Deprecated API
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Terminally Deprecated ElementsElementDescriptionWill be removed, no replacement.Will be removed, no replacement.This main method will be removed, CLI interfaces should not be used directly from Java code.This class has been moved to a new package, import and use it from its new location:
CalculatorPluginDisplayThis class has been moved to a new package, import and use it from its new location:CalculatorPluginOutputThis interface has been moved to a new package, import and use it from its new location:ParameterPanelHandlerThis class has been moved to a new package, import and use it from its new location:PluginFactoryThis main method will be removed, CLI interfaces should not be used directly from Java code.Deprecated for removal.Moved to a new package, use it from its new location:MolAligner.
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Deprecated InterfacesInterfaceDescription5.4Will be removed soon.This interface has been moved to a new package, import and use it from its new location:
ParameterPanelHandlersince 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.UseProgressObserverinstead. Will be removed.UseConsumerinstead.
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Deprecated ClassesClassDescriptionWill be removed from the public API.use
CheckerFixerFactoryinsteaduseCheckerFixerFactoryinsteadas of Marvin 5.2.3, useMolConverter.Builderinstead.as of Marvin 2014.07.21.0 intended for internal use onlyas of Marvin 2014.07.21.0 intended for internal use onlyas of Marvin 2014.07.21.0 intended for internal use onlyas of Marvin 2014.07.21.0 intended for internal use onlyas of Marvin 2014.07.21.0 not usedas of Marvin 2014.07.21.0 intended for internal use onlyThis class has been moved to a new package, import and use it from its new location:CalculatorPluginDisplayThis class has been moved to a new package, import and use it from its new location:CalculatorPluginOutputThis class has been moved to a new package, import and use it from its new location:PluginFactoryas of Marvin 5.11.1useSetAbsoluteStereoActionorRemoveAbsoluteStereoActioninsteadMoved to a new package, use it from its new location:MolAligner.
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Deprecated Enum ClassesEnum ClassDescriptionAs of Marvin 6.0, replaced by
MoleculeGraph.setValenceCheckOptions(ValenceCheckOptions)andValenceCheckOptions.As of Marvin 14.9.15, replaced byAtropStereoIUPACDescriptor.As of Marvin 14.9.15, replaced byAxialStereoIUPACDescriptor.As of Marvin 14.9.15, replaced byCisTransStereoIUPACDescriptor.As of Marvin 14.9.15, replaced byTetrahedralStereoIUPACDescriptor.
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Deprecated FieldsFieldDescriptionConfiguration file URL can be set in MarvinSketch preferences, and stored in UserSettings.as of Marvin 3.1, there is no possibility to do thatThis field will not be available from May 2016. Use
LogPMethodinstead.This field will not be available from May 2016. UseLogPMethodinstead.UseLogPMethod.USER_DEFINEDinstead.UseLogPMethod.CHEMAXONinstead.UseLogPMethod.CONSENSUSinstead.This field will not be available from May 2016. UseLogPMethodinstead.This field will not be available from May 2016. UseLogPMethodinstead.UseLogPMethod.USER_DEFINEDinstead.UseLogPMethod.CHEMAXONinstead.UseLogPMethod.CONSENSUSinstead.in 6.2.0 use atomNumberingType parameter instead.since 5.3.3 has no senseDeprecated since Marvin 6.4. No settings is used intead of this, only High Quality exists from now on.since 5.3UseAnyBondStyleinstead.UseAnyBondStyleinstead.UseAnyBondStyleinstead.UseAnyBondStyleinstead.UseAnyBondStyleinstead.UseAnyBondStyleinstead.UseAnyBondStyleinstead.UseAnyBondStyleinstead.UseAnyBondStyleinstead.As of Marvin 5.4.1, replaced byDispOptConsts.AUTOMATIC_FOGuseRenderingStyleinstead.useRenderingStyleinstead.since Marvin 6.4 only high quality existsSince Marvin 6.4 only high quality existsuseRenderingStyleinstead.useRenderingStyleinstead.useRenderingStyleinstead.useRenderingStyleinstead.useRenderingStyleinstead.useRenderingStyleinstead.useRenderingStyleinstead.useRenderingStyleinstead.useRenderingStyleinstead.As of Version 5.3.2, this method is deprecated and has no replacement. It will be removed in a future version of Marvin.will be deleted, no need to this constantwill be deleted, no need to this constantwill be deleted, no need to this constantwill be deleted, no need to this constantwill be deleted, no need to this constantwill be deleted, no need to this constantwill be deleted, no need to this constantwill be deleted, no need to this constantwill be deleted, no need to this constantAs of JChem 5.12, replaced bySearchConstants.SEARCH_TYPE_NAMES.As of Marvin 5.11
Graph invariants are checked by default when calculating CIS/TRANS stereo, so this option is out of use.As of Marvin 6.2, no replacement.
Not supported feature.As of Marvin 6.0, replaced byValenceCheckOptions.As of Marvin 6.2, no replacement.
Not supported feature.as of Marvin 6.2, useExpandable.LEAVE_COORDS_UNCHANGEDinsteadAs of Marvin 6.1,
Usage:In the specified methods the CIS|TRANS or CIS|TRANS|CTUNSPEC values are used instead.
As of Marvin 6.2, UseIteratorFactory.INCLUDE_CHEMICAL_ATOMS_ONLYinstead.Not used.
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Deprecated MethodsMethodDescriptionas of Marvin 6.0, replaced by
ElementalAnalyser.setMolecule(MoleculeGraph mol).since Marvin 5.11 use convertImplicitHToExplicit(MoleculeGraph) insteadsince Marvin 5.11 use convertImplicitHToExplicit(MoleculeGraph, MolAtom[]) insteadsince Marvin 5.11 use convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int) insteadsince Marvin 5.11 use convertImplicitLonePairsToExplicit(MoleculeGraph, MolAtom[]) isnteadas of Marvin 5.11.1, replaced byTopologyUtil.isBridgeHeadAtom(MoleculeGraph, int)since Marvin 5.11 use convertExplicitHToImplicit(MoleculeGraph) insteadsince Marvin 5.11 use convertExplicitHToImplicit(MoleculeGraph, int) insteadsince Marvin 5.11 use convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int) insteadsince Marvin 5.11 use convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean) insteadsince Marvin 5.11 use convertExplicitLonePairsToImplicit(MoleculeGraph) insteadas of release 5.5, replaced byRing.aliphaticAtomCount()as of release 5.5, replaced byRing.aliphaticBondCount()as of release 5.5, replaced byRing.aliphaticRingCount()as of release 5.5, replaced byRing.aliphaticRingCount(int)as of release 5.5, replaced byRing.aliphaticRings()as of release 5.5, replaced byRing.aliphaticRings(int)as of release 5.5, replaced byRing.aromaticAtomCount()as of release 5.5, replaced byRing.aromaticBondCount()as of release 5.5, replaced byRing.aromaticRingCount()as of release 5.5, replaced byRing.aromaticRingCount(int)as of release 5.5, replaced byRing.aromaticRings()as of release 5.5, replaced byRing.aromaticRings(int)as of release 5.5, replaced byStereochemistry.asymmetricAtomCount()as of release 5.5, replaced byStereochemistry.asymmetricAtoms()as of release 5.5, replaced byRing.carboaliphaticRingCount()as of release 5.5, replaced byRing.carboaromaticRingCount()as of release 5.5, replaced byRing.carboRingCount()as of release 5.5, replaced byRing.carboRingCount(int)as of release 5.5, replaced byRing.carboRings()as of release 5.5, replaced byRing.carboRings(int)as of release 5.5, replaced byRing.chainAtomCount()as of release 5.5, replaced byRing.chainBondCount()as of release 5.5, replaced byStereochemistry.chiralCenterCount()as of release 5.5, replaced byStereochemistry.chiralCenters()as of release 5.5, replaced byRing.fusedAliphaticRingCount()as of release 5.5, replaced byRing.fusedAliphaticRingCount(int)as of release 5.5, replaced byRing.fusedAliphaticRings()as of release 5.5, replaced byRing.fusedAliphaticRings(int)as of release 5.5, replaced byRing.fusedAromaticRingCount()as of release 5.5, replaced byRing.fusedAromaticRingCount(int)as of release 5.5, replaced byRing.fusedAromaticRings()as of release 5.5, replaced byRing.fusedAromaticRings(int)as of release 5.5, replaced byRing.fusedRingCount()as of release 5.5, replaced byRing.heteroaliphaticRingCount()as of release 5.5, replaced byRing.heteroaliphaticRingCount(int)as of release 5.5, replaced byRing.heteroaliphaticRings()as of release 5.5, replaced byRing.heteroaliphaticRings(int)as of release 5.5, replaced byRing.heteroaromaticRingCount()as of release 5.5, replaced byRing.heteroaromaticRingCount(int)as of release 5.5, replaced byRing.heteroaromaticRings()as of release 5.5, replaced byRing.heteroaromaticRings(int)as of release 5.5, replaced byRing.heteroRingCount()as of release 5.5, replaced byRing.heteroRingCount(int)as of release 5.5, replaced byRing.heteroRings()as of release 5.5, replaced byRing.heteroRings(int)as of release 5.5, replaced byRing.isAliphaticAtom(int)as of release 5.5, replaced byRing.isAromaticAtom(int)as of release 5.5, replaced byStereochemistry.isAsymmetricAtom(int)as of release 5.5, replaced byRing.isChainAtom(int)as of release 5.5, replaced byRing.isChainBond(int)as of release 5.5, replaced byStereochemistry.isChiral()as of release 5.5, replaced byStereochemistry.isChiralCenter(int)as of release 5.5, replaced byRing.isRingAtom(int)as of release 5.5, replaced byRing.isRingBond(int)as of release 5.5, replaced byRing.largestRing()as of release 5.5, replaced byRing.largestRingSize()as of release 5.5, replaced byRing.largestRingSizeOfAtom(int)as of release 5.5, replaced byRing.largestRingSystem()as of release 5.5, replaced byRing.largestRingSystemSize()as of release 5.5, replaced byRing.ringAtomCount()as of release 5.5, replaced byRing.ringBondCount()as of release 5.5, replaced byRing.ringCount()as of release 5.5, replaced byRing.ringCount(int)as of release 5.5, replaced byRing.ringCountOfAtom(int)as of release 5.5, replaced byRing.rings(int)as of release 5.5, replaced byRing.rings(int)as of release 5.5, replaced byRing.ringSystemCount()as of release 5.5, replaced byRing.ringSystemCount(int)as of release 5.5, replaced byRing.ringSystems()as of release 5.5, replaced byRing.ringSystems(int)as of release 5.5, replaced byRing.smallestRing()as of release 5.5, replaced byRing.smallestRingSize()as of release 5.5, replaced byRing.smallestRingSizeOfAtom(int)as of release 5.5, replaced byRing.smallestRingSystem()as of release 5.5, replaced byRing.smallestRingSystemSize()as of release 5.5, replaced byStereochemistry.stereo(int)as of release 5.5, replaced byStereochemistry.stereo(int, int)as of release 5.5, replaced byStereochemistry.stereoDoubleBondCount()This method isn't needed anymore and will be removed in 6.0This method isn't needed anymore and will be removed in 6.0This method isn't needed anymore and will be removed in 6.0This method isn't needed anymore and will be removed in 6.0This method isn't needed anymore and will be removed in 6.0This method isn't needed anymore and will be removed in 6.0This method isn't needed anymore and will be removed in 6.0This method isn't needed anymore and will be removed in 6.0This method isn't needed anymore and will be removed in 6.0This method isn't needed anymore and will be removed in 6.0This method isn't needed anymore and will be removed in 6.0This method isn't needed anymore and will be removed in 6.0This method isn't needed anymore and will be removed in 6.0This method isn't needed anymore and will be removed in 6.0chemaxon.core.calculations.valencecheck.ValenceCheckOptions.Builder.setLocalAromatiChecking(boolean) since Marvin 14.7.7, UseValenceCheckOptions.Builder.setLocalAromaticChecking(boolean)instead.As of JChem 5.4.1, replaced byfromIdentiferSet().As of JChem 5.4.1, replaced byECFP.getIdentiferCount().As of JChem 5.4.1, replaced byECFP.toIdentiferSet().Will be removed, no replacement.Will be removed, no replacement.as of Marvin 2014.07.21.0 useMFileFormat.createRecognizer()insteadas of Marvin 2014.07.21.0 not usedas of Marvin 2014.07.21.0 useMFileFormat.getSubFormatPriority(String)instead(Since Marvin 5.5) There is no need to specify an encoding for a String input. Instead, if you have a String to import, callMolImporter.importMol(String, String); if you have a byte array, callMolImporter.importMol(byte[], 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, callMolImporter.importMol(String, String); if you have a byte array, callMolImporter.importMol(byte[], String, String, Molecule).as of Marvin 6.2. It has no effect on the code.as of Marvin 14.7.7. useMolImporter.read()insteadas of Marvin 14.7.7. useMolImporter.nextDoc()insteadas of Marvin 14.7.7. useMolImporter.read()insteadas of Marvin 6.2. It has no effect on the code.as of Marvin 2014.07.21.0 intended for internal useas of Marvin 2014.07.21.0 not usedas of Marvin 2014.07.21.0 not used in recognition. ImplementRecognizer.tryToRecognize(String, int)instead.useReactionContext.setReaction(RxnMolecule)instead. Sets the map -> product atom array.UseReactionContext.setReaction(RxnMolecule)instead. Sets the products.useReactionContext.setReaction(RxnMolecule)instead. Sets the map -> reactant atom array.UseReactionContext.setReaction(RxnMolecule)instead. Sets the reactants.This main method will be removed, CLI interfaces should not be used directly from Java code.For internal use only.For internal use only.For internal use only.UseAlignmentMoleculeFactory.create(Molecule, AlignmentProperties.DegreeOfFreedomType)instead.Moleculebased on the values of the setters.The explicit Hydrogens are not removed from the original input structure. No need to use.The original input structure is not aromatized. No need to use.The explicit Hydrogens are not removed from the original input structure. No need to use.always false: Molecule is always converted before alignment, but coordinates are written back to the original one.Not used.as of Marvin 3.3.1, replaced by SwingUtil.createMenuas of Marvin 4.1, replaced byMarvinPane.getBondSpacing()use isAtomSymbolsVisible() insteadsince Marvin 5.1 when this and theMarvinPane.getSaveGlobalGUIProperties()function have been merged.as of Marvin 3.3, replaced by getAtomSetColoras of Marvin 3.3.1, replaced by SwingUtil.initActionas of Marvin 3.3.1, replaced by SwingUtil.initButtonin 6.2.0. Use getAtomNumberingType() instead.as of Marvin 3.5, use isGrinvVisible() insteadin 6.2.0. Use setAtomNumberingType() insteadas of Marvin 4.1, replaced byMarvinPane.setBondSpacing(double)as of Marvin 3.5, use setGrinvVisible(boolean) insteaduse setAtomSymbolsVisible(v) insteadas of Marvin 3.3, replaced by setAtomSetColorat N/A (before 02/12/2015)As of Marvin 2.8.1, replaced by getScale()useMSketchPane.getMol(String)insteadas of Marvin 3.5, replaced byMSketchPane.isBondDraggedAlong()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?
As of Marvin 2.8.1, replaced by setScale()useMSketchPane.setMol(Molecule)instead of this method.as of Marvin 3.5, replaced byMSketchPane.setBondDraggedAlong(boolean)as of Marvin 3.0, replaced by getVisibleCellComponentAs of Marvin 3.4,MarvinPane.addHelpMenu(java.awt.Container)should be used.As of Marvin 3.4,MarvinPane.addToolsMenu(java.awt.Container)should be used.As of Marvin 5.2.5, it is recommended to import the molecule in advance, e.g. by usingMolImporter, then set the cell synchronously usingMViewPane.setM(int, Molecule...). The reason is to simplify the public API and minimize the risk of related concurrency problems in user codes.As of Marvin 5.2.5, it is recommended to import the molecule in advance, e.g. by usingMolImporter, then set the cell synchronously usingMViewPane.setM(int, Molecule...). The reason is to simplify the public API and minimize the risk of related concurrency problems in user codes.As of Marvin 5.2.5, it is recommended to import the molecule in advance, e.g. by usingMolImporter, then set the cell synchronously usingMViewPane.setM(int, Molecule...). The reason is to simplify the public API and minimize the risk of related concurrency problems in user codes.as of Marvin 3.3, replaced by setAtomSetSeqOnly intended for internal use.UseHBDAPlugin.getAcceptorSiteCount()instead.UseHBDAPlugin.getAcceptorSiteCount()instead!UseHBDAPlugin.getDonorSiteCount()instead!UseHBDAPlugin.getDonorSiteCount(int)instead!Use {@link #setlogPMethod(LogPMethod))} instead.This function will not be available from May 2016. UselogDPlugin.setlogPMethod(LogPMethod)instead.Increments of implicit H-s are not calculated. Returns the same value aslogPPlugin.getAtomlogPIncrement(int)UselogPPlugin.setlogPMethod(LogPMethod)instead.This function will not be available from May 2016. UselogPPlugin.setlogPMethod(LogPMethod)instead.UsepKaPlugin.getMacropKaValues(int,double[],int[])insteadreplaced bysetModel(int)Not used.As of Marvin 5.0 pH effect is not consideredsince Marvin 5.9 replaced byTautomerizationPlugin.getStructure(int)obsolate methodNot used.Not used.as of Marvin 4.1, replaced byTPSAPlugin.getSurfaceArea()UseUserSettings.getCheckerConfigURL()instead. Deprecated in 5.12.UseUserSettings.setCheckerConfigURL(String)instead. Deprecated in 5.12 Sets the name of the configuration file for StructureChecker in marvin sketchAs of release 5.4, replaced byUserSettings.setCleanHOptionEnabled(boolean)Marvin 6.2 useMolExportModule.preconvert(chemaxon.struc.Molecule, boolean, int, boolean)insteadAs of Marvin 5.2.2, replaced byMolPrinter.getAtomSize().as of Marvin 4.1, replaced byMolPrinter.getBondSpacing()since Marvin 6.4 only high quality existsin 6.2.0. Use getAtomNumberingType instead.As of Marvin 5.5.1 this method always returns true. This method will be removed in a future release.As of Marvin 5.2.2, replaced byMolPrinter.isEZLabelsVisible()in 6.2.0. Use setAtomNumberingType() instead.As of Marvin 5.2.2, replaced byMolPrinter.setAtomSize(double).as of Marvin 4.1, replaced byMolPrinter.setBondSpacing(double)in Marvin 15.5.18since Marvin 6.4 only high quality existsAs of Marvin 5.5.1 this method does nothing. This method will be removed in a future release.As of Marvin 5.5.1 this method does nothing. This method will be removed in a future release.As of Marvin 5.2.2, replaced byMolPrinter.setEZLabelsVisible(boolean)MoleculeGraph.implicitizeHydrogens(int)with parameterMolAtom.ALL_Hdoes the same.useCodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)Creates aJTextPaneinstance with code assist capabilities.
Default toolbar configuration will be used for toolbars.useCodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)Creates aJTextPaneinstance with code assist capabilities.
Default toolbar configuration will be used for toolbars.useCodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)Creates aJTextPaneinstance with code assist capabilities.
Default toolbar configuration will be used for toolbars.useCodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)Creates aJTextPaneinstance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.useCodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)Creates aJTextPaneinstance 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.useCodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)Creates aJTextPaneinstance 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.useCodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)Creates aJTextPaneinstance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-spaceuseCodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)Creates aJTextPaneinstance with code assist capabilities.
Default toolbar configuration will be used for toolbars.useCodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)Creates aJTextPaneinstance with code assist capabilities.
Default toolbar configuration will be used for toolbars.useCodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)Creates aJTextPaneinstance with code assist capabilities.
Default toolbar configuration will be used for toolbars.useCodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)Creates aJTextPaneinstance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-spaceuseCodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)Creates aJTextPaneinstance 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.useCodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)Creates aJTextPaneinstance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-spaceuseCodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)Creates aJTextPaneinstance with code assist capabilities.
Default toolbar configuration will be used for toolbars.useCodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)Creates aJTextPaneinstance with code assist capabilities.
Default toolbar configuration will be used for toolbars.useCodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)Creates aJTextPaneinstance with code assist capabilities.
Default toolbar configuration will be used for toolbars.useCodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)Creates aJTextPaneinstance with code assist capabilities.useCodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)Creates aJTextPaneinstance with code assist capabilities.useCodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)Creates aJTextPaneinstance with code assist capabilities.useCodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)Creates aJTextPaneinstance with code assist capabilities.as of Marvin 5.11.1 useMoleculeGraph.setBond(int, MolBond)as of Marvin 5.11.1does nothing.does nothing.This main method will be removed, CLI interfaces should not be used directly from Java code.Deprecated for removal.The last three arguments are not used anymore, callConcurrentReactorProcessor.setReactantIterators(MoleculeIterator[], int)insteadcalling this method may result in very poor performance, callConcurrentReactorProcessor.setReactantIterators(MoleculeIterator[], int)insteadSince JChem 5.12, stereo is considered as default in tautomer regions, butSearchOptions.setTautomerSearch(int)with valueSearchConstants.TAUTOMER_SEARCH_ON_IGNORE_TAUTOMERSTEREOignores it.Since JChem 5.12, stereo is considered as default in tautomer regions, butSearchOptions.setTautomerSearch(int)with valueSearchConstants.TAUTOMER_SEARCH_ON_IGNORE_TAUTOMERSTEREOignores it.useTransformAction.setTransform(RxnMolecule)method insteaduseConfigurationUtility.filterGroups(StandardizerConfiguration, String[])on the configuration returned by the methodStandardizer.getConfiguration()useConfigurationUtility.filterGroups(StandardizerConfiguration, String[])on the configuration returned by the methodStandardizer.getConfiguration()useConfigurationUtility.setFinalClean(StandardizerConfiguration)on the configuration returned by the methodStandardizer.getConfiguration()useConfigurationUtility.setFinalClean(StandardizerConfiguration, int)on the configuration returned by the methodStandardizer.getConfiguration()useConfigurationUtility.setFinalClean(StandardizerConfiguration, int, boolean)on the configuration returned by the methodStandardizer.getConfiguration()As of Marvin 6.1, replaced byEFlowPlacementValidators.getValidSinkAtomPairs(Molecule, MolAtom).As of Marvin 6.1, replaced byEFlowPlacementValidators.getValidSinkAtomPairs(Molecule, MolBond).As of Marvin 6.1, replaced byEFlowPlacementValidators.getValidSinkAtoms(Molecule, MolAtom).As of Marvin 6.1, replaced byEFlowPlacementValidators.getValidSinkAtoms(Molecule, MolBond).As of Marvin 6.1, replaced byEFlowPlacementValidators.getValidSinkBonds(Molecule, MolAtom).As of Marvin 6.1, replaced byEFlowPlacementValidators.getValidSinkBonds(Molecule, MolBond).As of Marvin 6.1, replaced byEFlowPlacementValidators.getValidSourceAtomPairs(Molecule).As of Marvin 6.1, replaced byEFlowPlacementValidators.getValidSourceAtoms(Molecule).As of Marvin 6.1, replaced byEFlowPlacementValidators.getValidSourceBonds(Molecule).As of Marvin 6.1, replaced byEFlowPlacementValidators.isValidFlow(MolAtom, MolAtom, Molecule)or one of the other implementations instead.As of Marvin 6.1, replaced byEFlowPlacementValidators.isValidSource(MolAtom, Molecule)orEFlowPlacementValidators.isValidSource(MolAtom[], Molecule)orEFlowPlacementValidators.isValidSource(MolBond, Molecule).As of Marvin 6.1, replaced byCTransform3D.setRotation(double, double, double, double)andCTransform3D.setRotationCenter(DPoint3).useMTextBox.determinePosition(Graphics, DPoint3, boolean)in case you have a special graphics context to be used for font calculations.As of release 5.7, replaced byMolExporter.exportToBinFormat(MDocument, String).As of release 5.7, replaced byMolExporter.exportToFormat(MDocument, String)As of release 5.7, replaced byMolExporter.exportToObject(MDocument, String)As of release 5.7, replaced byMolImporter.parseMRV(String)As of release 5.7, replaced byMolExporter.convertToString(MDocument, String, int)As of Marvin 6.1, replaced byMDocument.setGUIPropertyContainer(MPropertyContainer).As of Marvin 5.9, replaced by a similar methodPeriodicSystem.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.as of Marvin 6.0 replaced bySuperatomSgroup.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.As of release 5.7, replaced byMolAtom.getQueryString()as of Marvin 6.2. useMolAtom.getRadicalValue()insteadAs of release 5.7, replaced bySmartsAtomQuerifier.hasSMARTSProps(MolAtom atom)As of release 5.7, replaced bySmartsAtomQuerifier.hasSMARTSPropsExcluding(MolAtom atom, String exclude)As of Marvin 5.9, replaced by a similar methodPeriodicSystem.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.as of Marvin 6.0, replaced bySuperatomSgroup.addAttachmentPoint(MolAtom), orSuperatomSgroup.addAttachmentPoint(MolAtom, int).as of Marvin 6.0, replaced bySuperatomSgroup.addAttachmentPoint(MolAtom), orSuperatomSgroup.addAttachmentPoint(MolAtom, int).as of Marvin 6.3. useMolAtom.setSpecIsotopeSymbolPreferred(boolean)andMolAtom.setMassno(int)instead.as of Marvin 6.0.1, exists only for internal usage
Usage:Internal usage only.
As of release 5.7, replaced bySmartsAtomQuerifier.setQuerystr(MolAtom atom, String s)andMolAtom.setQueryString(String).As of release 5.7, replaced bySmartsAtomQuerifier.setQuerystr(MolAtom atom, String s, int options)andMolAtom.setQueryString(String).as of Marvin 6.2. UseMolAtom.setRadicalValue(AtomProperty.Radical)instead.As of release 5.7, replaced bySmartsAtomQuerifier.setSMARTS(MolAtom atom, String s)since 5.11, replaced byMolBond.desiredLength(int, int, int, int).since 5.11, replaced byMolBond.desiredLength(int, int, int, int).As of Marvin 6.2, no replacement.
Not supported feature.As of Marvin 5.7, no replacement.
Not intended for public use, it was intended only for internal debugging.as of Marvin 6.3.
Not supported feature.as of Marvin 2014.09.01.0 useMolecule.clone()insteadAs of Marvin 5.7, replaced byMolExporter.exportToBinFormat(Molecule, String).As of Marvin 5.7, replaced byMolExporter.exportToFormat(Molecule, String).As of Marvin 5.7, replaced byMolExporter.exportToObject(Molecule, String).As of Marvin 5.7, replaced byMPropHandler.convertToString(MProp, String).
Usage:String property = MPropHandler.convertToString(mol.properties(), key);As of Marvin 4.1, replaced byproperties().getKeys()andproperties().getKeyEnumeration().
One-to-one replacement is methodgetKeyEnumeration()but methodgetKeys()is simpler to use.As of Marvin 5.7, replaced byHydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean).
Usage:Hydrogenize.convertExplicitHToImplicit(mol, atoms, f, check);as of Marvin 6.2 replaced byMolecule.hasContractedSgroup()As of Marvin 14.7.7, no replacement.
Not supported feature.As of Marvin 6.2, useMergeUtil.mergeAtoms(MolAtom, MolAtom, boolean)instead.as of Marvin 6.2, useMolecule.expandSgroups(int)orMolecule.contractSgroups(int)instead with option parameterExpandable.LEAVE_COORDS_UNCHANGEDas of Marvin 6.2, useMolecule.expandSgroups(int)orMolecule.contractSgroups(int)instead with option parameterExpandable.LEAVE_COORDS_UNCHANGEDAs of Marvin 5.12, no replacement.
Crossing bonds of aSuperatomSgroupdo 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.As of Marvin 5.7, replaced byMolExporter.exportToBinFormat(Molecule, String).As of Marvin 5.7, replaced byMolExporter.exportToFormat(Molecule, String).
To get exact replacement use:
try { String out = MolExporter.exportToFormat(this, fmt); } catch (IOException e) { throw new IllegalArgumentException(e); }As of Marvin 5.7, replaced byMolExporter.exportToObject(Molecule, String).as of Marvin 6.3. useMolecule.ungroupSgroup(Sgroup)instead.as of Marvin 6.3. useMolecule.ungroupSgroup(Sgroup)instead.as of Marvin 6.3. useMolecule.ungroupSgroups(EnumSet)instead.As of Marvin 5.7, replaced byHydrogenize.convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int).
Usage:Hydrogenize.convertImplicitHToExplicit(molecule, null, f);As of Marvin 5.7, replaced byHydrogenize.convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int).
Usage:Hydrogenize.convertImplicitHToExplicit(molecule, atoms, f);As of Marvin 5.7, replaced byHydrogenize.convertImplicitLonePairsToExplicit(MoleculeGraph, MolAtom[]).
Usage:Hydrogenize.convertImplicitLonePairsToExplicit(molecule, null);As of Marvin 5.7, replaced byCleanUtil.arrangeComponents(MoleculeGraph, boolean, boolean).
Usage:CleanUtil.arrangeComponents(molecule, true, true);As of Marvin 5.7, no replacement.
Not intended for public use, it was intended only for internal debugging.As of Marvin 5.7, replaced byCleaner.clean(MoleculeGraph, int, String).As of Marvin 5.7, replaced byCleaner.clean(MoleculeGraph, int, String, MProgressMonitor).as of Marvin 6.3.
Not supported feature.As of Marvin 6.0, replaced byMoleculeGraph.getFragIds(int)andMoleculeGraph.FRAG_BASIC.
Usage:mol.getFragIds(MoleculeGraph.FRAG_BASIC);As of Marvin 5.6, replaced byMoleculeGraph.findFrag(int, int, MoleculeGraph)andMoleculeGraph.FRAG_KEEPING_MULTICENTERS.
Usage:mol.findFrag(i, MoleculeGraph.FRAG_KEEPING_MULTICENTERS, frag);As of Marvin 5.6, replaced byMoleculeGraph.findFrags(Class, int)andMoleculeGraph.FRAG_KEEPING_MULTICENTERS.
Usage:mol.findFrags(cl, MoleculeGraph.FRAG_KEEPING_MULTICENTERS);UseMoleculeGraph.atoms()instead.As of Marvin 5.11, replaced byMolBond.desiredLength(int, int, int, int)andMoleculeGraph.getDim().
Usage:MolBond.desiredLength(atno1, atno2, type, getDim());As of Marvin 5.11, replaced byMolBond.desiredLength(int, int, int, int),MolBond.getType()andMoleculeGraph.getDim().
Usage:MolBond.desiredLength(atno1, atno2, b.getType, getDim());useMDocument.getExplicitLonePairCount()insteadas of Marvin 15.2.16 replaced byCIPStereoCalculator.calculateCIPStereoDescriptors(MoleculeGraph, boolean).As of Marvin 5.6, replaced byMoleculeGraph.getFragCount(int)andMoleculeGraph.FRAG_KEEPING_MULTICENTERS.
Usage:mol.getFragCount(MoleculeGraph.FRAG_KEEPING_MULTICENTERS);As of Marvin 4.0, replaced byMoleculeGraph.getGrinv(int[], int).
Usage:getGrinv(gi, uniqueFlag ? GRINV_OLDSTEREO : 0);useMDocument.getLonePairCount()insteadAs of Marvin 6.0, replaced bySuperatomSgroup.getAttachmentPointOrders(MolAtom)andMolAtom.getAttachParentSgroup().
Usage:SuperatomSgroup group = (SuperatomSgroup)molAtom.getAttachParentSgroup()); List<Integer> orders = group.getAttachmentPointOrders(molAtom);as of 15.09.2014, useMoleculeGraph.getSSSRBondSet()insteadas of Marvin 6.3 replaced byMoleculeGraph.getEZStereo(MolBond).As of Marvin 6.0, replaced byMoleculeGraph.getValenceCheckOptions()andMoleculeGraph.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;useMDocument.hasExplicitLonePairs()insteadAs of Marvin 5.7, replaced byHydrogenize.convertImplicitHToExplicit(MoleculeGraph)andHydrogenize.convertExplicitHToImplicit(MoleculeGraph).As of Marvin 5.7, replaced byHydrogenize.convertExplicitHToImplicit(MoleculeGraph, int).
Usage:Hydrogenize.convertExplicitHToImplicit(molecule, f);As of Marvin 5.7, replaced byHydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int).
Usage:Hydrogenize.convertExplicitHToImplicit(mol, atoms, f);As of Marvin 5.7, replaced byHydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean).
Usage:Hydrogenize.convertExplicitHToImplicit(mol, atoms, f, check);As of Marvin 5.7, replaced byHydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean).
Usage:Hydrogenize.convertExplicitHToImplicit(mol, atoms, f, check);as of Marvin 6.2, may construct inconsistentMoleculeGraph. Similar functionality is performed byMoleculeGraph.add(MolAtom).as of Marvin 6.2, may constructs inconsistentMoleculeGraph. Similar functionality is performed byMoleculeGraph.add(MolBond).As of Marvin 14.7.7, no replacement.
Not supported feature.As of Marvin 14.7.7, no replacement.
Not supported feature.as of Marvin 14.7.7, no replacement.
Usage:use
myObject instanceof MoleculeinsteadAs of Marvin 14.7.7, no replacement.
Not supported feature.As of Marvin 6.2, useMergeUtil.mergeAtoms(MolAtom, MolAtom, boolean)instead.As of Marvin 5.7, replaced byCleaner.partialClean(MoleculeGraph, int, int[], String).As of Marvin 5.7, replaced byCleaner.partialClean(Molecule, Molecule[], String).As of Marvin 5.7, replaced byCleaner.partialClean(MoleculeGraph, MoleculeGraph, int[], String).As of Marvin 5.7, replaced byHydrogenize.convertExplicitLonePairsToImplicit(MoleculeGraph).as of Marvin 6.2, may constructs inconsistentMoleculeGraph. UseMoleculeGraph.removeBond(MolBond)for removal andMoleculeGraph.add(MolBond)for adding a new bond to the molecule.as of Marvin 6.2, may construct inconsistentMoleculeGraph. UseMoleculeGraph.removeAtom(int)for atom removal andMoleculeGraph.add(MolAtom)for adding new atoms.as of Marvin 6.2, may constructs inconsistentMoleculeGraph. UseMoleculeGraph.removeBond(MolBond)for bond removal andMoleculeGraph.add(MolBond)for adding a new bond to the molecule.As of Marvin 6.0, replaced byMoleculeGraph.setValenceCheckOptions(ValenceCheckOptions)andMoleculeGraph.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));As of Marvin 5.7, replaced byMPropHandler.convertToString(MProp, String)As of Marvin 5.7, replaced byMPropHandler.convertToString(MProp, String).As of Marvin 5.7, replaced byMPropHandler.convertToString(MPropertyContainer, String)As of Marvin 5.9, replaced by a similar method which throws IllegalArgumentException in case of failurePeriodicSystem.findAtomicNumber(String).As of Marvin 5.7, replaced byMPropHandler.convertToString(MProp, String).As of Marvin 5.7, replaced byMPropHandler.convertToString(MProp, String)As of Marvin 5.7, replaced byMPropHandler.convertToString(MProp, String)As of Marvin 5.7, replaced byMPropHandler.convertToString(MProp, String)As of Marvin 5.7, replaced byMPropHandler.convertToString(MProp, String)As of Marvin 5.7, replaced byMPropHandler.convertToString(MProp, String)As of Marvin 5.7, replaced byMPropHandler.convertToString(MProp, String)As of Marvin 5.7, replaced byMPropHandler.convertToString(MProp, String)As of Marvin 5.7, replaced byMPropHandler.convertToString(MProp, String).As of Marvin 5.7, replaced byMPropHandler.convertToString(MProp, String)As of Marvin 5.7, replaced byMPropHandler.convertToString(MProp, String)As of Marvin 5.7, no replacement.
Not intended for public use, it was intended only for internal debugging.as of Marvin 6.3.
Not supported feature.As of Marvin 14.7.7, no replacement.
Not supported feature.As of Marvin 14.7.7, no replacement.
Not supported feature.As of Marvin 6.2, useMergeUtil.mergeAtoms(MolAtom, MolAtom, boolean)instead.as of Marvin 6.2, may constructs inconsistentMoleculeGraph. UseMoleculeGraph.removeBond(MolBond)for bond removal andRgMolecule.add(MolBond)for adding a new bond to the molecule.as of Marvin 6.2, may constructs inconsistentMoleculeGraph. UseMoleculeGraph.removeAtom(MolAtom)andRgMolecule.add(MolAtom)to modify the structure.as of Marvin 6.2, may constructs inconsistentMoleculeGraph. UseMoleculeGraph.removeBond(MolBond)for bond removal andRgMolecule.add(MolBond)for adding a new bond to the molecule.as of Marvin 6.3.
Not supported feature.Multi-step reactions not supported. Method performs no operations.As of Marvin 14.7.7, no replacement.
Not supported feature.As of Marvin 14.7.7, no replacement.
Not supported feature.As of Marvin 6.2, useMergeUtil.mergeAtoms(MolAtom, MolAtom, boolean)instead.as of Marvin 6.2, may constructs inconsistentMoleculeGraph. UseMoleculeGraph.removeBond(MolBond)for bond removal andRxnMolecule.add(MolBond)for adding a new bond to the molecule.As of Marvin 6.2, may constructs inconsistentMoleculeGraph. UseMoleculeGraph.removeAtom(MolAtom)andRxnMolecule.add(MolAtom)to modify the structure.as of Marvin 6.2, may constructs inconsistentMoleculeGraph. UseMoleculeGraph.removeBond(MolBond)for bond removal andRxnMolecule.add(MolBond)for adding a new bond to the molecule.Multi-step reactions not supported. Method performs no operations.as of Marvin 6.2. UseSelectionMolecule.removeBond(MolBond)for bond removal andSelectionMolecule.add(MolBond)for adding a new bond to the molecule.as of Marvin 6.3. useSgroup.getSgroupType()instead. Note that in case ofAminoAcidSgroups returnedSgroup.ST_SUPERATOMbutSgroup.getSgroupType()will returnSgroupType.AMINOACID.as of Marvin 2014.08.25.0, useMulticenterSgroup.setCentralAtom(chemaxon.struc.MolAtom)insteadas of Marvin 6.2 useMolecule.setGUIContracted(boolean), orMolecule.setGUIContracted(boolean, int)methods for such functionalityas of Marvin 6.2 useMolecule.setGUIContracted(boolean), orMolecule.setGUIContracted(boolean, int)methods for such functionalityas of Marvin 6.2, useSgroup.setXState(int)insteadAs of Marvin 6.2, no replacement.
Not supported feature.as of Marvin 6.2. useSuperatomSgroup.expand(int)instead on the s-groups desired to be expandedAs of Marvin 6.0, replaced bySuperatomSgroup.getBoundAttachAtoms().As of Marvin 6.0, replaced bySuperatomSgroup.getFreeAttachAtoms().As of Marvin 6.0, replaced bySuperatomSgroup.getAllAttachAtoms().as of Marvin 6.2, intended for internal use, similar functionality can be reached bySuperatomSgroup.getSgroupGraph()As of Marvin 6.0, replaced bySuperatomSgroup.isFreeAttachAtom(MolAtom a).As of Marvin 6.0, replaced bySuperatomSgroup.isAttachmentAtom(MolAtom).As of Marvin 6.2, no replacement.
Not supported feature.As of Marvin 6.2, no replacement.
Not supported feature.As of Marvin 6.2, no replacement.
Not supported feature.As of Marvin 6.2, no replacement.
Not supported feature.As of Marvin 6.2, no replacement.
Not supported feature.As of Marvin 6.2, no replacement.
Not supported feature.As of Marvin 5.12, no replacement.
Crossing bonds of aSuperatomSgroupdo 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.as of Marvin 6.2, useSuperatomSgroup.calculateAttachmentPoints()insteadAs of Marvin 6.2, UseIteratorFactory.AtomIterator.next()instead.As of Marvin 6.2, UseIteratorFactory.AtomNeighbourIterator.next()instead.As of Marvin 6.2, UseIteratorFactory.BondIterator.next()instead.As of Marvin 6.2, UseIteratorFactory.BondNeighbourIterator.next()instead.As of Marvin 6.2, UseIteratorFactory.RgComponentIterator.next()instead.As of Marvin 6.2, UseIteratorFactory.RxnComponentIterator.next()instead.Not used.MoleculeIterator.next()throwsNoSuchElementExceptionin case of error.Will be removed.UseProgressObservers.nullProgressObserver()instead.CloseableIterator.transform(java.util.function.Function)provides default method making this utility not necessaryAs of Marvin 14.9.15, replaced byAtropStereoCenter.getCIPValue().As of Marvin 14.9.15, replaced byAxialStereoCenter.getCIPValue().As of Marvin 14.9.15, replaced byCisTransStereoCenter.getCIPValue().As of Marvin 14.9.15, replaced byStereoCenter.getCIPValue().As of Marvin 14.9.15, replaced byTetrahedralStereoCenter.getCIPValue().This method is kept for compatibility reason. UseComparisonContext#descriptorComparator()on the instance returned byMetricFactory.defaultComparison()fromDescriptorGenerator.comparisonContextFactory()UseFloatVectorMetricFactory.forFloatMetrics(com.chemaxon.descriptors.metrics.FloatVectorMetrics)In various cases (euclid, euclid sqr, manhattan) this has no practical interpretationIn various cases (euclid, euclid sqr, manhattan) this has no practical interpretationUse#forTversky(double, double).UseFloatVectorMetricFactory.forFloatMetrics(com.chemaxon.descriptors.metrics.FloatVectorMetrics).
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Deprecated ConstructorsConstructorDescriptionNot used.Checker has no parameters.Please consider using
StructureCheckerFactory.getInstance()instead of calling this constructor directly.
Default constructor. Default configurations will be read.Please consider usingStructureCheckerFactory.getInstance(String, String)instead of calling this constructor directly.
With this constructor inner and external configuration location can be defined.Please consider usingStructureCheckerFactory.getInstance(String, String)instead of calling this constructor directly.
With this constructor inner and external configuration location can be defined.since Marvin 6.2, UseValenceCheckOptions.Builderfor building ValenceCheckOptions.since 5.4as of Marvin 5.2.3, useMolConverter.Builder.build()instead.as of Marvin 5.2.3, replaced byMolConverter(Builder)as of Marvin 5.2.3, replaced byMolConverter(Builder)as of Marvin 5.2.3, replaced byMolConverter(Builder)as of Marvin 5.2.3, replaced byMolConverter(Builder)as of Marvin 5.2.3, replaced byMolConverter(Builder)as of Marvin 5.2.3, replaced byMolConverter(Builder)Copy feature is no longer required. Constructor.UsePharmacophore3DGeneratorinstead.since 5.3.3 new descriptor parameter added.Won't be public in the futureWon't be public in the futureWon't be public in the futureAs of Marvin 5.12, replaced bySgroupFactory.createSgroup(Molecule, SgroupType).As of Marvin 5.12, replaced bySgroupFactory.createSgroup(Molecule, SgroupType)andSgroup.setXState(int).
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Deprecated Enum ConstantsEnum ConstantDescriptionAs of Marvin 6.0, replaced by
MoleculeGraph.setValenceCheckOptions(ValenceCheckOptions)andValenceCheckOptions.DEFAULT.
Usage:molecule.setValenceCheckOptions(ValenceCheckOptions.DEFAULT);As of Marvin 6.0, replaced byMoleculeGraph.setValenceCheckOptions(ValenceCheckOptions)andValenceCheckOptions(boolean, boolean).
Usage:molecule.setValenceCheckOptions(new ValenceCheckOptions(false,true);As of Marvin 6.0, replaced byMoleculeGraph.setValenceCheckEnabled(boolean). Usage:molecule.setValenceCheckEnabled(false);