Deprecated API


Contents
Deprecated Interfaces
chemaxon.jep.MolCondition
          Will be removed soon. 
 

Deprecated Classes
chemaxon.alchemist.AlchemistProgressObject
          Use AlchemistProgressLabel instead 
chemaxon.alchemist.utils.AlchemistSplitPane
          is it no longer used, will be removed 
chemaxon.alchemist.configbuilder.ConfigBuilder
          This class is no longer in use.
Use ConfigBuilderPanel instead.
 
chemaxon.alchemist.configbuilder.ConfigBuilderItemPanelHolder
          This class is no longer in use. All the functionality moved to ConfigBuilderPanel 
chemaxon.alchemist.configbuilder.ConfigBuilderListCellRenderer
          this class is no longer in use Use ConfigElementListCellRenderer instead 
chemaxon.alchemist.configbuilder.ConfigItem
          use ConfigElement instead 
chemaxon.alchemist.configbuilder.ConfigItemGroup
          This class is no longer in use. Configuration reading is handled by AbstractConfigurationReader inheritances
Presentation chooser system and item list customization is handled in ConfigBuilderPanel and described in XML
Notification is also handled by ConfigBuilderPanel
 
chemaxon.alchemist.configbuilder.ConfigItemList
          This item is no longer in use. To create custom action list, define the items in XML 
chemaxon.alchemist.configbuilder.ConfigItemPanel
          use ConfigElementPanel instead 
chemaxon.alchemist.configbuilder.ConfigItemTransferHandler
          This class is no longer in use.
Use ConfigElementTransferHandler instead.
 
chemaxon.alchemist.configbuilder.EmptyPanel
          This class is no longer in use. Use BasicConfigElementEditor instead. 
chemaxon.marvin.calculations.EnumerationPlugin
          Use MarkushEnumerationPlugin 
chemaxon.reaction.synthesis.ExhaustiveAlgorithm
          Will be removed soon. 
chemaxon.alchemist.configbuilder.GroupEditor
          This class is no longer in use. 
chemaxon.reaction.synthesis.LinearAlgorithm
          Will be removed soon. 
chemaxon.reaction.synthesis.MoleculeSet
          Will be removed soon. 
chemaxon.marvin.util.MolExportModule
          as of Marvin 5.0, replaced by MolExportModule 
chemaxon.marvin.util.MPainterUtil
          As of Marvin 4.1.8, replaced by MolPrinter 
chemaxon.alchemist.configbuilder.PresentationChooser
          This class is no longer in use. Use ConfigElementPresentationChooser instead 
chemaxon.reaction.synthesis.RandomAlgorithm
          Will be removed soon. 
chemaxon.reaction.SynthesisAlgorithm
          Will be removed soon. 
chemaxon.reaction.SynthesisGraph
          Will be removed soon. 
chemaxon.reaction.SynthesisGraph.Edge
          Will be removed soon. 
chemaxon.reaction.SynthesisGraph.Node
          Will be removed soon. 
chemaxon.reaction.Synthesizer
          Will be removed soon. 
 

Deprecated Exceptions
chemaxon.marvin.util.MolExportException
          as of Marvin 5.0, replaced by MolExportException 
 

Deprecated Fields
chemaxon.alchemist.utils.AlchemistUtilities.ALCHEMIST_BLUE
          See predefined colors in AlchemistGraphicsUtilities 
chemaxon.alchemist.utils.AlchemistUtilities.ALCHEMIST_GRAY
          See predefined colors in AlchemistGraphicsUtilities 
chemaxon.alchemist.utils.AlchemistUtilities.ALCHEMIST_ORANGE
          See predefined colors in AlchemistGraphicsUtilities 
chemaxon.alchemist.utils.AlchemistGraphicsUtilities.ALCHEMIST_TOOLTIP_YELLOW
          use ALCHEMIST_TOOLTIP_BGR instead 
chemaxon.alchemist.utils.AlchemistUtilities.ALCHEMIST_YELLOW
          See predefined colors in AlchemistGraphicsUtilities 
chemaxon.struc.MoleculeGraph.AROM_CHEMAXON
          please use AROM_BASIC instead. Chemaxon aromatization. 
chemaxon.struc.MoleculeGraph.AROM_DAYLIGHT
          please use AROM_GENERAL instead. Daylight aromatization (modified Huckel rule). 
chemaxon.struc.MolBond.COORDINATIVE
          As of Marvin 5.0, replaced by MolBond.COORDINATE 
chemaxon.sss.SearchConstants.DEFAULT_SIMILARITY_THRESHOLD
          use SearchConstants.DEFAULT_DISSIMILARITY_THRESHOLD instead 
chemaxon.sss.SearchConstants.DISSIMILARITY
          use SearchConstants.SIMILARITY instead 
chemaxon.sss.SearchConstants.EXACT_FRAGMENT_OFF
          since 5.0
Use SearchOptions.setExactFragment(boolean) instead.
 
chemaxon.sss.SearchConstants.EXACT_FRAGMENT_ON
          since 5.0
Use SearchOptions.setExactFragment(boolean) instead.
 
chemaxon.marvin.VersionInfo.IS_DEV_VERSION
          no more used 
chemaxon.jchem.db.Updater.UpdateInfo.isRegeneration
          since 5.1.2 use #isProgressMonitoringNeeded instead. 
chemaxon.sss.SearchConstants.KEEP_QUERY_ORDER
          since 5.0
Use SearchOptions.setKeepQueryOrder(boolean) instead.
 
chemaxon.sss.SearchConstants.MARKUSH_DISABLED
          since 5.0
Use MolSearchOptions.setMarkushEnabled(boolean) instead.
 
chemaxon.sss.SearchConstants.MARKUSH_ENABLED
          since 5.0
Use MolSearchOptions.setMarkushEnabled(boolean) instead.
 
chemaxon.sss.SearchConstants.MARKUSH_HIT_ORIGINAL
          since 5.0
Use MolSearchOptions.setMarkushHitSupergraph(boolean)
 
chemaxon.sss.SearchConstants.MARKUSH_HIT_SUPERGRAPH
          since 5.0
Use MolSearchOptions.setMarkushHitSupergraph(boolean)
 
chemaxon.sss.SearchConstants.MIX_SGROUP_MATCHING_OFF
          since 5.0
Use SearchOptions.setMixSgroupMatching(boolean) instead.
 
chemaxon.sss.SearchConstants.MIX_SGROUP_MATCHING_ON
          since 5.0
Use SearchOptions.setMixSgroupMatching(boolean) instead.
 
chemaxon.sss.SearchConstants.OPTION_CHARGE_MATCHING
          since 5.0
Use SearchOptions.setChargeMatching(int) instead.
 
chemaxon.sss.SearchConstants.OPTION_EXACT_FRAGMENT
          since 5.0
Use SearchOptions.setExactFragment(boolean) instead.
 
chemaxon.sss.SearchConstants.OPTION_ISOTOPE_MATCHING
          since 5.0
Use SearchOptions.setIsotopeMatching(int) instead.
 
chemaxon.sss.SearchConstants.OPTION_KEEP_QUERY_ORDER
          since 5.0
Use SearchOptions.setKeepQueryOrder(boolean) instead.
 
chemaxon.sss.SearchConstants.OPTION_MARKUSH_AROM
          since 5.0
Use MolSearchOptions.setMarkushArom(int) instead.
 
chemaxon.sss.SearchConstants.OPTION_MARKUSH_ENABLED
          since 5.0
Use MolSearchOptions.setMarkushEnabled(boolean) instead.
 
chemaxon.sss.SearchConstants.OPTION_MARKUSH_HIT
          since 5.0
Use MolSearchOptions.setMarkushHitSupergraph(boolean)
 
chemaxon.sss.SearchConstants.OPTION_MIX_SGROUP_MATCHING
          since 5.0
Use SearchOptions.setMixSgroupMatching(boolean) instead.
 
chemaxon.sss.SearchConstants.OPTION_RADICAL_MATCHING
          since 5.0
Use SearchOptions.setRadicalMatching(int) instead.
 
chemaxon.sss.SearchConstants.OPTION_STEREO_MODEL
          since 5.0
Use SearchOptions.setStereoModel(int) instead.
 
chemaxon.sss.SearchConstants.OPTION_TAUTOMER_SEARCH
          since 5.0
Use SearchOptions.setTautomerSearch(boolean) instead.
 
chemaxon.sss.SearchConstants.OPTION_VAGUE_BOND
          since 5.0 
chemaxon.sss.SearchConstants.OPTION_VALENCE_MATCHING
          since 5.0
Use SearchOptions.setValenceMatching(boolean) instead.
 
chemaxon.marvin.plugin.PluginFactory.PRELOAD
          Not used. 
chemaxon.jchem.db.JChemSearch.QM_ALWAYS_SMARTS
          since JChem 3.2. Will always use the default mode in the future. 
chemaxon.jchem.db.JChemSearch.QM_ALWAYS_SMILES
          since JChem 3.2. Will always use the default mode in the future. 
chemaxon.jchem.db.JChemSearch.QM_DEFAULT
          since JChem 3.2. Will always use the default mode in the future. 
chemaxon.sss.SearchConstants.REARRANGE_QUERY
          since 5.0
Use SearchOptions.setKeepQueryOrder(boolean) instead.
 
chemaxon.sss.SearchConstants.REGULAR_SEARCH
          use SearchConstants.SUBSTRUCTURE instead 
chemaxon.alchemist.AlchemistProgressObject.STATE_NOTNEEDED
          use STATE_DISABLED 
chemaxon.sss.SearchConstants.TAUTOMER_SEARCH_OFF
          since 5.0
Use SearchOptions.setTautomerSearch(boolean) instead.
 
chemaxon.sss.SearchConstants.TAUTOMER_SEARCH_ON
          since 5.0
Use SearchOptions.setTautomerSearch(boolean) instead.
 
chemaxon.formats.MdlCompressor.TEXTMODE
          as of Marvin 3.1, there is no possibility to do that 
chemaxon.struc.MolAtom.VALCHK_ATTACH
          as of Marvin 3.5, attachment points are always checked 
chemaxon.sss.SearchConstants.VALENCE_MATCHING_IGNORE
          since 5.0
Use SearchOptions.setValenceMatching(boolean) instead.
 
chemaxon.sss.SearchConstants.VALENCE_MATCHING_ON
          since 5.0
Use SearchOptions.setValenceMatching(boolean) instead.
 
 

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