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Deprecated API

Contents

  • Terminally Deprecated
  • Interfaces
  • Classes
  • Enum Classes
  • Fields
  • Methods
  • Constructors
  • Enum Constants
  • Terminally Deprecated Elements
    Element
    Description
    chemaxon.descriptors.MolecularDescriptor.main(String[])
    Will be removed, no replacement.
    chemaxon.descriptors.ReactionFingerprint.main(String[])
    Will be removed, no replacement.
    chemaxon.jep.Evaluator.main(String[])
    This main method will be removed, CLI interfaces should not be used directly from Java code.
    chemaxon.marvin.plugin.CalculatorPluginDisplay
    This class has been moved to a new package, import and use it from its new location: CalculatorPluginDisplay
    chemaxon.marvin.plugin.CalculatorPluginOutput
    This class has been moved to a new package, import and use it from its new location: CalculatorPluginOutput
    chemaxon.marvin.plugin.ParameterPanelHandler
    This interface has been moved to a new package, import and use it from its new location: ParameterPanelHandler
    chemaxon.marvin.plugin.PluginFactory
    This class has been moved to a new package, import and use it from its new location: PluginFactory
    chemaxon.pharmacophore.PMapper.main(String[])
    This main method will be removed, CLI interfaces should not be used directly from Java code.
    chemaxon.reaction.ConcurrentReactorProcessor.main(String[])
    Deprecated for removal.
    chemaxon.util.MolAligner
    Moved to a new package, use it from its new location: MolAligner.
  • Deprecated Interfaces
    Interface
    Description
    chemaxon.descriptors.MolecularDescriptorGenerator
    5.4
    chemaxon.jep.MolCondition
    Will be removed soon.
    chemaxon.marvin.plugin.ParameterPanelHandler
    This interface has been moved to a new package, import and use it from its new location: ParameterPanelHandler
    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.reaction.ReactantSetEnumeration
    com.chemaxon.calculations.common.SubProgressObserver
    Use ProgressObserver instead. Will be removed.
    com.chemaxon.calculations.io.Sink
    Use Consumer instead.
    com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue
  • Deprecated Classes
    Class
    Description
    chemaxon.checkers.result.ReactionCheckerResult
     
    chemaxon.checkers.runner.SketchCheckerRunner
    chemaxon.checkers.StereoCheckUtility
    Will be removed from the public API.
    chemaxon.checkers.StructureCheckerFactory
    use CheckerFixerFactory instead
    chemaxon.checkers.WedgeErrorChecker
    chemaxon.fixers.AbsentChiralFlagFixer
    use AddChiralFlagFixer
    chemaxon.fixers.AbsoluteStereoFixer
    use RemoveInvalidChiralFlagFixer
    chemaxon.fixers.CrossedDoubleBondFixer
    use ConvertToWigglyDoubleBondFixer
    chemaxon.fixers.ExplicitHydrogenFixer
    use RemoveExplicitHydrogenFixer
    chemaxon.fixers.IsotopeFixer
    use ConvertToElementalFormFixer
    chemaxon.fixers.StructureFixerFactory
    use CheckerFixerFactory instead
    chemaxon.fixers.WedgeCleanFixer
    chemaxon.fixers.WigglyDoubleBondFixer
    use ConvertToCrossedDoubleBondFixer
    chemaxon.formats.MolConverter.Options
    as of Marvin 5.2.3, use MolConverter.Builder instead.
    chemaxon.formats.recognizer.AbbrevGroupRecognizer
    as of Marvin 2014.07.21.0 intended for internal use only
    chemaxon.formats.recognizer.CubeRecognizer
    as of Marvin 2014.07.21.0 intended for internal use only
    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.formats.recognizer.RecognizerList
    as of Marvin 2014.07.21.0 not used
    chemaxon.formats.recognizer.SMILESRecognizer
    as of Marvin 2014.07.21.0 intended for internal use only
    chemaxon.marvin.calculations.StereoisomerPlugin
    chemaxon.marvin.plugin.CalculatorPluginDisplay
    This class has been moved to a new package, import and use it from its new location: CalculatorPluginDisplay
    chemaxon.marvin.plugin.CalculatorPluginOutput
    This class has been moved to a new package, import and use it from its new location: CalculatorPluginOutput
    chemaxon.marvin.plugin.PluginFactory
    This class has been moved to a new package, import and use it from its new location: PluginFactory
    chemaxon.marvin.util.MoleculeUtil
    as of Marvin 5.11.1
    chemaxon.standardizer.actions.AbsoluteStereoAction
    use SetAbsoluteStereoAction or RemoveAbsoluteStereoAction instead
    chemaxon.util.MolAligner
    Moved to a new package, use it from its new location: MolAligner.
  • Deprecated Enum Classes
    Enum Class
    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
    Description
    chemaxon.checkers.runner.configuration.reader.ConfigurationReader.USER_CHECKERS_CONFIG_PATH
    Configuration file URL can be set in MarvinSketch preferences, and stored in UserSettings.
    chemaxon.formats.MdlCompressor.TEXTMODE
    as of Marvin 3.1, there is no possibility to do that
    chemaxon.marvin.calculations.logDPlugin.METHOD_KLOP
    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.logDPlugin.METHOD_USER_DEFINED
    Use LogPMethod.USER_DEFINED instead.
    chemaxon.marvin.calculations.logDPlugin.METHOD_VG
    Use LogPMethod.CHEMAXON instead.
    chemaxon.marvin.calculations.logDPlugin.METHOD_WEIGHTED
    Use LogPMethod.CONSENSUS instead.
    chemaxon.marvin.calculations.logPPlugin.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.logPPlugin.METHOD_USER_DEFINED
    Use LogPMethod.USER_DEFINED instead.
    chemaxon.marvin.calculations.logPPlugin.METHOD_VG
    Use LogPMethod.CHEMAXON instead.
    chemaxon.marvin.calculations.logPPlugin.METHOD_WEIGHTED
    Use LogPMethod.CONSENSUS instead.
    chemaxon.marvin.common.ParameterConstants.ATOM_NUMBERS_VISIBLE
    in 6.2.0 use atomNumberingType parameter instead.
    chemaxon.marvin.common.ParameterConstants.COPY_OPTIONS
    since 5.3.3 has no sense
    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.marvin.common.ParameterConstants.VIEW_EXPLICIT_H
     
    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.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.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.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.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.marvin.paint.DispOptConsts.WIREFRAME
    use RenderingStyle instead.
    chemaxon.marvin.paint.DispOptConsts.WIREFRAME_RENDERING_S
    use RenderingStyle instead.
    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.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.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.sss.SearchConstants.SEARCH_MODE_NAMES
    As of JChem 5.12, replaced by SearchConstants.SEARCH_TYPE_NAMES.
    chemaxon.standardizer.Standardizer.FINAL_CLEAN_ID
     
    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.Molecule.RM_KEEP_LEAVINGGROUPS
    As of Marvin 6.2, no replacement.
    Not supported feature.
    chemaxon.struc.MoleculeGraph.VALENCE_CHECK_AMBIGUOUS
    As of Marvin 6.0, replaced by ValenceCheckOptions.
    chemaxon.struc.sgroup.Expandable.COORDS_UPDATE
    As of Marvin 6.2, no replacement.
    Not supported feature.
    chemaxon.struc.sgroup.Expandable.REVERSIBLE_EXPAND
    as of Marvin 6.2, use Expandable.LEAVE_COORDS_UNCHANGED 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.
     
    chemaxon.util.iterator.IteratorFactory.INCLUDE_CHEMICAL_ATOMS
    As of Marvin 6.2, Use IteratorFactory.INCLUDE_CHEMICAL_ATOMS_ONLY instead.
    com.chemaxon.calculations.gui.PluginFactory.PRELOAD
    Not used.
  • Deprecated Methods
    Method
    Description
    chemaxon.calculations.ElementalAnalyser.setMolecule(Smolecule)
    as of Marvin 6.0, replaced by ElementalAnalyser.setMolecule(MoleculeGraph mol).
    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.calculations.hydrogenize.Hydrogenize.addLonePairs(MoleculeGraph, MolAtom[])
    since Marvin 5.11 use convertImplicitLonePairsToExplicit(MoleculeGraph, MolAtom[]) isntead
    chemaxon.calculations.hydrogenize.Hydrogenize.isBridgeHeadAtom(MoleculeGraph, int)
    as of Marvin 5.11.1, replaced by TopologyUtil.isBridgeHeadAtom(MoleculeGraph, int)
    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.calculations.hydrogenize.Hydrogenize.removeLonePairs(MoleculeGraph)
    since Marvin 5.11 use convertExplicitLonePairsToImplicit(MoleculeGraph) 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.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.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.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.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.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.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.calculations.TopologyAnalyser.isAsymmetricAtom(int)
    as of release 5.5, replaced by Stereochemistry.isAsymmetricAtom(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.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.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.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.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.calculations.TopologyAnalyser.stereo(int)
    as of release 5.5, replaced by Stereochemistry.stereo(int)
    chemaxon.calculations.TopologyAnalyser.stereo(int, int)
    as of release 5.5, replaced by Stereochemistry.stereo(int, int)
    chemaxon.calculations.TopologyAnalyser.stereoDoubleBondCount()
    as of release 5.5, replaced by Stereochemistry.stereoDoubleBondCount()
    chemaxon.checkers.StructureChecker.getDescription()
    This method isn't needed anymore and will be removed in 6.0
    chemaxon.checkers.StructureChecker.getEditorClassName()
    This method isn't needed anymore and will be removed in 6.0
    chemaxon.checkers.StructureChecker.getHelpText()
    This method isn't needed anymore and will be removed in 6.0
    chemaxon.checkers.StructureChecker.getIcon()
    This method isn't needed anymore and will be removed in 6.0
    chemaxon.checkers.StructureChecker.getLocalMenuName()
    This method isn't needed anymore and will be removed in 6.0
    chemaxon.checkers.StructureChecker.getName()
    This method isn't needed anymore and will be removed in 6.0
    chemaxon.checkers.StructureChecker.setDescription(String)
    This method isn't needed anymore and will be removed in 6.0
    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.checkers.StructureChecker.setLocalMenuName(String)
    This method isn't needed anymore and will be removed in 6.0
    chemaxon.checkers.StructureChecker.setMoreErrorMessage(String)
    This method isn't needed anymore and will be removed in 6.0
    chemaxon.checkers.StructureChecker.setName(String)
    This method isn't needed anymore and will be removed in 6.0
    chemaxon.checkers.StructureChecker.setNoErrorMessage(String)
    This method isn't needed anymore and will be removed in 6.0
    chemaxon.checkers.StructureChecker.setOneErrorMessage(String)
    This method isn't needed anymore and will be removed in 6.0
    chemaxon.core.calculations.valencecheck.ValenceCheckOptions.Builder.setLocalAromatiChecking(boolean)
    since Marvin 14.7.7, Use ValenceCheckOptions.Builder.setLocalAromaticChecking(boolean) instead.
    chemaxon.descriptors.ECFP.fromFeatureSet(Set<Integer>)
    As of JChem 5.4.1, replaced by fromIdentiferSet().
    chemaxon.descriptors.ECFP.getFeatureCount()
    As of JChem 5.4.1, replaced by ECFP.getIdentiferCount().
    chemaxon.descriptors.ECFP.toFeatureSet()
    As of JChem 5.4.1, replaced by ECFP.toIdentiferSet().
    chemaxon.descriptors.MolecularDescriptor.main(String[])
    Will be removed, no replacement.
    chemaxon.descriptors.ReactionFingerprint.main(String[])
    Will be removed, no replacement.
    chemaxon.descriptors.ShapeDescriptor.getHistogramSimilarity(MolecularDescriptor)
    use ShapeDescriptor.getShapeSimilarity(MolecularDescriptor) instead
    chemaxon.fixers.StructureFixer.getDescription()
    chemaxon.fixers.StructureFixer.getName()
    chemaxon.fixers.StructureFixer.setDescription(String)
    chemaxon.fixers.StructureFixer.setName(String)
    chemaxon.formats.MFileFormat.createRecognizer(String)
    as of Marvin 2014.07.21.0 use MFileFormat.createRecognizer() instead
    chemaxon.formats.MFileFormat.getMIMEType()
    as of Marvin 2014.07.21.0 not used
    chemaxon.formats.MFileFormat.getPriority(String)
    as of Marvin 2014.07.21.0 use MFileFormat.getSubFormatPriority(String) instead
    chemaxon.formats.MolConverter.Options.addInput(File, String)
    chemaxon.formats.MolConverter.Options.addInput(InputStream, String)
    chemaxon.formats.MolConverter.Options.addInput(String, String)
    chemaxon.formats.MolConverter.Options.build()
    chemaxon.formats.MolConverter.Options.clean(int)
    chemaxon.formats.MolConverter.Options.clean(int, String)
    chemaxon.formats.MolConverter.Options.clear()
    chemaxon.formats.MolConverter.Options.clone()
    chemaxon.formats.MolConverter.Options.getInputCount()
    chemaxon.formats.MolConverter.Options.setEncodings(String)
    chemaxon.formats.MolConverter.Options.setFields(String[])
    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.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.formats.MolImporter.isGrabbingEnabled()
    as of Marvin 6.2. It has no effect on the code.
    chemaxon.formats.MolImporter.read(Molecule)
    as of Marvin 14.7.7. use MolImporter.read() instead
    chemaxon.formats.MolImporter.readDoc(MDocument, Molecule)
    as of Marvin 14.7.7. useMolImporter.nextDoc() instead
    chemaxon.formats.MolImporter.readMol(Molecule)
    as of Marvin 14.7.7. use MolImporter.read() instead
    chemaxon.formats.MolImporter.setGrabbingEnabled(boolean)
    as of Marvin 6.2. It has no effect on the code.
    chemaxon.formats.recognizer.PeptideRecognizer.guessPeptideFormat(String)
    as of Marvin 2014.07.21.0 intended for internal use
    chemaxon.formats.recognizer.Recognizer.getLastProcessedLineNum()
    as of Marvin 2014.07.21.0 not used
    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.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.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.jep.Evaluator.getFunctionParameterData()
    use Evaluator.getFunctionData()
    chemaxon.jep.Evaluator.getPluginIDs()
    use Evaluator.getFunctionData()
    chemaxon.jep.Evaluator.main(String[])
    This main method will be removed, CLI interfaces should not be used directly from Java code.
    chemaxon.jep.Evaluator.toString(Object)
    For internal use only.
    chemaxon.jep.Evaluator.toString(Object, int)
    For internal use only.
    chemaxon.jep.Evaluator.toString(Object, DecimalFormat)
    For internal use only.
    chemaxon.marvin.alignment.Alignment.setMinimumCommonSize(int)
    chemaxon.marvin.alignment.AlignmentMolecule.create(byte[])
    chemaxon.marvin.alignment.AlignmentMolecule.toData()
    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.alignment.AlignmentMoleculeFactory.isAromatize()
    chemaxon.marvin.alignment.AlignmentMoleculeFactory.isDehidrogenize()
    The explicit Hydrogens are not removed from the original input structure. No need to use.
    chemaxon.marvin.alignment.AlignmentMoleculeFactory.setAromatize(boolean)
    The original input structure is not aromatized. No need to use.
    chemaxon.marvin.alignment.AlignmentMoleculeFactory.setDehidrogenize(boolean)
    The explicit Hydrogens are not removed from the original input structure. No need to use.
    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.marvin.alignment.AlignmentMoleculeFactory.setUseOriginal(boolean)
    always false: Molecule is always converted before alignment, but coordinates are written back to the original one.
    chemaxon.marvin.beans.MarvinPane.addToolsMenu(Container)
    Not used.
    chemaxon.marvin.beans.MarvinPane.createMenu(ResourceBundle, String)
    as of Marvin 3.3.1, replaced by SwingUtil.createMenu
    chemaxon.marvin.beans.MarvinPane.getBondWidth()
    as of Marvin 4.1, replaced by MarvinPane.getBondSpacing()
    chemaxon.marvin.beans.MarvinPane.getCommonActions()
     
    chemaxon.marvin.beans.MarvinPane.getLabels()
    use isAtomSymbolsVisible() instead
    chemaxon.marvin.beans.MarvinPane.getReadGlobalGUIProperties()
    since Marvin 5.1 when this and the MarvinPane.getSaveGlobalGUIProperties() function have been merged.
    chemaxon.marvin.beans.MarvinPane.getSetColor(int)
    as of Marvin 3.3, replaced by getAtomSetColor
    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.beans.MarvinPane.isAtomNumbersVisible()
    in 6.2.0. Use getAtomNumberingType() instead.
    chemaxon.marvin.beans.MarvinPane.isGrinv()
    as of Marvin 3.5, use isGrinvVisible() instead
    chemaxon.marvin.beans.MarvinPane.setAtomNumbersVisible(boolean)
    in 6.2.0. Use setAtomNumberingType() instead
    chemaxon.marvin.beans.MarvinPane.setBondWidth(double)
    as of Marvin 4.1, replaced by MarvinPane.setBondSpacing(double)
    chemaxon.marvin.beans.MarvinPane.setGrinv(boolean)
    as of Marvin 3.5, use setGrinvVisible(boolean) instead
    chemaxon.marvin.beans.MarvinPane.setLabels(boolean)
    use setAtomSymbolsVisible(v) instead
    chemaxon.marvin.beans.MarvinPane.setSetColor(int, Color)
    as of Marvin 3.3, replaced by setAtomSetColor
    chemaxon.marvin.beans.MSketchPane.getCommonActions()
    at N/A (before 02/12/2015)
    chemaxon.marvin.beans.MSketchPane.getMag()
    As of Marvin 2.8.1, replaced by getScale()
    chemaxon.marvin.beans.MSketchPane.getMrvWithSettings()
    use MSketchPane.getMol(String) instead
    chemaxon.marvin.beans.MSketchPane.getSimpView()
    as of Marvin 3.5, replaced by MSketchPane.isBondDraggedAlong()
    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.marvin.beans.MSketchPane.setMag(double)
    As of Marvin 2.8.1, replaced by setScale()
    chemaxon.marvin.beans.MSketchPane.setMol(Molecule, boolean)
    use MSketchPane.setMol(Molecule) instead of this method.
    chemaxon.marvin.beans.MSketchPane.setMrvWithSettings(String)
    use MSketchPane.setMol(String)
    chemaxon.marvin.beans.MSketchPane.setSimpView(int)
    as of Marvin 3.5, replaced by MSketchPane.setBondDraggedAlong(boolean)
    chemaxon.marvin.beans.MViewPane.getCanvasComponent(int)
    as of Marvin 3.0, replaced by getVisibleCellComponent
    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.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.MViewPane.setSetSeq(int, int, int)
    as of Marvin 3.3, replaced by setAtomSetSeq
    chemaxon.marvin.calculations.AlignmentPlugin.setMinimumCommonSize(int)
    chemaxon.marvin.calculations.ConformerPlugin.getConformerWithConformerInfoProperty(int)
    Only intended for internal use.
    chemaxon.marvin.calculations.HBDAPlugin.getAcceptorCount()
    Use HBDAPlugin.getAcceptorSiteCount() instead.
    chemaxon.marvin.calculations.HBDAPlugin.getAcceptorCount(int)
    Use HBDAPlugin.getAcceptorSiteCount() instead!
    chemaxon.marvin.calculations.HBDAPlugin.getDonorCount()
    Use HBDAPlugin.getDonorSiteCount() instead!
    chemaxon.marvin.calculations.HBDAPlugin.getDonorCount(int)
    Use HBDAPlugin.getDonorSiteCount(int) instead!
    chemaxon.marvin.calculations.HBDAPlugin.setGUIMode(boolean)
     
    chemaxon.marvin.calculations.HuckelAnalysisPlugin.getEigenVector()
    Use HuckelAnalysisPlugin.getHMOEigenVector()
    chemaxon.marvin.calculations.HuckelAnalysisPlugin.getElectrophilicOrder(int)
    Use HuckelAnalysisPlugin.getHMOElectrophilicOrder(int)
    chemaxon.marvin.calculations.HuckelAnalysisPlugin.getHuckelOrbitalCoefficients()
    Use HuckelAnalysisPlugin.getHMOHuckelOrbitalCoefficients()
    chemaxon.marvin.calculations.HuckelAnalysisPlugin.getNucleophilicOrder(int)
    Use HuckelAnalysisPlugin.getHMONucleophilicOrder(int)
    chemaxon.marvin.calculations.HuckelAnalysisPlugin.getRealEigenValue()
    Use HuckelAnalysisPlugin.getHMORealEigenValue()
    chemaxon.marvin.calculations.HuckelAnalysisPlugin.getTotalPiEnergy()
    Use HuckelAnalysisPlugin.getHMOTotalPiEnergy()
    chemaxon.marvin.calculations.logDPlugin.setlogPMethod(int)
    Use {@link #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.marvin.calculations.logPPlugin.getAtomlogPHIncrement(int)
    Increments of implicit H-s are not calculated. Returns the same value as logPPlugin.getAtomlogPIncrement(int)
    chemaxon.marvin.calculations.logPPlugin.setlogPMethod(int)
    Use logPPlugin.setlogPMethod(LogPMethod) instead.
    chemaxon.marvin.calculations.logPPlugin.setTakeMajorTatomericForm(boolean)
    Use logPPlugin.setConsiderTautomerization(boolean)
    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.pKaPlugin.getpKa(int, int)
    Use pKaPlugin.getpKaValues(int, int)
    chemaxon.marvin.calculations.pKaPlugin.getSortedValues(int, double[], int[])
    Use pKaPlugin.getMacropKaValues(int,double[],int[]) instead
    chemaxon.marvin.calculations.pKaPlugin.setCalcAlways(boolean)
    replaced by setModel(int)
    chemaxon.marvin.calculations.pKaPlugin.setTakeMajorTatomericForm(boolean)
    Use pKaPlugin.setConsiderTautomerization(boolean)
    chemaxon.marvin.calculations.pKaPlugin.useCorrectionLibrary(boolean)
    Use pKaPlugin.setCorrectionLibrary(String)
    chemaxon.marvin.calculations.ResonancePlugin.createStandardizedMolecule(Molecule, boolean)
    Use ResonancePlugin.createStandardizedMolecule(Molecule) instead
    chemaxon.marvin.calculations.ResonancePlugin.setInputMoleculeModified(boolean)
    Not used.
    chemaxon.marvin.calculations.ResonancePlugin.setpH(double)
    As of Marvin 5.0 pH effect is not considered
    chemaxon.marvin.calculations.TautomerizationPlugin.createStandardizedMolecule(Molecule, boolean)
     
    chemaxon.marvin.calculations.TautomerizationPlugin.getStructures()
    since Marvin 5.9 replaced by TautomerizationPlugin.getStructure(int)
    chemaxon.marvin.calculations.TautomerizationPlugin.setCleanResultStructures(boolean)
    obsolate method
    chemaxon.marvin.calculations.TautomerizationPlugin.setInputMoleculeModified(boolean)
    Not used.
    chemaxon.marvin.calculations.TautomerizationPlugin.setRationalTautomerGenerationMode(boolean)
    chemaxon.marvin.calculations.TautomerizationPlugin.setTakeMostStableTautomer(boolean)
    Not used.
    chemaxon.marvin.calculations.TopologyAnalyserPlugin.getAliphaticRingCountOfSize(int)
    Use TopologyAnalyserPlugin.getAliphaticRingCount(int)
    chemaxon.marvin.calculations.TopologyAnalyserPlugin.getAromaticRingCountOfSize(int)
    Use TopologyAnalyserPlugin.getAromaticRingCount(int)
    chemaxon.marvin.calculations.TopologyAnalyserPlugin.getRingCountOfSize(int)
    Use TopologyAnalyserPlugin.getRingCount(int)
    chemaxon.marvin.calculations.TopologyAnalyserPlugin.getRingSystemCountOfSize(int)
    Use TopologyAnalyserPlugin.getRingSystemCount(int)
    chemaxon.marvin.calculations.TPSAPlugin.getTPSA()
    as of Marvin 4.1, replaced by TPSAPlugin.getSurfaceArea()
    chemaxon.marvin.common.UserSettings.getCheckerConfigFileName()
    Use UserSettings.getCheckerConfigURL() instead. Deprecated in 5.12.
    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.io.MolExportModule.preconvert(MoleculeGraph, boolean, int, boolean)
    Marvin 6.2 use MolExportModule.preconvert(chemaxon.struc.Molecule, boolean, int, boolean) instead
    chemaxon.marvin.modules.datatransfer.ClipboardHandler.addTransferable(String, String, Integer, Integer, boolean, boolean)
    use ClipboardHandler.addTransferable(String, String, Integer, Integer, boolean, boolean, boolean) instead.
    chemaxon.marvin.modules.datatransfer.ClipboardHandler.putFormattedTextToClipboard(Document, int, int)
    chemaxon.marvin.MolPrinter.getAtomsize()
    As of Marvin 5.2.2, replaced by MolPrinter.getAtomSize().
    chemaxon.marvin.MolPrinter.getBondWidth()
    as of Marvin 4.1, replaced by MolPrinter.getBondSpacing()
    chemaxon.marvin.MolPrinter.getDisplayQuality()
    since Marvin 6.4 only high quality exists
    chemaxon.marvin.MolPrinter.isAtomNumbersVisible()
    in 6.2.0. Use getAtomNumberingType 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.marvin.MolPrinter.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.marvin.MolPrinter.setBondWidth(double)
    as of Marvin 4.1, replaced by MolPrinter.setBondSpacing(double)
    chemaxon.marvin.MolPrinter.setChargeFont(Font)
    in Marvin 15.5.18
    chemaxon.marvin.MolPrinter.setDisplayQuality(int)
    since Marvin 6.4 only high quality exists
    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.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.marvin.plugin.CalculatorPlugin.getMainMolecule(Molecule)
    Use CalculatorPlugin.createModifiedInputMolecule(Molecule) instead
    chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(boolean, boolean)
    use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
    Default toolbar configuration will be used for toolbars.
    chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(boolean, boolean, boolean)
    use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
    Default toolbar configuration will be used for toolbars.
    chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(boolean, boolean, CodeAssistDataProvider.Context)
    use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
    Default toolbar configuration will be used for toolbars.
    chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(boolean, CodeAssistDataProvider.Context)
    use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
    Default toolbar configuration will be used for toolbars.
    Available function list will be shown when typing ctrl-space.
    chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(CodeAssistDataProvider.Context)
    use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
    Default toolbar configuration will be used for toolbars.
    Available function list will be shown when typing ctrl-space.
    Default help text will be shown in empty textpane.
    chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String)
    use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
    Default toolbar configuration will be used for toolbars.
    Available function list will be shown when typing ctrl-space.
    Default help text will be shown in empty textpane.
    chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, boolean)
    use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
    Default toolbar configuration will be used for toolbars.
    Available function list will be shown when typing ctrl-space
    chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, boolean, boolean)
    use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
    Default toolbar configuration will be used for toolbars.
    chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, boolean, boolean, boolean)
    use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
    Default toolbar configuration will be used for toolbars.
    chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, boolean, boolean, CodeAssistDataProvider.Context)
    use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
    Default toolbar configuration will be used for toolbars.
    chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, boolean, CodeAssistDataProvider.Context)
    use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
    Default toolbar configuration will be used for toolbars.
    Available function list will be shown when typing ctrl-space
    chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, CodeAssistDataProvider.Context)
    use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
    Default toolbar configuration will be used for toolbars.
    Available function list will be shown when typing ctrl-space.
    Default help text will be shown in empty textpane.
    chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, String)
    use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
    Default toolbar configuration will be used for toolbars.
    Available function list will be shown when typing ctrl-space
    chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, String, boolean)
    use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
    Default toolbar configuration will be used for toolbars.
    chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, String, boolean, boolean)
    use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
    Default toolbar configuration will be used for toolbars.
    chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, String, boolean, CodeAssistDataProvider.Context)
    use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
    Default toolbar configuration will be used for toolbars.
    chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, String, boolean, String)
    use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
    chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, String, boolean, String, boolean)
    use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
    chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, String, boolean, String, boolean, CodeAssistDataProvider.Context)
    use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
    chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, String, boolean, String, CodeAssistDataProvider.Context)
    use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
    chemaxon.marvin.util.MoleculeUtil.arrangeCrossingBonds(MolBond, Molecule, boolean)
    as of Marvin 5.11.1 use MoleculeGraph.setBond(int, MolBond)
    chemaxon.marvin.util.MoleculeUtil.getCrossingBonds(MolBond[], DPoint3, DPoint3)
    as of Marvin 5.11.1
    chemaxon.marvin.util.SwingUtil.initCtrlShortcutForMac(JMenuItem)
    does nothing.
    chemaxon.marvin.util.SwingUtil.initInApplet()
    does nothing.
    chemaxon.marvin.view.MDocStorage.countRecordsInFraction(double, int, MProgressMonitor)
     
    chemaxon.pharmacophore.PMapper.main(String[])
    This main method will be removed, CLI interfaces should not be used directly from Java code.
    chemaxon.reaction.ConcurrentReactorProcessor.main(String[])
    Deprecated for removal.
    chemaxon.reaction.ConcurrentReactorProcessor.setReactantIterators(MoleculeIterator[], int, String, double, boolean)
    The last three arguments are not used anymore, call ConcurrentReactorProcessor.setReactantIterators(MoleculeIterator[], int) instead
    chemaxon.reaction.ConcurrentReactorProcessor.setReactantSetEnumerator(ReactantSetEnumeration)
    calling this method may result in very poor performance, call ConcurrentReactorProcessor.setReactantIterators(MoleculeIterator[], int) instead
    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.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.standardizer.advancedactions.TransformAction.getStructure()
    chemaxon.standardizer.advancedactions.TransformAction.setStructure(String)
    use TransformAction.setTransform(RxnMolecule) method instead
    chemaxon.standardizer.Standardizer.getActiveGroups()
    use ConfigurationUtility.filterGroups(StandardizerConfiguration, String[]) on the configuration returned by the method Standardizer.getConfiguration()
    chemaxon.standardizer.Standardizer.setActiveGroups(String[])
    use ConfigurationUtility.filterGroups(StandardizerConfiguration, String[]) on the configuration returned by the method Standardizer.getConfiguration()
    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.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) .
    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.struc.graphics.MPolyline.rotate(DPoint3, double, DPoint3)
    As of Marvin 6.1, replaced by CTransform3D.setRotation(double, double, double, double) and CTransform3D.setRotationCenter(DPoint3).
    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.MDocument.exportToBinFormat(String)
    As of release 5.7, replaced by MolExporter.exportToBinFormat(MDocument, String).
    chemaxon.struc.MDocument.exportToFormat(String)
    As of release 5.7, replaced by MolExporter.exportToFormat(MDocument, String)
    chemaxon.struc.MDocument.exportToObject(String)
    As of release 5.7, replaced by MolExporter.exportToObject(MDocument, String)
    chemaxon.struc.MDocument.parseMRV(String)
    As of release 5.7, replaced by MolImporter.parseMRV(String)
    chemaxon.struc.MDocument.Prop.convertToString(String, int)
    As of release 5.7, replaced by MolExporter.convertToString(MDocument, String, int)
    chemaxon.struc.MDocument.setGUIProperyContainer(MPropertyContainer)
    As of Marvin 6.1, replaced by MDocument.setGUIPropertyContainer(MPropertyContainer).
    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.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.getQuerystr()
    As of release 5.7, replaced by MolAtom.getQueryString()
    chemaxon.struc.MolAtom.getRadical()
    as of Marvin 6.2. use MolAtom.getRadicalValue() 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.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.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.MolAtom.setImplicitHBasedOnValence(Valence)
    as of Marvin 6.0.1, exists only for internal usage
    Usage:
    Internal usage only.
    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.struc.MolAtom.setSMARTS(String)
    As of release 5.7, replaced by SmartsAtomQuerifier.setSMARTS(MolAtom atom, String s)
    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.MolBond.isRemovable()
    As of Marvin 6.2, no replacement.
    Not supported feature.
    chemaxon.struc.Molecule.checkConsistency()
    As of Marvin 5.7, no replacement.
    Not intended for public use, it was intended only for internal debugging.
    chemaxon.struc.Molecule.clonelesscopy(MoleculeGraph)
    as of Marvin 6.3.
    Not supported feature.
    chemaxon.struc.Molecule.cloneMolecule()
    as of Marvin 2014.09.01.0 use Molecule.clone() instead
    chemaxon.struc.Molecule.exportToBinFormat(String)
    As of Marvin 5.7, replaced by MolExporter.exportToBinFormat(Molecule, String).
    chemaxon.struc.Molecule.exportToFormat(String)
    As of Marvin 5.7, replaced by MolExporter.exportToFormat(Molecule, String).
    chemaxon.struc.Molecule.exportToObject(String)
    As of Marvin 5.7, replaced by MolExporter.exportToObject(Molecule, String).
    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.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.struc.Molecule.isGUIContracted()
    as of Marvin 6.2 replaced by Molecule.hasContractedSgroup()
    chemaxon.struc.Molecule.isSgroup()
    As of Marvin 14.7.7, no replacement.
    Not supported feature.
    chemaxon.struc.Molecule.mergeAtoms(MolAtom, MolAtom)
    As of Marvin 6.2, use MergeUtil.mergeAtoms(MolAtom, MolAtom, 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.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.Molecule.toBinFormat(String)
    As of Marvin 5.7, replaced by MolExporter.exportToBinFormat(Molecule, String).
    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) {
                     throw new IllegalArgumentException(e);
                 }
                 
    chemaxon.struc.Molecule.toObject(String)
    As of Marvin 5.7, replaced by MolExporter.exportToObject(Molecule, String).
    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.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.struc.MoleculeGraph.arrangeComponents()
    As of Marvin 5.7, replaced by CleanUtil.arrangeComponents(MoleculeGraph, boolean, boolean).
    Usage:
                 CleanUtil.arrangeComponents(molecule, true, true);
                 
    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.MoleculeGraph.clean(int, String)
    As of Marvin 5.7, replaced by Cleaner.clean(MoleculeGraph, int, String).
    chemaxon.struc.MoleculeGraph.clean(int, String, MProgressMonitor)
    As of Marvin 5.7, replaced by Cleaner.clean(MoleculeGraph, int, String, MProgressMonitor).
    chemaxon.struc.MoleculeGraph.clonelesscopy(MoleculeGraph)
    as of Marvin 6.3.
    Not supported feature.
    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.struc.MoleculeGraph.getAtomReferenceList()
    Use MoleculeGraph.atoms() instead.
    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.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.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.MoleculeGraph.getGrinv(int[], boolean)
    As of Marvin 4.0, replaced by MoleculeGraph.getGrinv(int[], int).
    Usage:
                 getGrinv(gi, uniqueFlag ? GRINV_OLDSTEREO : 0);
                 
    chemaxon.struc.MoleculeGraph.getLonePairCount(int)
    use MDocument.getLonePairCount() instead
    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&ltInteger&gt orders = group.getAttachmentPointOrders(molAtom);
                 
    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.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.MoleculeGraph.hasExplicitLonePairs()
    use MDocument.hasExplicitLonePairs() instead
    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.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.struc.MoleculeGraph.isAtom()
    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.MoleculeGraph.isMolecule()
    as of Marvin 14.7.7, no replacement.
    Usage:
     use myObject instanceof Molecule instead
                 
    chemaxon.struc.MoleculeGraph.isRing()
    As of Marvin 14.7.7, no replacement.
    Not supported feature.
    chemaxon.struc.MoleculeGraph.mergeAtoms(MolAtom, MolAtom)
    As of Marvin 6.2, use MergeUtil.mergeAtoms(MolAtom, MolAtom, boolean) instead.
    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.struc.MoleculeGraph.removeExplicitLonePairs()
    As of Marvin 5.7, replaced by Hydrogenize.convertExplicitLonePairsToImplicit(MoleculeGraph).
    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.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 constructs inconsistent MoleculeGraph. Use MoleculeGraph.removeBond(MolBond) for bond removal and MoleculeGraph.add(MolBond) for adding a new bond to the molecule.
    chemaxon.struc.MoleculeGraph.setValenceCheckState(MoleculeGraph.ValenceCheckState)
    As of Marvin 6.0, replaced by MoleculeGraph.setValenceCheckOptions(ValenceCheckOptions) and MoleculeGraph.setValenceCheckEnabled(boolean).
    Usage:
                 // Same as setValenceCheckState(ValenceCheckState.OFF):
                 setValenceCheckEnabled(false);
                 // Same as setValenceCheckState(ValenceCheckState.AMBIGUOUS_AROMATIC_ATOMS_IGNORED):
                 setValenceCheckOptions(ValenceCheckOptions.DEFAULT);
                 // Same as setValenceCheckState(ValenceCheckState.FULL):
                 setValenceCheckOptions(new ValenceCheckOptions(false, true));
                 
    chemaxon.struc.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.MPropertyContainer.getString(String)
    As of Marvin 5.7, replaced by MPropHandler.convertToString(MPropertyContainer, String)
    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.struc.prop.MBooleanProp.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.MHCoords3DProp.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.MIntegerProp.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.struc.prop.MMoleculeProp.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.MStringProp.convertToString(String, int)
    As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
    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.RgMolecule.clonelesscopy(MoleculeGraph)
    as of Marvin 6.3.
    Not supported feature.
    chemaxon.struc.RgMolecule.isAtom()
    As of Marvin 14.7.7, no replacement.
    Not supported feature.
    chemaxon.struc.RgMolecule.isBond()
    As of Marvin 14.7.7, no replacement.
    Not supported feature.
    chemaxon.struc.RgMolecule.mergeAtoms(MolAtom, MolAtom)
    As of Marvin 6.2, use MergeUtil.mergeAtoms(MolAtom, MolAtom, boolean) 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.getMSLogic()
    Multi-step reactions not supported. Method performs no operations.
    chemaxon.struc.RxnMolecule.isAtom()
    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.struc.RxnMolecule.isSingleStepReaction()
    chemaxon.struc.RxnMolecule.mergeAtoms(MolAtom, MolAtom)
    As of Marvin 6.2, use MergeUtil.mergeAtoms(MolAtom, MolAtom, boolean) instead.
    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.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.RxnMolecule.setMSLogic(Map<MRArrow, RxnMolecule>)
    Multi-step reactions not supported. Method performs no operations.
    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.getType()
    as of Marvin 6.3. use Sgroup.getSgroupType() instead. Note that in case of AminoAcidSgroups returned Sgroup.ST_SUPERATOM but Sgroup.getSgroupType() will return SgroupType.AMINOACID.
    chemaxon.struc.sgroup.MulticenterSgroup.replaceMulticenterAtom(MolAtom, MolAtom)
    as of Marvin 2014.08.25.0, use MulticenterSgroup.setCentralAtom(chemaxon.struc.MolAtom) instead
    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.struc.Sgroup.setXState(int, int)
    as of Marvin 6.2, use Sgroup.setXState(int) instead
    chemaxon.struc.sgroup.SuperatomSgroup.cloneLeavingGroups(SuperatomSgroup)
    As of Marvin 6.2, no replacement.
    Not supported feature.
    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.getAttachAtoms()
    As of Marvin 6.0, replaced by SuperatomSgroup.getBoundAttachAtoms().
    chemaxon.struc.sgroup.SuperatomSgroup.getFreeLegalAttachAtoms()
    As of Marvin 6.0, replaced by SuperatomSgroup.getFreeAttachAtoms().
    chemaxon.struc.sgroup.SuperatomSgroup.getLegalAttachAtoms()
    As of Marvin 6.0, replaced by SuperatomSgroup.getAllAttachAtoms().
    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.isFreeLegalAttachAtom(MolAtom)
    As of Marvin 6.0, replaced by SuperatomSgroup.isFreeAttachAtom(MolAtom a).
    chemaxon.struc.sgroup.SuperatomSgroup.isLegalAttachment(MolAtom)
    As of Marvin 6.0, replaced by SuperatomSgroup.isAttachmentAtom(MolAtom).
    chemaxon.struc.sgroup.SuperatomSgroup.removeLeavingGroup(int)
    As of Marvin 6.2, no replacement.
    Not supported feature.
    chemaxon.struc.sgroup.SuperatomSgroup.setCrossingBondType(int, BondType)
    As of Marvin 6.2, no replacement.
    Not supported feature.
    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.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.struc.sgroup.SuperatomSgroup.updateAttachmentPoints()
    as of Marvin 6.2, use SuperatomSgroup.calculateAttachmentPoints() 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.RgComponentIterator.nextComponent()
    As of Marvin 6.2, Use IteratorFactory.RgComponentIterator.next() instead.
    chemaxon.util.iterator.IteratorFactory.RxnComponentIterator.nextComponent()
    As of Marvin 6.2, Use IteratorFactory.RxnComponentIterator.next() instead.
    chemaxon.util.iterator.MoleculeIterator.getThrowable()
    Not used. MoleculeIterator.next() throws NoSuchElementException in case of error.
    com.chemaxon.calculations.cli.CalculatorPluginOutput.setPlugin(CalculatorPlugin)
    use CalculatorPluginOutput.setPluginChecked(CalculatorPlugin) instead
    com.chemaxon.calculations.common.ProgressObserver.subTask(String, long)
    Will be removed.
    com.chemaxon.calculations.common.ProgressObservers.createForgivingNullObserver()
    Use ProgressObservers.nullProgressObserver() instead.
    com.chemaxon.calculations.common.ProgressObservers.createNoCancelObserver()
    Use ProgressObservers.noCanceller()
    com.chemaxon.calculations.common.ProgressObservers.createNullObserver(String)
    Use ProgressObservers.createStrictNullObserver().
    com.chemaxon.calculations.gui.CalculatorPluginDisplay.setPlugin(CalculatorPlugin)
    use CalculatorPluginDisplay.setPluginChecked(CalculatorPlugin) instead
    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
    com.chemaxon.calculations.stereoanal.stereocenters.AtomSelection.primaryAtomIndexes()
    com.chemaxon.calculations.stereoanal.stereocenters.AtomSelection.secondaryAtomIndexes()
    com.chemaxon.calculations.stereoanal.stereocenters.AtropStereoCenter.getValue()
    As of Marvin 14.9.15, replaced by AtropStereoCenter.getCIPValue().
    com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter.getValue()
    As of Marvin 14.9.15, replaced by AxialStereoCenter.getCIPValue().
    com.chemaxon.calculations.stereoanal.stereocenters.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.descriptors.alignment.ShapeDescriptor.getDescriptorGenerator()
    Use Guarded.getGuardObject()
    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.cfp.CfpGenerator.getBinaryMetricsComparator(BinaryMetrics)
    Use BinaryVectorMetricFactory.forBinaryMetrics(com.chemaxon.descriptors.metrics.BinaryMetrics)
    com.chemaxon.descriptors.fingerprints.cfp.CfpGenerator.getDefaultComparator()
    com.chemaxon.descriptors.fingerprints.cfp.CfpGenerator.getTverskyComparator(double, double)
    Use BinaryVectorMetricFactory.forTverskyCoefficients(double, double)
    com.chemaxon.descriptors.fingerprints.cfp.CfpGenerator.getTverskyComparator(TverskyParameters)
    Use BinaryVectorMetricFactory.forTversky(com.chemaxon.descriptors.metrics.TverskyParameters)
    com.chemaxon.descriptors.fingerprints.ecfp.EcfpGenerator.getBinaryMetricsComparator(BinaryMetrics)
    Use BinaryVectorMetricFactory.forBinaryMetrics(com.chemaxon.descriptors.metrics.BinaryMetrics)
    com.chemaxon.descriptors.fingerprints.ecfp.EcfpGenerator.getDefaultComparator()
    com.chemaxon.descriptors.fingerprints.ecfp.EcfpGenerator.getTverskyComparator(double, double)
    Use BinaryVectorMetricFactory.forTverskyCoefficients(double, double)
    com.chemaxon.descriptors.fingerprints.ecfp.EcfpGenerator.getTverskyComparator(TverskyParameters)
    Use BinaryVectorMetricFactory.forTversky(com.chemaxon.descriptors.metrics.TverskyParameters)
    com.chemaxon.descriptors.fingerprints.pf2d.PfGenerator.getDefaultComparator()
    com.chemaxon.descriptors.fingerprints.pf2d.PfGenerator.getFloatVectorComparator(FloatVectorMetrics)
    Use FloatVectorMetricFactory.forFloatMetrics(com.chemaxon.descriptors.metrics.FloatVectorMetrics)
    com.chemaxon.descriptors.metrics.FloatVectorComparator.calculateFloatVectorSimilarity(float[], float[])
    In various cases (euclid, euclid sqr, manhattan) this has no practical interpretation
    com.chemaxon.descriptors.metrics.FloatVectorComparator.getUpperBoundForFloatVectors()
    In various cases (euclid, euclid sqr, manhattan) this has no practical interpretation
    com.chemaxon.descriptors.vectors.binary.BvGenerator.getBinaryMetricsComparator(BinaryMetrics)
    Use BinaryVectorMetricFactory.forBinaryMetrics(com.chemaxon.descriptors.metrics.BinaryMetrics).
    com.chemaxon.descriptors.vectors.binary.BvGenerator.getTverskyComparator(double, double)
    Use #forTversky(double, double).
    com.chemaxon.descriptors.vectors.binary.BvGenerator.getTverskyComparator(TverskyParameters)
    Use BinaryVectorMetricFactory.forBinaryMetrics(com.chemaxon.descriptors.metrics.BinaryMetrics).
    com.chemaxon.descriptors.vectors.floats.FvGenerator.getFloatMetricsComparator(FloatVectorMetrics)
    Use FloatVectorMetricFactory.forFloatMetrics(com.chemaxon.descriptors.metrics.FloatVectorMetrics).
  • 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.checkers.result.ReactionCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, List<Long>, StructureCheckerErrorType, Molecule, String, String, String, String, Icon)
    use ReactionCheckerResult(StructureChecker, List, List, List, StructureCheckerErrorType, Molecule, String, String, String, String, Icon, int) instead
    chemaxon.checkers.runner.configuration.reader.ActionStringBasedConfigurationReader(String, StructureCheckerFactory, StructureFixerFactory)
    use ActionStringBasedConfigurationReader(String, CheckerFixerFactory) instead
    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.
    chemaxon.core.calculations.valencecheck.ValenceCheckOptions(boolean, boolean)
    since Marvin 6.2, Use ValenceCheckOptions.Builder for building ValenceCheckOptions.
    chemaxon.descriptors.CFGenerator(int)
    since 5.4
    chemaxon.formats.MolConverter(MolConverter.Options)
    as of Marvin 5.2.3, use MolConverter.Builder.build() instead.
    chemaxon.formats.MolConverter(List<Object>, OutputStream, String, boolean)
    as of Marvin 5.2.3, replaced by MolConverter(Builder)
    chemaxon.formats.MolConverter(List<Object>, String, String, boolean)
    as of Marvin 5.2.3, replaced by MolConverter(Builder)
    chemaxon.formats.MolConverter(List<Object>, List<String>, OutputStream, String, boolean)
    as of Marvin 5.2.3, replaced by MolConverter(Builder)
    chemaxon.formats.MolConverter(List<Object>, List<String>, OutputStream, String, boolean, String[])
    as of Marvin 5.2.3, replaced by MolConverter(Builder)
    chemaxon.formats.MolConverter(List<Object>, List<String>, OutputStream, String, boolean, String[], String)
    as of Marvin 5.2.3, replaced by MolConverter(Builder)
    chemaxon.formats.MolConverter(List<Object>, List<String>, String, String, boolean)
    as of Marvin 5.2.3, replaced by MolConverter(Builder)
    chemaxon.formats.MolConverter.Options()
    chemaxon.jep.context.ReactionContext(boolean)
    Copy feature is no longer required. Constructor.
    chemaxon.jep.Evaluator(File, Standardizer, MolImporter, String)
     
    chemaxon.jep.Evaluator(String, Standardizer, MolImporter, String)
     
    chemaxon.marvin.alignment.MMPAlignmentProperties(AlignmentProperties.FlexibilityMode, AlignmentAccuracyMode)
    chemaxon.marvin.alignment.Pharmacophore3D(Molecule)
    Use Pharmacophore3DGenerator instead.
    chemaxon.marvin.modules.datatransfer.TransferableDescriptor(String, String, Integer, Integer, boolean, boolean)
    since 5.3.3 new descriptor parameter added.
    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.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).
    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>)
    com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter(AtomSelection, StereoConstants.StereoValue.CisTransStereo)
    com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter(AtomSelection, StereoConstants.StereoValue.CisTransStereo, List<AttachedData>)
    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>)
  • Deprecated Enum Constants
    Enum Constant
    Description
    chemaxon.checkers.StructureCheckerErrorType.INVALID_STEREO
    chemaxon.checkers.StructureCheckerErrorType.INVALID_WEDGE
    chemaxon.marvin.alignment.AlignmentProperties.GAUSS_FAST_EXTENDED_ATOMTYPE_MCS
    chemaxon.marvin.alignment.AlignmentProperties.OrientationType.MCS
    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(boolean, boolean).
    Usage:
     molecule.setValenceCheckOptions(new ValenceCheckOptions(false,true);
                 
    chemaxon.struc.MoleculeGraph.ValenceCheckState.OFF
    As of Marvin 6.0, replaced by MoleculeGraph.setValenceCheckEnabled(boolean). Usage:
                 molecule.setValenceCheckEnabled(false);