Deprecated API

Contents

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

Terminally Deprecated Elements

Element	Description
chemaxon.calculations.CalculatorPlugin.getpH()	Use CalculatorPlugin.getPh() instead. This method will be removed in a future version.
chemaxon.calculations.CalculatorPlugin.PLUGIN_DIR	Not used anymore, no replacement.
chemaxon.calculations.HBDAPlugin.getpHs()	Use HBDAPlugin.getPhValues() instead. This method will be removed in a future version.
chemaxon.calculations.HBDAPlugin.setpHLower(double)	Use HBDAPlugin.setPhLower(double) instead. This method will be removed in a future version.
chemaxon.calculations.HBDAPlugin.setpHStep(double)	Use HBDAPlugin.setPhStep(double) instead. This method will be removed in a future version.
chemaxon.calculations.HBDAPlugin.setpHUpper(double)	Use HBDAPlugin.setPhUpper(double) instead. This method will be removed in a future version.
chemaxon.calculations.HLBPlugin.Builder	Deprecated, use the constructor of HLBPlugin class directly instead.
chemaxon.calculations.HLBPlugin.getDaviesHlbValue()	Deprecated, use HLBPlugin.getDaviesHLBValue() instead.
chemaxon.calculations.HLBPlugin.getGriffinHlbValue()	Deprecated, use HLBPlugin.getGriffinHLBValue() instead.
chemaxon.calculations.HLBPlugin.getHlbValue()	Deprecated, use HLBPlugin.getHLBValue() instead.
chemaxon.calculations.HLBPlugin.getRequiredHlbValue()	Deprecated, use HLBPlugin.getRequiredHLBValue() instead.
chemaxon.calculations.HLBPlugin.setRHLB(boolean)	Deprecated, use HLBPlugin.enableRequiredHLBValue(boolean) instead.
chemaxon.calculations.IsoelectricPointPlugin.getpHs()	Use IsoelectricPointPlugin.getPhValues() instead. This method will be removed in a future version.
chemaxon.calculations.IsoelectricPointPlugin.getpI()	Use IsoelectricPointPlugin.getIsoelectricPoint() instead. This method will be removed in a future version.
chemaxon.calculations.IsoelectricPointPlugin.getpKaOfpI()	Use IsoelectricPointPlugin.getPkaOfIsoelectricPoint() instead. This method will be removed in a future version.
chemaxon.calculations.IsoelectricPointPlugin.setpH(double)	Use IsoelectricPointPlugin.setPh(double) instead. This method will be removed in a future version.
chemaxon.calculations.IsoelectricPointPlugin.setpHLower(double)	Use IsoelectricPointPlugin.setPhLower(double) instead. This method will be removed in a future version.
chemaxon.calculations.IsoelectricPointPlugin.setpHStep(double)	Use IsoelectricPointPlugin.setPhStep(double) instead. This method will be removed in a future version.
chemaxon.calculations.IsoelectricPointPlugin.setpHUpper(double)	Use IsoelectricPointPlugin.setPhUpper(double) instead. This method will be removed in a future version.
chemaxon.calculations.LogDPlugin.calclogD(double)	Use LogDPlugin.calcLogD(double) instead. This method will be removed in a future version.
chemaxon.calculations.LogDPlugin.getHidrophobicity()
chemaxon.calculations.LogDPlugin.getlogD()	Use LogDPlugin.getLogD() instead. This method will be removed in a future version.
chemaxon.calculations.LogDPlugin.getlogDs()	Use LogDPlugin.getLogDValues() instead. This method will be removed in a future version.
chemaxon.calculations.LogDPlugin.getpHs()	Use LogDPlugin.getPhValues() instead. This method will be removed in a future version.
chemaxon.calculations.LogDPlugin.getReflogDs()	Use LogDPlugin.getReferenceLogDValues() instead. This method will be removed in a future version.
chemaxon.calculations.LogDPlugin.getRefpHs()	Use LogDPlugin.getReferencePhValues() instead. This method will be removed in a future version.
chemaxon.calculations.LogDPlugin.setCloridIonConcentration(double)	Use LogDPlugin.setChlorideIonConcentration(double) instead. This method will be removed in a future version.
chemaxon.calculations.LogDPlugin.setlogPMethod(LogPMethod)	Use LogDPlugin.setLogPMethod(LogPMethod) instead. This method will be removed in a future version.
chemaxon.calculations.LogDPlugin.setpH(double)	Use LogDPlugin.setPh(double) instead. This method will be removed in a future version.
chemaxon.calculations.LogDPlugin.setpHLower(double)	Use LogDPlugin.setPhLower(double) instead. This method will be removed in a future version.
chemaxon.calculations.LogDPlugin.setpHStep(double)	Use LogDPlugin.setPhStep(double) instead. This method will be removed in a future version.
chemaxon.calculations.LogDPlugin.setpHUpper(double)	Use LogDPlugin.setPhUpper(double) instead. This method will be removed in a future version.
chemaxon.calculations.LogDPlugin.setpKaCorrectionLibrary(InputStream)	Use LogDPlugin.setPkaCorrectionLibrary(InputStream) instead. This method will be removed in a future version.
chemaxon.calculations.LogDPlugin.setpKaCorrectionLibrary(String)	Use LogDPlugin.setPkaCorrectionLibrary(String) instead. This method will be removed in a future version.
chemaxon.calculations.LogPPlugin.getAtomlogPIncrement(int)	Use LogPPlugin.getAtomLogPIncrement(int) instead. This method will be removed in a future version.
chemaxon.calculations.LogPPlugin.getlogDpI()	Use LogPPlugin.getLogDAtIsoelectricPoint() instead. This method will be removed in a future version.
chemaxon.calculations.LogPPlugin.getlogPMicro()	Use LogPPlugin.getLogPMicro() instead. This method will be removed in a future version.
chemaxon.calculations.LogPPlugin.getlogPNonionic()	Use LogPPlugin.getLogPNonionic() instead. This method will be removed in a future version.
chemaxon.calculations.LogPPlugin.getlogPTrue()	Use LogPPlugin.getLogPTrue() instead. This method will be removed in a future version.
chemaxon.calculations.LogPPlugin.getStructurallogPIncrement()	Use LogPPlugin.getStructuralLogPIncrement() instead. This method will be removed in a future version.
chemaxon.calculations.LogPPlugin.setCloridIonConcentration(double)	Use LogPPlugin.setChlorideIonConcentration(double) instead. This method will be removed in a future version.
chemaxon.calculations.LogPPlugin.setlogPMethod(LogPMethod)	Use LogPPlugin.setLogPMethod(LogPMethod) instead. This method will be removed in a future version.
chemaxon.calculations.MajorMicrospeciesAccessorPlugin.getpH()	Use MajorMicrospeciesAccessorPlugin.getPh() instead. This method will be removed in a future version.
chemaxon.calculations.MajorMicrospeciesAccessorPlugin.setpH(double)	Use MajorMicrospeciesAccessorPlugin.setPh(double) instead. This method will be removed in a future version.
chemaxon.calculations.MajorMicrospeciesPlugin.getpH()	Use MajorMicrospeciesPlugin.getPh() instead. This method will be removed in a future version.
chemaxon.calculations.MajorMicrospeciesPlugin.setpH(double)	Use MajorMicrospeciesPlugin.setPh(double) instead. This method will be removed in a future version.
chemaxon.calculations.PkaPlugin.DEF_IONICSTRENGTH	Use PkaPlugin.DEF_IONIC_STRENGTH instead. This constant will be removed in a future release.
chemaxon.calculations.PkaPlugin.DEF_MAXIONS	Use PkaPlugin.DEF_MAX_IONS instead. This constant will be removed in a future release.
chemaxon.calculations.PkaPlugin.DYNAMICpKaPREFIX	Use PkaPlugin.DYNAMIC_PKA_PREFIX instead. This constant will be removed in a future release.
chemaxon.calculations.PkaPlugin.getMacropKaValues(int)	Use PkaPlugin.getMacroPkaValues(int) instead. This method will be removed in a future version.
chemaxon.calculations.PkaPlugin.getMacropKaValues(int, double[], int[])	Use PkaPlugin.getMacroPkaValues(int, double[], int[]) instead. This method will be removed in a future version.
chemaxon.calculations.PkaPlugin.getMacroSpeciesCharge(int)	Use PkaPlugin.getMacrospeciesCharge(int) instead. This method will be removed in a future version.
chemaxon.calculations.PkaPlugin.getMacroSpeciesCount()	No replacement. This method will be removed in a future version.
chemaxon.calculations.PkaPlugin.getpHs()	Use PkaPlugin.getPhValues() instead. This method will be removed in a future version.
chemaxon.calculations.PkaPlugin.getpKa(int)	Use PkaPlugin.getPka(int) instead. This method will be removed in a future version.
chemaxon.calculations.PkaPlugin.getpKaConc(int)	Use PkaPlugin.getPkaConcentration(int) instead. This method will be removed in a future version.
chemaxon.calculations.PkaPlugin.getpKaMixed(int)	Use PkaPlugin.getPkaMixed(int) instead. This method will be removed in a future version.
chemaxon.calculations.PkaPlugin.getpKaPrefixType()	Use PkaPlugin.getPkaPrefixType() instead. This method will be removed in a future version.
chemaxon.calculations.PkaPlugin.getpKaType(int)	Use PkaPlugin.getPkaType(int) instead. This method will be removed in a future version.
chemaxon.calculations.PkaPlugin.getpKaValues(int, int)	Use PkaPlugin.getPkaValues(int, int) instead. This method will be removed in a future version.
chemaxon.calculations.PkaPlugin.setAcidicpKaUpperLimit(double)	Use PkaPlugin.setAcidicPkaUpperLimit(double) instead. This method will be removed in a future version.
chemaxon.calculations.PkaPlugin.setBasicpKaLowerLimit(double)	Use PkaPlugin.setBasicPkaLowerLimit(double) instead. This method will be removed in a future version.
chemaxon.calculations.PkaPlugin.setMicropKaCalc(boolean)	Use PkaPlugin.setMicroPkaCalc(boolean) instead. This method will be removed in a future version.
chemaxon.calculations.PkaPlugin.setpH(double)	Use PkaPlugin.setPh(double) instead. This method will be removed in a future version.
chemaxon.calculations.PkaPlugin.setpHLower(double)	Use PkaPlugin.setPhLower(double) instead. This method will be removed in a future version.
chemaxon.calculations.PkaPlugin.setpHStep(double)	Use PkaPlugin.setPhStep(double) instead. This method will be removed in a future version.
chemaxon.calculations.PkaPlugin.setpHUpper(double)	Use PkaPlugin.setPhUpper(double) instead. This method will be removed in a future version.
chemaxon.calculations.PkaPlugin.setpKaPrefixType(int)	Use PkaPlugin.setPkaPrefixType(int) instead. This method will be removed in a future version.
chemaxon.calculations.PkaPlugin.STATICpKaPREFIX	Use PkaPlugin.STATIC_PKA_PREFIX instead. This constant will be removed in a future release.
chemaxon.calculations.services.ServiceDescriptor.getIcon()	No longer used, always returns null.
chemaxon.calculations.TautomerPlugin.setpH(double)	Use TautomerPlugin.setPh(double) instead. This method will be removed in a future version.
chemaxon.checkers.StructureCheckerErrorType.INVALID_COORD_SYSTEM	StructureCheckerErrorType.INVALID_COORDINATION_SYSTEM is used instead
chemaxon.checkers.StructureCheckerErrorType.MULTI_COMPONENT	StructureCheckerErrorType.MULTIPLE_COMPONENT is used instead
chemaxon.checkers.StructureCheckerErrorType.PSEUDO_NO_GROUP	StructureCheckerErrorType.PSEUDO is used instead
chemaxon.checkers.StructureCheckerErrorType.SOLVENT_AMBIGOUS	StructureCheckerErrorType.SOLVENT_AMBIGUOUS is used instead
chemaxon.checkers.StructureCheckerErrorType.SUBSTRUCTURE_NOFIX	This error type is not used, will be removed
chemaxon.chemterms.ChemTermsExpression.evaluate_boolean(C)	Use ChemTermsExpression.evaluateBoolean(C) instead.
chemaxon.chemterms.ChemTermsExpression.evaluate_booleans(C)	Use ChemTermsExpression.evaluateBooleanArray(C) instead.
chemaxon.chemterms.ChemTermsExpression.evaluate_double(C)	Use ChemTermsExpression.evaluateDouble(C) instead.
chemaxon.chemterms.ChemTermsExpression.evaluate_doubles(C)	Use ChemTermsExpression.evaluateDoubleArray(C) instead.
chemaxon.core.calculations.stereo.StereoActivePart.getLigands()	Use StereoActivePart.getLigandIndexes() instead.
chemaxon.core.calculations.stereo.StereoActivePart.getStereoActiveAtom()	Use StereoActivePart.getActiveAtomIndex() instead.
chemaxon.core.util.MProgressMonitor	Use ProgressMonitor instead.
chemaxon.descriptors.ECFP.fromIdentiferSet(Set<Integer>)	Use ECFP.fromIdentifierSet(Set) instead.
chemaxon.descriptors.ECFP.getIdentiferCount()	Use ECFP.getIdentifierCount() instead.
chemaxon.descriptors.ECFP.toIdentiferSet()	Use ECFP.toIdentifierSet() instead
chemaxon.formats.MFileFormat.createRecordReader(MolInputStream, String)	Visibility will be restricted, no replacement method will be provided.
chemaxon.formats.MFileFormat.createUserDefined(String, String, String, MRecordReaderFactory, MolImportModuleFactory, MolExportModuleFactory, RecognizerFactory, String, long)	The support of user-defined formats will be removed.
chemaxon.formats.MFileFormat.createUserDefined(String, List<String>, List<String>, MRecordReaderFactory, MolImportModuleFactory, MolExportModuleFactory, RecognizerFactory, Map<String, Integer>, long)	The support of user-defined formats will be removed.
chemaxon.formats.MFileFormatUtil.createRecordReader(InputStream, String)	For in-house use only. Will be moved.
chemaxon.formats.MFileFormatUtil.createRecordReader(InputStream, String, String, String)	For in-house use only. Will be moved.
chemaxon.formats.MolImportModule.initMolImport(MRecord, String)	Should not be public. Visibility will be restricted in RemovalDate.JUL_01_2027
chemaxon.formats.PositionedInputStream.endGrabLines()
chemaxon.formats.PositionedInputStream.getGrabbedLines()
chemaxon.formats.PositionedInputStream.startGrabLines()
chemaxon.marvin.common.MDocStorage.getFieldAccessor()	designed for MarvinView, do not use.
chemaxon.marvin.common.MDocStorage.setFieldAccessor(MFieldAccessor)	designed for MarvinView, do not use.
chemaxon.marvin.common.UserSettings.isExperimentalFeaturesAreAllowed()	Not supported anymore
chemaxon.marvin.common.UserSettings.setAllowExperimentalFeatures(boolean)	Not supported anymore
chemaxon.reaction.mapper.AutoMapper.mapReaction(MolImporter, MolExporter)	Use AutoMapper.mapReactions(MolImporter, MolExporter) instead. This method will be removed in a future release.
chemaxon.reaction.mapper.AutoMapper.mapReaction(MolImporter, MolExporter, AutoMapper.Options)	Use AutoMapper.mapReactions(MolImporter, MolExporter, Options) instead. This method will be removed in a future release.
chemaxon.reaction.mapper.AutoMapper.mapReaction(MolImporter, MolExporter, ReactionMapper...)	No replacement. This method will be removed in a future release.
chemaxon.reaction.mapper.AutoMapper.mapReaction(AutoMapper.Options, Molecule...)	Use AutoMapper.mapReactions(Collection, Options) instead. This method will be removed in a future release.
chemaxon.reaction.mapper.AutoMapper.mapReaction(ReactionMapper[], Molecule...)	No replacement. This method will be removed in a future release.
chemaxon.reaction.mapper.AutoMapper.mapReaction(Molecule...)	Use AutoMapper.mapReactions(Molecule...) instead. This method will be removed in a future release.
chemaxon.reaction.mapper.AutoMapper.mapReaction(Collection<Molecule>)	Use AutoMapper.mapReactions(Collection) instead. This method will be removed in a future release.
chemaxon.reaction.mapper.AutoMapper.mapReaction(Collection<Molecule>, AutoMapper.Options)	Use AutoMapper.mapReactions(Collection, Options) instead. This method will be removed in a future release.
chemaxon.reaction.mapper.AutoMapper.mapReaction(Collection<Molecule>, ReactionMapper...)	No replacement. This method will be removed in a future release.
chemaxon.rendering.constants.DispOptConsts.RS_SELECTED	No longer supported, use DispOptConsts.RS_ALL option instead.
chemaxon.rendering.constants.DispOptConsts.RS_SELECTED_S	No longer supported, use DispOptConsts.RS_ALL_S option instead.
chemaxon.search.hitdisplay.HitDisplayTool.getHits(Molecule, Molecule, int)	This method will be removed in a future release, use HitDisplayTool.getHits(int) instead.
chemaxon.standardizer.configuration.ConfigurationUtility	Use StandardizerConfiguration.filterGroups(String...) instead
chemaxon.standardizer.Standardizer.setActiveGroups(String...)	use StandardizerConfiguration.filterGroups(String...) on the configuration returned by the method Standardizer.getConfiguration()
chemaxon.struc.IteratorFactory	This class is deprecated and subject to removal in a future release. Please use the appropriate methods of MoleculeGraph and Molecule instead.
chemaxon.struc.IteratorFactory.AtomIterator
chemaxon.struc.IteratorFactory.AtomNeighbourIterator
chemaxon.struc.IteratorFactory.BondIterator
chemaxon.struc.IteratorFactory.BondNeighbourIterator
chemaxon.struc.IteratorFactory.NeighbourIterator
chemaxon.struc.IteratorFactory.RgComponentIterator
chemaxon.struc.IteratorFactory.RxnComponentIterator
chemaxon.struc.IteratorFactory.SgroupIterator
chemaxon.struc.MolAtom.haveEqualProperties(MolAtom)	Deprecated for removal, no replacement.
chemaxon.struc.MolAtom.haveSimilarBonds(MolAtom)	Deprecated for removal, no replacement.
chemaxon.struc.MolAtom.SMARTS_H_DAYLIGHT_COMP_MODE	Not used anymore, will be removed in future releases.
chemaxon.struc.MolAtom.SMARTS_H_MARVIN_COMP_MODE	Not used anymore, will be removed in future releases.
chemaxon.struc.MolBond.haveEqualProperties(MolBond)	Deprecated for removal, no replacement.
chemaxon.struc.Molecule(Molecule, MolAtom)	use Molecule() and MoleculeGraph.add(MolAtom)
chemaxon.struc.Molecule(Molecule, MolBond)	use Molecule() and Molecule.add(MolBond)
chemaxon.struc.Molecule.countExpandableContractableSgroups()
chemaxon.struc.Molecule.countOrderedComponentSgroups()
chemaxon.struc.Molecule.findAllSgroupContaining(MolAtom)	Use Molecule.findSmallestSgroupsContaining(MolAtom)
chemaxon.struc.Molecule.getSgroupIterator()	use Molecule.getSgroupArray() instead.
chemaxon.struc.Molecule.isGUIContracted()	as of Marvin 6.2 replaced by Molecule.hasContractedSgroup()
chemaxon.struc.MoleculeGraph.findAtomClone(MolAtom)	Deprecated for removal, no replacement.
chemaxon.struc.MoleculeGraph.getAtomIterator()	use MoleculeGraph.atoms() or MoleculeGraph.getAtomArray() instead.
chemaxon.struc.MoleculeGraph.getBondIterator()	use MoleculeGraph.bonds() or MoleculeGraph.getBondArray() instead.
chemaxon.struc.MoleculeGraph.isAcceptedSpecialLigand(MolAtom)
chemaxon.struc.QueryBond.haveEqualProperties(MolBond)	Deprecated for removal, no replacement.
chemaxon.struc.RgMolecule.getAtomIterator()	use MoleculeGraph.atoms() or MoleculeGraph.getAtomArray() instead.
chemaxon.struc.RgMolecule.getBondIterator()	use MoleculeGraph.bonds() or MoleculeGraph.getBondArray() instead.
chemaxon.struc.RxnMolecule.getAtomIterator()	use MoleculeGraph.atoms() or MoleculeGraph.getAtomArray() instead.
chemaxon.struc.RxnMolecule.getBondIterator()	use MoleculeGraph.bonds() or MoleculeGraph.getBondArray() instead.
chemaxon.struc.Sgroup.checkConsistencyInEmbeddings()	replaced by Sgroup.checkConsistency()
chemaxon.struc.StereoConstants.CHIRALITYSUPPORT_SELECTED	No longer supported, use StereoConstants.CHIRALITYSUPPORT_ALL option instead.

Deprecated Interfaces

Interface	Description
chemaxon.core.util.MProgressMonitor	Use ProgressMonitor instead.

Deprecated Classes

Class	Description
chemaxon.calculations.HLBPlugin.Builder	Deprecated, use the constructor of HLBPlugin class directly instead.
chemaxon.calculations.StereoisomerPlugin	Use StereoisomerEnumeration instead.
chemaxon.checkers.AtropisomerChecker	This checker is no longer supported.
chemaxon.standardizer.configuration.ConfigurationUtility	Use StandardizerConfiguration.filterGroups(String...) instead
chemaxon.struc.IteratorFactory	This class is deprecated and subject to removal in a future release. Please use the appropriate methods of MoleculeGraph and Molecule instead.
chemaxon.struc.IteratorFactory.AtomIterator
chemaxon.struc.IteratorFactory.AtomNeighbourIterator
chemaxon.struc.IteratorFactory.BondIterator
chemaxon.struc.IteratorFactory.BondNeighbourIterator
chemaxon.struc.IteratorFactory.NeighbourIterator
chemaxon.struc.IteratorFactory.RgComponentIterator
chemaxon.struc.IteratorFactory.RxnComponentIterator
chemaxon.struc.IteratorFactory.SgroupIterator
chemaxon.structurechecker.BasicCheckerRunner	Don't use this class directly, use AdvancedCheckerRunner instead.

Deprecated Fields

Field	Description
chemaxon.calculations.CalculatorPlugin.PLUGIN_DIR	Not used anymore, no replacement.
chemaxon.calculations.PkaPlugin.DEF_IONICSTRENGTH	Use PkaPlugin.DEF_IONIC_STRENGTH instead. This constant will be removed in a future release.
chemaxon.calculations.PkaPlugin.DEF_MAXIONS	Use PkaPlugin.DEF_MAX_IONS instead. This constant will be removed in a future release.
chemaxon.calculations.PkaPlugin.DYNAMICpKaPREFIX	Use PkaPlugin.DYNAMIC_PKA_PREFIX instead. This constant will be removed in a future release.
chemaxon.calculations.PkaPlugin.STATICpKaPREFIX	Use PkaPlugin.STATIC_PKA_PREFIX instead. This constant will be removed in a future release.
chemaxon.marvin.common.ParameterConstants.ATOM_NUMBERS_VISIBLE	in 6.2.0 use atomNumberingType parameter instead.
chemaxon.rendering.constants.DispOptConsts.RS_SELECTED	No longer supported, use DispOptConsts.RS_ALL option instead.
chemaxon.rendering.constants.DispOptConsts.RS_SELECTED_S	No longer supported, use DispOptConsts.RS_ALL_S option instead.
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.MolAtom.SMARTS_H_DAYLIGHT_COMP_MODE	Not used anymore, will be removed in future releases.
chemaxon.struc.MolAtom.SMARTS_H_MARVIN_COMP_MODE	Not used anymore, will be removed in future releases.
chemaxon.struc.StereoConstants.CHIRALITYSUPPORT_SELECTED	No longer supported, use StereoConstants.CHIRALITYSUPPORT_ALL option instead.
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.

Deprecated Methods

Method	Description
chemaxon.alignment.AlignmentMolecule.toData()	use ShapeData.toData() instead.
chemaxon.alignment.AlignmentMoleculeFactory.generate(int, Molecule, boolean, boolean)	Use AlignmentMoleculeFactory.create(Molecule, AlignmentProperties.DegreeOfFreedomType) instead.
chemaxon.calculations.CalculatorPlugin.getpH()	Use CalculatorPlugin.getPh() instead. This method will be removed in a future version.
chemaxon.calculations.CalculatorPlugin.setChemicalTermsArgument(String)	For internal use only.
chemaxon.calculations.CalculatorPlugin.setChemicalTermsParameters(Properties, String)	For internal use only.
chemaxon.calculations.ConformerPlugin.getConformerWithConformerInfoProperty(int)	Only intended for internal use.
chemaxon.calculations.ElementalAnalysisPlugin.setChemicalTermsArgument(String)	For internal use only.
chemaxon.calculations.GeometryPlugin.setChemicalTermsArgument(String)	For internal use only.
chemaxon.calculations.HBDAPlugin.getpHs()	Use HBDAPlugin.getPhValues() instead. This method will be removed in a future version.
chemaxon.calculations.HBDAPlugin.setpHLower(double)	Use HBDAPlugin.setPhLower(double) instead. This method will be removed in a future version.
chemaxon.calculations.HBDAPlugin.setpHStep(double)	Use HBDAPlugin.setPhStep(double) instead. This method will be removed in a future version.
chemaxon.calculations.HBDAPlugin.setpHUpper(double)	Use HBDAPlugin.setPhUpper(double) instead. This method will be removed in a future version.
chemaxon.calculations.HLBPlugin.getDaviesHlbValue()	Deprecated, use HLBPlugin.getDaviesHLBValue() instead.
chemaxon.calculations.HLBPlugin.getGriffinHlbValue()	Deprecated, use HLBPlugin.getGriffinHLBValue() instead.
chemaxon.calculations.HLBPlugin.getHlbValue()	Deprecated, use HLBPlugin.getHLBValue() instead.
chemaxon.calculations.HLBPlugin.getRequiredHlbValue()	Deprecated, use HLBPlugin.getRequiredHLBValue() instead.
chemaxon.calculations.HLBPlugin.setRHLB(boolean)	Deprecated, use HLBPlugin.enableRequiredHLBValue(boolean) instead.
chemaxon.calculations.HuckelAnalysisPlugin.getEigenVector()	Use HuckelAnalysisPlugin.getHMOEigenVector()
chemaxon.calculations.HuckelAnalysisPlugin.getElectrophilicOrder(int)	Use HuckelAnalysisPlugin.getHMOElectrophilicOrder(int)
chemaxon.calculations.HuckelAnalysisPlugin.getHuckelOrbitalCoefficients()	Use HuckelAnalysisPlugin.getHMOHuckelOrbitalCoefficients()
chemaxon.calculations.HuckelAnalysisPlugin.getNucleophilicOrder(int)	Use HuckelAnalysisPlugin.getHMONucleophilicOrder(int)
chemaxon.calculations.HuckelAnalysisPlugin.getRealEigenValue()	Use HuckelAnalysisPlugin.getHMORealEigenValue()
chemaxon.calculations.HuckelAnalysisPlugin.getTotalPiEnergy()	Use HuckelAnalysisPlugin.getHMOTotalPiEnergy()
chemaxon.calculations.IsoelectricPointPlugin.getpHs()	Use IsoelectricPointPlugin.getPhValues() instead. This method will be removed in a future version.
chemaxon.calculations.IsoelectricPointPlugin.getpI()	Use IsoelectricPointPlugin.getIsoelectricPoint() instead. This method will be removed in a future version.
chemaxon.calculations.IsoelectricPointPlugin.getpKaOfpI()	Use IsoelectricPointPlugin.getPkaOfIsoelectricPoint() instead. This method will be removed in a future version.
chemaxon.calculations.IsoelectricPointPlugin.setChemicalTermsArgument(String)
chemaxon.calculations.IsoelectricPointPlugin.setpH(double)	Use IsoelectricPointPlugin.setPh(double) instead. This method will be removed in a future version.
chemaxon.calculations.IsoelectricPointPlugin.setpHLower(double)	Use IsoelectricPointPlugin.setPhLower(double) instead. This method will be removed in a future version.
chemaxon.calculations.IsoelectricPointPlugin.setpHStep(double)	Use IsoelectricPointPlugin.setPhStep(double) instead. This method will be removed in a future version.
chemaxon.calculations.IsoelectricPointPlugin.setpHUpper(double)	Use IsoelectricPointPlugin.setPhUpper(double) instead. This method will be removed in a future version.
chemaxon.calculations.LogDPlugin.calclogD(double)	Use LogDPlugin.calcLogD(double) instead. This method will be removed in a future version.
chemaxon.calculations.LogDPlugin.getHidrophobicity()
chemaxon.calculations.LogDPlugin.getlogD()	Use LogDPlugin.getLogD() instead. This method will be removed in a future version.
chemaxon.calculations.LogDPlugin.getlogDs()	Use LogDPlugin.getLogDValues() instead. This method will be removed in a future version.
chemaxon.calculations.LogDPlugin.getpHs()	Use LogDPlugin.getPhValues() instead. This method will be removed in a future version.
chemaxon.calculations.LogDPlugin.getReflogDs()	Use LogDPlugin.getReferenceLogDValues() instead. This method will be removed in a future version.
chemaxon.calculations.LogDPlugin.getRefpHs()	Use LogDPlugin.getReferencePhValues() instead. This method will be removed in a future version.
chemaxon.calculations.LogDPlugin.setChemicalTermsArgument(String)
chemaxon.calculations.LogDPlugin.setCloridIonConcentration(double)	Use LogDPlugin.setChlorideIonConcentration(double) instead. This method will be removed in a future version.
chemaxon.calculations.LogDPlugin.setlogPMethod(LogPMethod)	Use LogDPlugin.setLogPMethod(LogPMethod) instead. This method will be removed in a future version.
chemaxon.calculations.LogDPlugin.setpH(double)	Use LogDPlugin.setPh(double) instead. This method will be removed in a future version.
chemaxon.calculations.LogDPlugin.setpHLower(double)	Use LogDPlugin.setPhLower(double) instead. This method will be removed in a future version.
chemaxon.calculations.LogDPlugin.setpHStep(double)	Use LogDPlugin.setPhStep(double) instead. This method will be removed in a future version.
chemaxon.calculations.LogDPlugin.setpHUpper(double)	Use LogDPlugin.setPhUpper(double) instead. This method will be removed in a future version.
chemaxon.calculations.LogDPlugin.setpKaCorrectionLibrary(InputStream)	Use LogDPlugin.setPkaCorrectionLibrary(InputStream) instead. This method will be removed in a future version.
chemaxon.calculations.LogDPlugin.setpKaCorrectionLibrary(String)	Use LogDPlugin.setPkaCorrectionLibrary(String) instead. This method will be removed in a future version.
chemaxon.calculations.LogPPlugin.getAtomlogPIncrement(int)	Use LogPPlugin.getAtomLogPIncrement(int) instead. This method will be removed in a future version.
chemaxon.calculations.LogPPlugin.getlogDpI()	Use LogPPlugin.getLogDAtIsoelectricPoint() instead. This method will be removed in a future version.
chemaxon.calculations.LogPPlugin.getlogPMicro()	Use LogPPlugin.getLogPMicro() instead. This method will be removed in a future version.
chemaxon.calculations.LogPPlugin.getlogPNonionic()	Use LogPPlugin.getLogPNonionic() instead. This method will be removed in a future version.
chemaxon.calculations.LogPPlugin.getlogPTrue()	Use LogPPlugin.getLogPTrue() instead. This method will be removed in a future version.
chemaxon.calculations.LogPPlugin.getStructurallogPIncrement()	Use LogPPlugin.getStructuralLogPIncrement() instead. This method will be removed in a future version.
chemaxon.calculations.LogPPlugin.setCloridIonConcentration(double)	Use LogPPlugin.setChlorideIonConcentration(double) instead. This method will be removed in a future version.
chemaxon.calculations.LogPPlugin.setlogPMethod(LogPMethod)	Use LogPPlugin.setLogPMethod(LogPMethod) instead. This method will be removed in a future version.
chemaxon.calculations.MajorMicrospeciesAccessorPlugin.getpH()	Use MajorMicrospeciesAccessorPlugin.getPh() instead. This method will be removed in a future version.
chemaxon.calculations.MajorMicrospeciesAccessorPlugin.setChemicalTermsArgument(String)
chemaxon.calculations.MajorMicrospeciesAccessorPlugin.setpH(double)	Use MajorMicrospeciesAccessorPlugin.setPh(double) instead. This method will be removed in a future version.
chemaxon.calculations.MajorMicrospeciesPlugin.getpH()	Use MajorMicrospeciesPlugin.getPh() instead. This method will be removed in a future version.
chemaxon.calculations.MajorMicrospeciesPlugin.setChemicalTermsArgument(String)
chemaxon.calculations.MajorMicrospeciesPlugin.setpH(double)	Use MajorMicrospeciesPlugin.setPh(double) instead. This method will be removed in a future version.
chemaxon.calculations.MarkushEnumerationPlugin.setChemicalTermsArgument(String)	For internal use only.
chemaxon.calculations.PkaPlugin.getMacropKaValues(int)	Use PkaPlugin.getMacroPkaValues(int) instead. This method will be removed in a future version.
chemaxon.calculations.PkaPlugin.getMacropKaValues(int, double[], int[])	Use PkaPlugin.getMacroPkaValues(int, double[], int[]) instead. This method will be removed in a future version.
chemaxon.calculations.PkaPlugin.getMacroSpeciesCharge(int)	Use PkaPlugin.getMacrospeciesCharge(int) instead. This method will be removed in a future version.
chemaxon.calculations.PkaPlugin.getMacroSpeciesCount()	No replacement. This method will be removed in a future version.
chemaxon.calculations.PkaPlugin.getpHs()	Use PkaPlugin.getPhValues() instead. This method will be removed in a future version.
chemaxon.calculations.PkaPlugin.getpKa(int)	Use PkaPlugin.getPka(int) instead. This method will be removed in a future version.
chemaxon.calculations.PkaPlugin.getPka(int, int)	Use PkaPlugin.getPkaValues(int, int)
chemaxon.calculations.PkaPlugin.getpKaConc(int)	Use PkaPlugin.getPkaConcentration(int) instead. This method will be removed in a future version.
chemaxon.calculations.PkaPlugin.getpKaMixed(int)	Use PkaPlugin.getPkaMixed(int) instead. This method will be removed in a future version.
chemaxon.calculations.PkaPlugin.getpKaPrefixType()	Use PkaPlugin.getPkaPrefixType() instead. This method will be removed in a future version.
chemaxon.calculations.PkaPlugin.getpKaType(int)	Use PkaPlugin.getPkaType(int) instead. This method will be removed in a future version.
chemaxon.calculations.PkaPlugin.getpKaValues(int, int)	Use PkaPlugin.getPkaValues(int, int) instead. This method will be removed in a future version.
chemaxon.calculations.PkaPlugin.setAcidicpKaUpperLimit(double)	Use PkaPlugin.setAcidicPkaUpperLimit(double) instead. This method will be removed in a future version.
chemaxon.calculations.PkaPlugin.setBasicpKaLowerLimit(double)	Use PkaPlugin.setBasicPkaLowerLimit(double) instead. This method will be removed in a future version.
chemaxon.calculations.PkaPlugin.setChemicalTermsArgument(String)	For internal use only.
chemaxon.calculations.PkaPlugin.setMicropKaCalc(boolean)	Use PkaPlugin.setMicroPkaCalc(boolean) instead. This method will be removed in a future version.
chemaxon.calculations.PkaPlugin.setpH(double)	Use PkaPlugin.setPh(double) instead. This method will be removed in a future version.
chemaxon.calculations.PkaPlugin.setpHLower(double)	Use PkaPlugin.setPhLower(double) instead. This method will be removed in a future version.
chemaxon.calculations.PkaPlugin.setpHStep(double)	Use PkaPlugin.setPhStep(double) instead. This method will be removed in a future version.
chemaxon.calculations.PkaPlugin.setpHUpper(double)	Use PkaPlugin.setPhUpper(double) instead. This method will be removed in a future version.
chemaxon.calculations.PkaPlugin.setpKaPrefixType(int)	Use PkaPlugin.setPkaPrefixType(int) instead. This method will be removed in a future version.
chemaxon.calculations.PkaPlugin.useCorrectionLibrary(boolean)	Use PkaPlugin.setCorrectionLibrary(String)
chemaxon.calculations.services.ServiceDescriptor.getIcon()	No longer used, always returns null.
chemaxon.calculations.TautomerPlugin.setChemicalTermsArgument(String)
chemaxon.calculations.TautomerPlugin.setpH(double)	Use TautomerPlugin.setPh(double) instead. This method will be removed in a future version.
chemaxon.calculations.TopologyAnalysisPlugin.setChemicalTermsArgument(String)	For internal use only.
chemaxon.chemterms.ChemTermsExpression.evaluate_boolean(C)	Use ChemTermsExpression.evaluateBoolean(C) instead.
chemaxon.chemterms.ChemTermsExpression.evaluate_booleans(C)	Use ChemTermsExpression.evaluateBooleanArray(C) instead.
chemaxon.chemterms.ChemTermsExpression.evaluate_double(C)	Use ChemTermsExpression.evaluateDouble(C) instead.
chemaxon.chemterms.ChemTermsExpression.evaluate_doubles(C)	Use ChemTermsExpression.evaluateDoubleArray(C) instead.
chemaxon.chemterms.ReactionContext.setProductAtomsByMap(MolAtom[])	use ReactionContext.setReaction(RxnMolecule) instead. Sets the map -> product atom array.
chemaxon.chemterms.ReactionContext.setProducts(Molecule[])	Use ReactionContext.setReaction(RxnMolecule) instead. Sets the products.
chemaxon.chemterms.ReactionContext.setReactantAtomsByMap(MolAtom[])	use ReactionContext.setReaction(RxnMolecule) instead. Sets the map -> reactant atom array.
chemaxon.chemterms.ReactionContext.setReactants(Molecule[])	Use ReactionContext.setReaction(RxnMolecule) instead. Sets the reactants.
chemaxon.core.calculations.clean.CleanUtil.calcBracketEndPoints(Point3D[], Point3D, double)
chemaxon.core.calculations.clean.CleanUtil.calcDividingPoint(Point3D, Point3D, double)
chemaxon.core.calculations.clean.CleanUtil.calcSimplePolymerBracket(Point3D, Point3D, double)
chemaxon.core.calculations.clean.CleanUtil.createBracket(Sgroup, Point3D[], int)
chemaxon.core.calculations.stereo.StereoActivePart.getLigands()	Use StereoActivePart.getLigandIndexes() instead.
chemaxon.core.calculations.stereo.StereoActivePart.getStereoActiveAtom()	Use StereoActivePart.getActiveAtomIndex() instead.
chemaxon.descriptors.ECFP.fromIdentiferSet(Set<Integer>)	Use ECFP.fromIdentifierSet(Set) instead.
chemaxon.descriptors.ECFP.getIdentiferCount()	Use ECFP.getIdentifierCount() instead.
chemaxon.descriptors.ECFP.toIdentiferSet()	Use ECFP.toIdentifierSet() instead
chemaxon.formats.MFileFormat.createRecordReader(MolInputStream, String)	Visibility will be restricted, no replacement method will be provided.
chemaxon.formats.MFileFormat.createUserDefined(String, String, String, MRecordReaderFactory, MolImportModuleFactory, MolExportModuleFactory, RecognizerFactory, String, long)	The support of user-defined formats will be removed.
chemaxon.formats.MFileFormat.createUserDefined(String, List<String>, List<String>, MRecordReaderFactory, MolImportModuleFactory, MolExportModuleFactory, RecognizerFactory, Map<String, Integer>, long)	The support of user-defined formats will be removed.
chemaxon.formats.MFileFormatUtil.createRecordReader(InputStream, String)	For in-house use only. Will be moved.
chemaxon.formats.MFileFormatUtil.createRecordReader(InputStream, String, String, String)	For in-house use only. Will be moved.
chemaxon.formats.MolImporter.importMol(String, Object)	Use MolImporter.importMol(String, String) instead and pass the options as a string (call toString() on the object). This method will be removed in a future release.
chemaxon.formats.MolImportModule.initMolImport(MRecord, String)	Should not be public. Visibility will be restricted in RemovalDate.JUL_01_2027
chemaxon.formats.PositionedInputStream.endGrabLines()
chemaxon.formats.PositionedInputStream.getGrabbedLines()
chemaxon.formats.PositionedInputStream.startGrabLines()
chemaxon.marvin.beans.MarvinPane.getCommonActions()
chemaxon.marvin.beans.MSketchPane.getCommonActions()
chemaxon.marvin.beans.MViewPane.getCommonActions()
chemaxon.marvin.common.MDocStorage.getFieldAccessor()	designed for MarvinView, do not use.
chemaxon.marvin.common.MDocStorage.setFieldAccessor(MFieldAccessor)	designed for MarvinView, do not use.
chemaxon.marvin.common.UserSettings.isExperimentalFeaturesAreAllowed()	Not supported anymore
chemaxon.marvin.common.UserSettings.setAllowExperimentalFeatures(boolean)	Not supported anymore
chemaxon.reaction.mapper.AutoMapper.mapReaction(MolImporter, MolExporter)	Use AutoMapper.mapReactions(MolImporter, MolExporter) instead. This method will be removed in a future release.
chemaxon.reaction.mapper.AutoMapper.mapReaction(MolImporter, MolExporter, AutoMapper.Options)	Use AutoMapper.mapReactions(MolImporter, MolExporter, Options) instead. This method will be removed in a future release.
chemaxon.reaction.mapper.AutoMapper.mapReaction(MolImporter, MolExporter, ReactionMapper...)	No replacement. This method will be removed in a future release.
chemaxon.reaction.mapper.AutoMapper.mapReaction(AutoMapper.Options, Molecule...)	Use AutoMapper.mapReactions(Collection, Options) instead. This method will be removed in a future release.
chemaxon.reaction.mapper.AutoMapper.mapReaction(ReactionMapper[], Molecule...)	No replacement. This method will be removed in a future release.
chemaxon.reaction.mapper.AutoMapper.mapReaction(Molecule...)	Use AutoMapper.mapReactions(Molecule...) instead. This method will be removed in a future release.
chemaxon.reaction.mapper.AutoMapper.mapReaction(Collection<Molecule>)	Use AutoMapper.mapReactions(Collection) instead. This method will be removed in a future release.
chemaxon.reaction.mapper.AutoMapper.mapReaction(Collection<Molecule>, AutoMapper.Options)	Use AutoMapper.mapReactions(Collection, Options) instead. This method will be removed in a future release.
chemaxon.reaction.mapper.AutoMapper.mapReaction(Collection<Molecule>, ReactionMapper...)	No replacement. This method will be removed in a future release.
chemaxon.search.hitdisplay.HitDisplayTool.getHits(Molecule, Molecule, int)	This method will be removed in a future release, use HitDisplayTool.getHits(int) instead.
chemaxon.standardizer.configuration.ConfigurationUtility.filterGroups(StandardizerConfiguration, String[])	Use StandardizerConfiguration.filterGroups(String...) instead
chemaxon.standardizer.Standardizer.setActiveGroups(String...)	use StandardizerConfiguration.filterGroups(String...) on the configuration returned by the method Standardizer.getConfiguration()
chemaxon.struc.MolAtom.getAtomicNumber(String)	As of Marvin 5.9, replaced by a similar method PeriodicTable.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.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.MolAtom.haveEqualProperties(MolAtom)	Deprecated for removal, no replacement.
chemaxon.struc.MolAtom.haveSimilarBonds(MolAtom)	Deprecated for removal, no replacement.
chemaxon.struc.MolAtom.numOf(String)	As of Marvin 5.9, replaced by a similar method PeriodicTable.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.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.MolAtom.setForSpecIsotopeSymbol(String)	as of Marvin 6.3. use MolAtom.setSpecIsotopeSymbolPreferred(boolean) and MolAtom.setMassno(int) instead.
chemaxon.struc.MolBond.haveEqualProperties(MolBond)	Deprecated for removal, no replacement.
chemaxon.struc.Molecule.clonelesscopy(MoleculeGraph)	as of Marvin 6.3. Not supported feature.
chemaxon.struc.Molecule.countExpandableContractableSgroups()
chemaxon.struc.Molecule.countOrderedComponentSgroups()
chemaxon.struc.Molecule.findAllSgroupContaining(MolAtom)	Use Molecule.findSmallestSgroupsContaining(MolAtom)
chemaxon.struc.Molecule.findSgroupContaining(MolAtom)	Use Molecule.findAllSgroupsContaining(MolAtom), as there can be multiple largest S-groups containing a certain atom
chemaxon.struc.Molecule.findSgroupOf(MolAtom)	Use Molecule.findSmallestSgroupsContaining(MolAtom), as there can be multiple smallest S-groups containing a certain atom
chemaxon.struc.Molecule.findSmallestSgroupContaining(MolAtom)	Use Molecule.findSmallestSgroupsContaining(MolAtom), as there can be multiple smallest S-groups containing a certain atom
chemaxon.struc.Molecule.getSgroupIterator()	use Molecule.getSgroupArray() instead.
chemaxon.struc.Molecule.isGUIContracted()	as of Marvin 6.2 replaced by Molecule.hasContractedSgroup()
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.struc.Molecule.ungroupSgroup(int, int)	as of Marvin 6.3. use Molecule.ungroupSgroup(Sgroup) instead.
chemaxon.struc.MoleculeGraph.clonelesscopy(MoleculeGraph)	as of Marvin 6.3. Not supported feature.
chemaxon.struc.MoleculeGraph.findAtomClone(MolAtom)	Deprecated for removal, no replacement.
chemaxon.struc.MoleculeGraph.getAtomIterator()	use MoleculeGraph.atoms() or MoleculeGraph.getAtomArray() instead.
chemaxon.struc.MoleculeGraph.getBondIterator()	use MoleculeGraph.bonds() or MoleculeGraph.getBondArray() instead.
chemaxon.struc.MoleculeGraph.getExplicitLonePairCount(int)	For internal use only.
chemaxon.struc.MoleculeGraph.getLonePairCount(int)	use MolAtom.getLonePairCount() instead
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 construct inconsistent MoleculeGraph. Similar functionality is performed by MoleculeGraph.add(MolBond).
chemaxon.struc.MoleculeGraph.isAcceptedSpecialLigand(MolAtom)
chemaxon.struc.MoleculeGraph.replaceBond(MolBond, MolBond)	as of Marvin 6.2, may construct inconsistent MoleculeGraph. Use MoleculeGraph.removeBond(MolBond) for removal and MoleculeGraph.add(MolBond) for adding a new bond to the molecule.
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.MoleculeGraph.setBond(int, MolBond)	as of Marvin 6.2, may construct inconsistent MoleculeGraph. Use MoleculeGraph.removeBond(MolBond) for bond removal and MoleculeGraph.add(MolBond) for adding a new bond to the molecule.
chemaxon.struc.QueryBond.haveEqualProperties(MolBond)	Deprecated for removal, no replacement.
chemaxon.struc.RgMolecule.clonelesscopy(MoleculeGraph)	as of Marvin 6.3. Not supported feature.
chemaxon.struc.RgMolecule.getAtomIterator()	use MoleculeGraph.atoms() or MoleculeGraph.getAtomArray() instead.
chemaxon.struc.RgMolecule.getBondIterator()	use MoleculeGraph.bonds() or MoleculeGraph.getBondArray() 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.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.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.RxnMolecule.clonelesscopy(MoleculeGraph)	as of Marvin 6.3. Not supported feature.
chemaxon.struc.RxnMolecule.getAtomIterator()	use MoleculeGraph.atoms() or MoleculeGraph.getAtomArray() instead.
chemaxon.struc.RxnMolecule.getBondIterator()	use MoleculeGraph.bonds() or MoleculeGraph.getBondArray() instead.
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.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.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.Sgroup.checkConsistencyInEmbeddings()	replaced by Sgroup.checkConsistency()
chemaxon.struc.Sgroup.setGUIStateRecursively(boolean)	as of Marvin 6.2, use Molecule.setGUIContracted(boolean) for such functionality
chemaxon.struc.Sgroup.setGUIStateRecursively(boolean, int)	as of Marvin 6.2, use Molecule.setGUIContracted(boolean) for such functionality
chemaxon.struc.Sgroup.setXState(int, int)	as of Marvin 6.2, use Sgroup.setXState(int) instead
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.sgroup.SuperatomSgroup.getParentSgroupGraph()	as of Marvin 6.2, intended for internal use, similar functionality can be reached by SuperatomSgroup.getSgroupGraph()
chemaxon.struc.sgroup.SuperatomSgroup.setGUIStateRecursively(boolean)
chemaxon.struc.sgroup.SuperatomSgroup.updateAttachmentPoints()	as of Marvin 6.2, use SuperatomSgroup.calculateAttachmentPoints() instead

Deprecated Constructors

Constructor	Description
chemaxon.checkers.BondAngleChecker(double)	Not used.
chemaxon.checkers.BondLengthChecker(Map<String, String>)	Checker has no parameters.
chemaxon.checkers.result.DefaultExternalStructureCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, Molecule, String, String, String, String, String, Icon)	use 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(StructureChecker, List, List, StructureCheckerErrorType, Molecule, String, String, String, String, Icon, int) instead
chemaxon.checkers.result.MetalloceneCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, StructureCheckerErrorType, Molecule, String, String, String, String, Icon, List<List<MolAtom>>, List<MolAtom>)	use MetalloceneCheckerResult(StructureChecker, List, List, StructureCheckerErrorType, Molecule, String, String, String, String, Icon, List, List, int) instead
chemaxon.marvin.datatransfer.TransferableDescriptor(String, String, Integer, Integer, boolean, boolean)	since 5.3.3 new descriptor parameter added.
chemaxon.struc.Molecule(Molecule, MolAtom)	use Molecule() and MoleculeGraph.add(MolAtom)
chemaxon.struc.Molecule(Molecule, MolBond)	use Molecule() and Molecule.add(MolBond)
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).

Deprecated Enum Constants

Enum Constant	Description
chemaxon.alignment.AlignmentProperties.GAUSS_FAST_EXTENDED_ATOMTYPE_MCS
chemaxon.alignment.AlignmentProperties.OrientationType.MCS
chemaxon.checkers.StructureCheckerErrorType.INVALID_COORD_SYSTEM	StructureCheckerErrorType.INVALID_COORDINATION_SYSTEM is used instead
chemaxon.checkers.StructureCheckerErrorType.MULTI_COMPONENT	StructureCheckerErrorType.MULTIPLE_COMPONENT is used instead
chemaxon.checkers.StructureCheckerErrorType.PSEUDO_NO_GROUP	StructureCheckerErrorType.PSEUDO is used instead
chemaxon.checkers.StructureCheckerErrorType.SOLVENT_AMBIGOUS	StructureCheckerErrorType.SOLVENT_AMBIGUOUS is used instead
chemaxon.checkers.StructureCheckerErrorType.SUBSTRUCTURE_NOFIX	This error type is not used, will be removed