Serialized Form

  • Package chemaxon.calculations

    • Exception chemaxon.calculations.CalculationException

      class CalculationException extends RuntimeException implements Serializable
  • Package chemaxon.calculations.clean

    • Class chemaxon.calculations.clean.AtomChangeEvent

      class AtomChangeEvent extends EventObject implements Serializable
  • Package chemaxon.calculator

    • Exception chemaxon.calculator.CalculatorException

      class CalculatorException extends Exception implements Serializable
  • Package chemaxon.common.util

    • Class chemaxon.common.util.ByteVector

      class ByteVector extends Object implements Serializable
      • Serialized Fields

        • data
          byte[] data
        • size
          int size
    • Class chemaxon.common.util.DoubleVector

      class DoubleVector extends Object implements Serializable
      • Serialized Fields

        • data
          double[] data
        • size
          int size
    • Class chemaxon.common.util.FloatVector

      class FloatVector extends Object implements Serializable
      • Serialized Fields

        • data
          float[] data
        • size
          int size
    • Exception chemaxon.common.util.GeomCalc.GeomCalcException

      class GeomCalcException extends RuntimeException implements Serializable
    • Exception chemaxon.common.util.GeomCalc.Queue.Overflow

      class Overflow extends Exception implements Serializable
    • Exception chemaxon.common.util.GeomCalc.Queue.Underflow

      class Underflow extends Exception implements Serializable
    • Class chemaxon.common.util.IntMap

      class IntMap extends HashMap<K extends Object,Integer> implements Serializable
    • Class chemaxon.common.util.IntPair

      class IntPair extends Object implements Serializable
      • Serialized Fields

        • left
          int left
        • right
          int right
    • Class chemaxon.common.util.IntVector

      class IntVector extends Object implements Serializable
      • Serialized Fields

        • data
          int[] data
        • size
          int size
    • Class chemaxon.common.util.LongVector

      class LongVector extends Object implements Serializable
      • Serialized Fields

        • data
          long[] data
        • size
          int size
    • Class chemaxon.common.util.ShortVector

      class ShortVector extends Object implements Serializable
      • Serialized Fields

        • data
          short[] data
        • size
          int size
  • Package chemaxon.core

    • Exception chemaxon.core.SequenceBuildingException

      class SequenceBuildingException extends RuntimeException implements Serializable
      • Serialized Fields

  • Package chemaxon.core.calculations.valencecheck

    • Class chemaxon.core.calculations.valencecheck.ValenceCheckOptions

      class ValenceCheckOptions extends Object implements Serializable
      • Serialized Fields

        • localAromatic
          boolean localAromatic
        • traditionalNallowed
          boolean traditionalNallowed
    • Exception chemaxon.core.calculations.valencecheck.ValenceColumnException

      class ValenceColumnException extends chemaxon.core.calculations.valencecheck.ValenceException implements Serializable
    • Exception chemaxon.core.calculations.valencecheck.ValenceException

      class ValenceException extends Exception implements Serializable
    • Exception chemaxon.core.calculations.valencecheck.ValenceTypeException

      class ValenceTypeException extends chemaxon.core.calculations.valencecheck.ValenceException implements Serializable
  • Package chemaxon.core.util

    • Class chemaxon.core.util.BondTable

      class BondTable extends Object implements Serializable
      • Serialized Fields

        • atomCount
          int atomCount
          The size of the matrix, the number of atoms in the molecule it represents.
  • Package chemaxon.descriptors

  • Package chemaxon.formats

  • Package chemaxon.jchem.db

  • Package chemaxon.jep

    • Class chemaxon.jep.ChemFunction

      class ChemFunction extends chemaxon.nfunk.jep.function.PostfixMathCommand implements Serializable
      • Serialized Fields

        • cached
          boolean cached
        • jep
          ChemJEP jep
    • Class chemaxon.jep.ChemJEP

      class ChemJEP extends chemaxon.nfunk.jep.JEP implements Serializable
      • Serialized Fields

        • context
          ChemContext context
          The evaluation context object.
        • contextClass
          Class contextClass
          The evaluation context class.
    • Exception chemaxon.jep.ConditionException

      class ConditionException extends Exception implements Serializable
    • Class chemaxon.jep.ContextFunction

      class ContextFunction extends chemaxon.nfunk.jep.function.PostfixMathCommand implements Serializable
    • Class chemaxon.jep.DissimilarityFunction

      class DissimilarityFunction extends chemaxon.jep.ChemFunction implements Serializable
      • Serialized Fields

        • className
          String className
        • descriptors
          String[] descriptors
    • Class chemaxon.jep.Evaluator

      class Evaluator extends Object implements Serializable
      • Serialized Fields

        • builtInConfig
          chemaxon.jep.EvaluatorConfiguration builtInConfig
          The configuration object containing default function/plugin declarations.
        • config
          chemaxon.jep.EvaluatorConfiguration config
          The configuration object.
        • externalConfig
          chemaxon.jep.EvaluatorConfiguration externalConfig
          The configuration object containing external function/plugin declarations.
        • functionalGroupDisplayMolTable
          Hashtable<String,String> functionalGroupDisplayMolTable
          |functional group name| -> |displayable molecule representation|
        • licenseEnvironment
          String licenseEnvironment
        • servicesConfigurationPath
          String servicesConfigurationPath
          services configuration path
        • servicesFunctionTable
          Hashtable<String,chemaxon.nfunk.jep.function.PostfixMathCommandI> servicesFunctionTable
          Function table for services.
        • symtab
          chemaxon.nfunk.jep.SymbolTable symtab
          The base symbol table.
        • userConfig
          chemaxon.jep.EvaluatorConfiguration userConfig
          The configuration object containing user defined function/plugin declarations.
        • verbose
          boolean verbose
          True if verbose output.
    • Class chemaxon.jep.EvaluatorFunction

      class EvaluatorFunction extends chemaxon.jep.ChemFunction implements Serializable
      • Serialized Fields

    • Class chemaxon.jep.MatchFunction

      class MatchFunction extends chemaxon.jep.ChemFunction implements Serializable
      • Serialized Fields

        • attributes
          chemaxon.jep.util.SearchAttributes attributes
        • className
          String className
        • dir
          String dir
        • licenseEnvironment
          String licenseEnvironment
        • standardizer
          chemaxon.jep.Standardizer standardizer
        • subMatches
          Hashtable subMatches
        • type
          int type
  • Package chemaxon.jep.context

  • Package chemaxon.license

  • Package chemaxon.marvin

    • Class chemaxon.marvin.SketchApplication

      class SketchApplication extends chemaxon.marvin.AbstractApplication implements Serializable
      • Serialized Fields

    • Class chemaxon.marvin.ViewApplication

      class ViewApplication extends chemaxon.marvin.AbstractApplication implements Serializable
      • Serialized Fields

        • colorKeys
          List<String> colorKeys
        • exitAction
          Action exitAction
        • hasInitalized
          boolean hasInitalized
        • openAction
          Action openAction
        • printAction
          Action printAction
        • viewPane
          MViewPane viewPane
  • Package chemaxon.marvin.alignment

    • Exception chemaxon.marvin.alignment.AlignmentException

      class AlignmentException extends Exception implements Serializable
    • Exception chemaxon.marvin.alignment.NoConstraintException

      class NoConstraintException extends chemaxon.marvin.alignment.AlignmentException implements Serializable
    • Exception chemaxon.marvin.alignment.OptimizationException

      class OptimizationException extends RuntimeException implements Serializable
    • Class chemaxon.marvin.alignment.ShapeData

      class ShapeData extends Object implements Serializable
      • Serialized Fields

        • atoms
          chemaxon.marvin.alignment.ShapeData.Atom[] atoms
        • bonds
          chemaxon.marvin.alignment.ShapeData.Bond[] bonds
        • coloringScheme
          AlignmentProperties.ColoringScheme coloringScheme
        • maxs
          double[] maxs
        • mins
          double[] mins
        • shapeEnabledAtoms
          BitSet shapeEnabledAtoms
    • Exception chemaxon.marvin.alignment.TooDissimilarException

      class TooDissimilarException extends chemaxon.marvin.alignment.AlignmentException implements Serializable
  • Package chemaxon.marvin.beans

  • Package chemaxon.marvin.calculations

    • Class chemaxon.marvin.calculations.BitPattern

      class BitPattern extends BitSet implements Serializable
  • Package

  • Package chemaxon.marvin.modules.datatransfer

    • Class chemaxon.marvin.modules.datatransfer.CopyAsDialog

      class CopyAsDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable
      • Serialized Fields

  • Package chemaxon.marvin.plugin

  • Package chemaxon.marvin.plugin.concurrent

  • Package chemaxon.marvin.plugin.gui

  • Package

  • Package chemaxon.marvin.sketch

    • Class chemaxon.marvin.sketch.History

      class History extends Object implements Serializable
      • Serialized Fields

        • autoHydrogenizeHist
          int[] autoHydrogenizeHist
        • changeSupport
          PropertyChangeSupport changeSupport
        • cornerHist
          Point[] cornerHist
        • historyOverflow
          boolean historyOverflow
        • molgToZoomHist
          MoleculeGraph[][] molgToZoomHist
        • molHist
          MDocument[] molHist
        • molHistCur
          int molHistCur
        • molHistLen
          int molHistLen
        • molHistMax
          int molHistMax
        • rotateMatrHist
          CTransform3D[] rotateMatrHist
        • scaleHist
          double[] scaleHist
        • scrollBarHist
          int[][] scrollBarHist
        • selectionToZoomHist
          boolean[] selectionToZoomHist
    • Class chemaxon.marvin.sketch.MolEditor

      class MolEditor extends Object implements Serializable
      • Serialization Methods

      • Serialized Fields

        • atomBranchPiece
          Molecule atomBranchPiece
        • atomSelectionMode
          int atomSelectionMode
        • atomStrings
          Set<Integer> atomStrings
        • bondDraggedAlong
          boolean bondDraggedAlong
        • bondDrawMode
          boolean bondDrawMode
        • canMovCurfrag
          boolean canMovCurfrag
        • canRotCurfrag
          boolean canRotCurfrag
        • curfrag
          MDocument curfrag
        • curfragJoin
          com.chemaxon.marvin.editor.molecule.fusion.MolJoin curfragJoin
        • curfragMoved
          boolean curfragMoved
        • curfragR
          double curfragR
        • currentTool
          chemaxon.marvin.sketch.tool.EditorTool currentTool
        • dataSgroupObject
          DataSgroup dataSgroupObject
        • deleteRemovesTerminalAtoms
          boolean deleteRemovesTerminalAtoms
        • disabledAliases
          Set<String> disabledAliases
        • document
          MDocument document
        • documentEdited
          boolean documentEdited
        • elements
          List<Integer> elements
        • extraBonds
          Set<Integer> extraBonds
        • flyingBondMol
          MoleculeGraph flyingBondMol
        • hadSelection
          boolean hadSelection
        • historizeEnabled
          boolean historizeEnabled
        • historizeUnSelection
          boolean historizeUnSelection
        • history
          chemaxon.marvin.sketch.History history
        • isAxisSet
          boolean isAxisSet
        • isDataSgroupLabelPointed
          boolean isDataSgroupLabelPointed
        • isProbablyDotNetApplication
          boolean isProbablyDotNetApplication
        • isSketchApplication
          boolean isSketchApplication
        • jointAtom
          MolAtom jointAtom
        • lastBondFlags
          int lastBondFlags
        • lastQueryBondString
          String lastQueryBondString
        • lastSelectionCorner
          Point lastSelectionCorner
        • lastSelectionDoc
          MDocument lastSelectionDoc
        • lastSelectionScale
          double lastSelectionScale
        • lpEnabled
          boolean lpEnabled
        • mergedst
          double mergedst
        • moveMode
          int moveMode
        • newKeyboardMotion
          boolean newKeyboardMotion
        • painter
          chemaxon.marvin.paint.internal.MolPainter painter
        • persistentMoveMode
          boolean persistentMoveMode
        • piece
          Molecule piece
        • pieceOriginalObject
          Molecule pieceOriginalObject
        • prevCurfrag
          MDocument prevCurfrag
        • queryAtoms
          Set<Integer> queryAtoms
        • reactionSupported
          boolean reactionSupported
        • rotate3direction
          int rotate3direction
        • rotate3dPhi
          double rotate3dPhi
        • rotate3dPhiX
          double rotate3dPhiX
        • rotate3dPhiY
          double rotate3dPhiY
        • rotate3dx
          double rotate3dx
        • rotate3dy
          double rotate3dy
        • rotateZPhi
          double rotateZPhi
        • rotation3DMode
          int rotation3DMode
        • rotAxisPoint
          DPoint3 rotAxisPoint
        • rotO
          DPoint3 rotO
        • scrollBarVals
          int[] scrollBarVals
        • selectionDoc
          MSelectionDocument selectionDoc
        • selectionHistorized
          boolean selectionHistorized
        • selectionHPoints
          DPoint3[] selectionHPoints
        • showMolecule
          Molecule showMolecule
        • starEnabled
          boolean starEnabled
        • stickdst
          double stickdst
  • Package

    • Class

      class EventQueue extends Vector implements Serializable
    • Class

      class GraphicScene extends JPanel implements Serializable
      • Serialized Fields

        • _glListsToDelete
          ArrayList<Integer> _glListsToDelete
        • activeCell
          int activeCell
          index of the active cell: cells are numbered line-by-line
        • antialias
          boolean antialias
        • backgroundColor
          float[] backgroundColor
          we use java.awt.Color in the following cases - when the color does not change too often - when the user can change the given color - when we don't have to give it to OGL2 too often (like color of an atom, etc) These are e.g. : background color, constant component colors
        • backgroundColorChanged
          boolean backgroundColorChanged
        • canvas
          Component canvas
        • cellCount
          int cellCount
          number of cells (there might be fewer cells than cells.length())
        • cells
          GraphicCell[] cells
          components per cells, line-by-line 0 is the top-left corner
        • columnCount
          int columnCount
          layout of the graphic view: number of cells per column
        • defaultDrawProperties
          Map<Object,Object> defaultDrawProperties
        • eventHandler
        • gl
        • glAutoDrawable
        • globalDrawProperties
          Properties globalDrawProperties
        • gltext
          this is used to display warning about unregistered product
        • glu
        • height
          int height
          physical height of the entire scene (in pixels)
        • initialized
          boolean initialized
        • motionmode
          int motionmode
          standing or moving mode
        • needsRefresh
          int needsRefresh
          Indicates with internal index which cell needs redraw. -1 means none, cellCount means all cells.
        • needsReset
          int needsReset
        • progressBar
        • renderTargets
        • rowCount
          int rowCount
          layout of the graphic view: number of cells per row
        • rx
          double rx
          rotation around x-y-z axises
        • ry
          double ry
          rotation around x-y-z axises
        • rz
          double rz
          rotation around x-y-z axises
        • smoothBackground
          boolean smoothBackground
        • synchronousMode
          boolean synchronousMode
        • transparentBackground
          int transparentBackground
        • userSettings
          UserSettings userSettings
        • verboseLevel
          int verboseLevel
        • width
          int width
          physical width of the entire scene (in pixels)
  • Package chemaxon.marvin.uif.dialog

    • Class chemaxon.marvin.uif.dialog.CategoriesDialog

      class CategoriesDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable
      • Serialized Fields

        • bundle
          ResourceBundle bundle
        • model
          chemaxon.marvin.uif.dialog.model.CategoriesModel model
    • Class chemaxon.marvin.uif.dialog.ConfigurationDialog

      class ConfigurationDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable
      • Serialized Fields

        • module
          chemaxon.marvin.uif.module.GUIModule module
    • Class chemaxon.marvin.uif.dialog.CustomizeDialog

      class CustomizeDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable
      • Serialized Fields

        • bundle
          ResourceBundle bundle
        • guiRegistryClone
          chemaxon.marvin.uif.model.GUIRegistry guiRegistryClone
        • model
          chemaxon.marvin.uif.dialog.model.CustomizeGUIModel model
        • moduleConf
          chemaxon.marvin.uif.module.ModuleConfiguration moduleConf
    • Class chemaxon.marvin.uif.dialog.LicenseDialog

      class LicenseDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable
    • Class chemaxon.marvin.uif.dialog.MenuDialog

      class MenuDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable
      • Serialized Fields

        • bundle
          ResourceBundle bundle
        • model
          chemaxon.marvin.uif.dialog.model.MenuManagerModel model
    • Class chemaxon.marvin.uif.dialog.MenuMoveDialog

      class MenuMoveDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable
      • Serialized Fields

        • bundle
          ResourceBundle bundle
        • model
          chemaxon.marvin.uif.dialog.model.ItemGroupModel model
    • Class chemaxon.marvin.uif.dialog.PopupDialog

      class PopupDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable
      • Serialized Fields

        • bundle
          ResourceBundle bundle
        • model
          chemaxon.marvin.uif.dialog.model.PopupManagerModel model
    • Class chemaxon.marvin.uif.dialog.ShortcutEditorDialog

      class ShortcutEditorDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable
      • Serialized Fields

        • bundle
          ResourceBundle bundle
        • model
          chemaxon.marvin.uif.dialog.model.ShortcutModel model
    • Class chemaxon.marvin.uif.dialog.ToolBarDialog

      class ToolBarDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable
      • Serialized Fields

        • bundle
          ResourceBundle bundle
        • model
          chemaxon.marvin.uif.dialog.model.ToolBarManagerModel model
  • Package chemaxon.marvin.util

    • Exception chemaxon.marvin.util.CancelPrintException

      class CancelPrintException extends Exception implements Serializable
    • Class chemaxon.marvin.util.MarvinModule

      class MarvinModule extends Object implements Serializable
    • Class chemaxon.marvin.util.MarvinOLEFrame

      class MarvinOLEFrame extends JFrame implements Serializable
    • Class chemaxon.marvin.util.MarvinOLEPanel

      class MarvinOLEPanel extends JPanel implements Serializable
      • Serialized Fields

        • emfExportOptions
          String emfExportOptions
        • importExceptionCaught
          boolean importExceptionCaught
        • msketch
          MSketchPane msketch
        • retainGUIPropertiesOnPanel
          boolean retainGUIPropertiesOnPanel
        • semaphore
          Semaphore semaphore
        • sketchPanel
          chemaxon.marvin.sketch.swing.SketchPanel sketchPanel
        • structureGUIProperties
          MPropertyContainer structureGUIProperties
    • Class chemaxon.marvin.util.SwingUtil

      class SwingUtil extends Object implements Serializable
  • Package chemaxon.marvin.util.codeassist

  • Package chemaxon.marvin.view

  • Package chemaxon.marvin.view.swing

    • Class chemaxon.marvin.view.swing.TwoLists

      class TwoLists extends JPanel implements Serializable
      • Serialized Fields

        • addAllButton
          JButton addAllButton
        • addButton
          JButton addButton
        • allSelected
          boolean allSelected
        • list1
          JList list1
        • list2
          JList list2
        • listData1
          String[] listData1
        • listData2
          String[] listData2
        • removeAllButton
          JButton removeAllButton
        • removeButton
          JButton removeButton
    • Class chemaxon.marvin.view.swing.ViewCanvas

      class ViewCanvas extends chemaxon.marvin.common.swing.MolCanvas implements Serializable
      • Serialization Methods

      • Serialized Fields

        • cellIndex
          int cellIndex
        • document
          MDocument document
        • error
          boolean error
        • highlightedAtom
          int highlightedAtom
        • inZoomWindow
          boolean inZoomWindow
        • markedAtom
          int markedAtom
        • moleculeBackground
          Color moleculeBackground
        • moleculeCenter
          DPoint3 moleculeCenter
        • nextV
          Vector<Object[]> nextV
        • painter
          chemaxon.marvin.paint.internal.MolPainter painter
        • preferredSize1
          Dimension preferredSize1
        • rescaleNeeded
          boolean rescaleNeeded
        • rsize
          Dimension rsize
        • viewFrame
          chemaxon.marvin.view.swing.modules.MViewFrame viewFrame
        • viewPanel
          chemaxon.marvin.view.swing.ViewPanel viewPanel
        • windowAction
          chemaxon.marvin.swing.MAction windowAction
        • winScale
          double winScale
    • Class chemaxon.marvin.view.swing.ViewHandler

      class ViewHandler extends Object implements Serializable
      • Serialized Fields

        • cellFiller
          chemaxon.marvin.view.swing.CellFiller cellFiller
        • debug
          boolean debug
        • visibleDocs
          chemaxon.marvin.view.swing.VisibleDocuments visibleDocs
    • Class chemaxon.marvin.view.swing.ViewPanel

      class ViewPanel extends chemaxon.marvin.common.swing.MolPanel implements Serializable
      • Serialization Methods

      • Serialized Fields

        • animator
          chemaxon.marvin.view.swing.modules.MViewAnimator animator
        • animSynchronized
          boolean animSynchronized
        • atomMarkAndHighlightEnabled
          boolean atomMarkAndHighlightEnabled
        • autoTabScale
          boolean autoTabScale
        • borderColor
          Color borderColor
        • borderWidth
          int borderWidth
        • clearStateOnOpenAction
          Action clearStateOnOpenAction
        • cols
          int cols
        • commonActions
          chemaxon.marvin.common.swing.action.CommonActions commonActions
        • defaultFieldFont
          Font defaultFieldFont
        • detachable
          boolean detachable
        • draggable
          boolean draggable
        • editable
          int editable
        • fieldFontMap
          Map<String,Font> fieldFontMap
        • findAction
          Action findAction
        • findAgainAction
          Action findAgainAction
        • findTextModule
          chemaxon.marvin.view.swing.modules.FindText findTextModule
        • importEnabled
          boolean importEnabled
        • molbgMap
          Map<Integer,Color> molbgMap
        • moleculeSelections
          chemaxon.marvin.common.AtomSelectionHandler[] moleculeSelections
        • molEdited
          boolean molEdited
        • molFrame0
          Window molFrame0
        • molString
          String molString
        • molStrings
          String[] molStrings
        • navigationActions
          chemaxon.marvin.swing.MAction[] navigationActions
        • oldMarkedAtom
          int oldMarkedAtom
        • oldMarkedCell
          int oldMarkedCell
        • rasmolScripts
          String[] rasmolScripts
        • rows
          int rows
        • selectable
          boolean selectable
        • selected
          int selected
        • skbridge
          chemaxon.marvin.view.modules.sketchbridge.MViewSketch skbridge
        • startLoad
          boolean startLoad
        • tableSupport
          TableSupport tableSupport
        • tabScale
          double tabScale
        • tabScaleCalcInProgress
          int tabScaleCalcInProgress
        • tabScaleCalcNeeded
          boolean tabScaleCalcNeeded
        • viewActions
          chemaxon.marvin.view.swing.ViewActions viewActions
        • viewHandler
          chemaxon.marvin.view.swing.ViewHandler viewHandler
        • winScale
          double winScale
    • Class chemaxon.marvin.view.swing.WholeNumberField

      class WholeNumberField extends JTextField implements Serializable
      • Serialized Fields

    • Class chemaxon.marvin.view.swing.WholeNumberField.WholeNumberDocument

      class WholeNumberDocument extends PlainDocument implements Serializable
  • Package chemaxon.naming

  • Package chemaxon.naming.document

    • Exception chemaxon.naming.document.D2SOptionsParser.UnknownOptionException

      class UnknownOptionException extends Exception implements Serializable
    • Class chemaxon.naming.document.D2SPdfParser

      class D2SPdfParser extends org.apache.tika.parser.pdf.ExtendablePdfParser implements Serializable
    • Class chemaxon.naming.document.D2STextParser

      class D2STextParser extends Object implements Serializable
    • Exception chemaxon.naming.document.EncryptedDocumentException

      class EncryptedDocumentException extends IOException implements Serializable
    • Class chemaxon.naming.document.OsrParser

      class OsrParser extends org.apache.tika.parser.AbstractParser implements Serializable
    • Class chemaxon.naming.document.SafeOfficeParser

      class SafeOfficeParser extends implements Serializable
    • Exception chemaxon.naming.document.TimeoutException

      class TimeoutException extends IOException implements Serializable
      • Serialized Fields

        • timeoutMS
          long timeoutMS
    • Class chemaxon.naming.document.TrivialXmlParser

      class TrivialXmlParser extends org.apache.tika.parser.AbstractParser implements Serializable
  • Package chemaxon.naming.document.annotate

    • Exception chemaxon.naming.document.annotate.AnnotationException

      class AnnotationException extends IOException implements Serializable
  • Package chemaxon.reaction

  • Package

    • Class

      class MarkushFeature extends Object implements Serializable
    • Class

      class MolSearchOptions extends SearchOptions implements Serializable
      • Serialized Fields

        • hitIncludesRNodes
          boolean hitIncludesRNodes
          If true, the result hit will contain R-nodes with dummy indexes
        • hitIndexType
          int hitIndexType
          In case of Markush search specifies the representation of the Markush structure on which the hit indexes are retrieved. (default MARKUSH_HIT_ORIGINAL)
        • ignoreChiralityForAtoms
          chemaxon.common.util.IntVector ignoreChiralityForAtoms
          Contains query atom numbers which should be ignored at the chirality check in case of exact stereo searching. It has a package visibility.
        • markushEnabled
          boolean markushEnabled
          Decides whether targets with Markush features should be treated as Markush libraries (true) or just "strange" molecules (false) (default value: false).
        • queryAbsoluteStereo
          boolean queryAbsoluteStereo
          If true, chiral centers in the query molecules are regarded as absolute stereo, ignoring the chiral flag. If the molecule contains any enhanced stereo labels, this flag has no effect.
        • recursiveSMARTSMode
          boolean recursiveSMARTSMode
          true: at findAll searches only hits are retrieved where the first atom differs as well.
        • switchOffAllProtectsForTDF
          boolean switchOffAllProtectsForTDF
          If true, all protect features are switched of during generic tautomer creation
        • targetAbsoluteStereo
          boolean targetAbsoluteStereo
          If true, chiral centers in the target molecules are regarded as absolute stereo, ignoring the chiral flag. If the molecule contains any enhanced stereo labels, this flag has no effect.
        • tautomerEqualityMode
    • Exception

      class SearchException extends Exception implements Serializable
    • Class

      class SearchOptions extends Object implements Serializable
      • Serialized Fields

        • attachedDataMatch
          int attachedDataMatch
          Specifies attached data match type Default is SearchConstants.ATTACHED_DATA_MATCH_IGNORE
        • attachedDataPrefixes
          String attachedDataPrefixes
          Data sgroup name prefixes that will be used for comparison When null, all data sgroups will be used.
        • bridgingRAllowed
          boolean bridgingRAllowed
          True: different undefined R-atoms can match the same group of atoms. Default value: false.
        • changedUserComparator
          boolean changedUserComparator
          true if user-defined comparators has changed
        • chargeMatching
          int chargeMatching
          Specifies the charge searching behaviour. Default is CHARGE_MATCHING_DEFAULT (charged query matches only charged target, noncharged query matches all)
        • checkSpHyb
          boolean checkSpHyb
          If we need to check the sp-hybridization state of the atoms. If used together with vagueBond-4 (SearchConstants.VAGUE_BOND_LEVEL4) option then the bond types are ignored, but the sp hybridization state is still calculated considering the bond types. Benzene matches cyclohexene with double bonds outside (O=C1C(=O)C(=O)C(=O)C(=O)C(=O)1), both planar but different bonds.
        • chemTermsFilterOption
        • completeHG
          boolean completeHG
          Specifies if only complete structures should match on target homology groups.
        • copolymerMatching
          boolean copolymerMatching
          True: Polymers in copolymers can only be matched by copolymers. (default: false)
        • dirty
          boolean dirty
          This flag is set to true whenever any of the options change. It can be used by Search objects to check whether options changed since the previous initialization. (They set the dirty flag to false during their own initialization.)
        • doubleBondStereoMatchingMode
          int doubleBondStereoMatchingMode
          Defines the double bond stereo matching mode. Default is DBS_MARKED.
          JChem 2.2
          See Also:
        • endGroupMatching
          boolean endGroupMatching
          True: polymer endgroups must match (default: false)
        • exactBondMatching
          boolean exactBondMatching
          true, if query bonds match only the same query bonds
        • exactQueryAtomMatching
          boolean exactQueryAtomMatching
          If true, query information (eg atom list, any atom, number of hydrogens, aromaticity, etc) in atoms will not be evaluated, but rather exact matching of these information is required. It is useful for searching in query databases. Default is false.
          JChem 2.2
        • exactSpecialAtomMatching
          String exactSpecialAtomMatching
        • exhaustiveModeLimit
          int exhaustiveModeLimit
          Upon reaching this number of steps, the search switches to exhaustive mode from fast mode.
        • hCountMatching
          int hCountMatching
          Defines the interpretation of H count in the query. Default is HCOUNT_MATCHING_AUTO.
        • hitOrdering
          int hitOrdering
          Specifies hit ordering, currently used in ordering undefined R-atom group matchings Default is SearchConstants.HIT_ORDERING_NONE.
        • homologyBroadTranslation
          HomologyTranslationOption homologyBroadTranslation
          If pseudo atoms with homology names are present in the target, they should be handled as homology group not as pseudo atoms. false - handle as pseudo atoms.
        • homologyNarrowTranslation
          HomologyTranslationOption homologyNarrowTranslation
          If pseudo atoms with homology names are present in the query, they should be handled as homology group not as pseudo atoms. false - handle as pseudo atoms.
        • ignoreAxialStereo
          boolean ignoreAxialStereo
          See Also:
        • ignoreCumuleneCisTransStereo
          boolean ignoreCumuleneCisTransStereo
          See Also:
        • ignoreDoubleBondStereo
          boolean ignoreDoubleBondStereo
          See Also:
        • ignoreSynAntiStereo
          boolean ignoreSynAntiStereo
          See Also:
        • ignoreTetrahedralStereo
          boolean ignoreTetrahedralStereo
          See Also:
        • implicitHMatching
          int implicitHMatching
          Specifies match between explicit and implicit hydrogens. Default is IMPLICIT_H_MATCHING_DEFAULT (matching depends on the circumstances of search)
        • isotopeMatching
          int isotopeMatching
          Specifies the isotope searching behaviour. Default is ISOTOPE_MATCHING_DEFAULT (isotope query matches only isotope target, nonisotope query matches all)
        • keepQueryOrder
          boolean keepQueryOrder
          True: instructs search to rearrange query atoms for better search performance.
        • markushAromHandling
          MarkushAromaticityHandlingOption markushAromHandling
          Specifies handling Markush aromatization information (ambiguous aromatic rings) during Markush search. Currently, the default is MarkushAromaticityHandlingOption.ALL_MATCH_AMBIG: consider Markush aromatization during Markush search, but do not check the hit afterwards.
        • mixSgroupMatching
          boolean mixSgroupMatching
          True: consider COM, MIX and FOR sgroups during search (default value: true).
        • orderSensitiveSearch
          boolean orderSensitiveSearch
          Specifies whether the same set of target atoms found in a different order should be considered as a different hit.
        • phaseShift
          boolean phaseShift
          True: the phase-shifted polymers are matching on each other. (default: true)
        • polymerMatching
          boolean polymerMatching
          True: consider polymer sgroups during search (default value: true).
        • radicalMatching
          int radicalMatching
          Specifies the radical searching behaviour. Default is RADICAL_MATCHING_DEFAULT (radical query matches only radical target, nonradical query matches all)
        • reactionUnpairedMapMatching
          boolean reactionUnpairedMapMatching
          True: in reaction search unpaired (orphan and widow) atom maps can match any atom map (default value: true).
        • rLigandEqualityCheck
          boolean rLigandEqualityCheck
          True: undefined R-atoms with the same R-group ID should match the same structure. Default value: true.
        • searchType
          int searchType
          Search type: global mode of search.
        • ssrOption
          SetOfSmallestRingsOption ssrOption
          Which set of smallest rings to use for property calculations.
        • stereoModel
          int stereoModel
          Specifies the used stereo model.
        • stereoSearchType
          int stereoSearchType
          The way stereo information is considered in searching. Default is SearchConstants.STEREO_SPECIFIC.
          See Also:
        • targetHomologyMatchingMode
          TargetHomologyMatchingMode targetHomologyMatchingMode
        • tautomerSearch
          boolean tautomerSearch
          True: tautomer searching is enabled (default value: false).
        • tautomerSearchOption
          int tautomerSearchOption
          Specifies the tautomer searching behavior. Default: non-tautomer search, except: duplicate search in tautomer duplicate table
        • tautomerSearchOptionLeftDefault
          boolean tautomerSearchOptionLeftDefault
          Shows that tautomerSearch value has not been set.
        • throwExceptionOnTimeout
          boolean throwExceptionOnTimeout
          If the search should throw exception upon timeout.
        • timeoutLimitMilliseconds
          int timeoutLimitMilliseconds
          The search on a single target timeouts reaching this number of milliseconds.
        • transformMonomer
          boolean transformMonomer
          True: monomers are transformed to structural repeating units. (default: true)
        • undefinedRAtom
          int undefinedRAtom
          Specifies match of undefined r-atom in query Default is SearchConstants.UNDEF_R_MATCHING_GROUP.
        • undefinedRAtomUserDefined
          boolean undefinedRAtomUserDefined
          True if undefinedRAtom option is user defined, false if automatically set by RGroupDecomposition depending on whether the original query has undefined R-atoms. Used in RGroupDecomposition only.
        • userComparators
          ArrayList<MolComparator> userComparators
          User defined MolComparators
        • vagueBondLevel
          int vagueBondLevel
          Option for less strict evaluation of query bonds (e.g. ambiguious aromaticity). Default value is SearchConstants.VAGUE_BOND_LEVEL_HALF
        • valenceMatching
          boolean valenceMatching
          True: valence is checked during search (default value: true).
        • verbose
          boolean verbose
          For debugging purposes. Public, because it does not count for the dirty flag.
    • Exception

      class SearchTimeoutException extends SearchException implements Serializable
    • Exception

      class UnsupportedQueryException extends IllegalArgumentException implements Serializable
  • Package

    • Class

      class ChemTermsFilterOption extends Object implements Serializable
      • Serialized Fields

        • chemTermsFilter
          String chemTermsFilter
        • chemTermsFilterConfig
          String chemTermsFilterConfig
        • ignoreCTExceptions
          boolean ignoreCTExceptions
  • Package chemaxon.standardizer.advancedactions

  • Package chemaxon.struc

  • Package

  • Package chemaxon.struc.prop

  • Package chemaxon.struc.sgroup

  • Package chemaxon.util

    • Exception chemaxon.util.ArgumentException

      class ArgumentException extends Exception implements Serializable
    • Exception chemaxon.util.CmdLine.CmdLineException

      class CmdLineException extends RuntimeException implements Serializable
    • Class chemaxon.util.SearchAttributes

      class SearchAttributes extends chemaxon.jep.util.SearchAttributes implements Serializable
  • Package com.chemaxon.calculations.gui

    • Class com.chemaxon.calculations.gui.MChart

      class MChart extends chemaxon.marvin.util.MarvinModule implements Serializable
      • Serialized Fields

        • chart
          com.objectplanet.chart.LineChart chart
        • colors
          Color[] colors
        • legendMols
          Molecule[] legendMols
        • legendTexts
          String[] legendTexts
        • precision
          int precision
  • Package

  • Package com.chemaxon.calculations.util

    • Exception com.chemaxon.calculations.util.CmdlineContext.ExitWithNonZeroStatus

      class ExitWithNonZeroStatus extends RuntimeException implements Serializable
    • Exception com.chemaxon.calculations.util.CmdlineContext.ExitWithZeroStatus

      class ExitWithZeroStatus extends RuntimeException implements Serializable
  • Package com.chemaxon.clustering.framework

    • Class com.chemaxon.clustering.framework.RemoveSidechainsMolwalk

      class RemoveSidechainsMolwalk extends Object implements Serializable
    • Class com.chemaxon.clustering.framework.RemoveSidechainsSc

      class RemoveSidechainsSc extends Object implements Serializable
      • Serialized Fields

        • keepUnsaturatedConnections
          boolean keepUnsaturatedConnections
    • Class com.chemaxon.clustering.framework.SimpleFrameworkAssociation

      class SimpleFrameworkAssociation extends Object implements Serializable
      • Serialized Fields

        • indexToFramework
          List<T extends Object> indexToFramework
  • Package com.chemaxon.descriptors.alignment

  • Package com.chemaxon.descriptors.common

  • Package com.chemaxon.descriptors.fingerprints.cfp

    • Class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters

      class CfpParameters extends Object implements Serializable
      • Serialized Fields

        • bitsPerPattern
          int bitsPerPattern
          Bits set for each pattern.
        • bondCount
          int bondCount
          Max pattern length considered (bond count).
        • length
          int length
          Fingerprint length (bit count).
        • rings
          boolean rings
          Consider rings in fingerprint generation.
  • Package com.chemaxon.descriptors.fingerprints.ecfp

    • Class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters

      class EcfpParameters extends Object implements Serializable
      • Serialized Fields

        • atomTypizer
          EcfpAtomTypizers atomTypizer
          Atom typizer to use.
        • diameter
          int diameter
          Diameter parameter.
        • identifierConfigurationXml
<String> identifierConfigurationXml
          Identifier configuration for custom XML mode.
        • length
          int length
          Fingerprint length (bit count).
    • Class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpParameters

      class ThreadLocalizedEcfpParameters extends Object implements Serializable
  • Package com.chemaxon.descriptors.fingerprints.maccs

    • Class com.chemaxon.descriptors.fingerprints.maccs.GenerateMaccsFp

      class GenerateMaccsFp extends Object implements Serializable
      • Serialized Fields

        • bit1
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit1
        • bit100
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit100
        • bit101
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit101
        • bit102
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit102
        • bit104
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit104
        • bit105
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit105
        • bit106
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit106
        • bit107
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit107
        • bit108
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit108
        • bit109
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit109
        • bit11
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit11
        • bit110
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit110
        • bit111
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit111
        • bit112
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit112
        • bit113
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit113
        • bit114
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit114
        • bit115
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit115
        • bit116
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit116
        • bit117
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit117
        • bit118
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit118
        • bit119
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit119
        • bit120
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit120
        • bit121
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit121
        • bit122
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit122
        • bit123
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit123
        • bit124
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit124
        • bit126
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit126
        • bit127
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit127
        • bit128
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit128
        • bit129
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit129
        • bit13
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit13
        • bit131
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit131
        • bit132
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit132
        • bit133
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit133
        • bit135
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit135
        • bit136
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit136
        • bit138
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit138
        • bit139
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit139
        • bit14
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit14
        • bit140
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit140
        • bit141
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit141
        • bit142
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit142
        • bit144
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit144
        • bit145
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit145
        • bit147
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit147
        • bit148
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit148
        • bit149
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit149
        • bit15
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit15
        • bit150
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit150
        • bit151
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit151
        • bit152
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit152
        • bit154
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit154
        • bit155
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit155
        • bit156
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit156
        • bit157
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit157
        • bit158
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit158
        • bit16
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit16
        • bit162
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit162
        • bit163
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit163
        • bit165
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit165
        • bit17
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit17
        • bit19
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit19
        • bit2
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit2
        • bit21
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit21
        • bit22
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit22
        • bit23
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit23
        • bit24
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit24
        • bit25
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit25
        • bit26
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit26
        • bit28
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit28
        • bit30
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit30
        • bit31
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit31
        • bit32
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit32
        • bit33
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit33
        • bit34
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit34
        • bit36
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit36
        • bit37
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit37
        • bit38
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit38
        • bit39
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit39
        • bit40
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit40
        • bit41
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit41
        • bit43
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit43
        • bit44
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit44
        • bit45
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit45
        • bit47
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit47
        • bit48
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit48
        • bit49
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit49
        • bit50
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit50
        • bit51
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit51
        • bit52
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit52
        • bit53
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit53
        • bit54
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit54
        • bit55
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit55
        • bit56
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit56
        • bit57
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit57
        • bit58
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit58
        • bit59
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit59
        • bit60
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit60
        • bit61
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit61
        • bit62
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit62
        • bit63
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit63
        • bit64
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit64
        • bit65
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit65
        • bit66
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit66
        • bit67
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit67
        • bit68
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit68
        • bit69
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit69
        • bit70
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit70
        • bit71
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit71
        • bit72
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit72
        • bit73
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit73
        • bit74
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit74
        • bit75
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit75
        • bit76
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit76
        • bit77
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit77
        • bit78
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit78
        • bit79
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit79
        • bit8
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit8
        • bit80
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit80
        • bit81
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit81
        • bit82
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit82
        • bit83
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit83
        • bit84
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit84
        • bit85
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit85
        • bit86
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit86
        • bit87
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit87
        • bit89
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit89
        • bit90
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit90
        • bit91
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit91
        • bit92
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit92
        • bit93
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit93
        • bit94
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit94
        • bit95
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit95
        • bit96
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit96
        • bit97
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit97
        • bit98
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit98
        • bit99
          com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit99
    • Class com.chemaxon.descriptors.fingerprints.maccs.GsSearch

      class GsSearch extends Object implements Serializable
      • Serialized Fields

        • log
          org.apache.commons.logging.Log log
        • queries
          Molecule[] queries
        • sma
          String sma
    • Class com.chemaxon.descriptors.fingerprints.maccs.MaccsParameters

      class MaccsParameters extends Object implements Serializable
    • Class com.chemaxon.descriptors.fingerprints.maccs.RingAtomBs

      class RingAtomBs extends BitSet implements Serializable
    • Class com.chemaxon.descriptors.fingerprints.maccs.RingBondBs

      class RingBondBs extends BitSet implements Serializable
  • Package com.chemaxon.descriptors.fingerprints.pf2d

    • Class com.chemaxon.descriptors.fingerprints.pf2d.PfComparatorImpl

      class PfComparatorImpl extends Object implements Serializable
    • Class com.chemaxon.descriptors.fingerprints.pf2d.PfParameters

      class PfParameters extends Object implements Serializable
      • Serialized Fields

        • xmlConfig
<String> xmlConfig
          XML configuration string.
    • Class com.chemaxon.descriptors.fingerprints.pf2d.PharmacophoreFPImpl

      class PharmacophoreFPImpl extends com.chemaxon.descriptors.common.realvector.FloatVectorDescriptorImpl implements Serializable
    • Class com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfParameters

      class ThreadLocalizedPfParameters extends Object implements Serializable
      • Serialized Fields

        • xmlConfig
<String> xmlConfig
  • Package com.chemaxon.descriptors.metrics

  • Package com.chemaxon.descriptors.vectors.binary

  • Package com.chemaxon.descriptors.vectors.floats

  • Package

    • Class

      class AllAbsentMasterMoleculeStorage extends Object implements Serializable
      • Serialized Fields

        • size
          long size
    • Class

      class Builder extends Object implements Serializable
      • Serialized Fields

        • builtPages
          List<C extends Serializable> builtPages
        • currentPage
          List<E extends Serializable> currentPage
        • elementType
          Class<E extends Serializable> elementType
        • getFromPage
          com.chemaxon.descriptors.common.reflect.SerializableBiFunction<C extends Serializable,Integer,E extends Serializable> getFromPage
        • initialSkips
          long initialSkips
        • listToPage
          com.chemaxon.descriptors.common.reflect.SerializableFunction<List<E extends Serializable>,C extends Serializable> listToPage
        • pageSize
          int pageSize
        • totalAbsents
          long totalAbsents
        • totalSize
          long totalSize
    • Class

      class Storage extends Object implements Serializable
      • Serialized Fields

        • elementType
          Class<E extends Object> elementType
        • getFromPage
          com.chemaxon.descriptors.common.reflect.SerializableBiFunction<C extends Object,Integer,E extends Object> getFromPage
        • initialSkips
          long initialSkips
        • pages
          List<C extends Object> pages
        • pageSize
          int pageSize
        • totalAbsents
          long totalAbsents
        • totalSize
          long totalSize
    • Class

      class CompactStringStorage extends Object implements Serializable
      • Serialized Fields

        • absentCount
          long absentCount
        • pagesize
          int pagesize
        • size
          long size
        • skips
          long skips
        • starts
          int[][] starts
        • storage
          byte[][] storage
        • storedByteCount
          long storedByteCount
    • Class

      class Metadata extends Object implements Serializable
      • Serialized Fields

        • absentCount
          long absentCount
        • bytes
          long bytes
        • lastPageSize
          int lastPageSize
        • pageCount
          int pageCount
        • pageSize
          int pageSize
        • size
          long size
        • skips
          long skips
        • storeSizes
          int[] storeSizes
        • storeStart
          long storeStart
    • Class

      class MasterMoleculeStorageImpl extends Object implements Serializable
      • Serialized Fields

        • importOptsOrNull
          String importOptsOrNull
        • sources
  • Package

    • Exception

      class TransformationException extends Exception implements Serializable