Deprecated List (JChem Base API documentation (c) 1998-2023 Chemaxon Ltd.)

For Removal
Element	Description
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.PluginException(String, int)	Error level is never set or used by the API. This feature will be completely removed.
chemaxon.marvin.plugin.PluginException.getErrorLevel()	Error level is never set or used by the API. This feature will be completely removed.
chemaxon.marvin.plugin.PluginFactory	This class has been moved to a new package, import and use it from its new location: `PluginFactory`

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

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

Enums
Enum	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`.

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.jchem.db.DatabaseConstants.MSSQL_DRIVER	as of JChem 5.9, only the new MSSQL database is supported
chemaxon.jchem.db.DatabaseConstants.MSSQL_URL_EXAMPLE	as of JChem 5.9, only the new MSSQL database is supported
chemaxon.jchem.db.DatabaseConstants.MSSQL_URL_TEMPLATE	as of JChem 5.9, only the new MSSQL database is supported
chemaxon.jchem.db.JChemSearch.MAXIMAL_ACCEPTEDSEARCHTIME_MINUTES
chemaxon.jchem.db.Updater.UpdateInfo.isRegeneration	since 5.1.2 use `Updater.UpdateInfo.isProgressMonitoringSupported` instead.
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.

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, MolAtom[])	since Marvin 5.11 use convertImplicitHToExplicit(MoleculeGraph, MolAtom[]) 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, int)	since Marvin 5.11 use convertExplicitHToImplicit(MoleculeGraph, int) 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.aliphaticRings()	as of release 5.5, replaced by `Ring.aliphaticRings()`
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.aromaticRings()	as of release 5.5, replaced by `Ring.aromaticRings()`
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.carboRings()	as of release 5.5, replaced by `Ring.carboRings()`
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.fusedAliphaticRings()	as of release 5.5, replaced by `Ring.fusedAliphaticRings()`
chemaxon.calculations.TopologyAnalyser.fusedAromaticRingCount()	as of release 5.5, replaced by `Ring.fusedAromaticRingCount()`
chemaxon.calculations.TopologyAnalyser.fusedAromaticRings()	as of release 5.5, replaced by `Ring.fusedAromaticRings()`
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.heteroaliphaticRings()	as of release 5.5, replaced by `Ring.heteroaliphaticRings()`
chemaxon.calculations.TopologyAnalyser.heteroaromaticRingCount()	as of release 5.5, replaced by `Ring.heteroaromaticRingCount()`
chemaxon.calculations.TopologyAnalyser.heteroaromaticRings()	as of release 5.5, replaced by `Ring.heteroaromaticRings()`
chemaxon.calculations.TopologyAnalyser.heteroRingCount()	as of release 5.5, replaced by `Ring.heteroRingCount()`
chemaxon.calculations.TopologyAnalyser.heteroRings()	as of release 5.5, replaced by `Ring.heteroRings()`
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.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.ringSystemCount()	as of release 5.5, replaced by `Ring.ringSystemCount()`
chemaxon.calculations.TopologyAnalyser.ringSystems()	as of release 5.5, replaced by `Ring.ringSystems()`
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.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.MDSet.getUserData(int)	since 2.3
chemaxon.descriptors.MDSet.setUserData(float[])	since 2.3
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.build()
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.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.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. use`MolImporter.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.jchem.db.DatabaseProperties.isGenericTautomerProtectsChirality(String)	stereo is considered as default in tautomer regions during searching, `SearchOptions.setTautomerSearch(int)` with value `SearchConstants.TAUTOMER_SEARCH_ON_IGNORE_TAUTOMERSTEREO` ignores it.
chemaxon.jchem.db.DatabaseProperties.isSetSwitchOffAllProtectionsForTDF(String)	stereo is considered as default in tautomer regions during searching, `SearchOptions.setTautomerSearch(int)` with value `SearchConstants.TAUTOMER_SEARCH_ON_IGNORE_TAUTOMERSTEREO` ignores it.
chemaxon.jchem.db.Importer.getConnections()	since 2.2 replaced by `Importer.getFieldConnections()`.
chemaxon.jchem.db.Importer.setConnections(String)	since 2.2 replaced by `Importer.setFieldConnections(String)`.
chemaxon.jchem.db.Importer.setDuplicateImportAllowed(boolean)	since JChem 5.4. This import option has been table option, instead of this use `Importer.setDuplicateImportAllowed(int)` method
chemaxon.jchem.db.UpdateHandler.setDuplicateFiltering(boolean)	since JChem 5.4. This import option has been table option, instead of this use `UpdateHandler.setDuplicateFiltering(int)` method
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.toString(Object)	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, 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, 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(int)	Use `HBDAPlugin.getAcceptorSiteCount()` 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.plugin.PluginException.getErrorLevel()	Error level is never set or used by the API. This feature will be completely removed.
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.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.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.screen.Similarity.Tanimoto()
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.struc.graphics.MEFlow.getValidSinkAtomPairsForMolecule(Molecule, MolAtom)	As of Marvin 6.1, replaced by `EFlowPlacementValidators.getValidSinkAtomPairs(Molecule, MolAtom)` .
chemaxon.struc.graphics.MEFlow.getValidSinkAtomsForMolecule(Molecule, MolAtom)	As of Marvin 6.1, replaced by `EFlowPlacementValidators.getValidSinkAtoms(Molecule, MolAtom)` .
chemaxon.struc.graphics.MEFlow.getValidSinkBondsForMolecule(Molecule, MolAtom)	As of Marvin 6.1, replaced by `EFlowPlacementValidators.getValidSinkBonds(Molecule, MolAtom)` .
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.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.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.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.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.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.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.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.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<Integer> 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.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(Molecule[], String)	As of Marvin 5.7, replaced by `Cleaner.partialClean(Molecule, Molecule[], 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, 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.addReactionStep(List<Molecule>, List<Molecule>, List<Molecule>, MRArrow, int)	Deprecated without replacement. The method had no effect.
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.getReactionSteps()	Deprecated without replacement. The method never served a real purpose.
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 `AminoAcidSgroup`s 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.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.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(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(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.floats.FvGenerator.getFloatMetricsComparator(FloatVectorMetrics)	Use `FloatVectorMetricFactory.forFloatMetrics(com.chemaxon.descriptors.metrics.FloatVectorMetrics)`.

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.core.calculations.valencecheck.ValenceCheckOptions(boolean, boolean)	since Marvin 6.2, Use `ValenceCheckOptions.Builder` for building ValenceCheckOptions.
chemaxon.descriptors.CFGenerator(int)	since 5.4
chemaxon.descriptors.MDDBReader(ConnectionHandler, String, MDSet, String)	since 2.3 Use `MDDBReader(java.lang.String, chemaxon.util.ConnectionHandler, chemaxon.descriptors.MDSet, java.lang.String)` instead.
chemaxon.formats.MolConverter(List<Object>, OutputStream, String, boolean)	as of Marvin 5.2.3, replaced by `MolConverter(Builder)`
chemaxon.formats.MolConverter.Options()
chemaxon.jchem.db.DatabaseProperties(ConnectionHandler)	in JChem 5.8 Please use `DatabaseProperties(ConnectionHandler, boolean)` instead. The constructor DatabaseProperties(conh) is equivalent to DatabaseProperties(conh, false).
chemaxon.jep.context.ReactionContext(boolean)	Copy feature is no longer required. Constructor.
chemaxon.jep.Evaluator(File, 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.marvin.plugin.PluginException(String, int)	Error level is never set or used by the API. This feature will be completely removed.
chemaxon.sss.screen.Similarity(byte[], byte[])
chemaxon.standardizer.concurrent.StandardizerRunner(Iterator<Molecule>, StandardizerConfiguration)	Won't be public in the future
chemaxon.struc.Sgroup(Molecule, int)	As of Marvin 5.12, replaced by `SgroupFactory.createSgroup(Molecule, SgroupType)`.
com.chemaxon.calculations.stereoanal.stereocenters.AtomSelection(int[], int[])
com.chemaxon.calculations.stereoanal.stereocenters.AtropStereoCenter(AtomSelection, StereoConstants.StereoValue.AtropStereo, List<AttachedData>)
com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter(AtomSelection, StereoConstants.StereoValue.AxialStereo, List<AttachedData>)
com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter(AtomSelection, StereoConstants.StereoValue.CisTransStereo, List<AttachedData>)
com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter(AtomSelection, StereoConstants.StereoValue.TetrahedralStereo, Optional<EnhancedStereo>, List<AttachedData>)

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);

Deprecated API

Contents