Deprecated API
Contents
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Terminally Deprecated ElementsElementDescriptionsince Marvin 5.11, use
Hydrogenize.convertImplicitHToExplicit(MoleculeGraph)insteadsince Marvin 5.11, useHydrogenize.convertImplicitHToExplicit(MoleculeGraph, MolAtom[])insteadsince Marvin 5.11, useHydrogenize.convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int)insteadsince Marvin 5.11, useHydrogenize.convertImplicitLonePairsToExplicit(MoleculeGraph, MolAtom[])insteadas of Marvin 5.11.1, replaced byTopologyUtil.isBridgeHeadAtom(MoleculeGraph, int)since Marvin 5.11, useHydrogenize.convertExplicitHToImplicit(MoleculeGraph)insteadsince Marvin 5.11, useHydrogenize.convertExplicitHToImplicit(MoleculeGraph, int)insteadsince Marvin 5.11, useHydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int)insteadsince Marvin 5.11, useHydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean)insteadsince Marvin 5.11, useHydrogenize.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 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 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()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()Configuration file URL can be set in MarvinSketch preferences, and stored in UserSettings.Will be removed from the public API.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 6.0since Marvin 6.2, UseValenceCheckOptions.Builderfor building ValenceCheckOptions.chemaxon.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.No longer used, will be removed.Will be removed, no replacement.as of Marvin 3.1, there is no possibility to do thatas of Marvin 2014.07.21.0 useMFileFormat.createRecognizer()insteadas of Marvin 2014.07.21.0 not usedUseMFileFormat.getNameList()instead.as of Marvin 2014.07.21.0 useMFileFormat.getSubFormatPriority(String)insteadas 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)as of Marvin 5.2.3, useMolConverter.Builderinstead.UseMolImporter(String, Component, String)instead.As of 23.15, no replacementAs of 23.15, useMolImporter.importMol(byte[])insteadAs of 23.15, useMolImporter.importMol(byte[], String, String)insteadAs of 23.15, useMolImporter.importMol(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.No longer supported, useMolImporter.importMol(byte[])instead.as of Marvin 14.7.7. useMolImporter.read()insteadas of Marvin 14.7.7. useMolImporter.read()insteadas of Marvin 6.2. It has no effect on the code.No longer used, will be removed.No longer used, will be removed.No longer used, will be removed.No longer used, will be removed.as of Marvin 2014.07.21.0 not usedNot used in recognition and will be removed. ImplementRecognizer.tryToRecognize(String, int)instead.Not used, will be removedNo longer used, will be removed.UseChemContext.callContextFunction(String, List)instead.This method is the legacy option for specifying the supported context functions. Use theChemContext.ProvidesFunctionannotation instead.Direct creation of aChemJEPobject will no longer be supported, use theEvaluator.compile(java.lang.String)methods instead.Direct creation of aChemJEPobject will no longer be supported, use theEvaluator.compile(java.lang.String)methods instead.Complex number support will be removed without replacement.Complex number support will be removed without replacement.This class no longer collects exceptions but throws them when they are encountered. The list this method uses is filled but otherwise ignored.The function table will not be modifiable anymore. No replacement.The symbol table has been replaced with the constant table, and it will become unmodifiable. UseEvaluator.compile(String, Class, ConstantTable)instead.These functions will be removed without replacement.The symbol table has been replaced with the constant table, and it will become unmodifiable. UseEvaluator.compile(String, Class, ConstantTable)instead.The symbol table has been replaced with the constant table, and it will become unmodifiable. UseEvaluator.compile(String, Class, ConstantTable)instead.No longer used for accessing the context, will be removed without replacement.This class no longer collects exceptions but throws them when they are encountered. The list this method uses is filled but otherwise ignored.Complex number support will be removed without replacement.This class no longer collects exceptions but throws them when they are encountered. The list this method uses is filled but otherwise ignored.This class no longer collects exceptions but throws them when they are encountered. The list this method uses is filled but otherwise ignored.This class no longer collects exceptions but throws them when they are encountered. The list this method uses is filled but otherwise ignored.This class no longer collects exceptions but throws them when they are encountered. The list this method uses is filled but otherwise ignored.The function table will become an internal API. No replacement.This feature will be removed without replacement.UseChemJEP.constantTable()instead.This method returns an internal representation which will be hidden in the future. No replacement.UseChemJEP.evaluate_double(ChemContext)instead.UseChemJEP.evaluate(ChemContext)instead.This class no longer collects exceptions but throws them when they are encountered. The list this method uses is filled but otherwise ignored.The symbol table has been replaced with the constant table, and it will become unmodifiable. UseEvaluator.compile(String, Class, ConstantTable)instead.UseChemJEP.compile(String)instead.The symbol table has been replaced with the constant table, and it will become unmodifiable. UseEvaluator.compile(String, Class, ConstantTable)instead.Undeclared variables will always be allowed in the future, changing this will no longer be supported.This option will be removed without replacement.UseEvaluator.compile(String, Class, ConstantTable)instead.UseEvaluator.setVerbose(boolean)instead before creating theChemJEP.Use theChemContext.ProvidesFunctionannotation instead.Use theChemContext.ProvidesFunctionannotation instead.Copy feature is no longer required. Constructor.Use theChemContext.ProvidesFunctionannotation instead.UseEvaluator.compile(String, Class, ConstantTable)instead.No longer used, will be removed.Was only intended for internal use, will be removed.Was only intended for internal use, will be removed.Was only intended for internal use, will be removed.Was only intended for internal use, will be removed.Was only intended for internal use, will be removed.UseEvaluator.constantTable()instead.This main method will be removed, CLI interfaces should not be used directly from Java code.Was only intended for internal use, will be removed.Was only intended for internal use, will be removed.Was only intended for internal use, will be removed.Will be removed soon.useShapeData.toDatainstead.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 setAtomSetColorAs 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 setAtomSetSeqSome implementations of this method modify the state of the plugin, which is a very confusing behavior, so the method is now deprecated and should no longer be used. If you used this method with an index argument, parse the index instead, and callElementalAnalyserPlugin.getResult(Object, int). Otherwise, call the appropriate setter method of the plugin to configure it with the argument, and callElementalAnalyserPlugin.getResult(Object, int)with a 0 index.Some implementations of this method modify the state of the plugin, which is a very confusing behavior, so the method is now deprecated and should no longer be used. If you used this method with an index argument, parse the index instead, and callGeometryPlugin.getResult(Object, int). Otherwise, call the appropriate setter method of the plugin to configure it with the argument, and callGeometryPlugin.getResult(Object, int)with a 0 index.UseHBDAPlugin.getAcceptorSiteCount()instead.UseHBDAPlugin.getAcceptorSiteCount()instead!UseHBDAPlugin.getDonorSiteCount()instead!UseHBDAPlugin.getDonorSiteCount(int)instead!No longer used.Some implementations of this method modify the state of the plugin, which is a very confusing behavior, so the method is now deprecated and should no longer be used. If you used this method with an index argument, parse the index instead, and callIsoelectricPointPlugin.getResult(Object, int). Otherwise, call the appropriate setter method of the plugin to configure it with the argument, and callIsoelectricPointPlugin.getResult(Object, int)with a 0 index.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.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)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.UselogPPlugin.setlogPMethod(LogPMethod)instead.This function will not be available from May 2016. UselogPPlugin.setlogPMethod(LogPMethod)instead.Some implementations of this method modify the state of the plugin, which is a very confusing behavior, so the method is now deprecated and should no longer be used. If you used this method with an index argument, parse the index instead, and callMarkushEnumerationPlugin.getResult(Object, int). Otherwise, call the appropriate setter method of the plugin to configure it with the argument, and callMarkushEnumerationPlugin.getResult(Object, int)with a 0 index.Some implementations of this method modify the state of the plugin, which is a very confusing behavior, so the method is now deprecated and should no longer be used. If you used this method with an index argument, parse the index instead, and callpKaPlugin.getResult(Object, int). Otherwise, call the appropriate setter method of the plugin to configure it with the argument, and callpKaPlugin.getResult(Object, int)with a 0 index.replaced bysetModel(int)Not used.As of Marvin 5.0 pH effect is not consideredsince Marvin 5.9 replaced byTautomerizationPlugin.getStructure(int)obsolete methodNot used.CallTautomerizationPlugin.setTakeMajorTautomer(boolean)instead.Some implementations of this method modify the state of the plugin, which is a very confusing behavior, so the method is now deprecated and should no longer be used. If you used this method with an index argument, parse the index instead, and callTopologyAnalyserPlugin.getResult(Object, int). Otherwise, call the appropriate setter method of the plugin to configure it with the argument, and callTopologyAnalyserPlugin.getResult(Object, int)with a 0 index.as of Marvin 4.1, replaced byTPSAPlugin.getSurfaceArea()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 5.3As of release 5.3, this feature is deprecated and has no replacement. It will be removed in a future version of Marvin.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)Loading plugins from plugin-specific jars is no longer supported, useCalculatorPlugin.create(String)instead.Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, int)with parameterMolAtom.ALL_Hdoes the same.Some implementations of this method modify the state of the plugin, which is a very confusing behavior, so the method is now deprecated and should no longer be used. If you used this method with an index argument, parse the index instead, and callCalculatorPlugin.getResult(Object, int). Otherwise, call the appropriate setter method of the plugin to configure it with the argument, and callCalculatorPlugin.getResult(Object, int)with a 0 index.Some implementations of this method modify the state of the plugin, which is a very confusing behavior, so the method is now deprecated and should no longer be used. If you used this method with an index argument, parse the index instead, and callCalculatorPlugin.getResult(Object, int). Otherwise, call the appropriate setter method of the plugin to configure it with the argument, and callCalculatorPlugin.getResult(Object, int)with a 0 index.An instance-specific class loader is no longer used by this method. UseClass.forName(String)instead.Loading plugins from plugin-specific jars is no longer supported, useCalculatorPlugin.loadPluginClass(String)instead.Jar attributes are no longer used to store information related to calculator plugins. No replacement.As of Version 5.3.2, this method is deprecated and has no replacement. It will be removed in a future version of Marvin.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.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 constantdoes nothing.does nothing.This interface will be removed, useCustomFunctioninstead.Since 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.This option is no longer supported. This method always returns true.This option is no longer supported. This method does not change anything.As of JChem 5.12, replaced bySearchConstants.SEARCH_TYPE_NAMES.useSetAbsoluteStereoActionorRemoveAbsoluteStereoActioninsteaduseTransformAction.setTransform(RxnMolecule)method insteadWill be removed, no replacement.It's not required anymore.It's not required anymore.It's not required anymore.It's not required anymore.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()since 2014.06.04. useBondType.convertToBondType(int)instead.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 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 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 5.7, no replacement.
Not intended for public use, it was intended only for internal debugging.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, this method is deprecated. Replaced byMPropHandler.getPropertyString(MoleculeGraph, String).
Usage:String property = MPropHandler.getPropertyString(mol, 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 14.7.7, no replacement.
Not supported feature.As of Marvin 6.2, useMergeUtil.mergeAtoms(MolAtom, MolAtom, boolean)instead.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.Replaced byMolExporter.toBinFormat(Molecule, String).Replaced byMolExporter.toFormat(Molecule, String).Replaced byMolExporter.toObject(Molecule, String).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 6.0, 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());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);As of Marvin 6.0, replaced bySuperatomSgroup.getAttachmentPointOrders(MolAtom)andMolAtom.getAttachParentSgroup().
Usage:SuperatomSgroup group = (SuperatomSgroup)molAtom.getAttachParentSgroup()); List<Integer> orders = group.getAttachmentPointOrders(molAtom);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 14.7.7, no replacement.
Usage:use
myObject instanceof MoleculeinsteadAs 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 6.0, 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(ValenceCheckOptions.GLOBAL);As of Marvin 6.0, replaced byValenceCheckOptions.As of Marvin 6.0, replaced byMoleculeGraph.setValenceCheckOptions(ValenceCheckOptions)andValenceCheckOptions.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 5.7, 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, 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 6.2, useMergeUtil.mergeAtoms(MolAtom, MolAtom, boolean)instead.Multi-step reactions not supported. Method performs no operations.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.Multi-step reactions not supported. Method performs no operations.As of Marvin 6.2, no replacement.
Not supported feature.as of Marvin 6.2, useExpandable.LEAVE_COORDS_UNCHANGEDinsteadas of Marvin 2014.08.25.0, useMulticenterSgroup.setCentralAtom(chemaxon.struc.MolAtom)insteadAs 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 6.0, replaced bySuperatomSgroup.isFreeAttachAtom(MolAtom a).As of Marvin 6.0, replaced bySuperatomSgroup.isAttachmentAtom(MolAtom).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.UseSmolecule.getRadicalValue(int)instead.As 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.INCLUDE_CHEMICAL_ATOMS_ONLYinstead.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.ImplementProgressObserver.close()instead, and create instances of this interface in a try-with-resources block.No longer used, will be removed.No longer used, will be removed.This method depends on the now deprecatedCalculatorPlugin.getResult(Object, String)method, so this is deprecated as well and will be removed.Moved toMolecularFormulas.Not used.As 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().Check the implementing enums for details.No longer supported, usechemaxon.jchem.version.JChemVersionInfoinstead.
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Deprecated InterfacesInterfaceDescriptionNo longer used, will be removed.Will be removed soon.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.This interface will be removed, use
CustomFunctioninstead.Check the implementing enums for details.
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Deprecated ClassesClassDescriptionWill be removed from the public API.use
CheckerFixerFactoryinsteaduseCheckerFixerFactoryinsteadas of Marvin 5.2.3, useMolConverter.Builderinstead.No longer used, will be removed.No longer used, will be removed.No longer used, will be removed.No longer used, will be removed.Not used, will be removedNo longer used, will be removed.useSetAbsoluteStereoActionorRemoveAbsoluteStereoActioninsteadMoved toMolecularFormulas.
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Deprecated Enum ClassesEnum ClassDescriptionAs of Marvin 6.0, replaced by
MoleculeGraph.setValenceCheckOptions(ValenceCheckOptions)andValenceCheckOptions.
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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 class no longer collects exceptions but throws them when they are encountered. The list this method uses is filled but otherwise ignored.No longer used, will be removed.This 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 5.3As of release 5.3, this feature is deprecated and has no replacement. It will be removed in a future version of Marvin.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.It's not required anymore.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 6.0, 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, useHydrogenize.convertImplicitHToExplicit(MoleculeGraph)insteadsince Marvin 5.11, useHydrogenize.convertImplicitHToExplicit(MoleculeGraph, MolAtom[])insteadsince Marvin 5.11, useHydrogenize.convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int)insteadsince Marvin 5.11, useHydrogenize.convertImplicitLonePairsToExplicit(MoleculeGraph, MolAtom[])insteadas of Marvin 5.11.1, replaced byTopologyUtil.isBridgeHeadAtom(MoleculeGraph, int)since Marvin 5.11, useHydrogenize.convertExplicitHToImplicit(MoleculeGraph)insteadsince Marvin 5.11, useHydrogenize.convertExplicitHToImplicit(MoleculeGraph, int)insteadsince Marvin 5.11, useHydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int)insteadsince Marvin 5.11, useHydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean)insteadsince Marvin 5.11, useHydrogenize.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 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 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()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 6.0chemaxon.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 usedUseMFileFormat.getNameList()instead.as of Marvin 2014.07.21.0 useMFileFormat.getSubFormatPriority(String)insteadAs of 23.15, no replacementAs of 23.15, useMolImporter.importMol(byte[])insteadAs of 23.15, useMolImporter.importMol(byte[], String, String)insteadAs of 23.15, useMolImporter.importMol(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.No longer supported, useMolImporter.importMol(byte[])instead.as of Marvin 14.7.7. useMolImporter.read()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 not usedNot used in recognition and will be removed. ImplementRecognizer.tryToRecognize(String, int)instead.UseChemContext.callContextFunction(String, List)instead.This method is the legacy option for specifying the supported context functions. Use theChemContext.ProvidesFunctionannotation instead.Complex number support will be removed without replacement.Complex number support will be removed without replacement.This class no longer collects exceptions but throws them when they are encountered. The list this method uses is filled but otherwise ignored.The function table will not be modifiable anymore. No replacement.The symbol table has been replaced with the constant table, and it will become unmodifiable. UseEvaluator.compile(String, Class, ConstantTable)instead.These functions will be removed without replacement.The symbol table has been replaced with the constant table, and it will become unmodifiable. UseEvaluator.compile(String, Class, ConstantTable)instead.The symbol table has been replaced with the constant table, and it will become unmodifiable. UseEvaluator.compile(String, Class, ConstantTable)instead.No longer used for accessing the context, will be removed without replacement.Complex number support will be removed without replacement.This class no longer collects exceptions but throws them when they are encountered. The list this method uses is filled but otherwise ignored.This class no longer collects exceptions but throws them when they are encountered. The list this method uses is filled but otherwise ignored.This class no longer collects exceptions but throws them when they are encountered. The list this method uses is filled but otherwise ignored.This class no longer collects exceptions but throws them when they are encountered. The list this method uses is filled but otherwise ignored.The function table will become an internal API. No replacement.This feature will be removed without replacement.UseChemJEP.constantTable()instead.This method returns an internal representation which will be hidden in the future. No replacement.UseChemJEP.evaluate_double(ChemContext)instead.UseChemJEP.evaluate(ChemContext)instead.This class no longer collects exceptions but throws them when they are encountered. The list this method uses is filled but otherwise ignored.The symbol table has been replaced with the constant table, and it will become unmodifiable. UseEvaluator.compile(String, Class, ConstantTable)instead.UseChemJEP.compile(String)instead.The symbol table has been replaced with the constant table, and it will become unmodifiable. UseEvaluator.compile(String, Class, ConstantTable)instead.Undeclared variables will always be allowed in the future, changing this will no longer be supported.This option will be removed without replacement.UseEvaluator.compile(String, Class, ConstantTable)instead.UseEvaluator.setVerbose(boolean)instead before creating theChemJEP.Use theChemContext.ProvidesFunctionannotation instead.Use theChemContext.ProvidesFunctionannotation instead.Use theChemContext.ProvidesFunctionannotation 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.UseEvaluator.compile(String, Class, ConstantTable)instead.Was only intended for internal use, will be removed.Was only intended for internal use, will be removed.Was only intended for internal use, will be removed.Was only intended for internal use, will be removed.Was only intended for internal use, will be removed.UseEvaluator.constantTable()instead.This main method will be removed, CLI interfaces should not be used directly from Java code.Was only intended for internal use, will be removed.Was only intended for internal use, will be removed.Was only intended for internal use, will be removed.useShapeData.toData()instead.useShapeData.toDatainstead.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 setAtomSetColorAs 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.Some implementations of this method modify the state of the plugin, which is a very confusing behavior, so the method is now deprecated and should no longer be used. If you used this method with an index argument, parse the index instead, and callElementalAnalyserPlugin.getResult(Object, int). Otherwise, call the appropriate setter method of the plugin to configure it with the argument, and callElementalAnalyserPlugin.getResult(Object, int)with a 0 index.For internal use only.Some implementations of this method modify the state of the plugin, which is a very confusing behavior, so the method is now deprecated and should no longer be used. If you used this method with an index argument, parse the index instead, and callGeometryPlugin.getResult(Object, int). Otherwise, call the appropriate setter method of the plugin to configure it with the argument, and callGeometryPlugin.getResult(Object, int)with a 0 index.For internal use only.UseHBDAPlugin.getAcceptorSiteCount()instead.UseHBDAPlugin.getAcceptorSiteCount()instead!UseHBDAPlugin.getDonorSiteCount()instead!UseHBDAPlugin.getDonorSiteCount(int)instead!No longer used.Some implementations of this method modify the state of the plugin, which is a very confusing behavior, so the method is now deprecated and should no longer be used. If you used this method with an index argument, parse the index instead, and callIsoelectricPointPlugin.getResult(Object, int). Otherwise, call the appropriate setter method of the plugin to configure it with the argument, and callIsoelectricPointPlugin.getResult(Object, int)with a 0 index.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.Some implementations of this method modify the state of the plugin, which is a very confusing behavior, so the method is now deprecated and should no longer be used. If you used this method with an index argument, parse the index instead, and callMarkushEnumerationPlugin.getResult(Object, int). Otherwise, call the appropriate setter method of the plugin to configure it with the argument, and callMarkushEnumerationPlugin.getResult(Object, int)with a 0 index.For internal use only.Some implementations of this method modify the state of the plugin, which is a very confusing behavior, so the method is now deprecated and should no longer be used. If you used this method with an index argument, parse the index instead, and callpKaPlugin.getResult(Object, int). Otherwise, call the appropriate setter method of the plugin to configure it with the argument, and callpKaPlugin.getResult(Object, int)with a 0 index.replaced bysetModel(int)For internal use only.Not used.As of Marvin 5.0 pH effect is not consideredsince Marvin 5.9 replaced byTautomerizationPlugin.getStructure(int)obsolete methodNot used.CallTautomerizationPlugin.setTakeMajorTautomer(boolean)instead.Some implementations of this method modify the state of the plugin, which is a very confusing behavior, so the method is now deprecated and should no longer be used. If you used this method with an index argument, parse the index instead, and callTopologyAnalyserPlugin.getResult(Object, int). Otherwise, call the appropriate setter method of the plugin to configure it with the argument, and callTopologyAnalyserPlugin.getResult(Object, int)with a 0 index.For internal use only.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)Loading plugins from plugin-specific jars is no longer supported, useCalculatorPlugin.create(String)instead.Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, int)with parameterMolAtom.ALL_Hdoes the same.Some implementations of this method modify the state of the plugin, which is a very confusing behavior, so the method is now deprecated and should no longer be used. If you used this method with an index argument, parse the index instead, and callCalculatorPlugin.getResult(Object, int). Otherwise, call the appropriate setter method of the plugin to configure it with the argument, and callCalculatorPlugin.getResult(Object, int)with a 0 index.Some implementations of this method modify the state of the plugin, which is a very confusing behavior, so the method is now deprecated and should no longer be used. If you used this method with an index argument, parse the index instead, and callCalculatorPlugin.getResult(Object, int). Otherwise, call the appropriate setter method of the plugin to configure it with the argument, and callCalculatorPlugin.getResult(Object, int)with a 0 index.An instance-specific class loader is no longer used by this method. UseClass.forName(String)instead.Loading plugins from plugin-specific jars is no longer supported, useCalculatorPlugin.loadPluginClass(String)instead.Jar attributes are no longer used to store information related to calculator plugins. No replacement.For internal use only.For internal use only.does nothing.does nothing.Since 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.This option is no longer supported. This method always returns true.This option is no longer supported. This method does not change anything.useTransformAction.setTransform(RxnMolecule)method insteadWill be removed, no replacement.It's not required anymore.It's not required anymore.It's not required anymore.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()since 2014.06.04. useBondType.convertToBondType(int)instead.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 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, this method is deprecated. Replaced byMPropHandler.getPropertyString(MoleculeGraph, String).
Usage:String property = MPropHandler.getPropertyString(mol, 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.Replaced byMolExporter.toBinFormat(Molecule, String).Replaced byMolExporter.toFormat(Molecule, String).Replaced byMolExporter.toObject(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());For internal use only.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);useMolAtom.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 6.0, 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 construct 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 construct 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 construct 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(ValenceCheckOptions.GLOBAL);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 5.7, 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, 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 2014.08.25.0, useMulticenterSgroup.setCentralAtom(chemaxon.struc.MolAtom)insteadas of Marvin 6.2, useMolecule.setGUIContracted(boolean)for such functionalityas of Marvin 6.2, useMolecule.setGUIContracted(boolean)for such functionalityas of Marvin 6.2, useSgroup.setXState(int)insteadas 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 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()insteadUseSmolecule.getRadicalValue(int)instead.As 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.ImplementProgressObserver.close()instead, and create instances of this interface in a try-with-resources block.No longer used, will be removed.No longer used, will be removed.This method depends on the now deprecatedCalculatorPlugin.getResult(Object, String)method, so this is deprecated as well and will be removed.As 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().useAutoMapper.closeableIterator(Iterator)insteaduseAutoMapper.closeableIterator(Iterator, Options)insteadNo longer supported, usechemaxon.jchem.version.JChemVersionInfoinstead.
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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.as 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)UseMolImporter(String, Component, String)instead.Direct creation of aChemJEPobject will no longer be supported, use theEvaluator.compile(java.lang.String)methods instead.Direct creation of aChemJEPobject will no longer be supported, use theEvaluator.compile(java.lang.String)methods instead.Copy feature is no longer required. Constructor.since 5.3.3 new descriptor parameter added.As 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).
Usage:molecule.setValenceCheckOptions(new ValenceCheckOptions(false,true);As of Marvin 6.0, replaced byMoleculeGraph.setValenceCheckEnabled(boolean). Usage:molecule.setValenceCheckEnabled(false);
ElementalAnalyser.setMolecule(MoleculeGraph mol).