|
Deprecated Methods |
chemaxon.struc.MoleculeGraph.addExplicitHydrogens(int)
as of Marvin 5.7 replaced by
Hydrogenize.addHAtoms(MoleculeGraph, MolAtom[], int) |
chemaxon.struc.MoleculeGraph.addExplicitHydrogens(int, MolAtom[])
as of Marvin 5.7 replaced by
Hydrogenize.addHAtoms(MoleculeGraph, MolAtom[], int) |
chemaxon.struc.MoleculeGraph.addExplicitLonePairs()
as of Marvin 5.7 replaced by
Hydrogenize.addLonePairs(MoleculeGraph, MolAtom[]) |
chemaxon.sss.search.RGroupDecomposition.addHydrogens(Molecule)
as of JChem 5.3, full fragment matching is forced,
which means that ligands are accepted at R-atoms only
(and never in place of implicit hydrogens) |
chemaxon.formats.MolConverter.Options.addInput(File, String)
|
chemaxon.formats.MolConverter.Options.addInput(InputStream, String)
|
chemaxon.formats.MolConverter.Options.addInput(String, String)
|
chemaxon.struc.RxnMolecule.addStructure(Molecule, int)
as of Marvin 4.1, replaced by
RxnMolecule.addComponent(Molecule, int) |
chemaxon.struc.RxnMolecule.addStructure(Molecule, int, boolean)
as of Marvin 4.1, replaced by
RxnMolecule.addComponent(Molecule, int, boolean) |
chemaxon.marvin.common.UserSettings.addTo(Properties)
since 5.4. use p.putAll with the persistent properties |
chemaxon.marvin.beans.MarvinPane.addToolsMenu(Container)
Not used. |
chemaxon.marvin.modules.datatransfer.ClipboardHandler.addTransferable(String, String, Integer, Integer, boolean, boolean)
use
ClipboardHandler.addTransferable(String, String, Integer, Integer, boolean, boolean, boolean)
instead. |
chemaxon.marvin.common.UserSettings.addWithLCKeysTo(Properties)
since 5.4 no replacements. |
chemaxon.calculations.TopologyAnalyser.aliphaticAtomCount()
as of release 5.5, replaced by Ring.aliphaticAtomCount() |
chemaxon.calculations.TopologyAnalyser.aliphaticBondCount()
as of release 5.5, replaced by Ring.aliphaticBondCount() |
chemaxon.calculations.TopologyAnalyser.aliphaticRingCount()
as of release 5.5, replaced by Ring.aliphaticRingCount() |
chemaxon.calculations.TopologyAnalyser.aliphaticRingCount(int)
as of release 5.5, replaced by Ring.aliphaticRingCount(int) |
chemaxon.calculations.TopologyAnalyser.aliphaticRings()
as of release 5.5, replaced by Ring.aliphaticRings() |
chemaxon.calculations.TopologyAnalyser.aliphaticRings(int)
as of release 5.5, replaced by Ring.aliphaticRings(int) |
chemaxon.calculations.TopologyAnalyser.aromaticAtomCount()
as of release 5.5, replaced by Ring.aromaticAtomCount() |
chemaxon.calculations.TopologyAnalyser.aromaticBondCount()
as of release 5.5, replaced by Ring.aromaticBondCount() |
chemaxon.calculations.TopologyAnalyser.aromaticRingCount()
as of release 5.5, replaced by Ring.aromaticRingCount() |
chemaxon.calculations.TopologyAnalyser.aromaticRingCount(int)
as of release 5.5, replaced by Ring.aromaticRingCount(int) |
chemaxon.calculations.TopologyAnalyser.aromaticRings()
as of release 5.5, replaced by Ring.aromaticRings() |
chemaxon.calculations.TopologyAnalyser.aromaticRings(int)
as of release 5.5, replaced by Ring.aromaticRings(int) |
chemaxon.struc.MoleculeGraph.arrangeComponents()
as of Marvin 5.7 replaced by
CleanUtil.arrangeComponents(MoleculeGraph, boolean, boolean)
To keep the same functionality use with TRUE boolean parameters. |
chemaxon.calculations.TopologyAnalyser.asymmetricAtomCount()
as of release 5.5, replaced by Stereochemistry.asymmetricAtomCount() |
chemaxon.calculations.TopologyAnalyser.asymmetricAtoms()
as of release 5.5, replaced by Stereochemistry.asymmetricAtoms() |
chemaxon.formats.MolConverter.Options.build()
|
chemaxon.formats.MFileFormatUtil.canBeAbbrevgroup(String)
as of Marvin 5.0,
AbbrevGroupRecognizer.testLine(String)
must be used instead |
chemaxon.formats.MFileFormatUtil.canBeJTF(String)
as of Marvin 5.0,
JTFRecognizer.canBeJTFHeader(String)
must be used instead |
chemaxon.formats.MFileFormatUtil.canBePDBRecord(String)
as of Marvin 5.0,
PDBRecognizer.testRecord(String)
must be used instead |
chemaxon.calculations.TopologyAnalyser.carboaliphaticRingCount()
as of release 5.5, replaced by Ring.carboaliphaticRingCount() |
chemaxon.calculations.TopologyAnalyser.carboaromaticRingCount()
as of release 5.5, replaced by Ring.carboaromaticRingCount() |
chemaxon.calculations.TopologyAnalyser.carboRingCount()
as of release 5.5, replaced by Ring.carboRingCount() |
chemaxon.calculations.TopologyAnalyser.carboRingCount(int)
as of release 5.5, replaced by Ring.carboRingCount(int) |
chemaxon.calculations.TopologyAnalyser.carboRings()
as of release 5.5, replaced by Ring.carboRings() |
chemaxon.calculations.TopologyAnalyser.carboRings(int)
as of release 5.5, replaced by Ring.carboRings(int) |
chemaxon.calculations.TopologyAnalyser.chainAtomCount()
as of release 5.5, replaced by Ring.chainAtomCount() |
chemaxon.calculations.TopologyAnalyser.chainBondCount()
as of release 5.5, replaced by Ring.chainBondCount() |
chemaxon.marvin.common.UserSettings.checkBeforeSave(Properties, Vector)
since 5.4 use the isEmpty method of
UserSettings.getPropertiesDescriptionChangedByOtherApp() method
to retreive the return value of this method. If you really
need it. |
chemaxon.struc.Molecule.checkConsistency()
|
chemaxon.struc.MoleculeGraph.checkConsistency()
|
chemaxon.struc.RgMolecule.checkConsistency()
|
chemaxon.calculations.TopologyAnalyser.chiralCenterCount()
as of release 5.5, replaced by Stereochemistry.chiralCenterCount() |
chemaxon.calculations.TopologyAnalyser.chiralCenters()
as of release 5.5, replaced by Stereochemistry.chiralCenters() |
chemaxon.formats.MolConverter.Options.clean(int)
|
chemaxon.formats.MolConverter.Options.clean(int, String)
|
chemaxon.struc.MoleculeGraph.clean(int, String)
as of Marvin 5.7 replaced by
Cleaner.clean(MoleculeGraph, int, String) |
chemaxon.struc.MoleculeGraph.clean(int, String, MProgressMonitor)
as of Marvin 5.7 replaced by
Cleaner.clean(MoleculeGraph, int, String, MProgressMonitor) |
chemaxon.formats.MolConverter.Options.clear()
|
chemaxon.marvin.util.ClipboardHandler.clearClipboard()
see the documentation of the class |
chemaxon.formats.MolConverter.Options.clone()
|
chemaxon.marvin.util.MolImageSize.clone()
|
chemaxon.struc.MolBond.cloneEdge(MolAtom, MolAtom)
As of Marvin 5.3, replaced by MolBond.cloneBond(MolAtom a1, MolAtom a2). |
chemaxon.alchemist.configbuilder.ConfigElement.cloneElement()
use ConfigElement.clone()
Returns a clone of the element, or null if clone not supported |
chemaxon.util.ConnectionHandler.close_NE()
since JChem 5.2 use ConnectionHandler.close() |
chemaxon.fragmenter.Fragmenter.collect(String, String, String, String, String[], boolean)
as of JChem 5.3, use
Fragmenter.collect(java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String[])
to initiate data collecting and use Fragmenter.setDataInLabel(boolean) and
Fragmenter.setAttachmentPointType(int) to set attachment data storage options. |
chemaxon.util.ConnectionHandler.connect_NE()
since JChem 5.2 use ConnectionHandler.connect() |
chemaxon.util.ConnectionHandler.connect()
since JChem 5.4, use ConnectionHandler.connectToDatabase() to avoid having to catch useless exceptions. |
chemaxon.struc.MProp.convertToString(String)
As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String) |
chemaxon.struc.MDocument.Prop.convertToString(String, int)
As of release 5.7, replaced by MolExporter.convertToString(MDocument, String, int) |
chemaxon.struc.MProp.convertToString(String, int)
As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String).
Instead MProp.CONV_SELFREF flag use fmt + ":-selfrefprops" string in fmt. |
chemaxon.struc.prop.MBooleanProp.convertToString(String, int)
As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String) |
chemaxon.struc.prop.MDoubleArrayProp.convertToString(String, int)
As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String) |
chemaxon.struc.prop.MDoubleProp.convertToString(String, int)
As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String) |
chemaxon.struc.prop.MHCoords3DProp.convertToString(String, int)
As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String) |
chemaxon.struc.prop.MHashProp.convertToString(String, int)
As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String) |
chemaxon.struc.prop.MIntegerArrayProp.convertToString(String, int)
As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String) |
chemaxon.struc.prop.MIntegerProp.convertToString(String, int)
As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String) |
chemaxon.struc.prop.MListProp.convertToString(String, int)
As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String) |
chemaxon.struc.prop.MMoleculeProp.convertToString(String, int)
As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
Instead MProp.CONV_SELFREF flag use fmt + ":-selfrefprops" string in fmt. |
chemaxon.struc.prop.MObjectProp.convertToString(String, int)
As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String) |
chemaxon.struc.prop.MStringProp.convertToString(String, int)
As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String) |
chemaxon.marvin.view.MDocStorage.countRecordsInFraction(double, int, MProgressMonitor)
|
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(boolean, boolean)
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
|
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(boolean, boolean, boolean)
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
|
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(boolean, boolean, CodeAssistDataProvider.Context)
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
|
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(boolean, CodeAssistDataProvider.Context)
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
|
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(CodeAssistDataProvider.Context)
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
Default help text will be shown in empty textpane. |
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String)
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
Default help text will be shown in empty textpane. |
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, boolean)
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space |
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, boolean, boolean)
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
|
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, boolean, boolean, boolean)
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
|
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, boolean, boolean, CodeAssistDataProvider.Context)
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
|
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, boolean, CodeAssistDataProvider.Context)
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space |
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, CodeAssistDataProvider.Context)
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
Default help text will be shown in empty textpane. |
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, String)
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space |
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, String, boolean)
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars. |
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, String, boolean, boolean)
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars. |
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, String, boolean, CodeAssistDataProvider.Context)
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars. |
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, String, boolean, String)
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities. |
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, String, boolean, String, boolean)
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities. |
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, String, boolean, String, boolean, CodeAssistDataProvider.Context)
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities. |
chemaxon.marvin.util.codeassist.CodeAssistFactory.createChemicalTermsTextPane(String, String, boolean, String, CodeAssistDataProvider.Context)
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities. |
chemaxon.marvin.beans.MarvinPane.createMenu(ResourceBundle, String)
as of Marvin 3.3.1, replaced by SwingUtil.createMenu |
chemaxon.struc.RgMolecule.createMol(String)
As of Marvin 3.4,
MolImportModule.createMol() must be used. |
chemaxon.reaction.Reactor.createReactionObject(Molecule, String, String, String, double[])
Will be removed from the public API. |
chemaxon.reaction.Reactor.createReactionObject(Molecule, String, String, String, String)
Will be removed from the public API. |
chemaxon.marvin.calculations.ResonancePlugin.createStandardizedMolecule(Molecule, boolean)
Use ResonancePlugin.createStandardizedMolecule(Molecule) instead |
chemaxon.marvin.calculations.TautomerizationPlugin.createStandardizedMolecule(Molecule, boolean)
Use TautomerizationPlugin.createStandardizedMolecule(Molecule) instead |
chemaxon.marvin.plugin.CalculatorPlugin.createStandardizedMolecule(Molecule, boolean)
Use CalculatorPlugin.createStandardizedMolecule(Molecule) instead |
chemaxon.marvin.plugin.CalculatorPlugin.dehydrogenize(Molecule)
MoleculeGraph.implicitizeHydrogens(int)
with parameter MolAtom.ALL_H does the same. |
chemaxon.struc.MDocument.exportToBinFormat(String)
As of release 5.7, replaced by MolExporter.exportToBinFormat(MDocument, String) |
chemaxon.struc.Molecule.exportToBinFormat(String)
As of release 5.7, replaced by
MolExporter.exportToBinFormat(Molecule, String) |
chemaxon.struc.MDocument.exportToFormat(String)
As of release 5.7, replaced by MolExporter.exportToFormat(MDocument, String) |
chemaxon.struc.Molecule.exportToFormat(String)
As of release 5.7, replaced by
MolExporter.exportToFormat(Molecule, String) |
chemaxon.struc.MDocument.exportToObject(String)
As of release 5.7, replaced by MolExporter.exportToObject(MDocument, String) |
chemaxon.struc.Molecule.exportToObject(String)
As of release 5.7, replaced by
MolExporter.exportToObject(Molecule, String) |
chemaxon.sss.search.MCS.findFirst()
since 5.4 |
chemaxon.struc.MoleculeGraph.findFrag(int, MoleculeGraph)
since 5.6, replaced by MoleculeGraph.findFrag(int, int, MoleculeGraph),
to keep the same functionality, use value MoleculeGraph.FRAG_KEEPING_MULTICENTERS
for parameter fragmentationType, e.g.:
mol.findFrag(i, MoleculeGraph.FRAG_KEEPING_MULTICENTERS, frag);
|
chemaxon.struc.MoleculeGraph.findFragById(int, MoleculeGraph)
since 5.6, replaced by MoleculeGraph.findFragById(int, int, MoleculeGraph),
to keep the same functionality, use value MoleculeGraph.FRAG_KEEPING_MULTICENTERS
for parameter fragmentationType, e.g.:
mol.findFragById(fragId, MoleculeGraph.FRAG_KEEPING_MULTICENTERS, frag);
|
chemaxon.struc.MoleculeGraph.findFrags(Class)
since 5.6, replaced by MoleculeGraph.findFrags(Class, int),
to keep the same functionality, use value MoleculeGraph.FRAG_KEEPING_MULTICENTERS
for parameter fragmentationType, e.g.:
mol.findFrags(cl, MoleculeGraph.FRAG_KEEPING_MULTICENTERS);
|
chemaxon.sss.search.MCS.findNext()
since 5.4 |
chemaxon.descriptors.ECFP.fromFeatureSet(Set)
As of JChem 5.4.1, replaced by fromIdentiferSet(). |
chemaxon.calculations.TopologyAnalyser.fusedAliphaticRingCount()
as of release 5.5, replaced by Ring.fusedAliphaticRingCount() |
chemaxon.calculations.TopologyAnalyser.fusedAliphaticRingCount(int)
as of release 5.5, replaced by Ring.fusedAliphaticRingCount(int) |
chemaxon.calculations.TopologyAnalyser.fusedAliphaticRings()
as of release 5.5, replaced by Ring.fusedAliphaticRings() |
chemaxon.calculations.TopologyAnalyser.fusedAliphaticRings(int)
as of release 5.5, replaced by Ring.fusedAliphaticRings(int) |
chemaxon.calculations.TopologyAnalyser.fusedAromaticRingCount()
as of release 5.5, replaced by Ring.fusedAromaticRingCount() |
chemaxon.calculations.TopologyAnalyser.fusedAromaticRingCount(int)
as of release 5.5, replaced by Ring.fusedAromaticRingCount(int) |
chemaxon.calculations.TopologyAnalyser.fusedAromaticRings()
as of release 5.5, replaced by Ring.fusedAromaticRings() |
chemaxon.calculations.TopologyAnalyser.fusedAromaticRings(int)
as of release 5.5, replaced by Ring.fusedAromaticRings(int) |
chemaxon.calculations.TopologyAnalyser.fusedRingCount()
as of release 5.5, replaced by Ring.fusedRingCount() |
chemaxon.marvin.common.UserSettings.get(String)
since 5.4 use UserSettings.getProperty(String) instead. |
chemaxon.reaction.Standardizer.getActiveGroups()
Not used anymore. |
chemaxon.marvin.calculations.TopologyAnalyserPlugin.getAliphaticRingCountOfSize(int)
Use TopologyAnalyserPlugin.getAliphaticRingCount(int) |
chemaxon.marvin.calculations.TopologyAnalyserPlugin.getAromaticRingCountOfSize(int)
Use TopologyAnalyserPlugin.getAromaticRingCount(int) |
chemaxon.struc.MoleculeGraph.getAromrings()
please use getAromaticAndAliphaticRings instead. |
chemaxon.struc.MoleculeGraph.getAromrings(int)
please use getAromaticAndAliphaticRings instead. |
chemaxon.struc.MolAtom.getAtomicNumber(String)
As of Marvin 5.9, replaced by a similar method PeriodicSystem.findAtomicNumber(String). |
chemaxon.struc.PeriodicSystem.getAtomicNumber(String)
As of Marvin 5.9, replaced by a similar method which
throws IllegalArgumentException in case of failure
PeriodicSystem.findAtomicNumber(String). |
chemaxon.marvin.calculations.logPPlugin.getAtomlogPHIncrement(int)
Increments of implicit H-s are not calculated. Returns the same value as logPPlugin.getAtomlogPIncrement(int) |
chemaxon.marvin.beans.MarvinPane.getAtomNumbersVisible()
as of Marvin 2.9.13, replaced by isAtomNumbersVisible. |
chemaxon.marvin.MolPrinter.getAtomsize()
As of Marvin 5.2.2, replaced by MolPrinter.getAtomSize(). |
chemaxon.marvin.MolPrinter.getBondWidth()
as of Marvin 4.1, replaced by MolPrinter.getBondSpacing() |
chemaxon.marvin.beans.MarvinPane.getBondWidth()
as of Marvin 4.1, replaced by MarvinPane.getBondSpacing() |
chemaxon.struc.MoleculeGraph.getBtab()
as of Marvin 5.4, please use MoleculeGraph.getBondTable() instead |
chemaxon.struc.RgMolecule.getBtab()
as of Marvin 5.4, please use RgMolecule.getBondTable() instead |
chemaxon.struc.RxnMolecule.getBtab()
as of Marvin 5.4, please use RxnMolecule.getBondTable() instead |
chemaxon.marvin.beans.MViewPane.getCanvasComponent(int)
as of Marvin 3.0, replaced by getVisibleCellComponent |
chemaxon.marvin.util.ClipboardHandler.getClipboard()
see the documentation of the class |
chemaxon.marvin.util.ClipboardHandler.getClipboardClearerTask()
see the documentation of the class |
chemaxon.marvin.beans.MarvinPane.getCommonActions()
|
chemaxon.jchem.db.Importer.getConnections()
since 2.2 replaced by Importer.getFieldConnections(). |
chemaxon.marvin.util.ClipboardHandler.getDataFromClipboardOLE()
see the documentation of the class |
chemaxon.marvin.common.UserSettings.getDefaultMyTemplatesValue()
since 5.4 use
TemplateHandler.DEFAULT_MY_TEMPLATES_VALUE instead. |
chemaxon.marvin.util.ClipboardHandler.getDefaultOutputTransferFormatIds()
since 5.3 not needed anymore won't be supported after 5.4 |
chemaxon.marvin.util.ClipboardHandler.getDefaultTransferFormatId()
see the documentation of the class |
chemaxon.checkers.StructureChecker.getDescription()
This method isn't needed anymore and will be removed in 6.0 |
chemaxon.fixers.StructureFixer.getDescription()
|
chemaxon.struc.MolAtom.getEdge(int)
As of Marvin 5.3, replaced by MolAtom.getBond(int). |
chemaxon.struc.MoleculeGraph.getEdge(int)
As of Marvin 5.3, replaced by MoleculeGraph.getBond(int). |
chemaxon.struc.MoleculeGraph.getEdgeArray()
As of Marvin 5.3, replaced by MoleculeGraph.getBondArray(). |
chemaxon.struc.MolAtom.getEdgeCount()
As of Marvin 5.3, replaced by MolAtom.getBondCount(). |
chemaxon.struc.MoleculeGraph.getEdgeCount()
As of Marvin 5.3, replaced by MoleculeGraph.getBondCount(). |
chemaxon.struc.MolAtom.getEdgeTo(MolAtom)
As of Marvin 5.3, replaced by MolAtom.getBondTo(MolAtom). |
chemaxon.struc.MoleculeGraph.getEdgeVector()
As of Marvin 5.3, replaced by
Arrays.asList(getAtomArray()). |
chemaxon.checkers.StructureChecker.getEditorClassName()
This method isn't needed anymore and will be removed in 6.0 |
chemaxon.marvin.calculations.HuckelAnalysisPlugin.getEigenVector()
Use HuckelAnalysisPlugin.getHMOEigenVector() |
chemaxon.marvin.calculations.HuckelAnalysisPlugin.getElectrophilicOrder(int)
Use HuckelAnalysisPlugin.getHMOElectrophilicOrder(int) |
chemaxon.marvin.beans.MarvinPane.getExplicitH()
since 5.4 returns false. will be unsupported in 5.5 |
chemaxon.descriptors.ECFP.getFeatureCount()
As of JChem 5.4.1, replaced by ECFP.getIdentiferCount(). |
chemaxon.reaction.Reaction.getFID()
Not used. Returns null. |
chemaxon.util.MolHandler.getFingerprintInBytes(int, int, int)
since JChem 3.1 the usage of
MolHandler.generateFingerprintInBytes(int, int, int)
is recommended |
chemaxon.util.MolHandler.getFingerprintInInts(int, int, int)
since JChem 3.1 the usage of
MolHandler.generateFingerprintInInts(int, int, int)
is recommended |
chemaxon.struc.MoleculeGraph.getFragCount()
since 5.6, replaced by MoleculeGraph.getFragCount(int),
to keep the same functionality, use value MoleculeGraph.FRAG_KEEPING_MULTICENTERS
for parameter fragmentationType, e.g.:
mol.getFragCount(MoleculeGraph.FRAG_KEEPING_MULTICENTERS);
|
chemaxon.struc.MoleculeGraph.getFragIds()
since 5.6, replaced by MoleculeGraph.getFragIds(int),
to keep the same functionality, use value MoleculeGraph.FRAG_KEEPING_MULTICENTERS
for parameter fragmentationType, e.g.:
mol.getFragIds(MoleculeGraph.FRAG_KEEPING_MULTICENTERS);
|
chemaxon.jep.Evaluator.getFunctionParameterData()
use Evaluator.getFunctionData() |
chemaxon.struc.MoleculeGraph.getGrinv(int[], boolean)
Please use getGrinv(int[], int) instead. |
chemaxon.checkers.StructureChecker.getHelpText()
This method isn't needed anymore and will be removed in 6.0 |
chemaxon.marvin.calculations.HuckelAnalysisPlugin.getHuckelOrbitalCoefficients()
Use HuckelAnalysisPlugin.getHMOHuckelOrbitalCoefficients() |
chemaxon.checkers.StructureChecker.getIcon()
This method isn't needed anymore and will be removed in 6.0 |
chemaxon.marvin.util.ClipboardHandler.getImageToClipboardTask(Image)
see the documentation of the class |
chemaxon.formats.MolConverter.Options.getInputCount()
|
chemaxon.marvin.beans.MarvinPane.getLabels()
use isAtomSymbolsVisible() instead |
chemaxon.checkers.StructureChecker.getLocalMenuName()
This method isn't needed anymore and will be removed in 6.0 |
chemaxon.marvin.beans.MSketchPane.getMag()
As of Marvin 2.8.1, replaced by getScale() |
chemaxon.marvin.plugin.CalculatorPlugin.getMainMolecule(Molecule)
Use CalculatorPlugin.createModifiedInputMolecule(Molecule) instead |
chemaxon.marvin.util.ClipboardHandler.getMoleculeToClipboardTask(Molecule, Properties, String)
see the documentation of the class |
chemaxon.marvin.common.UserSettings.getMyTemplatesKey()
since 5.4 use TemplateHandler.MYTEMPLATES_KEY
instead. |
chemaxon.marvin.common.UserSettings.getMyTemplatesValue()
since 5.4 |
chemaxon.marvin.common.UserSettings.getMyTemplatesValue(Properties)
since 5.4 no replacements |
chemaxon.checkers.StructureChecker.getName()
This method isn't needed anymore and will be removed in 6.0 |
chemaxon.fixers.StructureFixer.getName()
|
chemaxon.struc.MoleculeGraph.getNode(int)
As of Marvin 5.3, replaced by MoleculeGraph.getAtom(int). |
chemaxon.struc.MolBond.getNode1()
As of Marvin 5.3, replaced by MolBond.getAtom1(). |
chemaxon.struc.MolBond.getNode2()
As of Marvin 5.3, replaced by MolBond.getAtom2(). |
chemaxon.struc.MoleculeGraph.getNodeCount()
As of Marvin 5.3, replaced by MoleculeGraph.getAtomCount(). |
chemaxon.struc.MoleculeGraph.getNodeVector()
As of Marvin 5.3, replaced by
Arrays.asList(getAtomArray()). |
chemaxon.struc.MoleculeGraph.getNonAromrings()
please use getAromaticAndAliphaticRings instead. |
chemaxon.struc.MoleculeGraph.getNonAromrings(int)
please use getAromaticAndAliphaticRings instead. |
chemaxon.marvin.calculations.HuckelAnalysisPlugin.getNucleophilicOrder(int)
Use HuckelAnalysisPlugin.getHMONucleophilicOrder(int) |
chemaxon.marvin.util.ClipboardHandler.getObjectFromClipboard(boolean)
see the documentation of the class |
chemaxon.marvin.util.ClipboardHandler.getObjectFromTransferable(Transferable, boolean)
see the documentation of the class |
chemaxon.marvin.util.ClipboardHandler.getOLEToClipboardTask(Molecule, Properties)
see the documentation of the class |
chemaxon.formats.MolImporter.getOptionFlags()
As of Marvin 5.2, use the "MOLMOVIE" and "NOMOLMOVIE" import
options instead. See MFileFormatUtil.MOLMOVIE,
MFileFormatUtil.NOMOLMOVIE, MolImporter.isMolMovie(). |
chemaxon.struc.MolBond.getOtherNode(MolAtom)
As of Marvin 5.3, replaced by MolBond.getOtherAtom(MolAtom). |
chemaxon.marvin.util.ClipboardHandler.getOutputTransferFormatIds()
see the documentation of the class |
chemaxon.marvin.calculations.pKaPlugin.getpKa(int, int)
Use pKaPlugin.getpKaValues(int, int) |
chemaxon.jep.Evaluator.getPluginIDs()
use Evaluator.getFunctionData() |
chemaxon.formats.recognizer.Recognizer.getPriority()
as of Marvin 5.1,
use MFileFormat.getPriority(java.lang.String) instead |
chemaxon.reaction.Reactor.getProductStandardizer()
Will be removed. Use Standardizer to standardize products. |
chemaxon.struc.Molecule.getProperty(String)
as of Marvin 5.7 replaced by
MPropHandler.convertToString(MProp, String),
the following usage will give the same results:
String property = MPropHandler.convertToString(mol.properties(), key);
|
chemaxon.struc.Molecule.getPropertyKeys()
as of Marvin 4.1, replaced by
properties().getKeys() |
chemaxon.struc.MolAtom.getQuerystr()
As of release 5.7, replaced by MolAtom.getQueryString() |
chemaxon.marvin.beans.MarvinPane.getReadGlobalGUIProperties()
since Marvin 5.1 when this and the MarvinPane.getSaveGlobalGUIProperties() function
have been merged. |
chemaxon.marvin.common.UserSettings.getReadGUIPropertiesFromMRV()
As of release 5.1, replaced by UserSettings.getSaveGUIPropertiesInMRV(). It will be removed in a future version of Marvin. |
chemaxon.marvin.calculations.HuckelAnalysisPlugin.getRealEigenValue()
Use HuckelAnalysisPlugin.getHMORealEigenValue() |
chemaxon.marvin.calculations.TopologyAnalyserPlugin.getRingCountOfSize(int)
Use TopologyAnalyserPlugin.getRingCount(int) |
chemaxon.marvin.calculations.TopologyAnalyserPlugin.getRingSystemCountOfSize(int)
Use TopologyAnalyserPlugin.getRingSystemCount(int) |
chemaxon.marvin.beans.MarvinPane.getSetColor(int)
as of Marvin 3.3, replaced by getAtomSetColor |
chemaxon.marvin.beans.MSketchPane.getSimpView()
as of Marvin 3.5, replaced by MSketchPane.isBondDraggedAlong() |
chemaxon.marvin.calculations.pKaPlugin.getSortedValues(int, double[], int[])
Use pKaPlugin.getMacropKaValues(int,double[],int[]) instead |
chemaxon.struc.MoleculeGraph.getSSSRBondSet()
please use getSSSRBondSetInLong() instead. |
chemaxon.reaction.Reactor.getStandardizer()
Will be removed. Use Standardizer to standardize reactants. |
chemaxon.struc.MPropertyContainer.getString(String)
As of Marvin 5.7, replaced by
MPropHandler.convertToString(MPropertyContainer, String) |
chemaxon.marvin.util.ClipboardHandler.getStringFromClipboard()
see the documentation of the class |
chemaxon.marvin.util.ClipboardHandler.getStringToClipboardTask(String)
see the documentation of the class |
chemaxon.struc.RxnMolecule.getStructure(int, int)
as of Marvin 4.1, replaced by RxnMolecule.getComponent(int, int) |
chemaxon.struc.RxnMolecule.getStructureCount(int)
as of Marvin 4.1, replaced by RxnMolecule.getComponentCount(int) |
chemaxon.marvin.calculations.TautomerizationPlugin.getStructures()
since Marvin 5.9 replaced by
TautomerizationPlugin.getStructure(int) |
chemaxon.util.iterator.MoleculeIterator.getThrowable()
Not used. MoleculeIterator.next() throws NoSuchElementException in case of error. |
chemaxon.sss.search.SearchOptions.getTimeoutLimit()
since 5.6 use SearchOptions.getTimeoutLimitMilliseconds() instead |
chemaxon.marvin.calculations.HuckelAnalysisPlugin.getTotalPiEnergy()
Use HuckelAnalysisPlugin.getHMOTotalPiEnergy() |
chemaxon.marvin.calculations.TPSAPlugin.getTPSA()
as of Marvin 4.1, replaced by
TPSAPlugin.getSurfaceArea() |
chemaxon.marvin.util.ClipboardHandler.getTransferableFor(Molecule, Properties)
see the documentation of the class |
chemaxon.marvin.util.ClipboardHandler.getTransferableFor(Molecule, Properties, String)
see the documentation of the class |
chemaxon.descriptors.MDSet.getUserData()
since 2.3 |
chemaxon.descriptors.MDSet.getUserData(int)
since 2.3 |
chemaxon.marvin.common.UserSettings.getViewExplicitH()
As of release 5.3, this method is deprecated and has no replacement. It will be removed in a future version of Marvin. |
chemaxon.formats.MFileFormatUtil.guessPeptideFormat(String)
as of Marvin 5.0,
PeptideRecognizer.guessPeptideFormat(String)
must be used instead |
chemaxon.struc.MolAtom.hasSMARTSProps()
As of release 5.7, replaced by SmartsAtomQuerifier.hasSMARTSProps(MolAtom atom) |
chemaxon.struc.MolAtom.hasSMARTSPropsExcluding(String)
As of release 5.7, replaced by SmartsAtomQuerifier.hasSMARTSPropsExcluding(MolAtom atom, String exclude) |
chemaxon.struc.MolAtom.haveSimilarEdges(MolAtom)
As of Marvin 5.3, replaced by MolAtom.haveSimilarBonds(MolAtom). |
chemaxon.calculations.TopologyAnalyser.heteroaliphaticRingCount()
as of release 5.5, replaced by Ring.heteroaliphaticRingCount() |
chemaxon.calculations.TopologyAnalyser.heteroaliphaticRingCount(int)
as of release 5.5, replaced by Ring.heteroaliphaticRingCount(int) |
chemaxon.calculations.TopologyAnalyser.heteroaliphaticRings()
as of release 5.5, replaced by Ring.heteroaliphaticRings() |
chemaxon.calculations.TopologyAnalyser.heteroaliphaticRings(int)
as of release 5.5, replaced by Ring.heteroaliphaticRings(int) |
chemaxon.calculations.TopologyAnalyser.heteroaromaticRingCount()
as of release 5.5, replaced by Ring.heteroaromaticRingCount() |
chemaxon.calculations.TopologyAnalyser.heteroaromaticRingCount(int)
as of release 5.5, replaced by Ring.heteroaromaticRingCount(int) |
chemaxon.calculations.TopologyAnalyser.heteroaromaticRings()
as of release 5.5, replaced by Ring.heteroaromaticRings() |
chemaxon.calculations.TopologyAnalyser.heteroaromaticRings(int)
as of release 5.5, replaced by Ring.heteroaromaticRings(int) |
chemaxon.calculations.TopologyAnalyser.heteroRingCount()
as of release 5.5, replaced by Ring.heteroRingCount() |
chemaxon.calculations.TopologyAnalyser.heteroRingCount(int)
as of release 5.5, replaced by Ring.heteroRingCount(int) |
chemaxon.calculations.TopologyAnalyser.heteroRings()
as of release 5.5, replaced by Ring.heteroRings() |
chemaxon.calculations.TopologyAnalyser.heteroRings(int)
as of release 5.5, replaced by Ring.heteroRings(int) |
chemaxon.struc.MoleculeGraph.hydrogenize(boolean)
as of Marvin 5.7 replaced by
Hydrogenize.addHAtoms(MoleculeGraph) and
Hydrogenize.removeHAtoms(MoleculeGraph) |
chemaxon.struc.MoleculeGraph.implicitizeHydrogens(int)
as of Marvin 5.7 replaced by
Hydrogenize.removeHAtoms(MoleculeGraph, int),
the following usage will give the same results:
chemaxon.calculations.hydrogenize.Hydrogenize.removeHAtoms(mol, f);
|
chemaxon.struc.MoleculeGraph.implicitizeHydrogens(int, MolAtom[])
as of Marvin 5.7 replaced by
Hydrogenize.removeHAtoms(MoleculeGraph, MolAtom[], int),
the following usage will give the same results:
chemaxon.calculations.hydrogenize.Hydrogenize.removeHAtoms(mol, atoms, f);
|
chemaxon.struc.MoleculeGraph.implicitizeHydrogens(int, MolAtom[], boolean)
as of Marvin 5.7 replaced by
Hydrogenize.removeHAtoms(MoleculeGraph, MolAtom[], int, boolean)
the following usage will give the same results:
chemaxon.calculations.hydrogenize.Hydrogenize.removeHAtoms(mol, atoms, f, check);
|
chemaxon.struc.Molecule.implicitizeHydrogens0(int, MolAtom[], boolean)
as of Marvin 5.7 replaced by
Hydrogenize.removeHAtoms(MoleculeGraph, MolAtom[], int, boolean) |
chemaxon.struc.MoleculeGraph.implicitizeHydrogens0(int, MolAtom[], boolean)
as of Marvin 5.7 replaced by
Hydrogenize.removeHAtoms(MoleculeGraph, MolAtom[], int, boolean) |
chemaxon.formats.MolImporter.importMol(String, String, String)
(Since Marvin 5.5) There is no need to specify an encoding for a String input. Instead,
if you have a String to import, call MolImporter.importMol(String,String);
if you have a byte array, call MolImporter.importMol(byte[], String, String). |
chemaxon.formats.MolImporter.importMol(String, String, String, Molecule)
(Since Marvin 5.5) There is no need to specify an encoding for a String input. Instead,
if you have a String to import, call MolImporter.importMol(String, String);
if you have a byte array, call MolImporter.importMol(byte[], String, String, Molecule). |
chemaxon.marvin.beans.MarvinPane.initAction(Action, ResourceBundle, String, KeyStroke)
as of Marvin 3.3.1, replaced by SwingUtil.initAction |
chemaxon.marvin.beans.MarvinPane.initButton(AbstractButton, ResourceBundle, String)
as of Marvin 3.3.1, replaced by SwingUtil.initButton |
chemaxon.marvin.util.SwingUtil.initCtrlShortcutForMac(JMenuItem)
does nothing. |
chemaxon.marvin.util.SwingUtil.initInApplet()
does nothing. |
chemaxon.struc.MoleculeGraph.insertEdge(int, MolBond)
As of Marvin 5.3, replaced by MoleculeGraph.insertBond(int, MolBond). |
chemaxon.struc.MoleculeGraph.insertEdgeInOrder(MolBond, MolBond[])
As of Marvin 5.3, replaced by MoleculeGraph.insertBondInOrder(MolBond, MolBond[]). |
chemaxon.struc.MoleculeGraph.insertNode(int, MolAtom)
As of Marvin 5.3, replaced by MoleculeGraph.insertAtom(int, MolAtom). |
chemaxon.calculations.TopologyAnalyser.isAliphaticAtom(int)
as of release 5.5, replaced by Ring.isAliphaticAtom(int) |
chemaxon.calculations.TopologyAnalyser.isAromaticAtom(int)
as of release 5.5, replaced by Ring.isAromaticAtom(int) |
chemaxon.struc.MolBond.isArrow()
As of Marvin 5.3, |
chemaxon.struc.MolAtom.isArrowEnd()
As of Marvin 5.3 |
chemaxon.calculations.TopologyAnalyser.isAsymmetricAtom(int)
as of release 5.5, replaced by Stereochemistry.isAsymmetricAtom(int) |
chemaxon.calculations.TopologyAnalyser.isChainAtom(int)
as of release 5.5, replaced by Ring.isChainAtom(int) |
chemaxon.calculations.TopologyAnalyser.isChainBond(int)
as of release 5.5, replaced by Ring.isChainBond(int) |
chemaxon.calculations.TopologyAnalyser.isChiral()
as of release 5.5, replaced by Stereochemistry.isChiral() |
chemaxon.calculations.TopologyAnalyser.isChiralCenter(int)
as of release 5.5, replaced by Stereochemistry.isChiralCenter(int) |
chemaxon.struc.MolBond.isCoordinative()
As of Marvin 5.0, replaced by
MolBond.isCoordinate() |
chemaxon.formats.MFileFormatUtil.isCubeLine(String, int)
as of Marvin 5.0,
CubeRecognizer.isCubeLine(String, int)
must be used instead |
chemaxon.sss.search.SearchOptions.isExactFragment()
since 5.6, replaced by SearchOptions.isFullFragment() |
chemaxon.marvin.MolPrinter.isExplicitHVisible()
As of Marvin 5.5.1 this method always returns true.
This method will be removed in a future release. |
chemaxon.marvin.MolPrinter.isEzVisible()
As of Marvin 5.2.2, replaced by MolPrinter.isEZLabelsVisible() |
chemaxon.marvin.beans.MarvinPane.isGrinv()
as of Marvin 3.5, use isGrinvVisible() instead |
chemaxon.struc.MolAtom.isNobleGas()
As of Marvin 5.4, replaced by PeriodicSystem.isNobleGas(int z). |
chemaxon.sss.search.SearchOptions.isQHomologyHandling()
since 5.6, use SearchOptions.getHomologyNarrowTranslation() |
chemaxon.marvin.beans.MSketchPane.isReactionErrorVisible()
As of Version 5.3.2, this method is deprecated and has no replacement. It will be removed in a future version of Marvin.
Are reaction errors highlighted? |
chemaxon.marvin.common.UserSettings.isReactionErrorVisible()
As of Version 5.3.2, this method is deprecated and has no replacement. It will be removed in a future version of Marvin.
Are reaction errors visible? |
chemaxon.calculations.TopologyAnalyser.isRingAtom(int)
as of release 5.5, replaced by Ring.isRingAtom(int) |
chemaxon.calculations.TopologyAnalyser.isRingBond(int)
as of release 5.5, replaced by Ring.isRingBond(int) |
chemaxon.marvin.util.ClipboardHandler.isSupportedTransferFormat(String)
see the documentation of the class |
chemaxon.sss.search.SearchOptions.isTautomerDuplicateFiltering()
since 5.5, replace with SearchOptions.getTautomerSearch() |
chemaxon.struc.MoleculeGraph.isValenceCheckEnabled()
since Marvin 5.9, please use
MoleculeGraph.getValenceCheckState() instead |
chemaxon.marvin.common.UserSettings.keys()
in 5.4 use the keySet method on the result of
UserSettings.getPropertyMap() instead. |
chemaxon.calculations.TopologyAnalyser.largestRing()
as of release 5.5, replaced by Ring.largestRing() |
chemaxon.calculations.TopologyAnalyser.largestRingSize()
as of release 5.5, replaced by Ring.largestRingSize() |
chemaxon.calculations.TopologyAnalyser.largestRingSizeOfAtom(int)
as of release 5.5, replaced by Ring.largestRingSizeOfAtom(int) |
chemaxon.calculations.TopologyAnalyser.largestRingSystem()
as of release 5.5, replaced by Ring.largestRingSystem() |
chemaxon.calculations.TopologyAnalyser.largestRingSystemSize()
as of release 5.5, replaced by Ring.largestRingSystemSize() |
chemaxon.reaction.Reactor.main(String[])
ConcurrentReactorProcessor provides command line interface for Reactor command line application. |
chemaxon.reaction.Standardizer.main(String[])
Use ConcurrentStandardizerProcessor.main(String[]) |
chemaxon.marvin.beans.MViewPane.makeHelpMenu(Container)
As of Marvin 3.4,
MarvinPane.addHelpMenu(java.awt.Container) should be used. |
chemaxon.marvin.beans.MViewPane.makeToolsMenu()
As of Marvin 3.4,
MarvinPane.addToolsMenu(java.awt.Container) should be used. |
chemaxon.struc.Molecule.mergeFrags()
since 5.6, it was used by an internal method, not intended
for public usage. |
chemaxon.struc.MoleculeGraph.mergeFrags()
since 5.6, it was an empty method in this class which is not
required any more, it's usage can simply be deleted. |
chemaxon.struc.MoleculeGraph.mergeFrags(int, int)
since 5.6, replaced by MoleculeGraph.mergeFrags(int, int, int),
to keep the same functionality, use value MoleculeGraph.FRAG_KEEPING_MULTICENTERS
for parameter fragmentationType, e.g.:
mol.mergeFrags(id1, id2, MoleculeGraph.FRAG_KEEPING_MULTICENTERS);
|
chemaxon.struc.MoleculeGraph.mergeNodes(MolAtom, MolAtom)
As of Marvin 5.3, replaced by MoleculeGraph.mergeAtoms(MolAtom, MolAtom). |
chemaxon.util.iterator.IteratorFactory.AtomIterator.nextAtom()
Use IteratorFactory.AtomIterator.next() instead. |
chemaxon.util.iterator.IteratorFactory.AtomNeighbourIterator.nextAtom()
Use IteratorFactory.AtomNeighbourIterator.next() instead. |
chemaxon.util.iterator.IteratorFactory.BondIterator.nextBond()
Use IteratorFactory.BondIterator.next() instead. |
chemaxon.util.iterator.IteratorFactory.BondNeighbourIterator.nextBond()
Use IteratorFactory.BondNeighbourIterator.next() instead. |
chemaxon.util.iterator.IteratorFactory.RxnComponentIterator.nextComponent()
Use IteratorFactory.RxnComponentIterator.next() instead. |
chemaxon.util.iterator.IteratorFactory.RgComponentIterator.nextComponent()
Use IteratorFactory.RgComponentIterator.next() instead. |
chemaxon.struc.MolAtom.numOf(String)
As of Marvin 5.6, replaced by MolAtom.getAtomicNumber(String). |
chemaxon.struc.MDocument.parseMRV(String)
As of release 5.7, replaced by MolImporter.parseMRV(String) |
chemaxon.struc.MoleculeGraph.partialClean(int, int[], String)
as of Marvin 5.7 replaced by
Cleaner.partialClean(MoleculeGraph, int, int[], String) |
chemaxon.struc.MoleculeGraph.partialClean(Molecule[], String)
as of Marvin 5.7 replaced by
Cleaner.partialClean(Molecule, Molecule[], String) |
chemaxon.struc.MoleculeGraph.partialClean(MoleculeGraph, int[], String)
as of Marvin 5.7 replaced by
Cleaner.partialClean(MoleculeGraph, MoleculeGraph, int[], String) |
chemaxon.marvin.common.UserSettings.put(String, String)
since 5.4 use UserSettings.setProperty(String, String) or
UserSettings.setProperty(String, String, boolean) instead. |
chemaxon.marvin.util.ClipboardHandler.putImageToClipboard(Image)
see the documentation of the class |
chemaxon.marvin.util.ClipboardHandler.putMoleculeToClipboard(Molecule, Properties)
see the documentation of the class |
chemaxon.marvin.util.ClipboardHandler.putMoleculeToClipboard(Molecule, Properties, String)
see the documentation of the class |
chemaxon.marvin.util.ClipboardHandler.putOLEToClipboard(Molecule, Properties)
see the documentation of the class |
chemaxon.marvin.util.ClipboardHandler.putStringToClipboard(String)
see the documentation of the class |
chemaxon.struc.MoleculeGraph.regenEdges()
As of Marvin 5.3, replaced by MoleculeGraph.regenBonds(). |
chemaxon.struc.MoleculeGraph.removeAllEdges()
As of Marvin 5.3, replaced by MoleculeGraph.removeAllBonds(). |
chemaxon.struc.MoleculeGraph.removeEdge(int)
As of Marvin 5.3, replaced by MoleculeGraph.removeBond(int). |
chemaxon.struc.MoleculeGraph.removeEdge(MolBond)
As of Marvin 5.3, replaced by MoleculeGraph.removeBond(MolBond). |
chemaxon.struc.MoleculeGraph.removeExplicitLonePairs()
as of Marvin 5.7 replaced by
Hydrogenize.removeLonePairs(MoleculeGraph) |
chemaxon.struc.MoleculeGraph.removeNode(int)
As of Marvin 5.3, replaced by MoleculeGraph.removeAtom(int). |
chemaxon.struc.MoleculeGraph.removeNode(int, int)
As of Marvin 5.3, replaced by MoleculeGraph.removeAtom(int, int). |
chemaxon.struc.MoleculeGraph.removeNode(MolAtom)
As of Marvin 5.3, replaced by MoleculeGraph.removeAtom(MolAtom). |
chemaxon.struc.MoleculeGraph.removeNode(MolAtom, int)
As of Marvin 5.3, replaced by MoleculeGraph.removeAtom(MolAtom, int). |
chemaxon.marvin.util.ClipboardHandler.removePermanentOLEEnsurerReference()
see the documentation of the class |
chemaxon.marvin.util.ClipboardHandler.removePermanentOLESupport()
see the documentation of the class |
chemaxon.struc.RxnMolecule.removeStructure(int, int)
as of Marvin 4.1, replaced by
RxnMolecule.removeComponent(int, int) |
chemaxon.struc.MoleculeGraph.replaceEdge(MolBond, MolBond)
As of Marvin 5.3, replaced by MoleculeGraph.replaceBond(MolBond, MolBond). |
chemaxon.util.HTMLUtil.replaceString(String, String, String)
as of Marvin 5.0, replaced by
chemaxon.util.StringUtil.replaceAll(String,String,String) |
chemaxon.calculations.TopologyAnalyser.ringAtomCount()
as of release 5.5, replaced by Ring.ringAtomCount() |
chemaxon.calculations.TopologyAnalyser.ringBondCount()
as of release 5.5, replaced by Ring.ringBondCount() |
chemaxon.calculations.TopologyAnalyser.ringCount()
as of release 5.5, replaced by Ring.ringCount() |
chemaxon.calculations.TopologyAnalyser.ringCount(int)
as of release 5.5, replaced by Ring.ringCount(int) |
chemaxon.calculations.TopologyAnalyser.ringCountOfAtom(int)
as of release 5.5, replaced by Ring.ringCountOfAtom(int) |
chemaxon.calculations.TopologyAnalyser.rings()
as of release 5.5, replaced by Ring.rings(int) |
chemaxon.calculations.TopologyAnalyser.rings(int)
as of release 5.5, replaced by Ring.rings(int) |
chemaxon.calculations.TopologyAnalyser.ringSystemCount()
as of release 5.5, replaced by Ring.ringSystemCount() |
chemaxon.calculations.TopologyAnalyser.ringSystemCount(int)
as of release 5.5, replaced by Ring.ringSystemCount(int) |
chemaxon.calculations.TopologyAnalyser.ringSystems()
as of release 5.5, replaced by Ring.ringSystems() |
chemaxon.calculations.TopologyAnalyser.ringSystems(int)
as of release 5.5, replaced by Ring.ringSystems(int) |
chemaxon.marvin.common.UserSettings.save(String, boolean)
As of Marvin 5.3, use UserSettings.save(String). |
chemaxon.struc.RgMolecule.setAbsStereo(boolean, int, int)
as of Marvin 5.1.1, please call
MoleculeGraph.setAbsStereo(boolean) for the
component |
chemaxon.reaction.Standardizer.setActiveGroup(String)
Not used anymore. Practical examples may use
Standardizer.setInactiveTasks(String) |
chemaxon.reaction.Standardizer.setActiveGroups(String[])
Not used anymore. |
chemaxon.marvin.MolPrinter.setAtomsize(double)
As of Marvin 5.2.2, replaced by MolPrinter.setAtomSize(double). |
chemaxon.marvin.MolPrinter.setBondWidth(double)
as of Marvin 4.1, replaced by MolPrinter.setBondSpacing(double) |
chemaxon.marvin.beans.MarvinPane.setBondWidth(double)
as of Marvin 4.1, replaced by MarvinPane.setBondSpacing(double) |
chemaxon.marvin.calculations.pKaPlugin.setCalcAlways(boolean)
replaced by setModel(int) |
chemaxon.marvin.common.UserSettings.setCleanHOption(boolean)
As of release 5.4, replaced by UserSettings.setCleanHOptionEnabled(boolean) |
chemaxon.jchem.db.Importer.setConnections(String)
since 2.2 replaced by Importer.setFieldConnections(String). |
chemaxon.checkers.StructureChecker.setDescription(String)
This method isn't needed anymore and will be removed in 6.0 |
chemaxon.fixers.StructureFixer.setDescription(String)
|
chemaxon.clustering.LibraryMCS.setDissimCutoff(float)
This method has no affect from version 0.7 of LibraryMCS (JChem version 5.0.1) due to internal
incompatibilities. |
chemaxon.sss.search.MCS.setDontBreakRingBonds(boolean)
since 5.4 |
chemaxon.jchem.db.UpdateHandler.setDuplicateFiltering(boolean)
since JChem 5.4. This import option has been table option,
instead of this use UpdateHandler.setDuplicateFiltering(int) method |
chemaxon.jchem.db.Importer.setDuplicateImportAllowed(boolean)
since JChem 5.4. This import option has been table option,
instead of this use Importer.setDuplicateImportAllowed(int) method |
chemaxon.struc.MoleculeGraph.setEdge(int, MolBond)
As of Marvin 5.3, replaced by MoleculeGraph.setBond(int, MolBond). |
chemaxon.formats.MolConverter.Options.setEncodings(String)
|
chemaxon.sss.search.SearchOptions.setExactFragment(boolean)
since 5.6, replaced by SearchOptions.SearchOptions(int) |
chemaxon.marvin.MolPrinter.setExplicitH(boolean)
As of Marvin 5.5.1 this method does nothing.
This method will be removed in a future release. |
chemaxon.marvin.beans.MarvinPane.setExplicitH(boolean)
since 5.4 does nothing, will not be supported after 5.5 |
chemaxon.marvin.MolPrinter.setExplicitHVisible(boolean)
As of Marvin 5.5.1 this method does nothing.
This method will be removed in a future release. |
chemaxon.marvin.MolPrinter.setEzVisible(boolean)
As of Marvin 5.2.2, replaced by MolPrinter.setEZLabelsVisible(boolean) |
chemaxon.clustering.LibraryMCS.setFastSearch(boolean)
Use setMCSMode(MCS.MODE_FAST) or setMCSMode(MCS.MODE_TURBO) instead, this method has no effect form version 5.0 of JChem. |
chemaxon.sss.search.MCS.setFastSearch(boolean)
use setMode(MODE_TURBO) instead |
chemaxon.reaction.Reaction.setFID(String)
Not used. |
chemaxon.formats.MolConverter.Options.setFields(String[])
|
chemaxon.formats.MolImporter.setFileName(String)
As of Marvin 5.2, use any non-empty constructor of MolImporter |
chemaxon.reaction.Standardizer.setFinalClean(int, boolean, HashSet)
Not used. |
chemaxon.sss.search.SearchOptions.setFullFragment(boolean)
since 5.6, replaced by SearchOptions.SearchOptions(int) |
chemaxon.marvin.beans.MarvinPane.setGrinv(boolean)
as of Marvin 3.5, use setGrinvVisible(boolean) instead |
chemaxon.struc.MDocument.setGUIProperyContainer(MPropertyContainer)
in 5.2.2 typo error fixed. |
chemaxon.checkers.StructureChecker.setHelpText(String)
This method isn't needed anymore and will be removed in 6.0 |
chemaxon.checkers.StructureChecker.setIcon(Icon)
This method isn't needed anymore and will be removed in 6.0 |
chemaxon.sss.search.MCS.setIgnoreQueryProperties(boolean)
since 5.0 |
chemaxon.reaction.Reactor.setIgnoreReactionDefinedStandardizer(boolean)
Will be removed. |
chemaxon.reaction.Standardizer.setInactiveTasks(String)
Use Standardizer.addInactiveTasks(String) instead |
chemaxon.marvin.calculations.ResonancePlugin.setInputMoleculeModified(boolean)
Not used. |
chemaxon.marvin.calculations.TautomerizationPlugin.setInputMoleculeModified(boolean)
Not used. |
chemaxon.marvin.beans.MarvinPane.setLabels(boolean)
use setAtomSymbolsVisible(v) instead |
chemaxon.checkers.StructureChecker.setLocalMenuName(String)
This method isn't needed anymore and will be removed in 6.0 |
chemaxon.marvin.beans.MViewPane.setM(int, File, String)
As of Marvin 5.2.5, it is recommended to import the molecule
in advance, e.g. by using MolImporter, then set the
cell synchronously using MViewPane.setM(int, Molecule). The
reason is to simplify the public API and minimize the risk
of related concurrency problems in user codes. |
chemaxon.marvin.beans.MViewPane.setM(int, String)
As of Marvin 5.2.5, it is recommended to import the molecule
in advance, e.g. by using MolImporter, then set the
cell synchronously using MViewPane.setM(int, Molecule). The
reason is to simplify the public API and minimize the risk
of related concurrency problems in user codes. |
chemaxon.marvin.beans.MViewPane.setM(int, String, String)
As of Marvin 5.2.5, it is recommended to import the molecule
in advance, e.g. by using MolImporter, then set the
cell synchronously using MViewPane.setM(int, Molecule). The
reason is to simplify the public API and minimize the risk
of related concurrency problems in user codes. |
chemaxon.marvin.beans.MSketchPane.setMag(double)
As of Marvin 2.8.1, replaced by setScale() |
chemaxon.marvin.modules.AutoMapper.setMappingMode(int)
Use setMappingStyle(int) instead. |
chemaxon.struc.MolAtom.setMassnoIfKnown(String)
as of Marvin 4.1, replaced by
MolAtom.setForSpecIsotopeSymbol(String) |
chemaxon.reaction.Reactor.setMaxNumberOfProductSets(int)
Not used. |
chemaxon.sss.search.MCS.setMCESMode(boolean)
MCES is the only structure matching mode supported by the MCS class from version 5.0. |
chemaxon.sss.search.MCS.setMCSMode(boolean)
Strict MCS (vs. MCES) is not available from version 5.0 |
chemaxon.clustering.LibraryMCS.setMCSSimilarityThreshold(float)
The similarity threshold is not used from version 0.7 of LibraryMCS |
chemaxon.clustering.LibraryMCS.setMinimalSimilarityMeasurement(float)
Minimal similarity measurement is not used from version 0.7 |
chemaxon.clustering.LibraryMCS.setMode(int)
Use setMCSMode instead. |
chemaxon.sss.search.MCS.setMode(int)
since 5.4 |
chemaxon.util.MolHandler.setMolecule_BNE(byte[])
since JChem 5.2 use MolHandler.setMolecule(byte[]) |
chemaxon.util.MolHandler.setMolecule_SNE(String)
since JChem 5.2 use MolHandler.setMolecule(String) |
chemaxon.checkers.StructureChecker.setMoreErrorMessage(String)
This method isn't needed anymore and will be removed in 6.0 |
chemaxon.checkers.StructureChecker.setName(String)
This method isn't needed anymore and will be removed in 6.0 |
chemaxon.fixers.StructureFixer.setName(String)
|
chemaxon.struc.MoleculeGraph.setNode(int, MolAtom)
As of Marvin 5.3, replaced by MoleculeGraph.setAtom(int, MolAtom). |
chemaxon.checkers.StructureChecker.setNoErrorMessage(String)
This method isn't needed anymore and will be removed in 6.0 |
chemaxon.checkers.StructureChecker.setOneErrorMessage(String)
This method isn't needed anymore and will be removed in 6.0 |
chemaxon.formats.MolImporter.setOptionFlags(int)
As of Marvin 5.2, use the "MOLMOVIE" and "NOMOLMOVIE" import
options instead. See MFileFormatUtil.MOLMOVIE,
MFileFormatUtil.NOMOLMOVIE, MolImporter.isMolMovie(). |
chemaxon.formats.MolImporter.setOptions(String)
As of Marvin 5.2.2, use any non-empty constructor of MolImporter |
chemaxon.formats.MolConverter.Options.setOutput(File, String)
|
chemaxon.formats.MolConverter.Options.setOutput(OutputStream, String)
|
chemaxon.formats.MolConverter.Options.setOutput(String, String)
|
chemaxon.formats.MolConverter.Options.setOutputFlags(int)
|
chemaxon.marvin.calculations.ResonancePlugin.setpH(double)
As of Marvin 5.0 pH effect is not considered |
chemaxon.reaction.ConcurrentStandardizerProcessor.setPreprocessing(int)
Use ConcurrentStandardizerProcessor.setPreprocessor(MolTransformer) |
chemaxon.reaction.Reactor.setProductStandardizer(Standardizer)
Will be removed. Use Standardizer to standardize products. |
chemaxon.sss.search.SearchOptions.setQHomologyHandling(boolean)
since 5.6, use SearchOptions.setHomologyNarrowTranslation(HomologyTranslationOption) |
chemaxon.sss.search.RGroupDecomposition.setQuery(Molecule, int)
as of JChem 5.9,
call SearchOptions.setUndefinedRAtom(int) and
RGroupDecomposition.setQuery(chemaxon.struc.Molecule) separately. |
chemaxon.struc.MolAtom.setQuerystr(String)
As of release 5.7, replaced by
SmartsAtomQuerifier.setQuerystr(MolAtom atom, String s)
and MolAtom.setQueryString(String) |
chemaxon.struc.MolAtom.setQuerystr(String, int)
As of release 5.7, replaced by SmartsAtomQuerifier.setQuerystr(MolAtom atom, String s, int options)
and MolAtom.setQueryString(String) |
chemaxon.reaction.Reactor.setReaction(Reaction)
Will be removed from the public API. |
chemaxon.marvin.beans.MSketchPane.setReactionErrorVisible(boolean)
As of Version 5.3.2, this method is deprecated and has no replacement. It will be removed in a future version of Marvin. |
chemaxon.marvin.common.UserSettings.setReactionErrorVisible(boolean)
As of Version 5.3.2, this method is deprecated and has no replacement. It will be removed in a future version of Marvin. |
chemaxon.marvin.common.UserSettings.setReadGUIPropertiesFromMRV(boolean)
As of release 5.1, replaced by UserSettings.setSaveGUIPropertiesInMRV(boolean). It will be removed in a future version of Marvin. |
chemaxon.sss.search.RGroupDecomposition.setSameRGroupSameStructure(boolean)
as of JChem 5.3, set search option "RLigandEqualityCheck"
in SearchOptions, see SearchOptions.setRLigandEqualityCheck(boolean)
and SearchOptions.setOption(java.lang.String, java.lang.String) |
chemaxon.sss.search.SearchOptions.setSearchType(int)
As of release 5.5, replaced by SearchOptions.SearchOptions(int) |
chemaxon.reaction.Reaction.setSelectivityRule(String, Evaluator)
Use Reaction.setSelectivityRule(String, double[], Evaluator) or
Reaction.setSelectivityRule(String, String, Evaluator) and set
tolerances parameter to null |
chemaxon.marvin.beans.MarvinPane.setSetColor(int, Color)
as of Marvin 3.3, replaced by setAtomSetColor |
chemaxon.marvin.beans.MViewPane.setSetSeq(int, int, int)
as of Marvin 3.3, replaced by setAtomSetSeq |
chemaxon.struc.MoleculeGraph.setSetSeqs(int)
as of Marvin 4.0, replaced by setAtomSetSeq |
chemaxon.marvin.beans.MSketchPane.setSimpView(int)
as of Marvin 3.5, replaced by MSketchPane.setBondDraggedAlong(boolean) |
chemaxon.struc.MolAtom.setSMARTS(String)
As of release 5.7, replaced by SmartsAtomQuerifier.setSMARTS(MolAtom atom, String s) |
chemaxon.sss.search.MCS.setSSSMode(boolean)
Substructure search is not supported by MCS form version 5.0 |
chemaxon.reaction.Reactor.setStandardizer(Standardizer)
Will be removed. Use Standardizer to standardize reactants. |
chemaxon.marvin.calculations.logPPlugin.setTakeMajorTatomericForm(boolean)
Use logPPlugin.setConsiderTautomerization(boolean) |
chemaxon.marvin.calculations.pKaPlugin.setTakeMajorTatomericForm(boolean)
Use pKaPlugin.setConsiderTautomerization(boolean) |
chemaxon.marvin.calculations.TautomerizationPlugin.setTakeMostStableTautomer(boolean)
Not used. |
chemaxon.sss.search.SearchOptions.setTautomerDuplicateFiltering(boolean)
As of release 5.5, replaced by SearchOptions.setTautomerSearch(int) |
chemaxon.sss.search.SearchOptions.setTimeoutLimit(int)
since 5.6 use SearchOptions.setTimeoutLimitMilliseconds(int) instead |
chemaxon.reaction.Reactor.setTransform(boolean)
Use Standardizer. |
chemaxon.descriptors.MDSet.setUserData(float[])
since 2.3 |
chemaxon.descriptors.MDSet.setUserData(int, float)
since 2.3 |
chemaxon.struc.MoleculeGraph.setValenceCheckEnabled(boolean)
since Marvin 5.9, please use
MoleculeGraph.setValenceCheckState(ValenceCheckState) instead |
chemaxon.marvin.common.UserSettings.setViewExplicitH(boolean)
As of release 5.3, this method is deprecated and has no replacement. It will be removed in a future version of Marvin. |
chemaxon.formats.MolImporter.skipToNext()
As of Marvin 5.0, the record reading/molecule import
separation makes this method unusable |
chemaxon.calculations.TopologyAnalyser.smallestRing()
as of release 5.5, replaced by Ring.smallestRing() |
chemaxon.calculations.TopologyAnalyser.smallestRingSize()
as of release 5.5, replaced by Ring.smallestRingSize() |
chemaxon.calculations.TopologyAnalyser.smallestRingSizeOfAtom(int)
as of release 5.5, replaced by Ring.smallestRingSizeOfAtom(int) |
chemaxon.calculations.TopologyAnalyser.smallestRingSystem()
as of release 5.5, replaced by Ring.smallestRingSystem() |
chemaxon.calculations.TopologyAnalyser.smallestRingSystemSize()
as of release 5.5, replaced by Ring.smallestRingSystemSize() |
chemaxon.struc.MoleculeGraph.sortEdgesAccordingTo(MolBond[])
As of Marvin 5.3, replaced by MoleculeGraph.sortBondsAccordingTo(MolBond[]). |
chemaxon.reaction.Standardizer.standardize(Molecule[])
Use Standardizer.standardize(Molecule). |
chemaxon.calculations.TopologyAnalyser.stereo(int)
as of release 5.5, replaced by Stereochemistry.stereo(int) |
chemaxon.calculations.TopologyAnalyser.stereo(int, int)
as of release 5.5, replaced by Stereochemistry.stereo(int, int) |
chemaxon.calculations.TopologyAnalyser.stereoDoubleBondCount()
as of release 5.5, replaced by Stereochemistry.stereoDoubleBondCount() |
chemaxon.sss.screen.Similarity.Tanimoto()
|
chemaxon.struc.Molecule.toBinFormat(String)
As of release 5.7, replaced by
MolExporter.exportToBinFormat(Molecule, String) |
chemaxon.descriptors.ECFP.toFeatureSet()
As of JChem 5.4.1, replaced by ECFP.toIdentiferSet(). |
chemaxon.struc.Molecule.toFormat(String)
As of release 5.7, replaced by
MolExporter.exportToFormat(Molecule, String) |
chemaxon.struc.Molecule.toObject(String)
As of release 5.7, replaced by
MolExporter.exportToObject(Molecule, String) |
chemaxon.marvin.util.MolImageSize.toString()
|
chemaxon.jep.Evaluator.toString(Object)
For internal use only. |
chemaxon.jep.Evaluator.toString(Object, DecimalFormat)
For internal use only. |
chemaxon.jep.Evaluator.toString(Object, int)
For internal use only. |
chemaxon.marvin.common.UserSettings.tryToLoad()
since Marvin 5.4 no replacements. |
chemaxon.marvin.common.UserSettings.tryToLoad(Properties)
since Marvin 5.4 no replacements. |
chemaxon.marvin.common.UserSettings.tryToLoadTemplates()
since 5.4 no replacements |
chemaxon.struc.sgroup.SuperatomSgroup.updateSgroupCrossings()
as of Marvin 3.3, replaced by Sgroup.findCrossingBonds() |
chemaxon.marvin.calculations.pKaPlugin.useCorrectionLibrary(boolean)
Use pKaPlugin.setCorrectionLibrary(String) |
chemaxon.struc.MolAtom.valenceCheck(int)
As of Marvin 5.4, replaced by MolAtom.valenceCheck(). |