|
Deprecated Methods |
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.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.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.marvin.util.ClipboardHandler.clearClipboard()
see the documentation of the class |
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.marvin.view.MDocStorage.countRecordsInFraction(double, int, MProgressMonitor)
|
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.createReaction(Molecule[])
use Reactor.setResultType(int) |
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.reaction.Reactor.createReactions(Molecule[])
Not used. Returns null. |
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.sss.search.MolSearchOptions.deepCopy(SearchOptions)
since 5.0.2
Please use MolSearchOptions.clonecopy(SearchOptions) instead |
chemaxon.sss.search.SearchOptions.deepCopy(SearchOptions)
since 5.0.2
Please use SearchOptions.clonecopy(SearchOptions) instead |
chemaxon.marvin.plugin.CalculatorPlugin.dehydrogenize(Molecule)
MoleculeGraph.implicitizeHydrogens(int)
with parameter MolAtom.ALL_H does the same. |
chemaxon.struc.Molecule.draw(Graphics, String)
As of release 4.1.6, replaced by chemaxon.marvin.util.MPainterUtil.draw(Molecule,Graphics,String) |
chemaxon.marvin.util.MPainterUtil.draw(MDocument, Graphics, String)
as of Marvin 4.1.8, replaced by
MolPrinter.paint(java.awt.Graphics,java.awt.Rectangle) |
chemaxon.marvin.util.MPainterUtil.draw(Molecule, Graphics, String)
as of Marvin 4.1.8, replaced by
MolPrinter.paint(java.awt.Graphics,java.awt.Rectangle) |
chemaxon.sss.search.RGroupDecomposition.findAllLigandIds(int[][])
as of JChem 5.3, use RGroupDecomposition.findFirstDecomposition() and
RGroupDecomposition.findNextDecomposition() to get decomposition results
(the current implementation ignores the hit parameter and uses
the latest groupHit found by the search process) |
chemaxon.sss.search.RGroupDecomposition.findAllLigands(int[][])
as of JChem 5.3, use RGroupDecomposition.findFirstDecomposition() and
RGroupDecomposition.findNextDecomposition() to get decomposition results
(the current implementation ignores the hit parameter and uses
the latest groupHit found by the search process) |
chemaxon.sss.search.MolSearch.findAllOrder()
Use setOrderSensitiveSearch(true) instead |
chemaxon.sss.search.RGroupDecomposition.findLigandIds(int[])
as of JChem 5.3, use RGroupDecomposition.findFirstDecomposition() and
RGroupDecomposition.findNextDecomposition() to get decomposition results
(the current implementation ignores the hit parameter and uses
the latest groupHit found by the search process) |
chemaxon.sss.search.RGroupDecomposition.findLigands(int[])
as of JChem 5.3, use RGroupDecomposition.findFirstDecomposition() and
RGroupDecomposition.findNextDecomposition() to get decomposition results
(the current implementation ignores the hit parameter and uses
the latest groupHit found by the search process) |
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.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.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.modules.datatransfer.ClipboardHandler.getClipboardClearerTask()
see ClipboardHandler.setWorkOnBackground(boolean) |
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.common.UserSettings.getCopyOpts()
since 5.3 won't be supported after 5.4 |
chemaxon.marvin.modules.datatransfer.ClipboardHandler.getDataFromClipboardOLE()
this method will not be available after 5.4 |
chemaxon.marvin.util.ClipboardHandler.getDataFromClipboardOLE()
see the documentation of the class |
chemaxon.marvin.common.UserSettings.getDefaultCopyAsFormat()
since 5.3 use instead |
chemaxon.marvin.common.UserSettings.getDefaultCopyOpts()
since 5.3 won't be supported after 5.4 |
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.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.marvin.calculations.HuckelAnalysisPlugin.getEigenVector()
Use HuckelAnalysisPlugin.getHMOEigenVector() |
chemaxon.marvin.calculations.HuckelAnalysisPlugin.getElectrophilicOrder(int)
Use HuckelAnalysisPlugin.getHMOElectrophilicOrder(int) |
chemaxon.marvin.MolPrinter.getExplicitH()
As of Marvin 5.2.2, replaced by MolPrinter.isExplicitHVisible(). |
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.jep.Evaluator.getFunctionParameterData()
use Evaluator.getFunctionData() |
chemaxon.struc.MoleculeGraph.getGrinv(int[], boolean)
Please use getGrinv(int[], int) instead. |
chemaxon.marvin.calculations.HuckelAnalysisPlugin.getHuckelOrbitalCoefficients()
Use HuckelAnalysisPlugin.getHMOHuckelOrbitalCoefficients() |
chemaxon.marvin.modules.datatransfer.ClipboardHandler.getImageToClipboardTask(Image)
see ClipboardHandler.setWorkOnBackground(boolean) |
chemaxon.marvin.util.ClipboardHandler.getImageToClipboardTask(Image)
see the documentation of the class |
chemaxon.marvin.beans.MarvinPane.getLabels()
use isAtomSymbolsVisible() instead |
chemaxon.sss.search.RGroupDecomposition.getLigandTable(int[][], int[][], int, int, String)
as of JChem 5.3, use RGroupDecomposition.findLigandTable(int, int, java.lang.String)
to get decomposition results
(the current implementation ignores the hits parameter and uses
all filtered group hits - skipping equivalent hits - instead) |
chemaxon.sss.search.RGroupDecomposition.getLigandTable(int[][], int, int)
as of JChem 5.3, use RGroupDecomposition.findLigandTable(int, int)
to get decomposition results
(the current implementation ignores the hits parameter and uses
all filtered group hits - skipping equivalent hits - instead) |
chemaxon.sss.search.RGroupDecomposition.getLigandTable(int[][], int, int, String)
as of JChem 5.3, use RGroupDecomposition.findLigandTable(int, int, java.lang.String)
to get decomposition results
(the current implementation ignores the hits parameter and uses
all filtered group hits - skipping equivalent hits - instead) |
chemaxon.sss.search.RGroupDecomposition.getLigandTableRow(int[], int)
as of JChem 5.3, use RGroupDecomposition.findLigandTableRow(int, java.lang.String)
to get decomposition results
(the current implementation ignores the hit parameter and and uses
the latest groupHit found by the search process) |
chemaxon.sss.search.RGroupDecomposition.getLigandTableRow(int[], int[], int, String)
as of JChem 5.3, use RGroupDecomposition.findLigandTableRow(int, java.lang.String)
to get decomposition results
(the current implementation ignores the hit and the ligandIds
parameters and and uses the latest groupHit found by the search process) |
chemaxon.sss.search.RGroupDecomposition.getLigandTableRow(int[], int, String)
as of JChem 5.3, use RGroupDecomposition.findLigandTableRow(int, java.lang.String)
to get decomposition results
(the current implementation ignores the hit parameter and and uses
the latest groupHit found by the search process) |
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.sss.search.MolSearch.getMolecule()
Use getTarget instead |
chemaxon.marvin.modules.datatransfer.ClipboardHandler.getMoleculeToClipboardTask(Molecule, Properties, String)
see ClipboardHandler.setWorkOnBackground(boolean) |
chemaxon.marvin.util.ClipboardHandler.getMoleculeToClipboardTask(Molecule, Properties, String)
see the documentation of the class |
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.modules.datatransfer.ClipboardHandler.getOLEToClipboardTask(Molecule, Properties)
see ClipboardHandler.setWorkOnBackground(boolean) |
chemaxon.marvin.util.ClipboardHandler.getOLEToClipboardTask(Molecule, Properties)
see the documentation of the class |
chemaxon.sss.search.Search.getOption(int)
Since 5.0
Please use getters instead. |
chemaxon.sss.search.SearchOptions.getOption(int)
Since 5.0
Please use getters instead.
isKeepQueryOrder()
isFullFragment()
isTautomerSearch()
getIsotopeMatching()
getChargeMatching()
isValenceMatching()
getRadicalMatching()
getVagueBondLevel()
isMixSgroupMatching()
getStereoModel()
getImplicitHMatching()
isReactionUnpairedMapMatching() |
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.sss.search.SearchOptions.getOptions()
since 5.0 |
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.getPropertyKeys()
as of Marvin 4.1, replaced by
properties().getKeys() |
chemaxon.sss.search.RGroupDecomposition.getQueryRMap()
as of JChem 5.3, use RGroupDecomposition.findFirstDecomposition() and
RGroupDecomposition.findNextDecomposition() to get decomposition results
(the current implementation ignores the hit parameter and uses
the latest groupHit found by the search process) |
chemaxon.sss.search.RGroupDecomposition.getQueryRMapString()
as of JChem 5.3, use RGroupDecomposition.findFirstDecomposition() and
RGroupDecomposition.findNextDecomposition() to get decomposition results
(the current implementation ignores the hit parameter and uses
the latest groupHit found by the search process) |
chemaxon.sss.search.MolSearch.getQueryStructure()
Use getQuery instead |
chemaxon.marvin.calculations.MarkushEnumerationPlugin.getRandomStructure()
Use MarkushEnumerationPlugin.getNextStructure() instead, set random mode by
calling MarkushEnumerationPlugin.setRandomEnumeration()
before setting the molecule by CalculatorPlugin.setMolecule(chemaxon.struc.Molecule). |
chemaxon.marvin.calculations.MarkushEnumerationPlugin.getRandomStructures(int)
Use MarkushEnumerationPlugin.getStructures() instead, set random mode by
calling MarkushEnumerationPlugin.setRandomEnumeration()
before setting the molecule by CalculatorPlugin.setMolecule(chemaxon.struc.Molecule). |
chemaxon.marvin.beans.MarvinPane.getReadGlobalGUIProperties()
since Marvin 5.1 when this and the MarvinPane.getSaveGlobalGUIProperties() function
have been merged. |
chemaxon.marvin.common.UserSettings.getReadGUIPropertiesFromMRV()
since Marvin 5.1 when this and the previous function have been merged. |
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.reaction.Reactor.getSearchAttributes()
Will be removed soon. |
chemaxon.alchemist.utils.AlchemistLinearMoleculeView.getSelectedIndex()
use AlchemistLinearMoleculeView.getSelectedIndexes() instead |
chemaxon.alchemist.utils.AlchemistLinearMoleculeView.getSelectedValue()
use AlchemistLinearMoleculeView.getSelectedValues() instead |
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.marvin.util.ClipboardHandler.getStringFromClipboard()
see the documentation of the class |
chemaxon.marvin.modules.datatransfer.ClipboardHandler.getStringToClipboardTask(String)
see ClipboardHandler.setWorkOnBackground(boolean) |
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.jchem.db.DatabaseProperties.getStructureTableNames(boolean)
Use DatabaseProperties.getStructureTableNames() in conjunction with
DatabaseProperties.DatabaseProperties(ConnectionHandler, boolean) to
indicate whether the names of JChem structure tables or JChem
Cartridge index tables are to be retrieved. |
chemaxon.marvin.common.UserSettings.getSupportedCopyAsFormats()
since 5.3 use ClipboardHandler.getCopyAsTransferFormatIds() |
chemaxon.sss.search.RGroupDecomposition.getTargetRMap(int[])
as of JChem 5.3, use RGroupDecomposition.findFirstDecomposition() and
RGroupDecomposition.findNextDecomposition() to get decomposition results
(the current implementation ignores the hit parameter and uses
the latest groupHit found by the search process) |
chemaxon.sss.search.RGroupDecomposition.getTargetRMapString(int[])
as of JChem 5.3, use RGroupDecomposition.findFirstDecomposition() and
RGroupDecomposition.findNextDecomposition() to get decomposition results
(the current implementation ignores the hit parameter and uses
the latest groupHit found by the search process) |
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.sss.search.RGroupDecomposition.getUniformRMap(int, Molecule)
as of JChem 5.3, use RGroupDecomposition.findFirstDecomposition() and
RGroupDecomposition.findNextDecomposition() to get decomposition results
(the current implementation ignores the hit parameter and uses
the latest groupHit found by the search process) |
chemaxon.sss.search.RGroupDecomposition.getUniformRMapString(int, Molecule)
as of JChem 5.3, use RGroupDecomposition.findFirstDecomposition() and
RGroupDecomposition.findNextDecomposition() to get decomposition results
(the current implementation ignores the hit parameter and uses
the latest groupHit found by the search process) |
chemaxon.descriptors.MDSet.getUserData()
since 2.3 |
chemaxon.descriptors.MDSet.getUserData(int)
since 2.3 |
chemaxon.marvin.common.UserSettings.getViewExplicitH()
since 5.3 |
chemaxon.formats.MFileFormatUtil.guessPeptideFormat(String)
as of Marvin 5.0,
PeptideRecognizer.guessPeptideFormat(String)
must be used instead |
chemaxon.struc.MolAtom.haveSimilarEdges(MolAtom)
As of Marvin 5.3, replaced by MolAtom.haveSimilarEdges(MolAtom). |
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.struc.MolBond.isArrow()
As of Marvin 5.3, |
chemaxon.struc.MolAtom.isArrowEnd()
As of Marvin 5.3 |
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.isDiastereomerMatching()
Please use SearchOptions.getStereoSearchType() instead. |
chemaxon.sss.search.Search.isExactAtomMatching()
since 2.2 |
chemaxon.sss.search.Search.isExactChargeMatching()
since JChem 3.2
Please use SearchOptions.getChargeMatching()
(SearchOptions.getChargeMatching()) instead. |
chemaxon.sss.search.Search.isExactIsotopeMatching()
since JChem 3.2
Please use SearchOptions.getIsotopeMatching()
(SearchOptions.getIsotopeMatching()) instead. |
chemaxon.sss.search.Search.isExactRadicalMatching()
since JChem 3.2
Please use SearchOptions.getRadicalMatching()
(SearchOptions.getRadicalMatching()) instead. |
chemaxon.sss.search.SearchOptions.isExactStereoMatching()
Please use SearchOptions.getStereoSearchType() instead. |
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.sss.search.MolSearchOptions.isMarkushHitSupergraph()
since 5.0 |
chemaxon.marvin.util.ClipboardHandler.isNativesRegistered()
since 5.3 always returns true, won't be supported after 5.4 |
chemaxon.sss.search.Search.isQueryAbsoluteStereo()
since JChem 5.0.1
Please use MolSearchOptions.isQueryAbsoluteStereo() instead. |
chemaxon.sss.search.SearchOptions.isStereoSearch()
Please use SearchOptions.getStereoSearchType() instead. |
chemaxon.marvin.common.UserSettings.isSupportedCopyOpt(String)
since 5.3 won't be supported after 5.4 |
chemaxon.marvin.util.ClipboardHandler.isSupportedTransferFormat(String)
see the documentation of the class |
chemaxon.sss.search.Search.isTargetAbsoluteStereo()
since JChem 5.0.1
Please use MolSearchOptions.isTargetAbsoluteStereo() instead. |
chemaxon.reaction.Reactor.isUnique()
Not used. |
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.MoleculeGraph.mergeNodes(MolAtom, MolAtom)
As of Marvin 5.3, replaced by MoleculeGraph.mergeAtoms(MolAtom, MolAtom). |
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.modules.datatransfer.ClipboardHandler.putOLEToClipboard(Molecule, Properties)
use simply
ClipboardHandler.putMoleculeToClipboard(Molecule, Properties) |
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.reaction.Reactor.removeDuplicateProductReferences(Molecule[])
Use Reactor.setRemoveDuplicateProductReferences(boolean) |
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.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.MDocument.removeReactionArrow(MDocument)
|
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.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.jchem.db.Importer.setConnections(String)
since 2.2 replaced by Importer.setFieldConnections(String). |
chemaxon.marvin.common.UserSettings.setCopyOpts(String)
since 5.3 won't be supported after 5.4 |
chemaxon.alchemist.AlchemistApplication.setCustomWaitAnimation(String)
custom animation is no longer supported |
chemaxon.sss.search.SearchOptions.setDiastereomerMatching(boolean)
Please use setStereoSearchType(STEREO_DIASTEREOMER) and setStereoSearchType(STEREO_SPECIFIC) instead. |
chemaxon.marvin.alignment.Alignment.setDisableAuto(boolean)
use setAlignmentType(AlignmentType.USER_ONLY) instead |
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.struc.MoleculeGraph.setEdge(int, MolBond)
As of Marvin 5.3, replaced by MoleculeGraph.setBond(int, MolBond). |
chemaxon.sss.search.Search.setExactAtomMatching(boolean)
since 2.2. |
chemaxon.sss.search.Search.setExactChargeMatching(boolean)
since JChem 3.2
Please use SearchOptions.setChargeMatching(...)
(SearchOptions.setChargeMatching(int)) instead. |
chemaxon.sss.search.Search.setExactIsotopeMatching(boolean)
since JChem 3.2
Please use SearchOptions.setIsotopeMatching(...)
(SearchOptions.setIsotopeMatching(int)) instead. |
chemaxon.sss.search.Search.setExactRadicalMatching(boolean)
since JChem 3.2
Please use SearchOptions.setRadicalMatching(...)
(SearchOptions.setRadicalMatching(int)) instead. |
chemaxon.sss.search.SearchOptions.setExactStereoMatching(boolean)
Please use setStereoSearchType(STEREO_EXACT) and setStereoSearchType(STEREO_SPECIFIC) instead. |
chemaxon.marvin.MolPrinter.setExplicitH(boolean)
As of Marvin 5.2.2, replaced by MolPrinter.setExplicitHVisible(boolean). |
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.MolImporter.setFileName(String)
As of Marvin 5.2, use any non-empty constructor of MolImporter |
chemaxon.sss.search.MolSearch.setFilterConfig(File, Standardizer)
Please use
MolSearch.setFilterConfig(File) and/or
MolSearch.setStandardizer(chemaxon.reaction.Standardizer, boolean, boolean)
instead. |
chemaxon.reaction.Standardizer.setFinalClean(int, boolean, HashSet)
Not used. |
chemaxon.reaction.Reactor.setFragmentTag(String)
Not used. |
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.sss.search.MolSearch.setHitIncludesRNodes(boolean)
Since 5.0
Use MolSearchOptions.setHitIncludesRNodes(boolean) instead. |
chemaxon.sss.search.MCS.setIgnoreQueryProperties(boolean)
Since version 5.0 query properties are not supported by the MCS search. |
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.reaction.Reactor.setJEP(ChemJEP)
Not used. |
chemaxon.marvin.beans.MarvinPane.setLabels(boolean)
use setAtomSymbolsVisible(v) instead |
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.sss.search.MolSearchOptions.setMarkushHitSupergraph(boolean)
use MolSearchOptions.setHitIndexType(int) |
chemaxon.struc.MolAtom.setMassnoIfKnown(String)
as of Marvin 4.1, replaced by
MolAtom.setForSpecIsotopeSymbol(String) |
chemaxon.sss.search.JChemSearchOptions.setMatchCountOptions(int, boolean, int, boolean)
since JChem 5.1 use JChemSearchOptions.setMatchCountOptions(MatchCountOptions) instead. |
chemaxon.sss.search.JChemSearchOptions.setMatchCountOptions(String, int)
since JChem 5.1 use JChemSearchOptions.setMatchCountOptions(MatchCountOptions) instead. |
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.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.sss.search.MolSearch.setMolecule(Molecule)
Use setTarget instead |
chemaxon.struc.MoleculeGraph.setNode(int, MolAtom)
As of Marvin 5.3, replaced by MoleculeGraph.setAtom(int, MolAtom). |
chemaxon.sss.search.MolSearchOptions.setOption(int, int)
Since 5.0
Use setters instead.
setHitIndexType(int),
setMarkushEnabled(boolean),
setMarkushArom(int) |
chemaxon.sss.search.Search.setOption(int, int)
Since 5.0
Please use setters instead. |
chemaxon.sss.search.SearchOptions.setOption(int, int)
Since 5.0
Please use setters instead.
setKeepQueryOrder(boolean)
setFullFragment(boolean)
setTautomerSearch(boolean)
setIsotopeMatching(int)
setChargeMatching(int)
setValenceMatching(boolean)
setRadicalMatching(int)
setVagueBondLevel(int)
setMixSgroupMatching(boolean)
setStereoModel(int)
setImplicitHMatching(int)
setReactionUnpairedMapMatching(boolean) |
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.sss.search.SearchOptions.setOptions(int[])
since 5.0 |
chemaxon.formats.MolImporter.setOptions(String)
As of Marvin 5.2.2, use any non-empty constructor of MolImporter |
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.sss.search.Search.setQueryAbsoluteStereo(boolean)
since JChem 5.0.1
Please use MolSearchOptions.setQueryAbsoluteStereo(boolean) instead. |
chemaxon.sss.search.MolSearch.setQueryStructure(Molecule)
Use setQuery instead |
chemaxon.reaction.Reactor.setReaction(Reaction)
Will be removed from the public API. |
chemaxon.reaction.Reactor.setReactions(Molecule[])
Reaction sequences are not supported. |
chemaxon.reaction.Reactor.setReactions(Reaction[])
Reaction sequences are not supported. |
chemaxon.reaction.Reactor.setReactions(Reaction[], String)
Reaction sequences are not supported. |
chemaxon.marvin.common.UserSettings.setReadGUIPropertiesFromMRV(boolean)
since Marvin 5.1 when this and the previous function have been merged. |
chemaxon.marvin.alignment.Alignment.setRigidPreAlignOnly(boolean)
use setTryFlexiblePreAlignment instead but note negate the boolean parameter is necessary |
chemaxon.marvin.alignment.Alignment.setRingSize(int)
use setRingFlexibility instead |
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.reaction.Reactor.setSearchAttributes(SearchAttributes)
Use Reactor.setSearchOptions(String). Will be removed soon. |
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.sss.search.MCS.setSSSMode(boolean)
Substructure search is not supported by MCS form version 5.0 |
chemaxon.sss.search.Search.setStereoCareChecking(boolean)
since 2.2.
Please use Search.setDoubleBondStereoMatchingMode(int) instead. |
chemaxon.sss.search.SearchOptions.setStereoSearch(boolean)
Please use setStereoSearchType(STEREO_SPECIFIC) and setStereoSearchType(STEREO_IGNORE) instead. |
chemaxon.marvin.calculations.TautomerizationPlugin.setTakeMostStableTautomer(boolean)
Not used. |
chemaxon.sss.search.Search.setTargetAbsoluteStereo(boolean)
since JChem 5.0.1
Please use MolSearchOptions.setTargetAbsoluteStereo(boolean) instead. |
chemaxon.reaction.Reactor.setTransform(boolean)
Use Standardizer. |
chemaxon.marvin.alignment.Alignment.setTryFlexiblePreAlignment(boolean)
|
chemaxon.reaction.Reactor.setUnique(boolean)
Use Reactor.setDuplicateFiltering(int) instead |
chemaxon.descriptors.MDSet.setUserData(float[])
since 2.3 |
chemaxon.descriptors.MDSet.setUserData(int, float)
since 2.3 |
chemaxon.marvin.common.UserSettings.setViewExplicitH(boolean)
since 5.3 |
chemaxon.formats.MolImporter.skipToNext()
As of Marvin 5.0, the record reading/molecule import
separation makes this method unusable |
chemaxon.struc.MoleculeGraph.sortEdgesAccordingTo(MolBond[])
As of Marvin 5.3, replaced by MoleculeGraph.sortBondsAccordingTo(MolBond[]). |
chemaxon.sss.screen.Similarity.Tanimoto()
|
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.struc.sgroup.SuperatomSgroup.updateSgroupCrossings()
as of Marvin 3.3, replaced by Sgroup.findCrossingBonds() |
chemaxon.alchemist.AlchemistApplication.virtualHide()
This method will be removed |
chemaxon.alchemist.AlchemistApplication.virtualShow()
This method will be removed |