Deprecated List (Marvin API documentation (c) 1998-2021 ChemAxon Ltd.)

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.
chemaxon.descriptors.MolecularDescriptorGenerator 5.4
com.chemaxon.calculations.io.Sink Use `Consumer` instead.
com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue
com.chemaxon.calculations.common.SubProgressObserver Use `ProgressObserver` instead. Will be removed.

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.standardizer.actions.AbsoluteStereoAction use `SetAbsoluteStereoAction` or `RemoveAbsoluteStereoAction` instead
chemaxon.fixers.AbsoluteStereoFixer use `RemoveInvalidChiralFlagFixer`
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.DocumentToStructure Please use the new name of this class, `DocumentToStructure`.
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.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.runner.SketchCheckerRunner
chemaxon.formats.recognizer.SMILESRecognizer as of Marvin 2014.07.21.0 intended for internal use only
chemaxon.checkers.StereoCheckUtility Will be removed from the public API.
chemaxon.marvin.calculations.StereoisomerPlugin
chemaxon.checkers.StructureCheckerFactory use `CheckerFixerFactory` instead
chemaxon.fixers.StructureFixerFactory use `CheckerFixerFactory` instead
chemaxon.fixers.WedgeCleanFixer
chemaxon.checkers.WedgeErrorChecker
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.marvin.paint.DispOptConsts.ANYBOND_AUTO Use `AnyBondStyle` instead.
chemaxon.marvin.paint.DispOptConsts.ANYBOND_AUTO_S Use `AnyBondStyle` instead.
chemaxon.marvin.paint.DispOptConsts.ANYBOND_DASHED Use `AnyBondStyle` instead.
chemaxon.marvin.paint.DispOptConsts.ANYBOND_DASHED_S Use `AnyBondStyle` instead.
chemaxon.marvin.paint.DispOptConsts.ANYBOND_MASK Use `AnyBondStyle` instead.
chemaxon.marvin.paint.DispOptConsts.ANYBOND_OFFSET Use `AnyBondStyle` instead.
chemaxon.marvin.paint.DispOptConsts.ANYBOND_SOLID Use `AnyBondStyle` instead.
chemaxon.marvin.paint.DispOptConsts.ANYBOND_SOLID_S Use `AnyBondStyle` instead.
chemaxon.marvin.paint.DispOptConsts.ANYBOND_STYLES Use `AnyBondStyle` instead.
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.marvin.paint.DispOptConsts.BALLSTICK use `RenderingStyle` instead.
chemaxon.marvin.paint.DispOptConsts.BALLSTICK_RENDERING_S use `RenderingStyle` instead.
chemaxon.marvin.paint.DispOptConsts.COORDINATE_BOND_ARROW_S
chemaxon.marvin.paint.DispOptConsts.COORDINATE_BOND_AT_MULTICENTER_FLAG
chemaxon.marvin.paint.DispOptConsts.COORDINATE_BOND_AT_MULTICENTER_OFFSET
chemaxon.marvin.paint.DispOptConsts.COORDINATE_BOND_AT_MULTICENTER_STYLES
chemaxon.marvin.paint.DispOptConsts.COORDINATE_BOND_HASHED_S
chemaxon.marvin.paint.DispOptConsts.COORDINATE_BOND_SOLID_S
chemaxon.marvin.paint.DispOptConsts.COORDINATE_BOND_STYLE_FLAG
chemaxon.marvin.paint.DispOptConsts.COORDINATE_BOND_STYLE_OFFSET
chemaxon.marvin.paint.DispOptConsts.COORDINATE_BOND_STYLES
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.marvin.common.ParameterConstants.EXPLICIT_H since 5.3
chemaxon.standardizer.Standardizer.FINAL_CLEAN_ID
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.util.iterator.IteratorFactory.INCLUDE_CHEMICAL_ATOMS As of Marvin 6.2, Use `IteratorFactory.INCLUDE_CHEMICAL_ATOMS_ONLY` instead.
chemaxon.marvin.calculations.logPPlugin.METHOD_KLOP This field will not be available from May 2016. Use `LogPMethod` instead.
chemaxon.marvin.calculations.logDPlugin.METHOD_KLOP This field will not be available from May 2016. Use `LogPMethod` instead.
chemaxon.marvin.calculations.logPPlugin.METHOD_PHYS This field will not be available from May 2016. Use `LogPMethod` instead.
chemaxon.marvin.calculations.logDPlugin.METHOD_PHYS This field will not be available from May 2016. Use `LogPMethod` instead.
chemaxon.marvin.calculations.logPPlugin.METHOD_USER_DEFINED Use `LogPMethod.USER_DEFINED` instead.
chemaxon.marvin.calculations.logDPlugin.METHOD_USER_DEFINED Use `LogPMethod.USER_DEFINED` instead.
chemaxon.marvin.calculations.logPPlugin.METHOD_VG Use `LogPMethod.CHEMAXON` instead.
chemaxon.marvin.calculations.logDPlugin.METHOD_VG Use `LogPMethod.CHEMAXON` instead.
chemaxon.marvin.calculations.logPPlugin.METHOD_WEIGHTED Use `LogPMethod.CONSENSUS` instead.
chemaxon.marvin.calculations.logDPlugin.METHOD_WEIGHTED Use `LogPMethod.CONSENSUS` instead.
chemaxon.marvin.plugin.PluginFactory.PRELOAD Not used.
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.marvin.paint.DispOptConsts.RENDERING_MASK use `RenderingStyle` instead.
chemaxon.marvin.paint.DispOptConsts.RENDERING_OFFSET use `RenderingStyle` instead.
chemaxon.marvin.paint.DispOptConsts.RENDERING_STYLES use `RenderingStyle` instead.
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.sss.SearchConstants.SEARCH_MODE_NAMES As of JChem 5.12, replaced by `SearchConstants.SEARCH_TYPE_NAMES`.
chemaxon.marvin.paint.DispOptConsts.SPACEFILL use `RenderingStyle` instead.
chemaxon.marvin.paint.DispOptConsts.SPACEFILL_RENDERING_S use `RenderingStyle` instead.
chemaxon.marvin.paint.DispOptConsts.STICKS use `RenderingStyle` instead.
chemaxon.marvin.paint.DispOptConsts.STICKS_RENDERING_S use `RenderingStyle` instead.
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.paint.DispOptConsts.WIREFRAME use `RenderingStyle` instead.
chemaxon.marvin.paint.DispOptConsts.WIREFRAME_RENDERING_S use `RenderingStyle` instead.

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.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()
com.chemaxon.descriptors.metrics.FloatVectorComparator.calculateFloatVectorSimilarity(float[], float[]) In various cases (euclid, euclid sqr, manhattan) this has no practical interpretation
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.RgMolecule.checkConsistency() As of Marvin 5.7, no replacement. Not intended for public use, it was intended only for internal debugging.
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.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.struc.sgroup.SuperatomSgroup.cloneLeavingGroups(SuperatomSgroup) As of Marvin 6.2, no replacement. Not supported feature.
chemaxon.struc.RgMolecule.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.Molecule.clonelesscopy(MoleculeGraph) as of Marvin 6.3. Not supported feature.
chemaxon.struc.RxnMolecule.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.naming.NameConverter.convert(String) This method is deprecated, because implementations of this interface are potentially used in multi-threaded environments, so they should not store a call-site-dependent state. The method is no longer called by the Name to Structure algorithm, `NameConverter.convert(String, boolean)` is used instead. The default implementation of this method throws `UnsupportedOperationException` to enable users to remove the implementing methods before this method is removed.
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.MMoleculeProp.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.MBooleanProp.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.MIntegerProp.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.MDoubleArrayProp.convertToString(String, int) As of Marvin 5.7, replaced by `MPropHandler.convertToString(MProp, String)`
chemaxon.struc.prop.MDoubleProp.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.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.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.struc.MoleculeGraph.createCHtab() As of version 20.22, no replacement.
com.chemaxon.calculations.common.ProgressObservers.createForgivingNullObserver() Use `ProgressObservers.nullProgressObserver()` instead.
chemaxon.core.util.BondTable.createMatrixArray() as of version 20.22, no replacement
chemaxon.marvin.beans.MarvinPane.createMenu(ResourceBundle, String) as of Marvin 3.3.1, replaced by SwingUtil.createMenu
com.chemaxon.calculations.common.ProgressObservers.createNoCancelObserver() Use `ProgressObservers.noCanceller()`
com.chemaxon.calculations.common.ProgressObservers.createNullObserver(String) Use `ProgressObservers.createStrictNullObserver()`.
chemaxon.formats.MFileFormat.createRecognizer(String) as of Marvin 2014.07.21.0 use `MFileFormat.createRecognizer()` instead
chemaxon.marvin.calculations.TautomerizationPlugin.createStandardizedMolecule(Molecule, boolean)
chemaxon.marvin.calculations.ResonancePlugin.createStandardizedMolecule(Molecule, boolean) Use `ResonancePlugin.createStandardizedMolecule(Molecule)` instead
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.graphics.MTextBox.determinePosition(DPoint3, boolean) use `MTextBox.determinePosition(Graphics, DPoint3, boolean)` in case you have a special graphics context to be used for font calculations.
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.MDocument.exportToBinFormat(String) As of release 5.7, replaced by `MolExporter.exportToBinFormat(MDocument, String)`.
chemaxon.struc.Molecule.exportToBinFormat(String) As of Marvin 5.7, replaced by `MolExporter.exportToBinFormat(Molecule, String)`.
chemaxon.struc.MDocument.exportToFormat(String) As of release 5.7, replaced by `MolExporter.exportToFormat(MDocument, String)`
chemaxon.struc.Molecule.exportToFormat(String) As of Marvin 5.7, replaced by `MolExporter.exportToFormat(Molecule, String)`.
chemaxon.struc.MDocument.exportToObject(String) As of release 5.7, replaced by `MolExporter.exportToObject(MDocument, String)`
chemaxon.struc.Molecule.exportToObject(String) As of Marvin 5.7, replaced by `MolExporter.exportToObject(Molecule, 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<C>) 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.descriptors.ECFP.fromFeatureSet(Set<Integer>) As of JChem 5.4.1, replaced by `fromIdentiferSet()`.
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.HBDAPlugin.getAcceptorCount() Use `HBDAPlugin.getAcceptorSiteCount()` instead.
chemaxon.marvin.calculations.HBDAPlugin.getAcceptorCount(int) Use `HBDAPlugin.getAcceptorSiteCount()` instead!
chemaxon.standardizer.Standardizer.getActiveGroups() use `ConfigurationUtility.filterGroups(StandardizerConfiguration, String[])` on the configuration returned by the method `Standardizer.getConfiguration()`
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.struc.MoleculeGraph.getAtomReferenceList() Use `MoleculeGraph.atoms()` instead.
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()`.
com.chemaxon.descriptors.vectors.binary.BvGenerator.getBinaryMetricsComparator(BinaryMetrics) Use `BinaryVectorMetricFactory.forBinaryMetrics(com.chemaxon.descriptors.metrics.BinaryMetrics)`.
com.chemaxon.descriptors.fingerprints.ecfp.EcfpGenerator.getBinaryMetricsComparator(BinaryMetrics) Use `BinaryVectorMetricFactory.forBinaryMetrics(com.chemaxon.descriptors.metrics.BinaryMetrics)`
com.chemaxon.descriptors.fingerprints.cfp.CfpGenerator.getBinaryMetricsComparator(BinaryMetrics) Use `BinaryVectorMetricFactory.forBinaryMetrics(com.chemaxon.descriptors.metrics.BinaryMetrics)`
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.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() at N/A (before 02/12/2015)
chemaxon.marvin.beans.MarvinPane.getCommonActions()
chemaxon.marvin.util.MoleculeUtil.getCrossingBonds(MolBond[], DPoint3, DPoint3) as of Marvin 5.11.1
com.chemaxon.descriptors.common.DescriptorGenerator.getDefaultComparator() This method is kept for compatibility reason. Use `ComparisonContext#descriptorComparator()` on the instance returned by `MetricFactory.defaultComparison()` from `DescriptorGenerator.comparisonContextFactory()`
com.chemaxon.descriptors.fingerprints.pf2d.PfGenerator.getDefaultComparator()
com.chemaxon.descriptors.fingerprints.ecfp.EcfpGenerator.getDefaultComparator()
com.chemaxon.descriptors.fingerprints.cfp.CfpGenerator.getDefaultComparator()
chemaxon.checkers.StructureChecker.getDescription() This method isn't needed anymore and will be removed in 6.0
chemaxon.fixers.StructureFixer.getDescription()
com.chemaxon.descriptors.alignment.ShapeDescriptor.getDescriptorGenerator() Use `Guarded.getGuardObject()`
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.calculations.HBDAPlugin.getDonorCount() Use `HBDAPlugin.getDonorSiteCount()` instead!
chemaxon.marvin.calculations.HBDAPlugin.getDonorCount(int) Use `HBDAPlugin.getDonorSiteCount(int)` instead!
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.getExplicitLonePairCount(int) use `MDocument.getExplicitLonePairCount()` instead
chemaxon.struc.MoleculeGraph.getEZStereo(MolBond) as of Marvin 15.2.16 replaced by `CIPStereoCalculator.calculateCIPStereoDescriptors(MoleculeGraph, boolean)`.
chemaxon.descriptors.ECFP.getFeatureCount() As of JChem 5.4.1, replaced by `ECFP.getIdentiferCount()`.
com.chemaxon.descriptors.vectors.floats.FvGenerator.getFloatMetricsComparator(FloatVectorMetrics) Use `FloatVectorMetricFactory.forFloatMetrics(com.chemaxon.descriptors.metrics.FloatVectorMetrics)`.
com.chemaxon.descriptors.fingerprints.pf2d.PfGenerator.getFloatVectorComparator(FloatVectorMetrics) Use `FloatVectorMetricFactory.forFloatMetrics(com.chemaxon.descriptors.metrics.FloatVectorMetrics)`
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.descriptors.ShapeDescriptor.getHistogramSimilarity(MolecularDescriptor) use `ShapeDescriptor.getShapeSimilarity(MolecularDescriptor)` instead
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.struc.MoleculeGraph.getLonePairCount(int) use `MDocument.getLonePairCount()` instead
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.core.util.BondTable.getMatrixArray() as of version 20.22, no replacement
chemaxon.formats.MFileFormat.getMIMEType() as of Marvin 2014.07.21.0 not used
chemaxon.marvin.beans.MSketchPane.getMrvWithSettings() use `MSketchPane.getMol(String)` instead
chemaxon.struc.RxnMolecule.getMSLogic() Multi-step reactions not supported. Method performs no operations.
chemaxon.checkers.StructureChecker.getName() This method isn't needed anymore and will be removed in 6.0
chemaxon.fixers.StructureFixer.getName()
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.standardizer.advancedactions.TransformAction.getStructure()
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 `TPSAPlugin.getSurfaceArea()`
com.chemaxon.descriptors.vectors.binary.BvGenerator.getTverskyComparator(double, double) Use `#forTversky(double, double)`.
com.chemaxon.descriptors.fingerprints.ecfp.EcfpGenerator.getTverskyComparator(double, double) Use `BinaryVectorMetricFactory.forTverskyCoefficients(double, double)`
com.chemaxon.descriptors.fingerprints.cfp.CfpGenerator.getTverskyComparator(double, double) Use `BinaryVectorMetricFactory.forTverskyCoefficients(double, double)`
com.chemaxon.descriptors.vectors.binary.BvGenerator.getTverskyComparator(TverskyParameters) Use `BinaryVectorMetricFactory.forBinaryMetrics(com.chemaxon.descriptors.metrics.BinaryMetrics)`.
com.chemaxon.descriptors.fingerprints.ecfp.EcfpGenerator.getTverskyComparator(TverskyParameters) Use `BinaryVectorMetricFactory.forTversky(com.chemaxon.descriptors.metrics.TverskyParameters)`
com.chemaxon.descriptors.fingerprints.cfp.CfpGenerator.getTverskyComparator(TverskyParameters) Use `BinaryVectorMetricFactory.forTversky(com.chemaxon.descriptors.metrics.TverskyParameters)`
chemaxon.struc.Sgroup.getType() as of Marvin 6.3. use `Sgroup.getSgroupType()` instead. Note that in case of `AminoAcidSgroup`s returned `Sgroup.ST_SUPERATOM` but `Sgroup.getSgroupType()` will return `SgroupType.AMINOACID`.
com.chemaxon.descriptors.metrics.FloatVectorComparator.getUpperBoundForFloatVectors() In various cases (euclid, euclid sqr, manhattan) this has no practical interpretation
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.CisTransStereoCenter.getValue() As of Marvin 14.9.15, replaced by `CisTransStereoCenter.getCIPValue()`.
com.chemaxon.calculations.stereoanal.stereocenters.StereoCenter.getValue() As of Marvin 14.9.15, replaced by `StereoCenter.getCIPValue()`.
com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter.getValue() As of Marvin 14.9.15, replaced by `TetrahedralStereoCenter.getCIPValue()`.
com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter.getValue() As of Marvin 14.9.15, replaced by `AxialStereoCenter.getCIPValue()`.
com.chemaxon.calculations.stereoanal.stereocenters.AtropStereoCenter.getValue() As of Marvin 14.9.15, replaced by `AtropStereoCenter.getCIPValue()`.
chemaxon.formats.recognizer.PeptideRecognizer.guessPeptideFormat(String) as of Marvin 2014.07.21.0 intended for internal use
chemaxon.struc.MoleculeGraph.hasExplicitLonePairs() use `MDocument.hasExplicitLonePairs()` instead
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 construct 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.RgMolecule.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.RxnMolecule.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.RgMolecule.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.RxnMolecule.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.checkers.StructureCheck.isErrorOccured() Misspelled method name, use `StructureCheck.isErrorOccurred()` instead.
chemaxon.standardizer.concurrent.StandardizerResult.isExceptionOccured() Misspelled method name, use `StandardizerResult.isExceptionOccurred()` instead.
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.struc.Molecule.isSgroup() As of Marvin 14.7.7, no replacement. Not supported feature.
chemaxon.struc.RxnMolecule.isSingleStepReaction()
chemaxon.sss.search.MolSearchOptions.isSwitchOffAllProtectsForTDF() Since JChem 5.12, stereo is considered as default in tautomer regions, but `SearchOptions.setTautomerSearch(int)` with value `SearchConstants.TAUTOMER_SEARCH_ON_IGNORE_TAUTOMERSTEREO` ignores it.
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.RgMolecule.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.Molecule.mergeAtoms(MolAtom, MolAtom) As of Marvin 6.2, use `MergeUtil.mergeAtoms(MolAtom, MolAtom, boolean)` instead.
chemaxon.struc.RxnMolecule.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.marvin.modules.datatransfer.ClipboardHandler.putFormattedTextToClipboard(Document, int, int)
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. use`MolImporter.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.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.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.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.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.standardizer.Standardizer.setActiveGroups(String[]) use `ConfigurationUtility.filterGroups(StandardizerConfiguration, String[])` on the configuration returned by the method `Standardizer.getConfiguration()`
chemaxon.marvin.alignment.AlignmentMoleculeFactory.setAromatize(boolean) The original input structure is not aromatized. No need to use.
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.struc.MoleculeGraph.setAtom(int, MolAtom) as of Marvin 6.2, may construct inconsistent `MoleculeGraph`. Use `MoleculeGraph.removeAtom(int)` for atom removal and `MoleculeGraph.add(MolAtom)` for adding new atoms.
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.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.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.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.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.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.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.MolPrinter.setChargeFont(Font) in Marvin 15.5.18
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.naming.document.annotate.DocumentAnnotator.setD2SOptions(String) use `DocumentAnnotator.setD2SOptions(D2SOptions)` instead An option String can be parsed to `D2SOptions` object using `D2SOptionsParser.parseOptions(String)`.
chemaxon.marvin.alignment.AlignmentMoleculeFactory.setDehidrogenize(boolean) The explicit Hydrogens are not removed from the original input structure. No need to use.
chemaxon.checkers.StructureChecker.setDescription(String) This method isn't needed anymore and will be removed in 6.0
chemaxon.fixers.StructureFixer.setDescription(String)
chemaxon.marvin.MolPrinter.setDisplayQuality(int) since Marvin 6.4 only high quality exists
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.standardizer.Standardizer.setFinalClean() use `ConfigurationUtility.setFinalClean(StandardizerConfiguration)` on the configuration returned by the method `Standardizer.getConfiguration()`
chemaxon.standardizer.Standardizer.setFinalClean(int) use `ConfigurationUtility.setFinalClean(StandardizerConfiguration, int)` on the configuration returned by the method `Standardizer.getConfiguration()`
chemaxon.standardizer.Standardizer.setFinalClean(int, boolean) use `ConfigurationUtility.setFinalClean(StandardizerConfiguration, int, boolean)` on the configuration returned by the method `Standardizer.getConfiguration()`
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.TautomerizationPlugin.setInputMoleculeModified(boolean) Not used.
chemaxon.marvin.calculations.ResonancePlugin.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.calculations.logPPlugin.setlogPMethod(int) Use `logPPlugin.setlogPMethod(LogPMethod)` instead.
chemaxon.marvin.calculations.logDPlugin.setlogPMethod(int) Use `#setlogPMethod(LogPMethod))` instead.
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.alignment.Alignment.setMinimumCommonSize(int)
chemaxon.marvin.calculations.AlignmentPlugin.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.marvin.beans.MSketchPane.setMrvWithSettings(String) use `MSketchPane.setMol(String)`
chemaxon.struc.RxnMolecule.setMSLogic(Map<MRArrow, RxnMolecule>) Multi-step reactions not supported. Method performs no operations.
chemaxon.checkers.StructureChecker.setName(String) This method isn't needed anymore and will be removed in 6.0
chemaxon.fixers.StructureFixer.setName(String)
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.naming.NameConverter.setPrefixMode(boolean) This method is deprecated, because implementations of this interface are potentially used in multi-threaded environments, so they should not store a call-site-dependent state. The method is no longer called by the Name to Structure algorithm, `NameConverter.isPrefixModeSupported()` and `NameConverter.convert(String, boolean)` is used instead. The default implementation of this method throws `UnsupportedOperationException` to enable users to remove the implementing methods before this method is removed.
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.marvin.calculations.TautomerizationPlugin.setRationalTautomerGenerationMode(boolean)
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.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.standardizer.advancedactions.TransformAction.setStructure(String) use `TransformAction.setTransform(RxnMolecule)` method instead
chemaxon.sss.search.MolSearchOptions.setSwitchOffAllProtectsForTDF(boolean) Since JChem 5.12, stereo is considered as default in tautomer regions, but `SearchOptions.setTautomerSearch(int)` with value `SearchConstants.TAUTOMER_SEARCH_ON_IGNORE_TAUTOMERSTEREO` ignores it.
chemaxon.marvin.calculations.logPPlugin.setTakeMajorTatomericForm(boolean) Use `logPPlugin.setConsiderTautomerization(boolean)`
chemaxon.marvin.calculations.pKaPlugin.setTakeMajorTatomericForm(boolean) Use `pKaPlugin.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.marvin.calculations.logPPlugin.setWeightOfMethods(double, double, double, double) This function will not be available from May 2016. Use `logPPlugin.setlogPMethod(LogPMethod)` instead.
chemaxon.marvin.calculations.logDPlugin.setWeightOfMethods(double, double, double, double) This function will not be available from May 2016. Use `logDPlugin.setlogPMethod(LogPMethod)` instead.
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()`
com.chemaxon.calculations.common.ProgressObserver.subTask(String, long) Will be removed.
chemaxon.struc.Molecule.toBinFormat(String) As of Marvin 5.7, replaced by `MolExporter.exportToBinFormat(Molecule, String)`.
chemaxon.marvin.alignment.AlignmentMolecule.toData()
chemaxon.descriptors.ECFP.toFeatureSet() As of JChem 5.4.1, replaced by `ECFP.toIdentiferSet()`.
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.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.
com.chemaxon.calculations.io.CloseableIterators.transform(CloseableIterator<T>, Function<T, U>) `CloseableIterator.transform(java.util.function.Function)` provides default method making this utility not necessary
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<AttachedData>)
com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter(AtomSelection, StereoConstants.StereoValue.AxialStereo)
com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter(AtomSelection, StereoConstants.StereoValue.AxialStereo, List<AttachedData>)
chemaxon.checkers.BondAngleChecker(double) Not used.
chemaxon.checkers.BondLengthChecker(Map<String, String>) Checker has no parameters.
chemaxon.descriptors.CFGenerator(int) since 5.4
com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter(AtomSelection, StereoConstants.StereoValue.CisTransStereo)
com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter(AtomSelection, StereoConstants.StereoValue.CisTransStereo, List<AttachedData>)
chemaxon.checkers.result.DefaultExternalStructureCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, 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<MolAtom>, List<MolBond>, 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<MolAtom>, List<MolBond>, StructureCheckerErrorType, Molecule, String, String, String, String, Icon, List<List<MolAtom>>, List<MolAtom>) 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(List<Object>, List<String>, OutputStream, String, boolean) as of Marvin 5.2.3, replaced by `MolConverter.MolConverter(Builder)`
chemaxon.formats.MolConverter(List<Object>, List<String>, OutputStream, String, boolean, String[]) as of Marvin 5.2.3, replaced by `MolConverter.MolConverter(Builder)`
chemaxon.formats.MolConverter(List<Object>, List<String>, OutputStream, String, boolean, String[], String) as of Marvin 5.2.3, replaced by `MolConverter.MolConverter(Builder)`
chemaxon.formats.MolConverter(List<Object>, List<String>, String, String, boolean) as of Marvin 5.2.3, replaced by `MolConverter.MolConverter(Builder)`
chemaxon.formats.MolConverter(List<Object>, OutputStream, String, boolean) as of Marvin 5.2.3, replaced by `MolConverter.MolConverter(Builder)`
chemaxon.formats.MolConverter(List<Object>, String, String, boolean) as of Marvin 5.2.3, replaced by `MolConverter.MolConverter(Builder)`
chemaxon.formats.MolConverter(MolConverter.Options) as of Marvin 5.2.3, use `MolConverter.Builder.build()` instead.
chemaxon.formats.MolConverter.Options()
chemaxon.marvin.alignment.Pharmacophore3D(Molecule) Use `Pharmacophore3DGenerator` instead.
chemaxon.checkers.result.ReactionCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, List<Long>, 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.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.standardizer.concurrent.StandardizerRunner(Iterator<Molecule>, StandardizerConfiguration) Won't be public in the future
chemaxon.standardizer.concurrent.StandardizerRunner(Iterator<Molecule>, StandardizerConfiguration, int) Won't be public in the future
chemaxon.standardizer.concurrent.StandardizerRunner(Iterator<Molecule>, StandardizerConfiguration, int, String) Won't be public in the future
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<AttachedData>)
com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter(AtomSelection, StereoConstants.StereoValue.TetrahedralStereo, Optional<EnhancedStereo>, List<AttachedData>)
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.checkers.StructureCheckerErrorType.INVALID_WEDGE
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);

Deprecated API

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