|
Deprecated Methods |
chemaxon.struc.MoleculeGraph.addExplicitHydrogens(int)
as of Marvin 5.7 replaced by
Hydrogenize.convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int) |
chemaxon.struc.MoleculeGraph.addExplicitHydrogens(int, MolAtom[])
as of Marvin 5.7 replaced by
Hydrogenize.convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int) |
chemaxon.struc.MoleculeGraph.addExplicitLonePairs()
as of Marvin 5.7 replaced by
Hydrogenize.convertImplicitLonePairsToExplicit(MoleculeGraph, MolAtom[]) |
chemaxon.calculations.hydrogenize.Hydrogenize.addHAtoms(MoleculeGraph)
since Marvin 5.11 use
convertImplicitHToExplicit(MoleculeGraph) instead |
chemaxon.calculations.hydrogenize.Hydrogenize.addHAtoms(MoleculeGraph, MolAtom[])
since Marvin 5.11 use
convertImplicitHToExplicit(MoleculeGraph, MolAtom[]) instead |
chemaxon.calculations.hydrogenize.Hydrogenize.addHAtoms(MoleculeGraph, MolAtom[], int)
since Marvin 5.11 use
convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int) instead |
chemaxon.formats.MolConverter.Options.addInput(File, String)
|
chemaxon.formats.MolConverter.Options.addInput(InputStream, String)
|
chemaxon.formats.MolConverter.Options.addInput(String, String)
|
chemaxon.calculations.hydrogenize.Hydrogenize.addLonePairs(MoleculeGraph, MolAtom[])
since Marvin 5.11 use
convertImplicitLonePairsToExplicit(MoleculeGraph, MolAtom[]) isntead |
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.marvin.util.MoleculeUtil.arrangeCrossingBonds(MolBond, Molecule, boolean)
as of Marvin 5.11.1 use MoleculeGraph#setBond(int, MolBond) |
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.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.marvin.calculations.ResonancePlugin.createStandardizedMolecule(Molecule, boolean)
Use ResonancePlugin.createStandardizedMolecule(Molecule) instead |
chemaxon.marvin.calculations.TautomerizationPlugin.createStandardizedMolecule(Molecule, boolean)
|
chemaxon.marvin.plugin.CalculatorPlugin.createStandardizedMolecule(Molecule, boolean)
Use CalculatorPlugin.createStandardizedMolecule(Molecule) instead |
chemaxon.marvin.plugin.CalculatorPlugin.dehydrogenize(Molecule)
MoleculeGraph.implicitizeHydrogens(int)
with parameter MolAtom.ALL_H does the same. |
chemaxon.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.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.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.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.marvin.util.MoleculeUtil.getCrossingBonds(MolBond[], DPoint3, DPoint3)
as of Marvin 5.11.1 |
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.MolBond.getDesiredLength()
use MolBond.desiredLength(int, int, int, int) instead |
chemaxon.struc.MolBond.getDesiredLength(boolean)
use MolBond.desiredLength(int, int, int, int) instead |
chemaxon.struc.MoleculeGraph.getDesiredLength(int, int, int)
since Marin 5.11 use MolBond.desiredLength(int, int, int, int) instead. |
chemaxon.struc.MoleculeGraph.getDesiredLength(MolBond)
since Marvin 5.11 use MolBond.desiredLength(int, int, int, int) instead. |
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.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.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.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.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.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.convertImplicitHToExplicit(MoleculeGraph) and
Hydrogenize.convertExplicitHToImplicit(MoleculeGraph) |
chemaxon.struc.MoleculeGraph.implicitizeHydrogens(int)
as of Marvin 5.7 replaced by
chemaxon.calculations.hydrogenize.Hydrogenize#convertExplicitHToImplicit(MoleculeGraph)(MoleculeGraph, int),
the following usage will give the same results:
chemaxon.calculations.hydrogenize.Hydrogenize.convertExplicitHToImplicit(mol, f);
|
chemaxon.struc.MoleculeGraph.implicitizeHydrogens(int, MolAtom[])
as of Marvin 5.7 replaced by
Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int),
the following usage will give the same results:
chemaxon.calculations.hydrogenize.Hydrogenize.convertExplicitHToImplicit(mol, atoms, f);
|
chemaxon.struc.MoleculeGraph.implicitizeHydrogens(int, MolAtom[], boolean)
as of Marvin 5.7 replaced by
Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean)
the following usage will give the same results:
chemaxon.calculations.hydrogenize.Hydrogenize.convertExplicitHToImplicit(mol, atoms, f, check);
|
chemaxon.struc.Molecule.implicitizeHydrogens0(int, MolAtom[], boolean)
as of Marvin 5.7 replaced by
Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean) |
chemaxon.struc.MoleculeGraph.implicitizeHydrogens0(int, MolAtom[], boolean)
as of Marvin 5.7 replaced by
Hydrogenize.convertExplicitHToImplicit(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.hydrogenize.Hydrogenize.isBridgeHeadAtom(MoleculeGraph, int)
as of Marvin 5.11.1, replaced by
TopologyUtil.isBridgeHeadAtom(MoleculeGraph, 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.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.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.checkers.RgroupReferenceErrorChecker.isSearchMissingRatom()
|
chemaxon.checkers.RgroupReferenceErrorChecker.isSearchSelfReference()
|
chemaxon.marvin.util.ClipboardHandler.isSupportedTransferFormat(String)
see the documentation of the class |
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.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.convertExplicitLonePairsToImplicit(MoleculeGraph) |
chemaxon.calculations.hydrogenize.Hydrogenize.removeHAtoms(MoleculeGraph)
since Marvin 5.11 use
convertExplicitHToImplicit(MoleculeGraph) instead |
chemaxon.calculations.hydrogenize.Hydrogenize.removeHAtoms(MoleculeGraph, int)
since Marvin 5.11 use
convertExplicitHToImplicit(MoleculeGraph, int) instead |
chemaxon.calculations.hydrogenize.Hydrogenize.removeHAtoms(MoleculeGraph, MolAtom[], int)
since Marvin 5.11 use
convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int) instead |
chemaxon.calculations.hydrogenize.Hydrogenize.removeHAtoms(MoleculeGraph, MolAtom[], int, boolean)
since Marvin 5.11 use convertExplicitHToImplicit(MoleculeGraph, MolAtom[],
int, boolean) instead |
chemaxon.calculations.hydrogenize.Hydrogenize.removeLonePairs(MoleculeGraph)
since Marvin 5.11 use
convertExplicitLonePairsToImplicit(MoleculeGraph) instead |
chemaxon.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.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.checkers.StructureChecker.setDescription(String)
This method isn't needed anymore and will be removed in 6.0 |
chemaxon.fixers.StructureFixer.setDescription(String)
|
chemaxon.struc.MoleculeGraph.setEdge(int, MolBond)
As of Marvin 5.3, replaced by MoleculeGraph.setBond(int, MolBond). |
chemaxon.formats.MolConverter.Options.setEncodings(String)
|
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.formats.MolConverter.Options.setFields(String[])
|
chemaxon.formats.MolImporter.setFileName(String)
As of Marvin 5.2, use any non-empty constructor of MolImporter |
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.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.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.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.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.checkers.RgroupReferenceErrorChecker.setSearchMissingRatom(boolean)
|
chemaxon.checkers.RgroupReferenceErrorChecker.setSearchSelfReference(boolean)
|
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.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.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.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.struc.Molecule.toBinFormat(String)
As of release 5.7, replaced by
MolExporter.exportToBinFormat(Molecule, String) |
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(). |