|
Deprecated Methods |
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.canBe1LetterPeptide(String)
as of Marvin 5.0,
PeptideRecognizer.canBe1LetterPeptide(String)
must be used instead |
chemaxon.formats.MFileFormatUtil.canBe3LetterPeptide(String)
as of Marvin 5.0,
PeptideRecognizer.canBe3LetterPeptide(String)
must be used instead |
chemaxon.formats.MFileFormatUtil.canBeAbbrevgroup(String)
as of Marvin 5.0,
AbbrevGroupRecognizer.testLine(String)
must be used instead |
chemaxon.formats.MolInputStream.canBeAbbrevgroup(String)
as of Marvin 5.0,
AbbrevGroupRecognizer.testLine(String)
must be used instead |
chemaxon.formats.MFileFormatUtil.canBeBase64(String)
as of Marvin 5.0,
Base64Recognizer.canBeBase64(String)
must be used instead |
chemaxon.formats.MolInputStream.canBeBase64(String)
as of Marvin 5.0,
Base64Recognizer.canBeBase64(String)
must be used instead |
chemaxon.formats.MFileFormatUtil.canBeChime(String)
as of Marvin 5.0,
ChimeRecognizer.canBeChime(String)
must be used instead |
chemaxon.formats.MolInputStream.canBeChime(String)
as of Marvin 5.0,
ChimeRecognizer.canBeChime(String)
must be used instead |
chemaxon.formats.MFileFormatUtil.canBeJTF(String)
as of Marvin 5.0,
JTFRecognizer.canBeJTFHeader(String)
must be used instead |
chemaxon.formats.MolInputStream.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.formats.MFileFormatUtil.canBeSMARTS(String)
as of Marvin 5.0,
SMILESRecognizer.canBeSMARTS(String)
must be used instead |
chemaxon.formats.MolInputStream.canBeSMARTS(String)
as of Marvin 5.0,
SMILESRecognizer.canBeSMARTS(String)
must be used instead |
chemaxon.formats.MFileFormatUtil.canBeSMILES(String)
as of Marvin 5.0,
SMILESRecognizer.canBeSMILES(String)
must be used instead |
chemaxon.formats.MolInputStream.canBeSMILES(String)
as of Marvin 5.0,
SMILESRecognizer.canBeSMILES(String)
must be used instead |
chemaxon.marvin.beans.MarvinPane.createMenu(ResourceBundle, String)
as of Marvin 3.3.1, replaced by SwingUtil.createMenu |
chemaxon.struc.RgMolecule.createMol(String)
As of Marvin 3.4,
MolImportModule.createMol() must be used. |
chemaxon.reaction.Reactor.createReactionObject(Molecule)
Use Reactor.setReaction(Molecule). |
chemaxon.reaction.Reactor.createReactionObject(Molecule, String, String, double[])
Use Reactor.setReaction(Molecule, String, String, String, double[])
and set rid parameter to null. |
chemaxon.reaction.Reactor.createReactionObject(Molecule, String, String, String)
Use Reactor.setReaction(Molecule, String, String, String, String)
and set rid parameter to 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.jchem.db.UpdateHandler.createStructureTable(ConnectionHandler, String, int, int, int, String)
since JChem 5.0.
Please use UpdateHandler.createStructureTable(chemaxon.util.ConnectionHandler, StructureTableOptions)
instead. |
chemaxon.jchem.db.UpdateHandler.createStructureTable(ConnectionHandler, String, int, int, int, String, String, boolean)
since JChem 5.0.
Please use UpdateHandler.createStructureTable(chemaxon.util.ConnectionHandler, StructureTableOptions)
instead. |
chemaxon.jchem.db.UpdateHandler.createStructureTable(ConnectionHandler, String, int, int, int, String, String, boolean, Map, int)
since JChem 5.0.
Please use UpdateHandler.createStructureTable(chemaxon.util.ConnectionHandler, StructureTableOptions)
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.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.MolSearch.findAllOrder()
Use setOrderSensitiveSearch(true) instead |
chemaxon.jchem.db.JChemSearch.getAbsoluteStereo()
since JChem 5.0. use JChemSearchOptions.getAbsoluteStereo() instead |
chemaxon.reaction.Standardizer.getActiveGroups()
Not used anymore. |
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.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.jchem.db.Importer.getConnections()
since 2.2 replaced by Importer.getFieldConnections(). |
chemaxon.jchem.db.JChemSearch.getDissimilarityThreshold()
since JChem 5.0.
Use JChemSearchOptions.getDissimilarityThreshold() instead |
chemaxon.jchem.db.JChemSearch.getDoubleBondStereoMatchingMode()
since JChem 5.0. use SearchOptions.getDoubleBondStereoMatchingMode() instead |
chemaxon.reaction.Reaction.getFID()
Not used. |
chemaxon.jchem.db.JChemSearch.getFilter()
Since 5.0
Use SearchOptions.getChemTermsFilter() instead. |
chemaxon.jchem.db.JChemSearch.getFilterConfigFileName()
Since 5.0
Use SearchOptions.getChemTermsFilterConfig() instead. |
chemaxon.jchem.db.JChemSearch.getFilterQuery()
since JChem 5.0.
use JChemSearchOptions.getFilterQuery() instead |
chemaxon.jchem.db.JChemSearch.getFilterTable()
since 2.3. Please use JChemSearch.setFilterQuery(String) instead. |
chemaxon.util.MolHandler.getFingerprintInBytes(int, int, int)
since JChem 3.1 the usage of
MolHandler.generateFingerprintInBytes(int, int, int)
is recommended |
chemaxon.util.MolHandler.getFingerprintInInts(int, int, int)
since JChem 3.1 the usage of
MolHandler.generateFingerprintInInts(int, int, int)
is recommended |
chemaxon.struc.MoleculeGraph.getGrinv(int[], boolean)
Please use getGrinv(int[], int) instead. |
chemaxon.jchem.db.JChemSearch.getHCountMatching()
since JChem 5.0. use SearchOptions.getHCountMatching() instead |
chemaxon.formats.MolInputStream.getJtfFields(String)
as of Marvin 4.1, MFileFormatUtil.getJTFFields(String)
must be used instead |
chemaxon.marvin.beans.MarvinPane.getLabels()
use isAtomSymbolsVisible() instead |
chemaxon.marvin.MolPrinter.getMag()
as of Marvin 2.9.11, replaced by MolPrinter.getScale(). |
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.jchem.db.JChemSearch.getMaxResultCount()
since JChem 5.0. use JChemSearchOptions.getMaxResultCount() instead |
chemaxon.jchem.db.JChemSearch.getMaxTime()
since JChem 5.0. use JChemSearchOptions.getMaxTime() instead |
chemaxon.sss.search.MolSearch.getMolecule()
Use getTarget instead |
chemaxon.marvin.beans.MViewPane.getMols()
as of Marvin 4.0, MViewPane.getDocuments() is recommended |
chemaxon.struc.MoleculeGraph.getNonAromrings()
please use getAromaticAndAliphaticRings instead. |
chemaxon.struc.MoleculeGraph.getNonAromrings(int)
please use getAromaticAndAliphaticRings instead. |
chemaxon.jchem.db.JChemSearch.getOption(int)
since 5.0, use getters in
see JChemSearch.getSearchOptions()
see SearchOptions
see JChemSearchOptions |
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()
isExactFragment()
isTautomerSearch()
getIsotopeMatching()
getChargeMatching()
isValenceMatching()
getRadicalMatching()
getVagueBondLevel()
isMixSgroupMatching()
getStereoModel()
getImplicitHMatching()
isReactionUnpairedMapMatching() |
chemaxon.reaction.Standardizer.getOptionalTasksEnabled()
as of JChem 3.2, replaced by Standardizer.getActiveGroups() |
chemaxon.sss.search.SearchOptions.getOptions()
since 5.0 |
chemaxon.marvin.calculations.HuckelAnalysisPlugin.getPiChargeDensity(int)
Use HuckelAnalysisPlugin.getElectronDensity(int) instead |
chemaxon.marvin.calculations.pKaPlugin.getpKa(int, int)
Use pKaPlugin.getpKaValues(int, int) |
chemaxon.formats.recognizer.Recognizer.getPriority()
as of Marvin 5.1,
use MFileFormat.getPriority(java.lang.String) instead |
chemaxon.alchemist.Alchemist.getProgressBackgroundColor()
Use getSideBarTopBackground() or getSideBarBottomBackground() instead |
chemaxon.struc.Molecule.getPropertyKeys()
as of Marvin 4.1, replaced by
properties().getKeys() |
chemaxon.jchem.db.JChemSearch.getQueryMode()
since JChem 3.2. Will always use the default mode in the
future. |
chemaxon.sss.search.MolSearch.getQueryStructure()
Use getQuery instead |
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.jchem.db.JChemSearch.getSearchType()
since JChem 5.0 use SearchOptions.getSearchType() instead |
chemaxon.marvin.beans.MarvinPane.getSetColor(int)
as of Marvin 3.3, replaced by getAtomSetColor |
chemaxon.jchem.db.JChemSearch.getSimilarity(int)
Use JChemSearch.getDissimilarity(int) instead. |
chemaxon.jchem.db.JChemSearch.getSimilarityThreshold()
Use JChemSearch.getDissimilarityThreshold() instead |
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.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.jchem.db.JChemSearch.getTautomerSearch()
since JChem 5.0. use
SearchOptions.isTautomerSearch() instead |
chemaxon.struc.MoleculeGraph.getTotalCharge()
Use MoleculeGraph.getFormalCharge() |
chemaxon.marvin.calculations.HuckelAnalysisPlugin.getTotalChargeDensity(int)
Use HuckelAnalysisPlugin.getChargeDensity(int) instead |
chemaxon.marvin.calculations.TPSAPlugin.getTPSA()
as of Marvin 4.1, replaced by
TPSAPlugin.getSurfaceArea() |
chemaxon.descriptors.MDSet.getUserData()
since 2.3 |
chemaxon.descriptors.MDSet.getUserData(int)
since 2.3 |
chemaxon.jchem.db.JChemSearch.getVagueBondLevel()
since JChem 5.0. use
SearchOptions.getVagueBondLevel()
instead |
chemaxon.formats.MFileFormatUtil.guessPeptideFormat(String)
as of Marvin 5.0,
Base64Recognizer.canBeBase64(String)
must be used instead |
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.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.jchem.db.JChemSearch.isDeleteFilterTableWhenReady()
since 2.3. Please use JChemSearchOptions.getFilterQuery() instead. |
chemaxon.sss.search.SearchOptions.isDiastereomerMatching()
Please use SearchOptions.getStereoSearchType() instead. |
chemaxon.sss.search.Search.isExactAtomMatching()
since 2.2 |
chemaxon.jchem.db.JChemSearch.isExactChargeMatching()
since JChem 3.2
Please use SearchOptions.getChargeMatching() instead. |
chemaxon.sss.search.Search.isExactChargeMatching()
since JChem 3.2
Please use SearchOptions.getChargeMatching()
(SearchOptions.getChargeMatching()) instead. |
chemaxon.jchem.db.JChemSearch.isExactIsotopeMatching()
since JChem 3.2
Please use SearchOptions.getIsotopeMatching() instead. |
chemaxon.sss.search.Search.isExactIsotopeMatching()
since JChem 3.2
Please use SearchOptions.getIsotopeMatching()
(SearchOptions.getIsotopeMatching()) instead. |
chemaxon.jchem.db.JChemSearch.isExactQueryAtomMatching()
since JChem 5.0.
use SearchOptions.isExactQueryAtomMatching() instead |
chemaxon.jchem.db.JChemSearch.isExactRadicalMatching()
since JChem 3.2
Please use SearchOptions.getRadicalMatching() instead. |
chemaxon.sss.search.Search.isExactRadicalMatching()
since JChem 3.2
Please use SearchOptions.getRadicalMatching()
(SearchOptions.getRadicalMatching()) instead. |
chemaxon.jchem.db.JChemSearch.isExactStereoMatching()
since JChem 5.0. use SearchOptions.isExactStereoMatching() instead |
chemaxon.sss.search.SearchOptions.isExactStereoMatching()
Please use SearchOptions.getStereoSearchType() instead. |
chemaxon.marvin.beans.MarvinPane.isGrinv()
as of Marvin 3.5, use isGrinvVisible() instead |
chemaxon.sss.search.Search.isQueryAbsoluteStereo()
since JChem 5.0.1
Please use MolSearchOptions.isQueryAbsoluteStereo() instead. |
chemaxon.jchem.db.JChemSearch.isStereoSearch()
since JChem 5.0. use SearchOptions.isStereoSearch() instead |
chemaxon.sss.search.SearchOptions.isStereoSearch()
Please use SearchOptions.getStereoSearchType() instead. |
chemaxon.sss.search.Search.isTargetAbsoluteStereo()
since JChem 5.0.1
Please use MolSearchOptions.isTargetAbsoluteStereo() instead. |
chemaxon.reaction.Reactor.isUnique()
Not used. |
chemaxon.jchem.db.JChemSearch.isWaitingForResult()
Replaced by JChemSearch.getRunMode(). |
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.marvin.MolPrinter.maxMag(Dimension)
as of Marvin 2.9.11, replaced by MolPrinter.maxScale(Dimension). |
chemaxon.jchem.db.UpdateHandler.regenerateTable(ConnectionHandler, String, boolean, String, Map, ProgressWriter)
since JChem 5.0. Please use
UpdateHandler.recalculateTable(chemaxon.util.ConnectionHandler, String, boolean, String, java.util.Map, Boolean, chemaxon.jchem.file.ProgressWriter)
instead. |
chemaxon.jchem.db.UpdateHandler.regenerateTable(ConnectionHandler, String, boolean, String, ProgressWriter)
since JChem 5.0. Please use
UpdateHandler.recalculateTable(chemaxon.util.ConnectionHandler, String, boolean, String, java.util.Map, Boolean, chemaxon.jchem.file.ProgressWriter)
instead. |
chemaxon.jchem.db.UpdateHandler.regenerateTable(ConnectionHandler, String, ProgressWriter)
since JChem 5.0. Please use
UpdateHandler.recalculateTable(chemaxon.util.ConnectionHandler, String, boolean, String, java.util.Map, Boolean, chemaxon.jchem.file.ProgressWriter)
instead. |
chemaxon.reaction.Reactor.removeDuplicateProductReferences(Molecule[])
Use Reactor.setRemoveDuplicateProductReferences(boolean) |
chemaxon.struc.MDocument.removeReactionArrow(MDocument)
|
chemaxon.struc.RxnMolecule.removeStructure(int, int)
as of Marvin 4.1, replaced by
RxnMolecule.removeComponent(int, int) |
chemaxon.util.HTMLUtil.replaceString(String, String, String)
as of Marvin 5.0, replaced by
chemaxon.util.StringUtil.replaceAll(String,String,String) |
chemaxon.jchem.db.JChemSearch.setAbsoluteStereo(int)
since JChem 5.0. use JChemSearchOptions.setAbsoluteStereo(int) instead |
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.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.JChemSearch.setConnection(Connection)
It is recommended to use
setConnectionHandler instead. |
chemaxon.jchem.db.Importer.setConnections(String)
since 2.2 replaced by Importer.setFieldConnections(String). |
chemaxon.jchem.db.JChemSearch.setDeleteFilterTableWhenReady(boolean)
since 2.3. Please use JChemSearchOptions.getFilterQuery() instead. |
chemaxon.jchem.db.JChemSearch.setDescriptorConfig(String)
since JChem 5.0
use JChemSearchOptions.setDescriptorConfig(String) instead |
chemaxon.jchem.db.JChemSearch.setDescriptorName(String)
since JChem 5.0
use JChemSearchOptions.setDescriptorName(String) instead |
chemaxon.sss.search.SearchOptions.setDiastereomerMatching(boolean)
Please use setStereoSearchType(STEREO_DIASTEREOMER) and setStereoSearchType(STEREO_SPECIFIC) 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.jchem.db.JChemSearch.setDissimilarityMetric(String)
since JChem 5.0. Use JChemSearchOptions.setDissimilarityMetric(String) instead |
chemaxon.jchem.db.JChemSearch.setDissimilarityThreshold(float)
since JChem 5.0. Use JChemSearchOptions.setDissimilarityThreshold(float) instead |
chemaxon.jchem.db.JChemSearch.setDoubleBondStereoMatchingMode(int)
since JChem 5.0. use SearchOptions.setDoubleBondStereoMatchingMode(int) instead |
chemaxon.sss.search.Search.setExactAtomMatching(boolean)
since 2.2. |
chemaxon.jchem.db.JChemSearch.setExactChargeMatching(boolean)
since JChem 3.2
Please use SearchOptions.setChargeMatching(int) instead. |
chemaxon.sss.search.Search.setExactChargeMatching(boolean)
since JChem 3.2
Please use SearchOptions.setChargeMatching(...)
(SearchOptions.setChargeMatching(int)) instead. |
chemaxon.jchem.db.JChemSearch.setExactIsotopeMatching(boolean)
since JChem 3.2
Please use SearchOptions.setIsotopeMatching(int) instead. |
chemaxon.sss.search.Search.setExactIsotopeMatching(boolean)
since JChem 3.2
Please use SearchOptions.setIsotopeMatching(...)
(SearchOptions.setIsotopeMatching(int)) instead. |
chemaxon.jchem.db.JChemSearch.setExactQueryAtomMatching(boolean)
since JChem 5.0. use SearchOptions.setExactQueryAtomMatching(boolean) instead |
chemaxon.jchem.db.JChemSearch.setExactRadicalMatching(boolean)
since JChem 3.2
Please use SearchOptions.setRadicalMatching(int) instead. |
chemaxon.sss.search.Search.setExactRadicalMatching(boolean)
since JChem 3.2
Please use SearchOptions.setRadicalMatching(...)
(SearchOptions.setRadicalMatching(int)) instead. |
chemaxon.jchem.db.JChemSearch.setExactStereoMatching(boolean)
since JChem 5.0.
use SearchOptions.setExactStereoMatching(boolean) instead |
chemaxon.sss.search.SearchOptions.setExactStereoMatching(boolean)
Please use setStereoSearchType(STEREO_EXACT) and setStereoSearchType(STEREO_SPECIFIC) instead. |
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.jchem.db.JChemSearch.setFilter(String)
Since 5.0
Use SearchOptions.setChemTermsFilter(String) instead. |
chemaxon.sss.search.MolSearch.setFilterConfig(File, Standardizer)
Please use
MolSearch.setFilterConfig(File) and/or
MolSearch.setStandardizer(chemaxon.reaction.Standardizer, boolean, boolean)
instead. |
chemaxon.jchem.db.JChemSearch.setFilterConfigFileName(String)
Since 5.0
Use SearchOptions.setChemTermsFilterConfig(String) instead,
using the content of the file as parameter. |
chemaxon.jchem.db.JChemSearch.setFilterQuery(String)
since JChem 5.0
use JChemSearchOptions.setFilterQuery(String) |
chemaxon.jchem.db.JChemSearch.setFilterTable(String)
since 2.3. Please use
JChemSearchOptions.getFilterQuery() instead. |
chemaxon.marvin.beans.MarvinPane.setGrinv(boolean)
as of Marvin 3.5, use setGrinvVisible(boolean) instead |
chemaxon.jchem.db.JChemSearch.setHCountMatching(int)
since JChem 5.0.
use SearchOptions.setHCountMatching(int) instead |
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.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.marvin.MolPrinter.setMag(double)
as of Marvin 2.9.11, replaced by MolPrinter.setScale(double). |
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.jchem.db.JChemSearch.setMatchCountBetween(int, boolean, int, boolean)
since JChem 5.0
use JChemSearchOptions.setMatchCountOptions(MatchCountOptions) instead |
chemaxon.jchem.db.JChemSearch.setMatchCountInRelation(String, int)
since JChem 5.0
use JChemSearchOptions.setMatchCountOptions(MatchCountOptions) instead |
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.jchem.db.JChemSearch.setMaxResultCount(int)
since JChem 5.0.
use JChemSearchOptions.setMaxResultCount(int) instead |
chemaxon.jchem.db.JChemSearch.setMaxTime(long)
since JChem 5.0. use JChemSearchOptions.setMaxTime(long) instead |
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.alchemist.AlchemistApplication.setMenubar()
This method is no longer need to be called.
Menu will automatically added when calling setMenuResources |
chemaxon.clustering.LibraryMCS.setMinimalSimilarityMeasurement(float)
Minimal similarity measurement is not used from version 0.7 |
chemaxon.clustering.LibraryMCS.setMode(int)
Use setMCSMode instead. |
chemaxon.sss.search.MolSearch.setMolecule(Molecule)
Use setTarget instead |
chemaxon.jchem.db.JChemSearch.setOption(int, int)
since 5.0, use setters in SearchOptions
see JChemSearch.getSearchOptions()
see SearchOptions
see JChemSearchOptions |
chemaxon.sss.search.MolSearchOptions.setOption(int, int)
Since 5.0
Use setters instead.
setMarkushHitSupergraph(boolean),
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)
setExactFragment(boolean)
setTautomerSearch(boolean)
setIsotopeMatching(int)
setChargeMatching(int)
setValenceMatching(boolean)
setRadicalMatching(int)
setVagueBondLevel(int)
setMixSgroupMatching(boolean)
setStereoModel(int)
setImplicitHMatching(int)
setReactionUnpairedMapMatching(boolean) |
chemaxon.reaction.Standardizer.setOptionalTasksEnabled(boolean)
as of JChem 3.2, replaced by Standardizer.setActiveGroups(java.lang.String[])
and Standardizer.setActiveGroup(java.lang.String) which in turn were replaced
by Standardizer.setInactiveTasks(String) as of 5.0 |
chemaxon.sss.search.SearchOptions.setOptions(int[])
since 5.0 |
chemaxon.alchemist.configbuilder.ConfigBuilder.setParentInitialized(boolean)
This method is no longer in use |
chemaxon.marvin.calculations.ResonancePlugin.setpH(double)
As of Marvin 5.0 pH effect is not considered |
chemaxon.alchemist.Alchemist.setProgressBackgroundColor(Color)
Use setSidebarBackground(Color top, Color bottom) instead |
chemaxon.marvin.calculations.TautomerizationPlugin.setProtectAromacity(boolean)
Use TautomerizationPlugin.setProtectAromaticity(boolean) |
chemaxon.sss.search.Search.setQueryAbsoluteStereo(boolean)
since JChem 5.0.1
Please use MolSearchOptions.setQueryAbsoluteStereo(boolean) instead. |
chemaxon.jchem.db.JChemSearch.setQueryMode(int)
since JChem 3.2. Will always use the default mode in the
future. |
chemaxon.sss.search.MolSearch.setQueryStructure(Molecule)
Use setQuery instead |
chemaxon.reaction.Reactor.setReaction(Molecule, String)
Use Reactor.setReaction(Molecule, String, String, String, double[])
or Reactor.setReaction(Molecule, String, String, String, String)
and set rid, selectivity and
tolerances parameters to null. |
chemaxon.reaction.Reactor.setReaction(Molecule, String, String)
Use Reactor.setReaction(Molecule, String, String, String, double[])
or Reactor.setReaction(Molecule, String, String, String, String)
and set rid and tolerances parameters
to null. |
chemaxon.reaction.Reactor.setReaction(Molecule, String, String, double[])
Use Reactor.setReaction(Molecule, String, String, String, double[])
and set rid parameter to null. |
chemaxon.reaction.Reactor.setReaction(Molecule, String, String, String)
Use Reactor.setReaction(Molecule, String, String, String, String)
and set rid parameter to null. |
chemaxon.reaction.Reactor.setReaction(String)
As of JChem 3.2 Reactor configuration XML files are not supported. |
chemaxon.marvin.common.UserSettings.setReadGUIPropertiesFromMRV(boolean)
since Marvin 5.1 when this and the previous function have been merged. |
chemaxon.jchem.db.JChemSearch.setReturnsNonHits(boolean)
since JChem 5.0 use
JChemSearchOptions.setReturnsNonHits(boolean) instead |
chemaxon.jchem.db.JChemSearch.setSearchType(int)
since JChem 5.0
use SearchOptions.setSearchType(int) instead |
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.jchem.db.JChemSearch.setSimilarityThreshold(float)
Use instead |
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.jchem.db.JChemSearch.setStereoSearch(boolean)
since JChem 5.0. use SearchOptions.setStereoSearch(boolean) instead |
chemaxon.sss.search.SearchOptions.setStereoSearch(boolean)
Please use setStereoSearchType(STEREO_SPECIFIC) and setStereoSearchType(STEREO_IGNORE) instead. |
chemaxon.sss.search.Search.setTargetAbsoluteStereo(boolean)
since JChem 5.0.1
Please use MolSearchOptions.setTargetAbsoluteStereo(boolean) instead. |
chemaxon.jchem.db.JChemSearch.setTautomerSearch(boolean)
since JChem 5.0.
use SearchOptions.setTautomerSearch(boolean) instead |
chemaxon.reaction.Reactor.setTransform(boolean)
Use Standardizer. |
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.jchem.db.JChemSearch.setVagueBondLevel(int)
since JChem 5.0. use
|