolAtom.getAtomicNumber(String) 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.
chemaxon.struc.PeriodicSystem.getAtomicNumber(String) As of Marvin 5.9, replaced by a similar method which throws IllegalArgumentException in case of failure PeriodicSystem.findAtomicNumber(String).
chemaxon.marvin.calculations.logPPlugin.getAtomlogPHIncrement(int) Increments of implicit H-s are not calculated. Returns the same value as logPPlugin.getAtomlogPIncrement(int)
chemaxon.marvin.MolPrinter.getAtomsize() As of Marvin 5.2.2, replaced by MolPrinter.getAtomSize().
chemaxon.struc.MolAtom.getAttach() as of Marvin 6.0 replaced by SuperatomSgroup.getAttachmentPointOrders(MolAtom). If the atom takes place in a Superatom S-group then it's attachment point orders can be reached through the Superatom S-group.
chemaxon.struc.sgroup.SuperatomSgroup.getAttachAtoms() As of Marvin 6.0, replaced by SuperatomSgroup.getBoundAttachAtoms().
chemaxon.marvin.MolPrinter.getBondWidth() as of Marvin 4.1, replaced by MolPrinter.getBondSpacing()
chemaxon.marvin.beans.MarvinPane.getBondWidth() as of Marvin 4.1, replaced by MarvinPane.getBondSpacing()
chemaxon.struc.MoleculeGraph.getBtab() As of Marvin 5.4, replaced by MoleculeGraph.getBondTable() and BondTable.getMatrixArray(). Usage: molecule.getBondTable().getMatrixArray();
chemaxon.marvin.beans.MViewPane.getCanvasComponent(int) as of Marvin 3.0, replaced by getVisibleCellComponent
chemaxon.marvin.common.UserSettings.getCheckerConfigFileName() Use UserSettings.getCheckerConfigURL() instead. Deprecated in 5.12.
chemaxon.marvin.beans.MSketchPane.getCommonActions()
chemaxon.marvin.beans.MarvinPane.getCommonActions()
chemaxon.marvin.util.MoleculeUtil.getCrossingBonds(MolBond[], DPoint3, DPoint3) as of Marvin 5.11.1
chemaxon.fixers.StructureFixer.getDescription()
chemaxon.checkers.StructureChecker.getDescription() This method isn't needed anymore and will be removed in 6.0
chemaxon.struc.MolBond.getDesiredLength() since 5.11, replaced by MolBond.desiredLength(int, int, int, int).
chemaxon.struc.MolBond.getDesiredLength(boolean) since 5.11, replaced by MolBond.desiredLength(int, int, int, int).
chemaxon.struc.MoleculeGraph.getDesiredLength(int, int, int) As of Marvin 5.11, replaced by MolBond.desiredLength(int, int, int, int) and MoleculeGraph.getDim(). Usage: MolBond.desiredLength(atno1, atno2, type, getDim());
chemaxon.struc.MoleculeGraph.getDesiredLength(MolBond) As of Marvin 5.11, replaced by MolBond.desiredLength(int, int, int, int), MolBond.getType() and MoleculeGraph.getDim(). Usage: MolBond.desiredLength(atno1, atno2, b.getType, getDim());
chemaxon.marvin.MolPrinter.getDisplayQuality() since Marvin 6.4 only high quality exists
chemaxon.marvin.beans.MarvinPane.getDispQuality() always return 1. Deprecated Since Marvin 6.4.
chemaxon.checkers.StructureChecker.getEditorClassName() This method isn't needed anymore and will be removed in 6.0
chemaxon.marvin.calculations.HuckelAnalysisPlugin.getEigenVector() Use HuckelAnalysisPlugin.getHMOEigenVector()
chemaxon.marvin.calculations.HuckelAnalysisPlugin.getElectrophilicOrder(int) Use HuckelAnalysisPlugin.getHMOElectrophilicOrder(int)
chemaxon.struc.MoleculeGraph.getFragCount() As of Marvin 5.6, replaced by MoleculeGraph.getFragCount(int) and MoleculeGraph.FRAG_KEEPING_MULTICENTERS. Usage: mol.getFragCount(MoleculeGraph.FRAG_KEEPING_MULTICENTERS);
chemaxon.struc.sgroup.SuperatomSgroup.getFreeLegalAttachAtoms() As of Marvin 6.0, replaced by SuperatomSgroup.getFreeAttachAtoms().
chemaxon.jep.Evaluator.getFunctionParameterData() use Evaluator.getFunctionData()
chemaxon.struc.MoleculeGraph.getGrinv(int[], boolean) As of Marvin 4.0, replaced by MoleculeGraph.getGrinv(int[], int). Usage: getGrinv(gi, uniqueFlag ? GRINV_OLDSTEREO : 0);
chemaxon.checkers.StructureChecker.getHelpText() This method isn't needed anymore and will be removed in 6.0
chemaxon.marvin.calculations.HuckelAnalysisPlugin.getHuckelOrbitalCoefficients() Use HuckelAnalysisPlugin.getHMOHuckelOrbitalCoefficients()
chemaxon.checkers.StructureChecker.getIcon() This method isn't needed anymore and will be removed in 6.0
chemaxon.formats.MolConverter.Options.getInputCount()
chemaxon.marvin.beans.MarvinPane.getLabels() use isAtomSymbolsVisible() instead
chemaxon.formats.recognizer.Recognizer.getLastProcessedLineNum() as of Marvin 2014.07.21.0 not used
chemaxon.struc.sgroup.SuperatomSgroup.getLegalAttachAtoms() As of Marvin 6.0, replaced by SuperatomSgroup.getAllAttachAtoms().
chemaxon.checkers.StructureChecker.getLocalMenuName() This method isn't needed anymore and will be removed in 6.0
chemaxon.marvin.beans.MSketchPane.getMag() As of Marvin 2.8.1, replaced by getScale()
chemaxon.marvin.plugin.CalculatorPlugin.getMainMolecule(Molecule) Use CalculatorPlugin.createModifiedInputMolecule(Molecule) instead
chemaxon.formats.MFileFormat.getMIMEType() as of Marvin 2014.07.21.0 not used
chemaxon.fixers.StructureFixer.getName()
chemaxon.checkers.StructureChecker.getName() This method isn't needed anymore and will be removed in 6.0
chemaxon.marvin.calculations.HuckelAnalysisPlugin.getNucleophilicOrder(int) Use HuckelAnalysisPlugin.getHMONucleophilicOrder(int)
chemaxon.struc.sgroup.SuperatomSgroup.getParentSgroupGraph() as of Marvin 6.2, intended for internal use, similar functionality can be reached by SuperatomSgroup.getSgroupGraph()
chemaxon.marvin.calculations.pKaPlugin.getpKa(int, int) Use pKaPlugin.getpKaValues(int, int)
chemaxon.jep.Evaluator.getPluginIDs() use Evaluator.getFunctionData()
chemaxon.struc.MoleculeGraph.getPossibleAttachmentPoints(MolAtom) As of Marvin 6.0, replaced by SuperatomSgroup.getAttachmentPointOrders(MolAtom) and MolAtom.getAttachParentSgroup(). Usage: SuperatomSgroup group = (SuperatomSgroup)molAtom.getAttachParentSgroup()); List<Integer> orders = group.getAttachmentPointOrders(molAtom);
chemaxon.formats.MFileFormat.getPriority(String) as of Marvin 2014.07.21.0 use MFileFormat.getSubFormatPriority(String) instead
chemaxon.struc.Molecule.getProperty(String) As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String). Usage: String property = MPropHandler.convertToString(mol.properties(), key);
chemaxon.struc.Molecule.getPropertyKeys() As of Marvin 4.1, replaced by properties().getKeys() and properties().getKeyEnumeration(). One-to-one replacement is method getKeyEnumeration() but method getKeys() is simpler to use.
chemaxon.struc.MolAtom.getQuerystr() As of release 5.7, replaced by MolAtom.getQueryString()
chemaxon.struc.MolAtom.getRadical() as of Marvin 6.2. use MolAtom.getRadicalValue() instead
chemaxon.marvin.beans.MarvinPane.getReadGlobalGUIProperties() since Marvin 5.1 when this and the MarvinPane.getSaveGlobalGUIProperties() function have been merged.
chemaxon.marvin.calculations.HuckelAnalysisPlugin.getRealEigenValue() Use HuckelAnalysisPlugin.getHMORealEigenValue()
chemaxon.marvin.calculations.TopologyAnalyserPlugin.getRingCountOfSize(int) Use TopologyAnalyserPlugin.getRingCount(int)
chemaxon.marvin.calculations.TopologyAnalyserPlugin.getRingSystemCountOfSize(int) Use TopologyAnalyserPlugin.getRingSystemCount(int)
chemaxon.marvin.beans.MarvinPane.getSetColor(int) as of Marvin 3.3, replaced by getAtomSetColor
chemaxon.marvin.beans.MSketchPane.getSimpView() as of Marvin 3.5, replaced by MSketchPane.isBondDraggedAlong()
chemaxon.marvin.calculations.pKaPlugin.getSortedValues(int, double[], int[]) Use pKaPlugin.getMacropKaValues(int,double[],int[]) instead
chemaxon.struc.MoleculeGraph.getSSSRBondSetInLong() as of 15.09.2014, use MoleculeGraph.getSSSRBondSet() instead
chemaxon.struc.MoleculeGraph.getStereo2(MolBond) as of Marvin 6.3 replaced by MoleculeGraph.getEZStereo(MolBond).
chemaxon.struc.MPropertyContainer.getString(String) As of Marvin 5.7, replaced by MPropHandler.convertToString(MPropertyContainer, String)
chemaxon.marvin.calculations.TautomerizationPlugin.getStructures() since Marvin 5.9 replaced by TautomerizationPlugin.getStructure(int)
chemaxon.util.iterator.MoleculeIterator.getThrowable() Not used. MoleculeIterator.next() throws NoSuchElementException in case of error.
chemaxon.marvin.calculations.HuckelAnalysisPlugin.getTotalPiEnergy() Use HuckelAnalysisPlugin.getHMOTotalPiEnergy()
chemaxon.marvin.calculations.TPSAPlugin.getTPSA() as of Marvin 4.1, replaced by getSurfaceArea()
chemaxon.struc.Sgroup.getType() as of Marvin 6.3. use Sgroup.getSgroupType() instead. Note that in case of AminoAcidSgroups returned Sgroup.ST_SUPERATOM but Sgroup.getSgroupType() will return SgroupType.AMINOACID.
chemaxon.struc.MoleculeGraph.getValenceCheckState() 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;
chemaxon.struc.graphics.MEFlow.getValidSinkAtomPairsForMolecule(Molecule, MolAtom) As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSinkAtomPairs(Molecule, MolAtom) .
chemaxon.struc.graphics.MEFlow.getValidSinkAtomPairsForMolecule(Molecule, MolBond) As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSinkAtomPairs(Molecule, MolBond) .
chemaxon.struc.graphics.MEFlow.getValidSinkAtomsForMolecule(Molecule, MolAtom) As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSinkAtoms(Molecule, MolAtom) .
chemaxon.struc.graphics.MEFlow.getValidSinkAtomsForMolecule(Molecule, MolBond) As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSinkAtoms(Molecule, MolBond) .
chemaxon.struc.graphics.MEFlow.getValidSinkBondsForMolecule(Molecule, MolAtom) As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSinkBonds(Molecule, MolAtom) .
chemaxon.struc.graphics.MEFlow.getValidSinkBondsForMolecule(Molecule, MolBond) As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSinkBonds(Molecule, MolBond) .
chemaxon.struc.graphics.MEFlow.getValidSourceAtomPairsForMolecule(Molecule) As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSourceAtomPairs(Molecule) .
chemaxon.struc.graphics.MEFlow.getValidSourceAtomsForMolecule(Molecule) As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSourceAtoms(Molecule) .
chemaxon.struc.graphics.MEFlow.getValidSourceBondsForMolecule(Molecule) As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSourceBonds(Molecule) .
com.chemaxon.calculations.stereoanal.stereocenters.AtropStereoCenter.getValue() As of Marvin 14.9.15, replaced by AtropStereoCenter.getCIPValue().
com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter.getValue() As of Marvin 14.9.15, replaced by AxialStereoCenter.getCIPValue().
com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter.getValue() As of Marvin 14.9.15, replaced by TetrahedralStereoCenter.getCIPValue().
com.chemaxon.calculations.stereoanal.stereocenters.StereoCenter.getValue() As of Marvin 14.9.15, replaced by StereoCenter.getCIPValue().
com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter.getValue() As of Marvin 14.9.15, replaced by CisTransStereoCenter.getCIPValue().
chemaxon.formats.recognizer.PeptideRecognizer.guessPeptideFormat(String) as of Marvin 2014.07.21.0 intended for internal use
chemaxon.struc.MolAtom.hasSMARTSProps() As of release 5.7, replaced by SmartsAtomQuerifier.hasSMARTSProps(MolAtom atom)
chemaxon.struc.MolAtom.hasSMARTSPropsExcluding(String) As of release 5.7, replaced by SmartsAtomQuerifier.hasSMARTSPropsExcluding(MolAtom atom, String exclude)
chemaxon.calculations.TopologyAnalyser.heteroaliphaticRingCount() as of release 5.5, replaced by Ring.heteroaliphaticRingCount()
chemaxon.calculations.TopologyAnalyser.heteroaliphaticRingCount(int) as of release 5.5, replaced by Ring.heteroaliphaticRingCount(int)
chemaxon.calculations.TopologyAnalyser.heteroaliphaticRings() as of release 5.5, replaced by Ring.heteroaliphaticRings()
chemaxon.calculations.TopologyAnalyser.heteroaliphaticRings(int) as of release 5.5, replaced by Ring.heteroaliphaticRings(int)
chemaxon.calculations.TopologyAnalyser.heteroaromaticRingCount() as of release 5.5, replaced by Ring.heteroaromaticRingCount()
chemaxon.calculations.TopologyAnalyser.heteroaromaticRingCount(int) as of release 5.5, replaced by Ring.heteroaromaticRingCount(int)
chemaxon.calculations.TopologyAnalyser.heteroaromaticRings() as of release 5.5, replaced by Ring.heteroaromaticRings()
chemaxon.calculations.TopologyAnalyser.heteroaromaticRings(int) as of release 5.5, replaced by Ring.heteroaromaticRings(int)
chemaxon.calculations.TopologyAnalyser.heteroRingCount() as of release 5.5, replaced by Ring.heteroRingCount()
chemaxon.calculations.TopologyAnalyser.heteroRingCount(int) as of release 5.5, replaced by Ring.heteroRingCount(int)
chemaxon.calculations.TopologyAnalyser.heteroRings() as of release 5.5, replaced by Ring.heteroRings()
chemaxon.calculations.TopologyAnalyser.heteroRings(int) as of release 5.5, replaced by Ring.heteroRings(int)
chemaxon.struc.MoleculeGraph.hydrogenize(boolean) As of Marvin 5.7, replaced by Hydrogenize.convertImplicitHToExplicit(MoleculeGraph) and Hydrogenize.convertExplicitHToImplicit(MoleculeGraph).
chemaxon.struc.MoleculeGraph.implicitizeHydrogens(int) As of Marvin 5.7, replaced by Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, int). Usage: Hydrogenize.convertExplicitHToImplicit(molecule, f);
chemaxon.struc.MoleculeGraph.implicitizeHydrogens(int, MolAtom[]) As of Marvin 5.7, replaced by Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int). Usage: Hydrogenize.convertExplicitHToImplicit(mol, atoms, f);
chemaxon.struc.MoleculeGraph.implicitizeHydrogens(int, MolAtom[], boolean) As of Marvin 5.7, replaced by Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean). Usage: Hydrogenize.convertExplicitHToImplicit(mol, atoms, f, check);
chemaxon.struc.MoleculeGraph.implicitizeHydrogens0(int, MolAtom[], boolean) As of Marvin 5.7, replaced by Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean). Usage: Hydrogenize.convertExplicitHToImplicit(mol, atoms, f, check);
chemaxon.struc.Molecule.implicitizeHydrogens0(int, MolAtom[], boolean) As of Marvin 5.7, replaced by Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean). Usage: Hydrogenize.convertExplicitHToImplicit(mol, atoms, f, check);
chemaxon.formats.MolImporter.importMol(String, String, String) (Since Marvin 5.5) There is no need to specify an encoding for a String input. Instead, if you have a String to import, call MolImporter.importMol(String,String); if you have a byte array, call MolImporter.importMol(byte[], String, String).
chemaxon.formats.MolImporter.importMol(String, String, String, Molecule) (Since Marvin 5.5) There is no need to specify an encoding for a String input. Instead, if you have a String to import, call MolImporter.importMol(String, String); if you have a byte array, call MolImporter.importMol(byte[], String, String, Molecule).
chemaxon.marvin.beans.MarvinPane.initAction(Action, ResourceBundle, String, KeyStroke) as of Marvin 3.3.1, replaced by SwingUtil.initAction
chemaxon.marvin.beans.MarvinPane.initButton(AbstractButton, ResourceBundle, String) as of Marvin 3.3.1, replaced by SwingUtil.initButton
chemaxon.marvin.util.SwingUtil.initCtrlShortcutForMac(JMenuItem) does nothing.
chemaxon.marvin.util.SwingUtil.initInApplet() does nothing.
chemaxon.struc.MoleculeGraph.insertAtom(int, MolAtom) as of Marvin 6.2, may constructs inconsistent MoleculeGraph. Similar functionality is performed by MoleculeGraph.add(MolAtom).
chemaxon.struc.MoleculeGraph.insertBond(int, MolBond) as of Marvin 6.2, may constructs inconsistent MoleculeGraph. Similar functionality is performed by MoleculeGraph.add(MolBond).
chemaxon.calculations.TopologyAnalyser.isAliphaticAtom(int) as of release 5.5, replaced by Ring.isAliphaticAtom(int)
chemaxon.calculations.TopologyAnalyser.isAromaticAtom(int) as of release 5.5, replaced by Ring.isAromaticAtom(int)
chemaxon.marvin.alignment.AlignmentMoleculeFactory.isAromatize()
chemaxon.calculations.TopologyAnalyser.isAsymmetricAtom(int) as of release 5.5, replaced by Stereochemistry.isAsymmetricAtom(int)
chemaxon.struc.RxnMolecule.isAtom() As of Marvin 14.7.7, no replacement. Not supported feature.
chemaxon.struc.MoleculeGraph.isAtom() As of Marvin 14.7.7, no replacement. Not supported feature.
chemaxon.struc.RgMolecule.isAtom() As of Marvin 14.7.7, no replacement. Not supported feature.
chemaxon.marvin.MolPrinter.isAtomNumbersVisible() in 6.2.0. Use getAtomNumberingType instead.
chemaxon.marvin.beans.MarvinPane.isAtomNumbersVisible() in 6.2.0. Use getAtomNumberingType() instead.
chemaxon.struc.RxnMolecule.isBond() As of Marvin 14.7.7, no replacement. Not supported feature.
chemaxon.struc.MoleculeGraph.isBond() As of Marvin 14.7.7, no replacement. Not supported feature.
chemaxon.struc.RgMolecule.isBond() As of Marvin 14.7.7, no replacement. Not supported feature.
chemaxon.calculations.hydrogenize.Hydrogenize.isBridgeHeadAtom(MoleculeGraph, int) as of Marvin 5.11.1, replaced by TopologyUtil.isBridgeHeadAtom(MoleculeGraph, int)
chemaxon.calculations.TopologyAnalyser.isChainAtom(int) as of release 5.5, replaced by Ring.isChainAtom(int)
chemaxon.calculations.TopologyAnalyser.isChainBond(int) as of release 5.5, replaced by Ring.isChainBond(int)
chemaxon.calculations.TopologyAnalyser.isChiral() as of release 5.5, replaced by Stereochemistry.isChiral()
chemaxon.calculations.TopologyAnalyser.isChiralCenter(int) as of release 5.5, replaced by Stereochemistry.isChiralCenter(int)
chemaxon.marvin.alignment.AlignmentMoleculeFactory.isDehidrogenize() The explicit Hydrogens are not removed from the original input structure. No need to use.
chemaxon.marvin.MolPrinter.isExplicitHVisible() As of Marvin 5.5.1 this method always returns true. This method will be removed in a future release.
chemaxon.marvin.MolPrinter.isEzVisible() As of Marvin 5.2.2, replaced by MolPrinter.isEZLabelsVisible()
chemaxon.struc.sgroup.SuperatomSgroup.isFreeLegalAttachAtom(MolAtom) As of Marvin 6.0, replaced by SuperatomSgroup.isFreeAttachAtom(MolAtom a).
chemaxon.formats.MolImporter.isGrabbingEnabled() as of Marvin 6.2. It has no effect on the code.
chemaxon.marvin.beans.MarvinPane.isGrinv() as of Marvin 3.5, use isGrinvVisible() instead
chemaxon.struc.Molecule.isGUIContracted() as of Marvin 6.2 replaced by Molecule.hasContractedSgroup()
chemaxon.struc.sgroup.SuperatomSgroup.isLegalAttachment(MolAtom) As of Marvin 6.0, replaced by SuperatomSgroup.isAttachmentAtom(MolAtom).
chemaxon.struc.MoleculeGraph.isMolecule() as of Marvin 14.7.7, no replacement. Usage: use myObject instanceof Molecule instead
chemaxon.marvin.beans.MSketchPane.isReactionErrorVisible() 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?
chemaxon.struc.MolBond.isRemovable() As of Marvin 6.2, no replacement. Not supported feature.
chemaxon.struc.MoleculeGraph.isRing() As of Marvin 14.7.7, no replacement. Not supported feature.
chemaxon.calculations.TopologyAnalyser.isRingAtom(int) as of release 5.5, replaced by Ring.isRingAtom(int)
chemaxon.calculations.TopologyAnalyser.isRingBond(int) as of release 5.5, replaced by Ring.isRingBond(int)
chemaxon.checkers.RgroupReferenceErrorChecker.isSearchMissingRatom()
chemaxon.checkers.RgroupReferenceErrorChecker.isSearchSelfReference()
chemaxon.struc.Molecule.isSgroup() As of Marvin 14.7.7, no replacement. Not supported feature.
chemaxon.struc.graphics.MEFlow.isValidSourceAndSinkForMolecule(Object, Object, Molecule) As of Marvin 6.1, replaced by EFlowPlacementValidators.isValidFlow(MolAtom, MolAtom, Molecule) or one of the other implementations instead.
chemaxon.struc.graphics.MEFlow.isValidSourceForMolecule(Object, Molecule) As of Marvin 6.1, replaced by EFlowPlacementValidators.isValidSource(MolAtom, Molecule) or EFlowPlacementValidators.isValidSource(MolAtom[], Molecule) or EFlowPlacementValidators.isValidSource(MolBond, Molecule) .
chemaxon.calculations.TopologyAnalyser.largestRing() as of release 5.5, replaced by Ring.largestRing()
chemaxon.calculations.TopologyAnalyser.largestRingSize() as of release 5.5, replaced by Ring.largestRingSize()
chemaxon.calculations.TopologyAnalyser.largestRingSizeOfAtom(int) as of release 5.5, replaced by Ring.largestRingSizeOfAtom(int)
chemaxon.calculations.TopologyAnalyser.largestRingSystem() as of release 5.5, replaced by Ring.largestRingSystem()
chemaxon.calculations.TopologyAnalyser.largestRingSystemSize() as of release 5.5, replaced by Ring.largestRingSystemSize()
chemaxon.marvin.beans.MViewPane.makeHelpMenu(Container) As of Marvin 3.4, MarvinPane.addHelpMenu(java.awt.Container) should be used.
chemaxon.marvin.beans.MViewPane.makeToolsMenu() As of Marvin 3.4, MarvinPane.addToolsMenu(java.awt.Container) should be used.
chemaxon.struc.RxnMolecule.mergeAtoms(MolAtom, MolAtom) As of Marvin 6.2, use MergeUtil.mergeAtoms(MolAtom, MolAtom, boolean) instead.
chemaxon.struc.MoleculeGraph.mergeAtoms(MolAtom, MolAtom) As of Marvin 6.2, use MergeUtil.mergeAtoms(MolAtom, MolAtom, boolean) instead.
chemaxon.struc.RgMolecule.mergeAtoms(MolAtom, MolAtom) As of Marvin 6.2, use MergeUtil.mergeAtoms(MolAtom, MolAtom, boolean) instead.
chemaxon.struc.Molecule.mergeAtoms(MolAtom, MolAtom) As of Marvin 6.2, use MergeUtil.mergeAtoms(MolAtom, MolAtom, boolean) instead.
chemaxon.util.iterator.IteratorFactory.AtomIterator.nextAtom() As of Marvin 6.2, Use IteratorFactory.AtomIterator.next() instead.
chemaxon.util.iterator.IteratorFactory.AtomNeighbourIterator.nextAtom() As of Marvin 6.2, Use IteratorFactory.AtomNeighbourIterator.next() instead.
chemaxon.util.iterator.IteratorFactory.BondIterator.nextBond() As of Marvin 6.2, Use IteratorFactory.BondIterator.next() instead.
chemaxon.util.iterator.IteratorFactory.BondNeighbourIterator.nextBond() As of Marvin 6.2, Use IteratorFactory.BondNeighbourIterator.next() instead.
chemaxon.util.iterator.IteratorFactory.RxnComponentIterator.nextComponent() As of Marvin 6.2, Use IteratorFactory.RxnComponentIterator.next() instead.
chemaxon.util.iterator.IteratorFactory.RgComponentIterator.nextComponent() As of Marvin 6.2, Use IteratorFactory.RgComponentIterator.next() instead.
chemaxon.struc.MolAtom.numOf(String) As of Marvin 5.9, replaced by a similar method PeriodicSystem.findAtomicNumber(String). The recommended method does not work for symbol that does not represent a chemical element (e.g. R-atom, any atom), as this method should not have worked on them either.
chemaxon.struc.MDocument.parseMRV(String) As of release 5.7, replaced by MolImporter.parseMRV(String)
chemaxon.struc.MoleculeGraph.partialClean(int, int[], String) As of Marvin 5.7, replaced by Cleaner.partialClean(MoleculeGraph, int, int[], String).
chemaxon.struc.MoleculeGraph.partialClean(Molecule[], String) As of Marvin 5.7, replaced by Cleaner.partialClean(Molecule, Molecule[], String).
chemaxon.struc.MoleculeGraph.partialClean(MoleculeGraph, int[], String) As of Marvin 5.7, replaced by Cleaner.partialClean(MoleculeGraph, MoleculeGraph, int[], String).
chemaxon.marvin.io.MolExportModule.preconvert(MoleculeGraph, boolean, int, boolean) Marvin 6.2 use MolExportModule.preconvert(chemaxon.struc.Molecule, boolean, int, boolean) instead
com.chemaxon.calculations.stereoanal.stereocenters.AtomSelection.primaryAtomIndexes()
chemaxon.formats.MolImporter.read(Molecule) as of Marvin 14.7.7. use MolImporter.read() instead
chemaxon.formats.MolImporter.readDoc(MDocument, Molecule) as of Marvin 14.7.7. useMolImporter.nextDoc() instead
chemaxon.formats.MolImporter.readMol(Molecule) as of Marvin 14.7.7. use MolImporter.read() instead
chemaxon.struc.MoleculeGraph.removeExplicitLonePairs() As of Marvin 5.7, replaced by Hydrogenize.convertExplicitLonePairsToImplicit(MoleculeGraph).
chemaxon.calculations.hydrogenize.Hydrogenize.removeHAtoms(MoleculeGraph) since Marvin 5.11 use convertExplicitHToImplicit(MoleculeGraph) instead
chemaxon.calculations.hydrogenize.Hydrogenize.removeHAtoms(MoleculeGraph, int) since Marvin 5.11 use convertExplicitHToImplicit(MoleculeGraph, int) instead
chemaxon.calculations.hydrogenize.Hydrogenize.removeHAtoms(MoleculeGraph, MolAtom[], int) since Marvin 5.11 use convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int) instead
chemaxon.calculations.hydrogenize.Hydrogenize.removeHAtoms(MoleculeGraph, MolAtom[], int, boolean) since Marvin 5.11 use convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean) instead
chemaxon.struc.sgroup.SuperatomSgroup.removeLeavingGroup(int) As of Marvin 6.2, no replacement. Not supported feature.
chemaxon.calculations.hydrogenize.Hydrogenize.removeLonePairs(MoleculeGraph) since Marvin 5.11 use convertExplicitLonePairsToImplicit(MoleculeGraph) instead
chemaxon.struc.MObject.removeNotify() As of Marvin 6.1, replaced by MObject.removeNotify(MDocument).
chemaxon.struc.RxnMolecule.replaceBond(MolBond, MolBond) as of Marvin 6.2, may constructs inconsistent MoleculeGraph. Use MoleculeGraph.removeBond(MolBond) for bond removal and RxnMolecule.add(MolBond) for adding a new bond to the molecule.
chemaxon.struc.MoleculeGraph.replaceBond(MolBond, MolBond) as of Marvin 6.2, may constructs inconsistent MoleculeGraph. Use MoleculeGraph.removeBond(MolBond) for removal and MoleculeGraph.add(MolBond) for adding a new bond to the molecule.
chemaxon.struc.RgMolecule.replaceBond(MolBond, MolBond) as of Marvin 6.2, may constructs inconsistent MoleculeGraph. Use MoleculeGraph.removeBond(MolBond) for bond removal and RgMolecule.add(MolBond) for adding a new bond to the molecule.
chemaxon.struc.sgroup.MulticenterSgroup.replaceMulticenterAtom(MolAtom, MolAtom) as of Marvin 2014.08.25.0, use MulticenterSgroup.setCentralAtom(chemaxon.struc.MolAtom) instead
chemaxon.calculations.TopologyAnalyser.ringAtomCount() as of release 5.5, replaced by Ring.ringAtomCount()
chemaxon.calculations.TopologyAnalyser.ringBondCount() as of release 5.5, replaced by Ring.ringBondCount()
chemaxon.calculations.TopologyAnalyser.ringCount() as of release 5.5, replaced by Ring.ringCount()
chemaxon.calculations.TopologyAnalyser.ringCount(int) as of release 5.5, replaced by Ring.ringCount(int)
chemaxon.calculations.TopologyAnalyser.ringCountOfAtom(int) as of release 5.5, replaced by Ring.ringCountOfAtom(int)
chemaxon.calculations.TopologyAnalyser.rings() as of release 5.5, replaced by Ring.rings(int)
chemaxon.calculations.TopologyAnalyser.rings(int) as of release 5.5, replaced by Ring.rings(int)
chemaxon.calculations.TopologyAnalyser.ringSystemCount() as of release 5.5, replaced by Ring.ringSystemCount()
chemaxon.calculations.TopologyAnalyser.ringSystemCount(int) as of release 5.5, replaced by Ring.ringSystemCount(int)
chemaxon.calculations.TopologyAnalyser.ringSystems() as of release 5.5, replaced by Ring.ringSystems()
chemaxon.calculations.TopologyAnalyser.ringSystems(int) as of release 5.5, replaced by Ring.ringSystems(int)
chemaxon.struc.graphics.MPolyline.rotate(DPoint3, double, DPoint3) As of Marvin 6.1, replaced by CTransform3D.setRotation(double, double, double, double) and CTransform3D.setRotationCenter(DPoint3).
com.chemaxon.calculations.stereoanal.stereocenters.AtomSelection.secondaryAtomIndexes()
chemaxon.marvin.alignment.AlignmentMoleculeFactory.setAromatize(boolean) The original input structure is not aromatized. No need to use.
chemaxon.struc.RxnMolecule.setAtom(int, MolAtom) As of Marvin 6.2, may constructs inconsistent MoleculeGraph. Use MoleculeGraph.removeAtom(MolAtom) and RxnMolecule.add(MolAtom) to modify the structure.
chemaxon.struc.MoleculeGraph.setAtom(int, MolAtom) as of Marvin 6.2, may constructs inconsistent MoleculeGraph. Use MoleculeGraph.removeAtom(int) for atom removal and MoleculeGraph.add(MolAtom) for adding new MolAtoms.
chemaxon.struc.RgMolecule.setAtom(int, MolAtom) as of Marvin 6.2, may constructs inconsistent MoleculeGraph. Use MoleculeGraph.removeAtom(MolAtom) and RgMolecule.add(MolAtom) to modify the structure.
chemaxon.marvin.MolPrinter.setAtomNumbersVisible(boolean) in 6.2.0. Use setAtomNumberingType() instead.
chemaxon.marvin.beans.MarvinPane.setAtomNumbersVisible(boolean) in 6.2.0. Use setAtomNumberingType() instead
chemaxon.marvin.MolPrinter.setAtomsize(double) As of Marvin 5.2.2, replaced by MolPrinter.setAtomSize(double).
chemaxon.struc.MolAtom.setAttach(int) as of Marvin 6.0, replaced by SuperatomSgroup.addAttachmentPoint(MolAtom), or SuperatomSgroup.addAttachmentPoint(MolAtom, int).
chemaxon.struc.MolAtom.setAttach(int, Sgroup) as of Marvin 6.0, replaced by SuperatomSgroup.addAttachmentPoint(MolAtom), or SuperatomSgroup.addAttachmentPoint(MolAtom, int).
chemaxon.struc.RxnMolecule.setBond(int, MolBond) as of Marvin 6.2, may constructs inconsistent MoleculeGraph. Use MoleculeGraph.removeBond(MolBond) for bond removal and RxnMolecule.add(MolBond) for adding a new bond to the molecule.
chemaxon.struc.MoleculeGraph.setBond(int, MolBond) as of Marvin 6.2, may constructs inconsistent MoleculeGraph. Use MoleculeGraph.removeBond(MolBond) for bond removal and MoleculeGraph.add(MolBond) for adding a new bond to the molecule.
chemaxon.struc.RgMolecule.setBond(int, MolBond) as of Marvin 6.2, may constructs inconsistent MoleculeGraph. Use MoleculeGraph.removeBond(MolBond) for bond removal and RgMolecule.add(MolBond) for adding a new bond to the molecule.
chemaxon.struc.SelectionMolecule.setBond(int, MolBond) as of Marvin 6.2. Use SelectionMolecule.removeBond(MolBond) for bond removal and SelectionMolecule.add(MolBond) for adding a new bond to the molecule.
chemaxon.marvin.MolPrinter.setBondWidth(double) as of Marvin 4.1, replaced by MolPrinter.setBondSpacing(double)
chemaxon.marvin.beans.MarvinPane.setBondWidth(double) as of Marvin 4.1, replaced by MarvinPane.setBondSpacing(double)
chemaxon.marvin.calculations.pKaPlugin.setCalcAlways(boolean) replaced by setModel(int)
chemaxon.marvin.common.UserSettings.setCheckerConfigFileName(String) Use UserSettings.setCheckerConfigURL(String) instead. Deprecated in 5.12 Sets the name of the configuration file for StructureChecker in marvin sketch
chemaxon.marvin.common.UserSettings.setCleanHOption(boolean) As of release 5.4, replaced by UserSettings.setCleanHOptionEnabled(boolean)
chemaxon.marvin.calculations.TautomerizationPlugin.setCleanResultStructures(boolean) obsolate method
chemaxon.struc.sgroup.SuperatomSgroup.setCrossingBondType(int, BondType) As of Marvin 6.2, no replacement. Not supported feature.
chemaxon.marvin.alignment.AlignmentMoleculeFactory.setDehidrogenize(boolean) The explicit Hydrogens are not removed from the original input structure. No need to use.
chemaxon.fixers.StructureFixer.setDescription(String)
chemaxon.checkers.StructureChecker.setDescription(String) This method isn't needed anymore and will be removed in 6.0
chemaxon.marvin.MolPrinter.setDisplayQuality(int) since Marvin 6.4 only high quality exists
chemaxon.marvin.beans.MarvinPane.setDispQuality(int) Does nothing. Deprecated since Marvin 6.4.
chemaxon.formats.MolConverter.Options.setEncodings(String)
chemaxon.marvin.MolPrinter.setExplicitH(boolean) As of Marvin 5.5.1 this method does nothing. This method will be removed in a future release.
chemaxon.marvin.MolPrinter.setExplicitHVisible(boolean) As of Marvin 5.5.1 this method does nothing. This method will be removed in a future release.
chemaxon.marvin.MolPrinter.setEzVisible(boolean) As of Marvin 5.2.2, replaced by MolPrinter.setEZLabelsVisible(boolean)
chemaxon.formats.MolConverter.Options.setFields(String[])
chemaxon.marvin.alignment.AlignmentMoleculeFactory.setForcedFlexible(boolean) use AlignmentProperties.DegreeOfFreedomType.TRANSLATE_ROTATE_FLEXIBLE_EXTRA to get the same behavior in the AlignmentMoleculeFactory.create(chemaxon.marvin.alignment.ShapeData, chemaxon.marvin.alignment.AlignmentProperties.DegreeOfFreedomType) methods.
chemaxon.struc.MolAtom.setForSpecIsotopeSymbol(String) as of Marvin 6.3. use MolAtom.setSpecIsotopeSymbolPreferred(boolean) and MolAtom.setMassno(int) instead.
chemaxon.formats.MolImporter.setGrabbingEnabled(boolean) as of Marvin 6.2. It has no effect on the code.
chemaxon.marvin.beans.MarvinPane.setGrinv(boolean) as of Marvin 3.5, use setGrinvVisible(boolean) instead
chemaxon.struc.Molecule.setGUIContracted(boolean) as of Marvin 6.2, use Molecule.expandSgroups(int) or Molecule.contractSgroups(int) instead with option parameter Expandable.LEAVE_COORDS_UNCHANGED
chemaxon.struc.Molecule.setGUIContracted(boolean, int) as of Marvin 6.2, use Molecule.expandSgroups(int) or Molecule.contractSgroups(int) instead with option parameter Expandable.LEAVE_COORDS_UNCHANGED
chemaxon.marvin.calculations.HBDAPlugin.setGUIMode(boolean)
chemaxon.struc.MDocument.setGUIProperyContainer(MPropertyContainer) As of Marvin 6.1, replaced by MDocument.setGUIPropertyContainer(MPropertyContainer).
chemaxon.struc.Sgroup.setGUIStateRecursively(boolean) as of Marvin 6.2 use Molecule.setGUIContracted(boolean), or Molecule.setGUIContracted(boolean, int) methods for such functionality
chemaxon.struc.Sgroup.setGUIStateRecursively(boolean, int) as of Marvin 6.2 use Molecule.setGUIContracted(boolean), or Molecule.setGUIContracted(boolean, int) methods for such functionality
chemaxon.checkers.StructureChecker.setHelpText(String) This method isn't needed anymore and will be removed in 6.0
chemaxon.checkers.StructureChecker.setIcon(Icon) This method isn't needed anymore and will be removed in 6.0
chemaxon.struc.MolAtom.setImplicitHBasedOnValence(Valence) as of Marvin 6.0.1, exists only for internal usage Usage: Internal usage only.
chemaxon.marvin.calculations.ResonancePlugin.setInputMoleculeModified(boolean) Not used.
chemaxon.marvin.calculations.TautomerizationPlugin.setInputMoleculeModified(boolean) Not used.
chemaxon.marvin.beans.MarvinPane.setLabels(boolean) use setAtomSymbolsVisible(v) instead
chemaxon.struc.sgroup.SuperatomSgroup.setLeavingGroup(int, int) As of Marvin 6.2, no replacement. Not supported feature.
chemaxon.struc.sgroup.SuperatomSgroup.setLeavingGroup(int, int, String) As of Marvin 6.2, no replacement. Not supported feature.
chemaxon.struc.sgroup.SuperatomSgroup.setLeavingGroup(int, int, String, BondType) As of Marvin 6.2, no replacement. Not supported feature.
chemaxon.struc.sgroup.SuperatomSgroup.setLeavingGroupAlternativeName(int, String) As of Marvin 6.2, no replacement. Not supported feature.
chemaxon.core.calculations.valencecheck.ValenceCheckOptions.Builder.setLocalAromatiChecking(boolean) since Marvin 14.7.7, Use ValenceCheckOptions.Builder.setLocalAromaticChecking(boolean) instead.
chemaxon.checkers.StructureChecker.setLocalMenuName(String) This method isn't needed anymore and will be removed in 6.0
chemaxon.marvin.beans.MViewPane.setM(int, File, String) 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.
chemaxon.marvin.beans.MViewPane.setM(int, String) 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.
chemaxon.marvin.beans.MViewPane.setM(int, String, String) 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.
chemaxon.marvin.beans.MSketchPane.setMag(double) As of Marvin 2.8.1, replaced by setScale()
chemaxon.marvin.calculations.AlignmentPlugin.setMinimumCommonSize(int)
chemaxon.marvin.alignment.Alignment.setMinimumCommonSize(int)
chemaxon.marvin.beans.MSketchPane.setMol(Molecule, boolean) use MSketchPane.setMol(Molecule) instead of this method.
chemaxon.calculations.ElementalAnalyser.setMolecule(Smolecule) as of Marvin 6.0, replaced by ElementalAnalyser.setMolecule(MoleculeGraph mol).
chemaxon.checkers.StructureChecker.setMoreErrorMessage(String) This method isn't needed anymore and will be removed in 6.0
chemaxon.fixers.StructureFixer.setName(String)
chemaxon.checkers.StructureChecker.setName(String) This method isn't needed anymore and will be removed in 6.0
chemaxon.checkers.StructureChecker.setNoErrorMessage(String) This method isn't needed anymore and will be removed in 6.0
chemaxon.checkers.StructureChecker.setOneErrorMessage(String) This method isn't needed anymore and will be removed in 6.0
chemaxon.formats.MolConverter.Options.setOutput(File, String)
chemaxon.formats.MolConverter.Options.setOutput(OutputStream, String)
chemaxon.formats.MolConverter.Options.setOutput(String, String)
chemaxon.formats.MolConverter.Options.setOutputFlags(int)
chemaxon.marvin.calculations.ResonancePlugin.setpH(double) As of Marvin 5.0 pH effect is not considered
chemaxon.jep.context.ReactionContext.setProductAtomsByMap(MolAtom[]) use ReactionContext.setReaction(RxnMolecule) instead. Sets the map -> product atom array.
chemaxon.jep.context.ReactionContext.setProducts(Molecule[]) Use ReactionContext.setReaction(RxnMolecule) instead. Sets the products.
chemaxon.struc.MolAtom.setQuerystr(String) As of release 5.7, replaced by SmartsAtomQuerifier.setQuerystr(MolAtom atom, String s) and MolAtom.setQueryString(String).
chemaxon.struc.MolAtom.setQuerystr(String, int) As of release 5.7, replaced by SmartsAtomQuerifier.setQuerystr(MolAtom atom, String s, int options) and MolAtom.setQueryString(String).
chemaxon.struc.MolAtom.setRadical(int) as of Marvin 6.2. Use MolAtom.setRadicalValue(AtomProperty.Radical) instead.
chemaxon.jep.context.ReactionContext.setReactantAtomsByMap(MolAtom[]) use ReactionContext.setReaction(RxnMolecule) instead. Sets the map -> reactant atom array.
chemaxon.jep.context.ReactionContext.setReactants(Molecule[]) Use ReactionContext.setReaction(RxnMolecule) instead. Sets the reactants.
chemaxon.checkers.RgroupReferenceErrorChecker.setSearchMissingRatom(boolean)
chemaxon.checkers.RgroupReferenceErrorChecker.setSearchSelfReference(boolean)
chemaxon.marvin.beans.MarvinPane.setSetColor(int, Color) as of Marvin 3.3, replaced by setAtomSetColor
chemaxon.marvin.beans.MViewPane.setSetSeq(int, int, int) as of Marvin 3.3, replaced by setAtomSetSeq
chemaxon.marvin.beans.MSketchPane.setSimpView(int) as of Marvin 3.5, replaced by MSketchPane.setBondDraggedAlong(boolean)
chemaxon.struc.MolAtom.setSMARTS(String) As of release 5.7, replaced by SmartsAtomQuerifier.setSMARTS(MolAtom atom, String s)
chemaxon.marvin.calculations.pKaPlugin.setTakeMajorTatomericForm(boolean) Use pKaPlugin.setConsiderTautomerization(boolean)
chemaxon.marvin.calculations.logPPlugin.setTakeMajorTatomericForm(boolean) Use logPPlugin.setConsiderTautomerization(boolean)
chemaxon.marvin.calculations.TautomerizationPlugin.setTakeMostStableTautomer(boolean) Not used.
chemaxon.marvin.alignment.AlignmentMoleculeFactory.setUseOriginal(boolean) always false: Molecule is always converted before alignment, but coordinates are written back to the original one.
chemaxon.struc.MoleculeGraph.setValenceCheckState(MoleculeGraph.ValenceCheckState) As of Marvin 6.0, replaced by MoleculeGraph.setValenceCheckOptions(ValenceCheckOptions) and MoleculeGraph.setValenceCheckEnabled(boolean). Usage: // Same as setValenceCheckState(ValenceCheckState.OFF): setValenceCheckEnabled(false); // Same as setValenceCheckState(ValenceCheckState.AMBIGUOUS_AROMATIC_ATOMS_IGNORED): setValenceCheckOptions(ValenceCheckOptions.DEFAULT); // Same as setValenceCheckState(ValenceCheckState.FULL): setValenceCheckOptions(new ValenceCheckOptions(false, true));
chemaxon.struc.Sgroup.setXState(int, int) as of Marvin 6.2, use Sgroup.setXState(int) instead
chemaxon.calculations.TopologyAnalyser.smallestRing() as of release 5.5, replaced by Ring.smallestRing()
chemaxon.calculations.TopologyAnalyser.smallestRingSize() as of release 5.5, replaced by Ring.smallestRingSize()
chemaxon.calculations.TopologyAnalyser.smallestRingSizeOfAtom(int) as of release 5.5, replaced by Ring.smallestRingSizeOfAtom(int)
chemaxon.calculations.TopologyAnalyser.smallestRingSystem() as of release 5.5, replaced by Ring.smallestRingSystem()
chemaxon.calculations.TopologyAnalyser.smallestRingSystemSize() as of release 5.5, replaced by Ring.smallestRingSystemSize()
chemaxon.struc.Molecule.sortSgroupXBonds() 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.
chemaxon.struc.sgroup.SuperatomSgroup.sortXBonds() 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.
chemaxon.calculations.TopologyAnalyser.stereo(int) as of release 5.5, replaced by Stereochemistry.stereo(int)
chemaxon.calculations.TopologyAnalyser.stereo(int, int) as of release 5.5, replaced by Stereochemistry.stereo(int, int)
chemaxon.calculations.TopologyAnalyser.stereoDoubleBondCount() as of release 5.5, replaced by Stereochemistry.stereoDoubleBondCount()
chemaxon.struc.Molecule.toBinFormat(String) As of Marvin 5.7, replaced by MolExporter.exportToBinFormat(Molecule, String).
chemaxon.marvin.alignment.AlignmentMolecule.toData()
chemaxon.struc.Molecule.toFormat(String) As of Marvin 5.7, replaced by MolExporter.exportToFormat(Molecule, String). To get exact replacement use: try { String out = MolExporter.exportToFormat(this, fmt); } catch (IOException e){ }
chemaxon.struc.Molecule.toObject(String) As of Marvin 5.7, replaced by MolExporter.exportToObject(Molecule, String).
chemaxon.marvin.util.MolImageSize.toString()
chemaxon.jep.Evaluator.toString(Object) For internal use only.
chemaxon.jep.Evaluator.toString(Object, DecimalFormat) For internal use only.
chemaxon.jep.Evaluator.toString(Object, int) For internal use only.
chemaxon.formats.recognizer.Recognizer.tryToRecognize(String, int, RecognizerList) as of Marvin 2014.07.21.0 not used in recognition. Implement Recognizer.tryToRecognize(String, int) instead.
chemaxon.struc.Molecule.ungroupSgroup(int) as of Marvin 6.3. use Molecule.ungroupSgroup(Sgroup) instead.
chemaxon.struc.Molecule.ungroupSgroup(int, int) as of Marvin 6.3. use Molecule.ungroupSgroup(Sgroup) instead.
chemaxon.struc.Molecule.ungroupSgroups(int) as of Marvin 6.3. use Molecule.ungroupSgroups(EnumSet) instead.
chemaxon.struc.sgroup.SuperatomSgroup.updateAttachmentPoints() as of Marvin 6.2, use SuperatomSgroup.calculateAttachmentPoints() instead
chemaxon.marvin.calculations.pKaPlugin.useCorrectionLibrary(boolean) Use pKaPlugin.setCorrectionLibrary(String)

Deprecated Constructors

Constructor and Description
chemaxon.checkers.runner.configuration.reader.ActionStringBasedConfigurationReader(String, StructureCheckerFactory, StructureFixerFactory) use ActionStringBasedConfigurationReader.ActionStringBasedConfigurationReader(String, CheckerFixerFactory) instead
com.chemaxon.calculations.stereoanal.stereocenters.AtomSelection(int[], int[])
com.chemaxon.calculations.stereoanal.stereocenters.AtomSelection(int, int[])
com.chemaxon.calculations.stereoanal.stereocenters.AtropStereoCenter(AtomSelection, StereoConstants.StereoValue.AtropStereo)
com.chemaxon.calculations.stereoanal.stereocenters.AtropStereoCenter(AtomSelection, StereoConstants.StereoValue.AtropStereo, List)
com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter(AtomSelection, StereoConstants.StereoValue.AxialStereo)
com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter(AtomSelection, StereoConstants.StereoValue.AxialStereo, List)
chemaxon.checkers.runner.BasicCheckerRunner(ConfigurationReader, StructureFixerFactory) use BasicCheckerRunner.BasicCheckerRunner(ConfigurationReader, CheckerFixerFactory) instead
chemaxon.checkers.BondAngleChecker(double) Not used.
chemaxon.checkers.BondLengthChecker(Map) Checker has no parameters.
com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter(AtomSelection, StereoConstants.StereoValue.CisTransStereo)
com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter(AtomSelection, StereoConstants.StereoValue.CisTransStereo, List)
chemaxon.checkers.result.DefaultExternalStructureCheckerResult(StructureChecker, List, List, Molecule, String, String, String, String, String, Icon) use DefaultExternalStructureCheckerResult.DefaultExternalStructureCheckerResult(StructureChecker, List, List, Molecule, String, String, String, String, String, Icon, int)
chemaxon.checkers.result.DefaultStructureCheckerResult(StructureChecker, List, List, StructureCheckerErrorType, Molecule, String, String, String, String, Icon) use DefaultStructureCheckerResult.DefaultStructureCheckerResult(StructureChecker, List, List, StructureCheckerErrorType, Molecule, String, String, String, String, Icon, int) instead
chemaxon.jep.Evaluator(File, Standardizer, MolImporter, String)
chemaxon.jep.Evaluator(String, Standardizer, MolImporter, String)
chemaxon.checkers.result.MetalloceneCheckerResult(StructureChecker, List, List, StructureCheckerErrorType, Molecule, String, String, String, String, Icon, List>, List) use MetalloceneCheckerResult.MetalloceneCheckerResult(StructureChecker, List, List, StructureCheckerErrorType, Molecule, String, String, String, String, Icon, List, List, int) instead
chemaxon.marvin.alignment.MMPAlignmentProperties(AlignmentProperties.FlexibilityMode, AlignmentAccuracyMode)
chemaxon.formats.MolConverter.Options()
chemaxon.formats.MolConverter(List
chemaxon.formats.MolConverter(List
chemaxon.formats.MolConverter(List
chemaxon.formats.MolConverter(List
chemaxon.formats.MolConverter(List
chemaxon.formats.MolConverter(List
chemaxon.formats.MolConverter(MolConverter.Options) as of Marvin 5.2.3, use MolConverter.Builder.build() instead.
chemaxon.marvin.util.MolImageSize()
chemaxon.marvin.util.MolImageSize(int, int, double)
chemaxon.marvin.util.MolImageSize(MolImageSize)
chemaxon.marvin.alignment.Pharmacophore3D(Molecule) Use Pharmacophore3DGenerator instead.
chemaxon.checkers.result.ReactionCheckerResult(StructureChecker, List, List, List, StructureCheckerErrorType, Molecule, String, String, String, String, Icon) use ReactionCheckerResult.ReactionCheckerResult(StructureChecker, List, List, List, StructureCheckerErrorType, Molecule, String, String, String, String, Icon, int) instead
chemaxon.jep.context.ReactionContext(boolean) Copy feature is no longer required. Constructor.
chemaxon.checkers.result.RgroupCheckerResult(StructureChecker, List, List, List, StructureCheckerErrorType, Molecule, String, String, String, String, Icon) use RgroupCheckerResult.RgroupCheckerResult(StructureChecker, List, List, List, StructureCheckerErrorType, Molecule, String, String, String, String, Icon, int) instead
chemaxon.struc.Sgroup(Molecule, int) As of Marvin 5.12, replaced by SgroupFactory.createSgroup(Molecule, SgroupType).
chemaxon.struc.Sgroup(Molecule, int, int) As of Marvin 5.12, replaced by SgroupFactory.createSgroup(Molecule, SgroupType) and Sgroup.setXState(int).
chemaxon.checkers.StructureCheckerFactory() Please consider using StructureCheckerFactory.getInstance() instead of calling this constructor directly. Default constructor. Default configurations will be read.
chemaxon.checkers.StructureCheckerFactory(InputStream, InputStream) Please consider using StructureCheckerFactory.getInstance(String, String) instead of calling this constructor directly. With this constructor inner and external configuration location can be defined.
chemaxon.checkers.StructureCheckerFactory(String, String) Please consider using StructureCheckerFactory.getInstance(String, String) instead of calling this constructor directly. With this constructor inner and external configuration location can be defined.
com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter(AtomSelection, StereoConstants.StereoValue.TetrahedralStereo)
com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter(AtomSelection, StereoConstants.StereoValue.TetrahedralStereo, EnhancedStereo)
com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter(AtomSelection, StereoConstants.StereoValue.TetrahedralStereo, EnhancedStereo, List)
com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter(AtomSelection, StereoConstants.StereoValue.TetrahedralStereo, Optional, List)
chemaxon.marvin.modules.datatransfer.TransferableDescriptor(String, String, Integer, Integer, boolean, boolean) since 5.3.3 new descriptor parameter added.
chemaxon.core.calculations.valencecheck.ValenceCheckOptions(boolean, boolean) since Marvin 6.2, Use ValenceCheckOptions.Builder for building ValenceCheckOptions.

Deprecated Enum Constants

Enum Constant and Description
chemaxon.struc.MoleculeGraph.ValenceCheckState.AMBIGUOUS_AROMATIC_ATOMS_IGNORED As of Marvin 6.0, replaced by MoleculeGraph.setValenceCheckOptions(ValenceCheckOptions) and ValenceCheckOptions.DEFAULT. Usage: molecule.setValenceCheckOptions(ValenceCheckOptions.DEFAULT);
chemaxon.struc.MoleculeGraph.ValenceCheckState.FULL As of Marvin 6.0, replaced by MoleculeGraph.setValenceCheckOptions(ValenceCheckOptions) and ValenceCheckOptions.ValenceCheckOptions(boolean, boolean). Usage: molecule.setValenceCheckOptions(new ValenceCheckOptions(false,true);
chemaxon.marvin.alignment.AlignmentProperties.GAUSS_FAST_EXTENDED_ATOMTYPE_MCS
chemaxon.checkers.StructureCheckerErrorType.INVALID_STEREO
chemaxon.marvin.alignment.AlignmentProperties.OrientationType.MCS
chemaxon.struc.MoleculeGraph.ValenceCheckState.OFF As of Marvin 6.0, replaced by MoleculeGraph.setValenceCheckEnabled(boolean). Usage: molecule.setValenceCheckEnabled(false);