Serialized Form

  • Package chemaxon.calculations

    • Exception chemaxon.calculations.CalculationException

      class CalculationException extends RuntimeException implements Serializable
      serialVersionUID:
      1L
  • 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
      serialVersionUID:
      1L
  • Package chemaxon.clustering

    • Class chemaxon.clustering.ChemicalSpace

      class ChemicalSpace extends Vector implements Serializable
      • Serialized Fields

        • dimensions
          int dimensions
        • fpsize
          int fpsize
        • weights
          float[] weights
    • Exception chemaxon.clustering.ClusteringException

      class ClusteringException extends Exception implements Serializable
    • Exception chemaxon.clustering.InvalidLicenseKeyException

      class InvalidLicenseKeyException extends Exception implements Serializable
  • Package chemaxon.clustering.libmcs

  • Package chemaxon.common.util

    • Class chemaxon.common.util.ByteVector

      class ByteVector extends Object implements Serializable
      serialVersionUID:
      -1393815508326465236L
      • Serialized Fields

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

      class DoubleVector extends Object implements Serializable
      serialVersionUID:
      -5138497375635267024L
      • Serialized Fields

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

      class FloatVector extends Object implements Serializable
      serialVersionUID:
      -2327634131748729635L
      • Serialized Fields

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

      class GeomCalcException extends RuntimeException implements Serializable
      serialVersionUID:
      -1705490613297709773L
    • Exception chemaxon.common.util.GeomCalc.Queue.Overflow

      class Overflow extends Exception implements Serializable
      serialVersionUID:
      -6957894135268794743L
    • Exception chemaxon.common.util.GeomCalc.Queue.Underflow

      class Underflow extends Exception implements Serializable
      serialVersionUID:
      -1972826041963082169L
    • Class chemaxon.common.util.IntMap

      class IntMap extends HashMap<K extends Object,Integer> implements Serializable
      serialVersionUID:
      4318465509620546463L
    • Record Class chemaxon.common.util.IntPair

      class IntPair extends Record implements Serializable
      serialVersionUID:
      1961353781713733629L
      • Serialized Fields

        • left
          int left
          Deprecated, for removal: This API element is subject to removal in a future version.
        • right
          int right
          Deprecated, for removal: This API element is subject to removal in a future version.
    • Class chemaxon.common.util.IntVector

      class IntVector extends Object implements Serializable
      serialVersionUID:
      -9011852065319440166L
      • Serialized Fields

        • data
          int[] data
        • size
          int size
    • Exception chemaxon.common.util.LazyCalculationAlreadyFailedException

      class LazyCalculationAlreadyFailedException extends RuntimeException implements Serializable
    • Class chemaxon.common.util.LongVector

      class LongVector extends Object implements Serializable
      serialVersionUID:
      8437448887389765952L
      • Serialized Fields

        • data
          long[] data
        • size
          int size
    • Exception chemaxon.common.util.ResourceCleaner.ResourceClosingException

      class ResourceClosingException extends RuntimeException implements Serializable
    • Exception chemaxon.common.util.ServiceNotFoundException

      class ServiceNotFoundException extends RuntimeException implements Serializable
      • Serialized Fields

        • serviceType
          Class<?> serviceType
    • Class chemaxon.common.util.ShortVector

      class ShortVector extends Object implements Serializable
      serialVersionUID:
      8407562362886825374L
      • 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
      serialVersionUID:
      568843891825099500L
      • 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
      serialVersionUID:
      -8372436801118701137L
      • 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.formats.documents.jchemoffice

    • Exception chemaxon.formats.documents.jchemoffice.BatchProcessingException

      class BatchProcessingException extends IOException implements Serializable
      serialVersionUID:
      1L
    • Exception chemaxon.formats.documents.jchemoffice.InvalidSizeScaleArgumentException

      class InvalidSizeScaleArgumentException extends chemaxon.util.ArgumentException implements Serializable
      serialVersionUID:
      1L
  • Package chemaxon.jchem.db

    • Exception chemaxon.jchem.db.DatabaseSearchException

      class DatabaseSearchException extends Exception implements Serializable
    • Exception chemaxon.jchem.db.MaxSearchFrequencyExceededException

      class MaxSearchFrequencyExceededException extends DatabaseSearchException implements Serializable
    • Exception chemaxon.jchem.db.RecalculationException

      class RecalculationException extends Exception implements Serializable
      serialVersionUID:
      -2767058042924323545L
    • Exception chemaxon.jchem.db.TransferException

      class TransferException extends Exception implements Serializable
      serialVersionUID:
      -5241498055624956036L
    • Class chemaxon.jchem.db.UpdateHandler.RowData

      class RowData extends Object implements Serializable
      serialVersionUID:
      -4040824446004135801L
      • Serialized Fields

        • chemTermColValues
          Map<String,Object> chemTermColValues
        • descriptorData
          byte[][] descriptorData
        • fingerprint
          int[] fingerprint
        • flags
          String flags
        • formula
          String formula
        • hashCode
          int hashCode
        • markushData
          byte[] markushData
        • molecule
          Molecule molecule
        • molName
          String molName
        • molString
          byte[] molString
        • molWeight
          Double molWeight
        • noRingInfoInFP
          boolean noRingInfoInFP
        • reactionMappingIncomplete
          boolean reactionMappingIncomplete
        • screenDescriptor
          byte[] screenDescriptor
        • smiles
          String smiles
        • sortableFormula
          String sortableFormula
        • tautomer
          Molecule tautomer
        • tautomerFragmentHashCode
          int[] tautomerFragmentHashCode
        • tautomerHashCode
          int tautomerHashCode
    • Exception chemaxon.jchem.db.UpdateHandlerException

      class UpdateHandlerException extends Exception implements Serializable
      serialVersionUID:
      -8755169336283449997L
    • Class chemaxon.jchem.db.UpdateHandlerMetaData

      class UpdateHandlerMetaData extends Object implements Serializable
      serialVersionUID:
      -6512295793385774884L
      • Serialized Fields

        • chemTermColumns
          String[] chemTermColumns
        • chemTermForColumn
          Map<String,String> chemTermForColumn
        • collectionType
          chemaxon.jchem.base.storage.StructureCollectionType collectionType
        • compressedStructureFieldSupported
          boolean compressedStructureFieldSupported
        • descriptorSettings
          Map<String,String> descriptorSettings
        • descriptorTypes
          Map<String,String> descriptorTypes
        • duplicateFilteringOption
          boolean duplicateFilteringOption
        • insertDescriptorNames
          List<String> insertDescriptorNames
        • numberOfCombinedFPColumns
          int numberOfCombinedFPColumns
        • numberOfEdges
          int numberOfEdges
        • numberOfOnes
          int numberOfOnes
        • numberOfStructuralFPColumns
          int numberOfStructuralFPColumns
        • standardizerConfig
          String standardizerConfig
        • structuralKeys
          String structuralKeys
        • tableType
          int tableType
        • tautomerDuplicateFilteringEnabled
          boolean tautomerDuplicateFilteringEnabled
        • tautomerEqualityMode
          chemaxon.sss.search.options.TautomerEqualityMode tautomerEqualityMode
        • updateDescriptorNames
          List<String> updateDescriptorNames
    • Exception chemaxon.jchem.db.UpdateHandlerRowDataException

      class UpdateHandlerRowDataException extends UpdateHandlerException implements Serializable
      serialVersionUID:
      -7274357064259684370L
    • Class chemaxon.jchem.db.Updater.UpdateInfo

      class UpdateInfo extends Object implements Serializable
      serialVersionUID:
      4160146885445230514L
      • Serialized Fields

        • additionalInformation
          String[] additionalInformation
          Additional information for the entities in same order, if needed.
          Since:
          JChem 6.0
        • entityList
          String[] entityList
          The names of entities (e.g. table names) to be updated, or null.
        • isOperationRequired
          boolean isOperationRequired
          Indicates whether the operation is required or not.
          Since:
          JChem 5.3
        • isProgressMonitoringSupported
          boolean isProgressMonitoringSupported
          Indicates whether update process supports progress monitoring.
          Since:
          JChem 5.1.2
        • isRegeneration
          boolean isRegeneration
          Deprecated, for removal: This API element is subject to removal in a future version.
          Indicates if the update process is the regeneration of all tables. Since this can be a lengthy process, progress monitoring may be needed. In this case the table names in Updater.UpdateInfo.entityList can be used directly for UpdateHandler.recalculateTable(chemaxon.util.ConnectionHandler, String, boolean, String, java.util.Map, Boolean, chemaxon.jchem.file.ProgressWriter)
        • isStructuralChange
          boolean isStructuralChange
          Indicates whether the operation is required or not.
          Since:
          JChem 5.8
        • message
          String message
          Massage describing what update is necessary and why.
        • processingMessage
          String processingMessage
          A message that can be displayed during the update, e.g. "Recalculating tables"
        • regenerationType
          int regenerationType
          Indicates the regeneration type.
          Since:
          JChem 5.2.4
  • Package chemaxon.jchem.db.cache

    • Class chemaxon.jchem.db.cache.CachePool

      class CachePool extends Object implements Serializable
      serialVersionUID:
      1L
      • Serialized Fields

        • cacheHash
          Hashtable<String,chemaxon.jchem.db.cache.JChemCache> cacheHash
        • cacheRemovalMethod
          chemaxon.jchem.db.cache.CacheRemovalMethod cacheRemovalMethod
        • expirationTime
          double expirationTime
        • maxCacheMemory
          long maxCacheMemory
        • maxCacheMemoryCalculated
          boolean maxCacheMemoryCalculated
        • maxCacheSizeMB
          int maxCacheSizeMB
        • minFreeMemMB
          int minFreeMemMB
    • Exception chemaxon.jchem.db.cache.CacheRegistrationException

      class CacheRegistrationException extends RuntimeException implements Serializable
      serialVersionUID:
      1L
      • Serialized Fields

        • reason
          chemaxon.jchem.db.cache.CacheRegistrationException.Reason reason
  • Package chemaxon.jep

    • Class chemaxon.jep.ChemFunction

      class ChemFunction extends chemaxon.nfunk.jep.function.PostfixMathCommand implements Serializable
      serialVersionUID:
      -3446599636099344973L
      • Serialized Fields

        • context
          chemaxon.jep.function.base.FunctionContext context
          Deprecated, for removal: This API element is subject to removal in a future version.
    • Class chemaxon.jep.ChemJEP

      class ChemJEP extends Object implements Serializable
      • Serialized Fields

        • allowUndeclared
          boolean allowUndeclared
          Deprecated, for removal: This API element is subject to removal in a future version.
          Allow undeclared variables option. Only used if ChemJEP.legacyMode is true.
        • context
          C extends ChemContext context
          Deprecated, for removal: This API element is subject to removal in a future version.
          The evaluation context object.
        • contextClass
          Class<? extends C extends ChemContext> contextClass
          The type of the context, never null.
        • errorList
          Vector<Throwable> errorList
          Deprecated, for removal: This API element is subject to removal in a future version.
          This class no longer collects exceptions but throws them when they are encountered. The list this method uses is filled but otherwise ignored.
          The error list of this parser.
        • evaluator
          chemaxon.jep.ImmutableEvaluator evaluator
          The evaluator that created this ChemJEP object, never null.
        • expression
          String expression
          The input expression.
        • funTab
          chemaxon.nfunk.jep.FunctionTable funTab
          Deprecated, for removal: This API element is subject to removal in a future version.
          Function Table. Only used if ChemJEP.legacyMode is true, otherwise it is null.
        • implicitMul
          boolean implicitMul
          Deprecated, for removal: This API element is subject to removal in a future version.
          Implicit multiplication option. Only used if ChemJEP.legacyMode is true.
        • legacyMode
          boolean legacyMode
          Until JUL 2025, ChemJEP has two modes: the default mode, which is fast but cannot support some deprecated legacy features, and the slower legacy mode. The package-private constructor creates a ChemJEP in the default mode and switches to legacy mode when necessary, the two (deprecated) public constructors start in legacy mode.

          There is no transition from the legacy mode back to the default mode.

          Fields that are handled differently in the two modes:

          • ChemJEP.symTab and ChemJEP.funTab are null and ignored in the default mode. They are filled in ChemJEP.switchToLegacyMode() and after that, they are used instead of the function table and constant table of ChemJEP.evaluator.
          • ChemJEP.traverse, ChemJEP.allowUndeclared and ChemJEP.implicitMul have a default value (evaluator.isVerbose(), true and false, respectively) and the default mode assume their value to remain unchanged, so we must switch to legacy mode when they are changed.
        • symTab
          chemaxon.nfunk.jep.SymbolTable symTab
          Deprecated, for removal: This API element is subject to removal in a future version.
          Symbol Table. Only used if ChemJEP.legacyMode is true, otherwise it is null.
        • traverse
          boolean traverse
          Traverse option. Only used if ChemJEP.legacyMode is true.
    • Exception chemaxon.jep.ConditionException

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

      class Evaluator extends Object implements Serializable
      • Serialized Fields

        • config
          chemaxon.jep.EvaluatorConfiguration config
          Deprecated, for removal: This API element is subject to removal in a future version.
        • immutable
          chemaxon.jep.ImmutableEvaluator immutable
          The base function table.
        • servicesConfigurationPath
          String servicesConfigurationPath
          services configuration path
          Since:
          5.10
    • Class chemaxon.jep.ImmutableEvaluator

      class ImmutableEvaluator extends Object implements Serializable
    • Exception chemaxon.jep.JepException

      class JepException extends Exception implements Serializable
  • Package chemaxon.jep.context

  • Package chemaxon.license

  • Package chemaxon.marvin

    • Class chemaxon.marvin.SketchApplication

      class SketchApplication extends chemaxon.marvin.AbstractApplication implements Serializable
      serialVersionUID:
      1L
      • Serialized Fields

    • Class chemaxon.marvin.ViewApplication

      class ViewApplication extends chemaxon.marvin.AbstractApplication implements Serializable
      serialVersionUID:
      1L
      • 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
      serialVersionUID:
      1L
    • Class chemaxon.marvin.alignment.ShapeData

      class ShapeData extends Object implements Serializable
      serialVersionUID:
      1L
      • 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 chemaxon.marvin.io

  • Package chemaxon.marvin.modules.datatransfer

    • Class chemaxon.marvin.modules.datatransfer.CopyAsDialog

      class CopyAsDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable
      serialVersionUID:
      -4564761584830399025L
  • Package chemaxon.marvin.plugin

  • Package chemaxon.marvin.plugin.concurrent

  • Package chemaxon.marvin.plugin.gui

  • Package chemaxon.marvin.services

  • 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
      serialVersionUID:
      2463379690025911142L
      • 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 chemaxon.marvin.space

    • Class chemaxon.marvin.space.EventQueue

      class EventQueue extends Vector<Object> implements Serializable
    • Class chemaxon.marvin.space.GraphicScene

      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
          chemaxon.marvin.space.MSpaceEventHandler eventHandler
        • gl
          com.jogamp.opengl.GL2 gl
        • glAutoDrawable
          com.jogamp.opengl.GLAutoDrawable glAutoDrawable
        • globalDrawProperties
          Properties globalDrawProperties
        • glu
          com.jogamp.opengl.glu.GLU 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
          chemaxon.marvin.space.gui.JMSpaceProgressBar progressBar
          Deprecated, for removal: This API element is subject to removal in a future version.
        • renderTargets
          chemaxon.marvin.space.gl.shader.RenderTargets 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
      serialVersionUID:
      7380116746554005158L
    • Class chemaxon.marvin.util.MarvinModule

      class MarvinModule extends Object implements Serializable
      serialVersionUID:
      2763330874643316763L
    • Class chemaxon.marvin.util.MarvinOLEFrame

      class MarvinOLEFrame extends JFrame implements Serializable
      serialVersionUID:
      7801720334170069726L
    • Class chemaxon.marvin.util.MarvinOLEPanel

      class MarvinOLEPanel extends JPanel implements Serializable
      serialVersionUID:
      -6975415959061110410L
      • 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
      serialVersionUID:
      -1600625160321014724L
  • 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
      serialVersionUID:
      3979819797881974530L
      • 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
      serialVersionUID:
      802342314015862847L
      • 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 org.apache.tika.parser.microsoft.OfficeParser 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 chemaxon.sss.search

    • Class chemaxon.sss.search.JChemSearchOptions

      class JChemSearchOptions extends SearchOptions implements Serializable
      serialVersionUID:
      -6025435983286725061L
      • Serialized Fields

        • absoluteStereo
          int absoluteStereo
        • cacheRegistrationNeeded
          boolean cacheRegistrationNeeded
          Can be set to false in case of readonly databases and jcsearch. Only for internal use!
        • descriptorConfig
          String descriptorConfig
          configuration for descriptor dissim. calculations
        • descriptorName
          String descriptorName
          the identifier of stored descriptor used for dissim. calculations, null means pure fingerprint similarity is performed
        • dissimilarityMetric
          String dissimilarityMetric
          Dissimilarity metric name, or null for default.
        • dissimilarityMetricParameters
          String dissimilarityMetricParameters
          Dissimilarity metric parameters.
        • dissimilarityThreshold
          float dissimilarityThreshold
        • dissimilarityThresholdExcluded
          boolean dissimilarityThresholdExcluded
        • filterQuery
          String filterQuery
        • formulaSearchQuery
          String formulaSearchQuery
          Query of the formula search.
        • formulaSearchType
          int formulaSearchType
          Type of the formula search. See: chemaxon.sss.formula.FormulaSearch
        • haltOnError
          HaltOnErrorOption haltOnError
          Error handling of the search.
          See Also:
        • markushScreeningOptions
          Set<chemaxon.sss.search.options.MarkushScreeningType> markushScreeningOptions
          Set containing all enabled Markush screen methods
        • matchCountOptions
          MatchCountOptions matchCountOptions
        • maxResultCount
          int maxResultCount
        • optimizeQueries
          boolean optimizeQueries
          Shows whether the query should be enumerated to improve search
        • returnsNonHits
          boolean returnsNonHits
        • totalSearchTimeoutLimitMilliseconds
          int totalSearchTimeoutLimitMilliseconds
          The search on a database timeouts reaching this number of milliseconds.
    • Class chemaxon.sss.search.MarkushFeature

      class MarkushFeature extends Object implements Serializable
      serialVersionUID:
      8770437891053649928L
      • Serialized Fields

        • data
          int[] data
          Deprecated, for removal: This API element is subject to removal in a future version.
          Reference data to expanded object. Different for each type: R-group definition index: the index returned by RgMolecule.findRgroupIndex(int).
        • hashCode
          int hashCode
          Deprecated, for removal: This API element is subject to removal in a future version.
        • type
          int type
          Deprecated, for removal: This API element is subject to removal in a future version.
          Expansion type.
    • Class chemaxon.sss.search.MatchCountOptions

      class MatchCountOptions extends Object implements Serializable
      serialVersionUID:
      6422092438307828424L
      • Serialized Fields

        • matchCountHighLimit
          int matchCountHighLimit
        • matchCountHighLimitInclusive
          boolean matchCountHighLimitInclusive
        • matchCounthitLimit
          int matchCounthitLimit
        • matchCountIncludesZero
          boolean matchCountIncludesZero
        • matchCountLowLimit
          int matchCountLowLimit
        • matchCountLowLimitInclusive
          boolean matchCountLowLimitInclusive
        • matchCountRelation
          String matchCountRelation
        • mode
          int mode
    • Class chemaxon.sss.search.MolSearchOptions

      class MolSearchOptions extends SearchOptions implements Serializable
      serialVersionUID:
      -6364233804214700841L
      • 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
          chemaxon.sss.search.options.TautomerEqualityMode tautomerEqualityMode
          The way tautomer duplication is checked. Used only at duplicate, full and full fragment searches. Internal use only.
    • Exception chemaxon.sss.search.SearchException

      class SearchException extends Exception implements Serializable
      serialVersionUID:
      1698586463587833734L
    • Class chemaxon.sss.search.SearchOptions

      class SearchOptions extends Object implements Serializable
      serialVersionUID:
      -6845044337680993338L
      • 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.
          Since:
          5.1
        • chemTermsFilterOption
          chemaxon.sss.search.options.ChemTermsFilterOption chemTermsFilterOption
        • 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.
          Since:
          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 (e.g. atom list, any atom, number of hydrogens, aromaticity, etc.) in atoms will not be evaluated, but rather exact matching of this information is required. It is useful for searching in query databases. Default value is false.
          Since:
          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 behavior. Default is RADICAL_MATCHING_DEFAULT (radical query matches only radical target, non-radical 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 chemaxon.sss.search.SearchTimeoutException

      class SearchTimeoutException extends SearchException implements Serializable
      serialVersionUID:
      -78126823565453833L
    • Exception chemaxon.sss.search.UnsupportedQueryException

      class UnsupportedQueryException extends IllegalArgumentException implements Serializable
      serialVersionUID:
      6255906179820229430L
  • Package chemaxon.sss.search.options

    • Class chemaxon.sss.search.options.ChemTermsFilterOption

      class ChemTermsFilterOption extends Object implements Serializable
      serialVersionUID:
      8226348996476285704L
      • Serialized Fields

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

  • Package chemaxon.struc

  • Package chemaxon.struc.graphics

  • Package chemaxon.struc.prop

  • Package chemaxon.struc.sgroup

  • Package chemaxon.util

  • 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 com.chemaxon.calculations.io

  • Package com.chemaxon.clustering.framework

    • 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
      serialVersionUID:
      0L
      • 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
      serialVersionUID:
      0L
      • Serialized Fields

        • atomTypizer
          EcfpAtomTypizers atomTypizer
          Atom typizer to use.
        • diameter
          int diameter
          Diameter parameter.
        • identifierConfigurationXml
          com.google.common.base.Optional<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
      serialVersionUID:
      0L
  • Package com.chemaxon.descriptors.fingerprints.maccs

  • 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
      serialVersionUID:
      0L
      • Serialized Fields

        • xmlConfig
          com.google.common.base.Optional<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
      serialVersionUID:
      0L
      • Serialized Fields

        • xmlConfig
          com.google.common.base.Optional<String> xmlConfig
  • Package com.chemaxon.descriptors.metrics

  • Package com.chemaxon.descriptors.vectors.binary

  • Package com.chemaxon.descriptors.vectors.floats

  • Package com.chemaxon.overlap.io

    • Class com.chemaxon.overlap.io.AllAbsentMasterMoleculeStorage

      class AllAbsentMasterMoleculeStorage extends Object implements Serializable
      • Serialized Fields

        • size
          long size
          Deprecated, for removal: This API element is subject to removal in a future version.
    • Class com.chemaxon.overlap.io.ArraysBackedStorageTools.Builder

      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 com.chemaxon.overlap.io.ArraysBackedStorageTools.Storage

      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 com.chemaxon.overlap.io.CompactStringStorage

      class CompactStringStorage extends Object implements Serializable
      serialVersionUID:
      0L
      • Serialized Fields

        • absentCount
          long absentCount
          Deprecated, for removal: This API element is subject to removal in a future version.
        • pagesize
          int pagesize
          Deprecated, for removal: This API element is subject to removal in a future version.
        • size
          long size
          Deprecated, for removal: This API element is subject to removal in a future version.
        • skips
          long skips
          Deprecated, for removal: This API element is subject to removal in a future version.
        • starts
          int[][] starts
          Deprecated, for removal: This API element is subject to removal in a future version.
        • storage
          byte[][] storage
          Deprecated, for removal: This API element is subject to removal in a future version.
        • storedByteCount
          long storedByteCount
          Deprecated, for removal: This API element is subject to removal in a future version.
    • Class com.chemaxon.overlap.io.CompactStringStorage.Metadata

      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 com.chemaxon.overlap.io.MasterMoleculeStorageImpl

      class MasterMoleculeStorageImpl extends Object implements Serializable
      serialVersionUID:
      0L
      • Serialized Fields

        • importOptsOrNull
          String importOptsOrNull
          Deprecated, for removal: This API element is subject to removal in a future version.
        • sources
          com.chemaxon.overlap.io.CompactStringStorage sources
          Deprecated, for removal: This API element is subject to removal in a future version.
  • Package com.chemaxon.search.transformation

    • Exception com.chemaxon.search.transformation.TransformationException

      class TransformationException extends Exception implements Serializable