Serialized Form (Marvin API documentation (c) 1998-2024 Chemaxon Ltd.)

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.common.util
- Exception chemaxon.common.util.ArgumentException
  
  class ArgumentException extends Exception implements Serializable
  
  serialVersionUID:
  
  -8949782741678573705L
- 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
- 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
- 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
    
    errorKey
    
    String errorKey
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
- Exception chemaxon.descriptors.MDGeneratorException
  
  class MDGeneratorException extends Exception implements Serializable
- Exception chemaxon.descriptors.MDParametersException
  
  class MDParametersException extends RuntimeException implements Serializable
- Exception chemaxon.descriptors.SimilarityException
  
  class SimilarityException extends Exception implements Serializable
Package chemaxon.formats
- Exception chemaxon.formats.MolFormatException
  
  class MolFormatException extends IOException implements Serializable
  - Serialized Fields
    
    lineNumberInFile
    
    int lineNumberInFile
    
    lineNumberInRecord
    
    int lineNumberInRecord
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
  - Serialization Methods
    
    writeReplace
    
    private Object writeReplace() throws ObjectStreamException
    
    Throws:
    
    ObjectStreamException
- Exception chemaxon.jep.JepException
  
  class JepException extends Exception implements Serializable
Package chemaxon.jep.context
- Class chemaxon.jep.context.AtomContext
  
  class AtomContext extends MolContext implements Serializable
  - Serialized Fields
    
    atom
    
    int atom
    
    The input atom index.
- Class chemaxon.jep.context.MolContext
  
  class MolContext extends Object implements Serializable
  - Serialized Fields
    
    fingerprint
    
    int[] fingerprint
    
    Fingerprint of the input molecule.
    
    init
    
    boolean init
    
    reactionContext
    
    ReactionContext reactionContext
    
    reaction wrapped in this context
    
    supplier
    
    Supplier<Molecule> supplier
    
    The molecule supplier.
- Class chemaxon.jep.context.ReactionContext
  
  class ReactionContext extends Object implements Serializable
  
  serialVersionUID:
  
  -9162272287141708299L
  - Serialized Fields
    
    agentAtomMapping
    
    Map<Integer,MolAtom> agentAtomMapping
    
    mapping of AtomMap -> Agent Atom
    
    productAtomMapping
    
    Map<Integer,MolAtom> productAtomMapping
    
    mapping of AtomMap -> Product Atom
    
    reactantAtomMapping
    
    Map<Integer,MolAtom> reactantAtomMapping
    
    mapping of AtomMap -> Reactant Atom
    
    reaction
    
    RxnMolecule reaction
    
    reaction wrapped in this context
- Class chemaxon.jep.context.SearchContext
  
  class SearchContext extends MolContext implements Serializable
  - Serialized Fields
    
    hit
    
    int[] hit
    
    map
    
    int[] map
    
    query
    
    Molecule query
    
    queryFingerprint
    
    int[] queryFingerprint
    
    target
    
    Molecule target
    
    targetFingerprint
    
    int[] targetFingerprint
Package chemaxon.license
- Exception chemaxon.license.LicenseException
  
  class LicenseException extends RuntimeException implements Serializable
  - Serialized Fields
    
    product
    
    String product
- Exception chemaxon.license.LicenseProcessingException
  
  class LicenseProcessingException extends Exception implements Serializable
Package chemaxon.marvin
- Class chemaxon.marvin.SketchApplication
  
  class SketchApplication extends chemaxon.marvin.AbstractApplication implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    
    exitAction
    
    Action exitAction
    
    newWindowAction
    
    Action newWindowAction
    
    outSerName
    
    String outSerName
    
    sketchPane
    
    MSketchPane sketchPane
- 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 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 AlignmentException implements Serializable
Package chemaxon.marvin.beans
- Class chemaxon.marvin.beans.MarvinPane
  
  class MarvinPane extends JRootPane implements Serializable
  
  serialVersionUID:
  
  -9042549845769941129L
  - Serialized Fields
    
    actionListener
    
    chemaxon.marvin.beans.MarvinPane.MarvinActionListener actionListener
    
    molPanel
    
    chemaxon.marvin.common.swing.MolPanel molPanel
    
    Underlying panel.
    
    params
    
    String params
    
    Parameter string.
- Class chemaxon.marvin.beans.MolRenderer
  
  class MolRenderer extends JPanel implements Serializable
  
  serialVersionUID:
  
  7229361698115302929L
  - Serialized Fields
    
    printer
    
    MolPrinter printer
- Class chemaxon.marvin.beans.MSketch
  
  class MSketch extends Object implements Externalizable
  
  serialVersionUID:
  
  0L
  - Serialization Methods
    
    readExternal
    
    public void readExternal(ObjectInput in) throws IOException, ClassNotFoundException
    
    Restores the sketcher's state.
    
    Parameters:
    
    in - the stream to read data from in order to restore the object
    
    Throws:
    
    IOException - if I/O errors occur
    
    ClassNotFoundException - If the class for an object being restored cannot be found.
    
    writeExternal
    
    public void writeExternal(ObjectOutput out) throws IOException
    
    Saves the sketcher's state.
    
    Parameters:
    
    out - the stream to write the object to
    
    Throws:
    
    IOException - Includes any I/O exceptions that may occur
- Class chemaxon.marvin.beans.MSketchPane
  
  class MSketchPane extends MarvinPane implements Serializable
  
  serialVersionUID:
  
  602496692422927170L
  - Serialized Fields
    
    commonActions
    
    chemaxon.marvin.common.swing.action.CommonActions commonActions
- Class chemaxon.marvin.beans.MView
  
  class MView extends Object implements Externalizable
  
  serialVersionUID:
  
  0L
  - Serialization Methods
    
    readExternal
    
    public void readExternal(ObjectInput in) throws IOException, ClassNotFoundException
    
    Restores the viewer's state.
    
    Parameters:
    
    in - the stream to read data from in order to restore the object
    
    Throws:
    
    IOException - if I/O errors occur
    
    ClassNotFoundException - If the class for an object being restored cannot be found.
    
    writeExternal
    
    public void writeExternal(ObjectOutput out) throws IOException
    
    Saves the viewer's state.
    
    Parameters:
    
    out - the stream to write the object to
    
    Throws:
    
    IOException - Includes any I/O exceptions that may occur
- Class chemaxon.marvin.beans.MViewEditor
  
  class MViewEditor extends AbstractCellEditor implements Serializable
  
  serialVersionUID:
  
  1549621132660875966L
  - Serialized Fields
    
    editorComponent
    
    MViewPane editorComponent
- Class chemaxon.marvin.beans.MViewPane
  
  class MViewPane extends MarvinPane implements Serializable
  
  serialVersionUID:
  
  -4430811090653077262L
  - Serialized Fields
    
    delayedRepainter
    
    chemaxon.marvin.beans.MViewPane.DelayedRepainter delayedRepainter
    
    preferredSizeSet
    
    boolean preferredSizeSet
    
    tableSupport
    
    TableSupport tableSupport
- Class chemaxon.marvin.beans.MViewRenderer
  
  class MViewRenderer extends MViewPane implements Serializable
  
  serialVersionUID:
  
  5566509759455312369L
Package chemaxon.marvin.io
- Class chemaxon.marvin.io.Encoding
  
  class Encoding extends Object implements Externalizable
  - Serialization Methods
    
    readExternal
    
    public void readExternal(ObjectInput in) throws IOException
    
    Restores object state. For internal use only!
    
    Parameters:
    
    in - the stream to read data from in order to restore the object
    
    Throws:
    
    IOException - if I/O errors occur
    
    writeExternal
    
    public void writeExternal(ObjectOutput out) throws IOException
    
    Saves object state.
    
    Parameters:
    
    out - the stream to write the object to
    
    Throws:
    
    IOException - Includes any I/O exceptions that may occur
- Exception chemaxon.marvin.io.MolExportException
  
  class MolExportException extends IOException implements Serializable
  - Serialized Fields
    
    molIndex
    
    int molIndex
- Exception chemaxon.marvin.io.MRecordParseException
  
  class MRecordParseException extends Exception implements Serializable
  - Serialized Fields
    
    position
    
    MRecordReader.Position position
Package chemaxon.marvin.modules.datatransfer
- Class chemaxon.marvin.modules.datatransfer.CopyAsDialog
  
  class CopyAsDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable
  
  serialVersionUID:
  
  -4564761584830399025L
  - Serialized Fields
    
    bundle
    
    ResourceBundle bundle
    
    defaultFormat
    
    String defaultFormat
    
    formats
    
    List<String> formats
    
    prevSelectedIdx
    
    int prevSelectedIdx
    
    selectorList
    
    JList<String> selectorList
Package chemaxon.marvin.plugin
- Exception chemaxon.marvin.plugin.PluginException
  
  class PluginException extends Exception implements Serializable
- Exception chemaxon.marvin.plugin.PluginInputCheckerException
  
  class PluginInputCheckerException extends PluginException implements Serializable
Package chemaxon.marvin.plugin.concurrent
- Exception chemaxon.marvin.plugin.concurrent.PluginExecutionException
  
  class PluginExecutionException extends ExecutionException implements Serializable
  - Serialized Fields
    
    plugin
    
    CalculatorPlugin plugin
Package chemaxon.marvin.plugin.gui
- Class chemaxon.marvin.plugin.gui.CheckList
  
  class CheckList extends JPanel implements Serializable
  - Serialized Fields
    
    checkboxes
    
    chemaxon.marvin.plugin.gui.CheckList.MCheckBox[] checkboxes
- Class chemaxon.marvin.plugin.gui.OptionsPane
  
  class OptionsPane extends JDialog implements Serializable
  - Serialized Fields
    
    cancel
    
    chemaxon.marvin.swing.ActionButton cancel
    
    key
    
    String key
    
    ok
    
    chemaxon.marvin.swing.ActionButton ok
    
    okActionListener
    
    ActionListener okActionListener
    
    parameterPanel
    
    ParameterPanelHandler parameterPanel
    
    restoreDefaults
    
    chemaxon.marvin.swing.ActionButton restoreDefaults
- Class chemaxon.marvin.plugin.gui.ParameterPanel
  
  class ParameterPanel extends JPanel implements Serializable
  - Serialized Fields
    
    items
    
    chemaxon.marvin.plugin.gui.ParameterItem[] items
- Class chemaxon.marvin.plugin.gui.ResultView
  
  class ResultView extends JDialog implements Serializable
  
  serialVersionUID:
  
  -5728800883025815500L
  - Serialized Fields
    
    bottomComponent
    
    JComponent bottomComponent
    
    bottomTextArea
    
    JTextArea bottomTextArea
    
    chart
    
    MChart chart
    
    chartPanel
    
    JPanel chartPanel
    
    copymi
    
    JMenuItem copymi
    
    detachmi
    
    JMenuItem detachmi
    
    imageFormat
    
    String imageFormat
    
    mpan
    
    chemaxon.marvin.common.swing.MolPanel mpan
    
    popup
    
    JPopupMenu popup
    
    popupcopymi
    
    JMenuItem popupcopymi
    
    resetmi
    
    JMenuItem resetmi
    
    topComponent
    
    JComponent topComponent
    
    topTextArea
    
    JTextArea topTextArea
    
    viewMenu
    
    JMenu viewMenu
    
    viewMol
    
    Molecule viewMol
    
    viewMols
    
    Molecule[] viewMols
    
    viewPanel
    
    chemaxon.marvin.view.swing.ViewPanel viewPanel
    
    viewText
    
    String viewText
    
    viewTexts
    
    String[] viewTexts
Package chemaxon.marvin.services
- Exception chemaxon.marvin.services.ServiceException
  
  class ServiceException extends Exception implements Serializable
  
  serialVersionUID:
  
  328496720368460819L

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
- readObject
  
  private void readObject(ObjectInputStream arg0) throws ClassNotFoundException, IOException
  
  Throws:
  
  ClassNotFoundException
  
  IOException

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.swing
- Class chemaxon.marvin.swing.ActionButton
  
  class ActionButton extends JButton implements Serializable
  
  serialVersionUID:
  
  2230794873504101456L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream arg0) throws ClassNotFoundException, IOException
    
    Throws:
    
    ClassNotFoundException
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream arg0) throws IOException
    
    Throws:
    
    IOException
- Class chemaxon.marvin.swing.ActionCheckBox
  
  class ActionCheckBox extends JCheckBox implements Serializable
  
  serialVersionUID:
  
  6131344149171552165L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream arg0) throws ClassNotFoundException, IOException
    
    Throws:
    
    ClassNotFoundException
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream arg0) throws IOException
    
    Throws:
    
    IOException
- Class chemaxon.marvin.swing.ActionCheckBoxMenuItem
  
  class ActionCheckBoxMenuItem extends JCheckBoxMenuItem implements Serializable
  
  serialVersionUID:
  
  7947549730058920376L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream arg0) throws ClassNotFoundException, IOException
    
    Throws:
    
    ClassNotFoundException
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream arg0) throws IOException
    
    Throws:
    
    IOException
- Class chemaxon.marvin.swing.ActionMenuItem
  
  class ActionMenuItem extends JMenuItem implements Serializable
  
  serialVersionUID:
  
  2939865755214258229L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream arg0) throws ClassNotFoundException, IOException
    
    Throws:
    
    ClassNotFoundException
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream arg0) throws IOException
    
    Throws:
    
    IOException
  - Serialized Fields
    
    listener
    
    PropertyChangeListener listener
- Class chemaxon.marvin.swing.ActionRadioButtonMenuItem
  
  class ActionRadioButtonMenuItem extends JRadioButtonMenuItem implements Serializable
  
  serialVersionUID:
  
  5384729187647889557L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream arg0) throws ClassNotFoundException, IOException
    
    Throws:
    
    ClassNotFoundException
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream arg0) throws IOException
    
    Throws:
    
    IOException
- Class chemaxon.marvin.swing.ActionToggleButton
  
  class ActionToggleButton extends JToggleButton implements Serializable
  
  serialVersionUID:
  
  -5185314081498476700L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream arg0) throws ClassNotFoundException, IOException
    
    Throws:
    
    ClassNotFoundException
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream arg0) throws IOException
    
    Throws:
    
    IOException
- Class chemaxon.marvin.swing.DelegatingAction
  
  class DelegatingAction extends AbstractAction implements Serializable
  - Serialized Fields
    
    listenerList
    
    EventListenerList listenerList
- Class chemaxon.marvin.swing.ListWithDisabledItemsRenderer
  
  class ListWithDisabledItemsRenderer extends JLabel implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    
    isEnabled
    
    boolean[] isEnabled
- Class chemaxon.marvin.swing.MAction
  
  class MAction extends chemaxon.marvin.swing.DelegatingAction implements Serializable
  
  serialVersionUID:
  
  7192487516820206101L
  - Serialized Fields
    
    accelerators
    
    KeyStroke[] accelerators
    
    actionCommand
    
    String actionCommand
    
    labelDo
    
    String labelDo
    
    labelWhat
    
    String labelWhat
- Class chemaxon.marvin.swing.ToggleButtonAction
  
  class ToggleButtonAction extends MAction implements Serializable
  
  serialVersionUID:
  
  3577603063753471241L
  - Serialized Fields
    
    selected
    
    boolean selected
- Class chemaxon.marvin.swing.ToggleButtonActionGroup
  
  class ToggleButtonActionGroup extends Object implements Serializable
  
  serialVersionUID:
  
  5722808204737522586L
  - Serialized Fields
    
    actionListeners
    
    EventListenerList actionListeners
    
    actions
    
    chemaxon.marvin.swing.ToggleButtonAction[] actions
    
    changeListeners
    
    PropertyChangeSupport changeListeners
    
    currentIndex
    
    int currentIndex
    
    emptyAction
    
    chemaxon.marvin.swing.ToggleButtonAction emptyAction
    
    emptyRadioButtons
    
    Vector<chemaxon.marvin.swing.ActionRadioButtonMenuItem> emptyRadioButtons
    
    enabled
    
    boolean enabled
    
    keyStrokes
    
    KeyStroke[][] keyStrokes
    
    propertyName
    
    String propertyName
    
    values
    
    Object[] values
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.MarvinOLEFrame
  
  class MarvinOLEFrame extends JFrame implements Serializable
  
  serialVersionUID:
  
  7801720334170069726L
  - Serialized Fields
    
    sp
    
    Semaphore sp
- 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.view
- Exception chemaxon.marvin.view.MDocStorage.CancellationException
  
  class CancellationException extends Exception implements Serializable
- Exception chemaxon.marvin.view.MDocStorage.RecordUnavailableException
  
  class RecordUnavailableException extends Exception implements Serializable
  - Serialized Fields
    
    recordIndex
    
    int recordIndex
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
    
    writeObject
    
    private void writeObject(ObjectOutputStream arg0) throws IOException
    
    Throws:
    
    IOException
  - 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
    
    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
    
    readObject
    
    private void readObject(ObjectInputStream arg0) throws ClassNotFoundException, IOException
    
    Throws:
    
    ClassNotFoundException
    
    IOException
  - 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
    
    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
    
    integerFormatter
    
    NumberFormat integerFormatter
    
    options
    
    int options
    
    toolkit
    
    Toolkit toolkit
- Class chemaxon.marvin.view.swing.WholeNumberField.WholeNumberDocument
  
  class WholeNumberDocument extends PlainDocument implements Serializable
Package chemaxon.naming
- Exception chemaxon.naming.NameFormatException
  
  class NameFormatException extends MolFormatException implements Serializable
  - Serialized Fields
    
    prefix
    
    String prefix
- Exception chemaxon.naming.NameFormatException.FilteredCase
  
  class FilteredCase extends NameFormatException implements Serializable
- Exception chemaxon.naming.NamePrefixException
  
  class NamePrefixException extends NameFormatException implements Serializable
  - Serialized Fields
    
    token
    
    String token
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.nfunk.jep.function
- Class chemaxon.nfunk.jep.function.Abs
  
  class Abs extends chemaxon.jep.function.AbstractUnaryPureFunction implements Serializable
- Class chemaxon.nfunk.jep.function.Add
  
  class Add extends chemaxon.jep.function.AbstractVarargPureFunction implements Serializable
- Class chemaxon.nfunk.jep.function.Angle
  
  class Angle extends chemaxon.nfunk.jep.function.PostfixMathCommand implements Serializable
- Class chemaxon.nfunk.jep.function.ArcCosine
  
  class ArcCosine extends chemaxon.nfunk.jep.function.PostfixMathCommand implements Serializable
- Class chemaxon.nfunk.jep.function.ArcCosineH
  
  class ArcCosineH extends chemaxon.nfunk.jep.function.PostfixMathCommand implements Serializable
- Class chemaxon.nfunk.jep.function.ArcSine
  
  class ArcSine extends chemaxon.nfunk.jep.function.PostfixMathCommand implements Serializable
- Class chemaxon.nfunk.jep.function.ArcSineH
  
  class ArcSineH extends chemaxon.nfunk.jep.function.PostfixMathCommand implements Serializable
- Class chemaxon.nfunk.jep.function.ArcTangent
  
  class ArcTangent extends chemaxon.nfunk.jep.function.PostfixMathCommand implements Serializable
- Class chemaxon.nfunk.jep.function.ArcTanH
  
  class ArcTanH extends chemaxon.nfunk.jep.function.PostfixMathCommand implements Serializable
- Class chemaxon.nfunk.jep.function.Comparative
  
  class Comparative extends chemaxon.jep.function.AbstractBinaryPureFunction implements Serializable
  - Serialized Fields
    
    id
    
    int id
- Class chemaxon.nfunk.jep.function.Cosine
  
  class Cosine extends chemaxon.nfunk.jep.function.PostfixMathCommand implements Serializable
- Class chemaxon.nfunk.jep.function.CosineH
  
  class CosineH extends chemaxon.nfunk.jep.function.PostfixMathCommand implements Serializable
- Class chemaxon.nfunk.jep.function.Divide
  
  class Divide extends chemaxon.jep.function.AbstractBinaryPureFunction implements Serializable
- Class chemaxon.nfunk.jep.function.Imaginary
  
  class Imaginary extends chemaxon.nfunk.jep.function.PostfixMathCommand implements Serializable
- Class chemaxon.nfunk.jep.function.Logarithm
  
  class Logarithm extends chemaxon.nfunk.jep.function.PostfixMathCommand implements Serializable
- Class chemaxon.nfunk.jep.function.Logical
  
  class Logical extends Object implements Serializable
  - Serialized Fields
    
    nullValue
    
    boolean nullValue
- Class chemaxon.nfunk.jep.function.Modulus
  
  class Modulus extends chemaxon.jep.function.AbstractBinaryPureFunction implements Serializable
- Class chemaxon.nfunk.jep.function.Multiply
  
  class Multiply extends chemaxon.jep.function.AbstractVarargPureFunction implements Serializable
- Class chemaxon.nfunk.jep.function.NaturalLogarithm
  
  class NaturalLogarithm extends chemaxon.nfunk.jep.function.PostfixMathCommand implements Serializable
- Class chemaxon.nfunk.jep.function.Not
  
  class Not extends chemaxon.jep.function.AbstractUnaryPureFunction implements Serializable
- Class chemaxon.nfunk.jep.function.PostfixMathCommand
  
  class PostfixMathCommand extends Object implements Serializable
  
  serialVersionUID:
  
  8592522537301237765L
  - Serialized Fields
    
    curNumberOfParameters
    
    int curNumberOfParameters
    
    Deprecated, for removal: This API element is subject to removal in a future version.
    
    numberOfParameters
    
    int numberOfParameters
    
    Deprecated, for removal: This API element is subject to removal in a future version.
- Class chemaxon.nfunk.jep.function.Power
  
  class Power extends chemaxon.jep.function.AbstractBinaryPureFunction implements Serializable
- Class chemaxon.nfunk.jep.function.Random
  
  class Random extends chemaxon.nfunk.jep.function.PostfixMathCommand implements Serializable
- Class chemaxon.nfunk.jep.function.Real
  
  class Real extends chemaxon.nfunk.jep.function.PostfixMathCommand implements Serializable
- Class chemaxon.nfunk.jep.function.Sine
  
  class Sine extends chemaxon.nfunk.jep.function.PostfixMathCommand implements Serializable
- Class chemaxon.nfunk.jep.function.SineH
  
  class SineH extends chemaxon.nfunk.jep.function.PostfixMathCommand implements Serializable
- Class chemaxon.nfunk.jep.function.SquareRoot
  
  class SquareRoot extends chemaxon.nfunk.jep.function.PostfixMathCommand implements Serializable
- Class chemaxon.nfunk.jep.function.Subtract
  
  class Subtract extends chemaxon.jep.function.AbstractBinaryPureFunction implements Serializable
  
  serialVersionUID:
  
  -7730006408517854747L
- Class chemaxon.nfunk.jep.function.Sum
  
  class Sum extends chemaxon.nfunk.jep.function.PostfixMathCommand implements Serializable
- Class chemaxon.nfunk.jep.function.Tangent
  
  class Tangent extends chemaxon.nfunk.jep.function.PostfixMathCommand implements Serializable
- Class chemaxon.nfunk.jep.function.TanH
  
  class TanH extends chemaxon.nfunk.jep.function.PostfixMathCommand implements Serializable
- Class chemaxon.nfunk.jep.function.UMinus
  
  class UMinus extends chemaxon.jep.function.AbstractUnaryPureFunction implements Serializable
Package chemaxon.sss.search
- 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:
    
    MarkushFeature.RGROUP: {R-atom union index, R-group definition index}
    
    MarkushFeature.LINKNODE: {link atom union index}
    
    MarkushFeature.REPUNIT: {RepeatingUnitSgroup sgroup index in markush}
    
    MarkushFeature.ATOMLIST: {list atom union index}
    
    MarkushFeature.BONDLIST: {list bond union bond index}
    
    MarkushFeature.MULTIBOND: {union bond index, MulticenterSgroup sgroup index in markush}
    
    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.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
    
    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 behavior. 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:
    
    SearchOptions.setDoubleBondStereoMatchingMode(int)
    
    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:
    
    SearchOptions.setIgnoreAxialStereo(boolean)
    
    ignoreCumuleneCisTransStereo
    
    boolean ignoreCumuleneCisTransStereo
    
    See Also:
    
    SearchOptions.setIgnoreCumuleneOrRingCisTransStereo(boolean)
    
    ignoreDoubleBondStereo
    
    boolean ignoreDoubleBondStereo
    
    See Also:
    
    SearchOptions.setIgnoreDoubleBondStereo(boolean)
    
    ignoreSynAntiStereo
    
    boolean ignoreSynAntiStereo
    
    See Also:
    
    SearchOptions.setIgnoreSynAntiStereo(boolean)
    
    ignoreTetrahedralStereo
    
    boolean ignoreTetrahedralStereo
    
    See Also:
    
    SearchOptions.setIgnoreTetrahedralStereo(boolean)
    
    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 behavior. 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:
    
    SearchOptions.setStereoSearchType(int)
    
    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
- Class chemaxon.standardizer.advancedactions.GroupList
  
  class GroupList extends ArrayList<GroupDefinition> implements Serializable
Package chemaxon.struc
- Class chemaxon.struc.CTransform3D
  
  class CTransform3D extends Object implements Externalizable
  
  serialVersionUID:
  
  0L
  - Serialization Methods
    
    readExternal
    
    public void readExternal(ObjectInput in) throws IOException
    
    Deserializes a transformation matrix.
    
    Parameters:
    
    in - the object input stream
    
    Throws:
    
    IOException
    
    Since:
    
    3.5, 11/02/2004
    
    writeExternal
    
    public void writeExternal(ObjectOutput out) throws IOException
    
    Serializes a transformation matrix.
    
    Parameters:
    
    out - the object output stream
    
    Throws:
    
    IOException
    
    Since:
    
    3.5, 11/02/2004
- Class chemaxon.struc.DefaultDictionary
  
  class DefaultDictionary extends HashMap<String,SuperatomSgroup> implements Serializable
  
  serialVersionUID:
  
  8013155936541949713L
- Class chemaxon.struc.DPoint3
  
  class DPoint3 extends Object implements Externalizable
  
  serialVersionUID:
  
  0L
  - Serialization Methods
    
    readExternal
    
    public void readExternal(ObjectInput in) throws IOException, ClassNotFoundException
    
    Deserializes a 3D point.
    
    Parameters:
    
    in - the object input stream
    
    Throws:
    
    IOException
    
    ClassNotFoundException
    
    writeExternal
    
    public void writeExternal(ObjectOutput out) throws IOException
    
    Serializes a 3D point.
    
    Parameters:
    
    out - the object output stream
    
    Throws:
    
    IOException
- Class chemaxon.struc.ExtraAtomProperties
  
  class ExtraAtomProperties extends Object implements Serializable
  
  serialVersionUID:
  
  -1980229820290558380L
  - Serialized Fields
    
    aliasstr
    
    String aliasstr
    
    attachParentSgroup
    
    Sgroup attachParentSgroup
    
    countFlags
    
    int countFlags
    
    electronProp
    
    int electronProp
    
    extrargbs
    
    long extrargbs
    
    extrastr
    
    String extrastr
    
    flags
    
    int flags
    
    linkNodeOuterBonds
    
    int linkNodeOuterBonds
    
    list
    
    int[] list
    
    order
    
    int order
    
    qprops
    
    Map<String,Object> qprops
    
    querystr
    
    String querystr
    
    repetitionBits
    
    int repetitionBits
    
    rgroupId
    
    short rgroupId
    
    temporaryObjects
    
    Map<String,Object> temporaryObjects
    
    valence1
    
    short valence1
- Exception chemaxon.struc.MacroMolecule.BadMoleculeException
  
  class BadMoleculeException extends Exception implements Serializable
  
  serialVersionUID:
  
  9037472982065239933L
- Class chemaxon.struc.MDocument
  
  class MDocument extends Object implements Serializable
  
  serialVersionUID:
  
  553557622036381832L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
    
    Deserializes a document. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    ois - the object input stream
    
    Throws:
    
    ClassNotFoundException
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream oos) throws IOException
    
    Serializes a document. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    oos - the object output stream
    
    Throws:
    
    IOException
- Class chemaxon.struc.MDocument.Prop
  
  class Prop extends MProp implements Serializable
- Class chemaxon.struc.MDocumentUtil
  
  class MDocumentUtil extends Object implements Serializable
  
  serialVersionUID:
  
  12600100100892L
  - Serialized Fields
    
    doc
    
    MDocument doc
- Class chemaxon.struc.MObject
  
  class MObject extends Object implements Serializable
  
  serialVersionUID:
  
  2435517510938087080L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream ois) throws IOException
    
    Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    ois - the object input stream
    
    Throws:
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream oos) throws IOException
    
    Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    oos - the object output stream
    
    Throws:
    
    IOException
- Class chemaxon.struc.MolAtom
  
  class MolAtom extends Object implements Serializable
  
  serialVersionUID:
  
  -3974070468228529467L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
    
    Deserializes an atom. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    ois - the object input stream
    
    Throws:
    
    ClassNotFoundException
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream oos) throws IOException
    
    Serializes an atom. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    oos - the object output stream
    
    Throws:
    
    IOException
  - Serialized Fields
    
    angle
    
    double angle
    
    isValenceCheckNeeded
    
    boolean isValenceCheckNeeded
- Class chemaxon.struc.MolBond
  
  class MolBond extends Object implements Serializable
  
  serialVersionUID:
  
  3656012871856958335L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
    
    Deserializes a bond. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    ois - the object input stream
    
    Throws:
    
    ClassNotFoundException
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream oos) throws IOException
    
    Serializes a bond. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    oos - the object output stream
    
    Throws:
    
    IOException
- Class chemaxon.struc.Molecule
  
  class Molecule extends MoleculeGraph implements Serializable
  
  serialVersionUID:
  
  7275486436840296305L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
    
    Deserializes a molecule. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    ois - the object input stream
    
    Throws:
    
    ClassNotFoundException
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream oos) throws IOException
    
    Serializes a molecule. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    oos - the object output stream
    
    Throws:
    
    IOException
  - Serialized Fields
    
    id
    
    String id
- Class chemaxon.struc.MoleculeGraph
  
  class MoleculeGraph extends Object implements Serializable
  
  serialVersionUID:
  
  -2053719583816270190L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
    
    Deserializes a molecule graph. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    ois - the object input stream
    
    Throws:
    
    ClassNotFoundException
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream oos) throws IOException
    
    Serializes a molecule graph. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    oos - the object output stream
    
    Throws:
    
    IOException
  - Serialized Fields
    
    fragmentTracker
    
    chemaxon.struc.MoleculeGraph.FragmentTracker fragmentTracker
    
    hasBicycloStereo
    
    boolean hasBicycloStereo
    
    Molecule has bicyclo stereo information. Can be set by MolAtom.setBicycloStereo(BicycloStereoDescriptor[]).
    
    valenceCheckOptions
    
    ValenceCheckOptions valenceCheckOptions
    
    Valence check options for the molecule.
- Class chemaxon.struc.MPoint
  
  class MPoint extends MObject implements Serializable
  
  serialVersionUID:
  
  -3067277054033050963L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
    
    Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    ois - the object input stream
    
    Throws:
    
    ClassNotFoundException
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream oos) throws IOException
    
    Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    oos - the object output stream
    
    Throws:
    
    IOException
- Class chemaxon.struc.MProp
  
  class MProp extends Object implements Serializable
  
  serialVersionUID:
  
  -5699803671884637223L
  - Serialized Fields
    
    coordDependent
    
    boolean coordDependent
    
    grinvCC
    
    long grinvCC
- Class chemaxon.struc.MPropertyContainer
  
  class MPropertyContainer extends Object implements Externalizable
  
  serialVersionUID:
  
  -2575268570438177098L
  - Serialization Methods
    
    readExternal
    
    public void readExternal(ObjectInput in) throws IOException, ClassNotFoundException
    
    Restores the property container's state.
    
    Parameters:
    
    in - the stream to read data from in order to restore the object
    
    Throws:
    
    IOException - if I/O errors occur
    
    ClassNotFoundException - If the class for an object being restored cannot be found.
    
    writeExternal
    
    public void writeExternal(ObjectOutput out) throws IOException
    
    Saves the property container's state.
    
    Parameters:
    
    out - the stream to write the object to
    
    Throws:
    
    IOException - Includes any I/O exceptions that may occur
- Class chemaxon.struc.MSelectionDocument
  
  class MSelectionDocument extends MDocument implements Serializable
  
  serialVersionUID:
  
  2379294894434293119L
- Class chemaxon.struc.PageSettings
  
  class PageSettings extends Object implements Externalizable
  
  serialVersionUID:
  
  -7674028514396457694L
  - Serialization Methods
    
    readExternal
    
    public void readExternal(ObjectInput in) throws IOException, ClassNotFoundException
    
    Throws:
    
    IOException
    
    ClassNotFoundException
    
    writeExternal
    
    public void writeExternal(ObjectOutput out) throws IOException
    
    Throws:
    
    IOException
- Class chemaxon.struc.QueryBond
  
  class QueryBond extends MolBond implements Serializable
  
  serialVersionUID:
  
  -5025485107616067648L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
    
    Deserializes a bond. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    ois - the object input stream
    
    Throws:
    
    ClassNotFoundException
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream oos) throws IOException
    
    Serializes a bond. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    oos - the object output stream
    
    Throws:
    
    IOException
- Class chemaxon.struc.RgMolecule
  
  class RgMolecule extends Molecule implements Serializable
  
  serialVersionUID:
  
  -939153732283455787L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
    
    Deserializes an RgMolecule. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    ois - the object input stream
    
    Throws:
    
    ClassNotFoundException
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream oos) throws IOException
    
    Serializes an RgMolecule. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    oos - the object output stream
    
    Throws:
    
    IOException
- Class chemaxon.struc.RxnMolecule
  
  class RxnMolecule extends Molecule implements Serializable
  
  serialVersionUID:
  
  -2863036104564183121L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
    
    Deserializes a reaction. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    ois - the object input stream
    
    Throws:
    
    ClassNotFoundException
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream oos) throws IOException
    
    Serializes a reaction. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    oos - the object output stream
    
    Throws:
    
    IOException
- Class chemaxon.struc.SelectionMolecule
  
  class SelectionMolecule extends MoleculeGraph implements Serializable
  
  serialVersionUID:
  
  234062772192819675L
- Class chemaxon.struc.SelectionRgMolecule
  
  class SelectionRgMolecule extends SelectionMolecule implements Serializable
- Class chemaxon.struc.Sgroup
  
  class Sgroup extends Object implements Serializable
  
  serialVersionUID:
  
  -6209766549185582411L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
    
    Deserializes an Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    ois - the object input stream
    
    Throws:
    
    ClassNotFoundException
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream oos) throws IOException
    
    Serializes an Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    oos - the object output stream
    
    Throws:
    
    IOException
  - Serialized Fields
    
    atomSet
    
    Set<MolAtom> atomSet
    
    Set for storing the atoms of the s-group's graph.
    
    id
    
    String id
- Class chemaxon.struc.StaticMolecule
  
  class StaticMolecule extends Object implements Serializable
  
  serialVersionUID:
  
  -6974806277329432018L
  - Serialized Fields
    
    arrayFlags
    
    int arrayFlags
    
    atomCount
    
    int atomCount
    
    atomLists
    
    byte[][] atomLists
    
    atomMap
    
    short[] atomMap
    
    atomStereo
    
    byte[] atomStereo
    
    atomType
    
    short[] atomType
    
    bondAtom1
    
    short[] bondAtom1
    
    bondAtom2
    
    short[] bondAtom2
    
    bondCount
    
    int bondCount
    
    bondFlags
    
    int[] bondFlags
    
    charge
    
    byte[] charge
    
    connectionTable
    
    short[] connectionTable
    
    explicitHcount
    
    byte[] explicitHcount
    
    extendedAtomType
    
    int[] extendedAtomType
    
    hybridization
    
    byte[] hybridization
    
    implicitHcount
    
    byte[] implicitHcount
    
    massno
    
    byte[] massno
    
    name
    
    String name
    
    neighborCount
    
    byte[] neighborCount
    
    nodeEdgeList
    
    short[][] nodeEdgeList
    
    queryProperty
    
    byte[][] queryProperty
    
    radical
    
    byte[] radical
    
    rgroupId
    
    short[] rgroupId
    
    ringPerception
    
    boolean ringPerception
    
    sgroupId
    
    String[] sgroupId
    
    valence
    
    byte[] valence
Package chemaxon.struc.graphics
- Class chemaxon.struc.graphics.MAnalysisBox
  
  class MAnalysisBox extends MTextBox implements Serializable
  
  serialVersionUID:
  
  -7630363128405095856L
  - Serialized Fields
    
    mol
    
    Molecule mol
    
    terms
    
    List<chemaxon.struc.graphics.analysis.MAnalysisBoxTerm> terms
- Class chemaxon.struc.graphics.MAssigner
  
  class MAssigner extends MPolyline implements Serializable
  - Serialized Fields
    
    order
    
    int order
- Class chemaxon.struc.graphics.MAtomSetPoint
  
  class MAtomSetPoint extends MPoint implements Serializable
  
  serialVersionUID:
  
  5932389976054063500L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
    
    Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    ois - the object input stream
    
    Throws:
    
    ClassNotFoundException
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream oos) throws IOException
    
    Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    oos - the object output stream
    
    Throws:
    
    IOException
- Class chemaxon.struc.graphics.MBracket
  
  class MBracket extends MRectangle implements Serializable
  
  serialVersionUID:
  
  -5775562691065011181L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream ois) throws IOException
    
    Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    ois - the object input stream
    
    Throws:
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream oos) throws IOException
    
    Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    oos - the object output stream
    
    Throws:
    
    IOException
  - Serialized Fields
    
    bracketOrientation
    
    int bracketOrientation
    
    Bracket orientation, bracket can have two sides (T_DOUBLE) or just one (T_SINGLE). Possible values: T_SINGLE, T_DOUBLE
    
    bracketType
    
    int bracketType
- Class chemaxon.struc.graphics.MChemicalStruct
  
  class MChemicalStruct extends MObject implements Serializable
  
  serialVersionUID:
  
  7098670860634457343L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
    
    Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    ois - the object input stream
    
    Throws:
    
    ClassNotFoundException
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream oos) throws IOException
    
    Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    oos - the object output stream
    
    Throws:
    
    IOException
- Class chemaxon.struc.graphics.MEFlow
  
  class MEFlow extends MPolyline implements Serializable
  
  serialVersionUID:
  
  891769518407563834L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream ois) throws IOException
    
    Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    ois - the object input stream
    
    Throws:
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream oos) throws IOException
    
    Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    oos - the object output stream
    
    Throws:
    
    IOException
  - Serialized Fields
    
    baseElectronContainerIndex
    
    int baseElectronContainerIndex
    
    baseElectronIndexInContainer
    
    int baseElectronIndexInContainer
- Class chemaxon.struc.graphics.MEFlowBasePoint
  
  class MEFlowBasePoint extends MPoint implements Serializable
  
  serialVersionUID:
  
  1053944912020926984L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
    
    Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    ois - the object input stream
    
    Throws:
    
    ClassNotFoundException
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream oos) throws IOException
    
    Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    oos - the object output stream
    
    Throws:
    
    IOException
  - Serialized Fields
    
    electronIndex
    
    int electronIndex
    
    electronLabel
    
    String electronLabel
- Class chemaxon.struc.graphics.MElectron
  
  class MElectron extends MAtomSetPoint implements Serializable
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream ois) throws IOException
    
    Throws:
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream oos) throws IOException
    
    Throws:
    
    IOException
  - Serialized Fields
    
    difLoc
    
    DPoint3 difLoc
    
    isPointed
    
    boolean isPointed
- Class chemaxon.struc.graphics.MElectronContainer
  
  class MElectronContainer extends MObject implements Serializable
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream ois) throws IOException, ClassNotFoundException
    
    Throws:
    
    IOException
    
    ClassNotFoundException
    
    writeObject
    
    private void writeObject(ObjectOutputStream oos) throws IOException
    
    Throws:
    
    IOException
  - Serialized Fields
    
    electronOccupation
    
    boolean[] electronOccupation
    
    electrons
    
    MElectron[] electrons
    
    radical
    
    boolean radical
- Class chemaxon.struc.graphics.MEllipse
  
  class MEllipse extends MRectangle implements Serializable
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
    
    Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    ois - the object input stream
    
    Throws:
    
    ClassNotFoundException
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream oos) throws IOException
    
    Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    oos - the object output stream
    
    Throws:
    
    IOException
- Class chemaxon.struc.graphics.MFont
  
  class MFont extends Object implements Serializable
  
  serialVersionUID:
  
  -7769715209509613515L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
    
    Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    ois - the object input stream
    
    Throws:
    
    ClassNotFoundException
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream oos) throws IOException
    
    Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    oos - the object output stream
    
    Throws:
    
    IOException
- Class chemaxon.struc.graphics.MMidPoint
  
  class MMidPoint extends MPoint implements Serializable
  
  serialVersionUID:
  
  5307361876930807239L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
    
    Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    ois - the object input stream
    
    Throws:
    
    ClassNotFoundException
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream oos) throws IOException
    
    Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    oos - the object output stream
    
    Throws:
    
    IOException
- Class chemaxon.struc.graphics.MMidPoint.Sticky
  
  class Sticky extends MMidPoint implements Serializable
  
  serialVersionUID:
  
  3223068581543532992L
- Class chemaxon.struc.graphics.MMoleculeMovie
  
  class MMoleculeMovie extends MObject implements Serializable
  
  serialVersionUID:
  
  6476041884742537582L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
    
    Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    ois - the object input stream
    
    Throws:
    
    ClassNotFoundException
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream oos) throws IOException
    
    Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    oos - the object output stream
    
    Throws:
    
    IOException
- Class chemaxon.struc.graphics.MNameTextBox
  
  class MNameTextBox extends MTextBox implements Serializable
  
  serialVersionUID:
  
  6302424343157644471L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
    
    Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    ois - the object input stream
    
    Throws:
    
    ClassNotFoundException
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream oos) throws IOException
    
    Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    oos - the object output stream
    
    Throws:
    
    IOException
- Class chemaxon.struc.graphics.MPolyline
  
  class MPolyline extends MObject implements Serializable
  
  serialVersionUID:
  
  4958026600768388648L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
    
    Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    ois - the object input stream
    
    Throws:
    
    ClassNotFoundException
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream oos) throws IOException
    
    Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    oos - the object output stream
    
    Throws:
    
    IOException
  - Serialized Fields
    
    internalPointAddCount
    
    int internalPointAddCount
    
    internalPointPos
    
    int internalPointPos
- Class chemaxon.struc.graphics.MRArrow
  
  class MRArrow extends MPolyline implements Serializable
  
  serialVersionUID:
  
  8638690394107448092L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
    
    Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    ois - the object input stream
    
    Throws:
    
    ClassNotFoundException
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream oos) throws IOException
    
    Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    oos - the object output stream
    
    Throws:
    
    IOException
- Class chemaxon.struc.graphics.MReactionSign
  
  class MReactionSign extends MTextBox implements Serializable
  
  serialVersionUID:
  
  -7025949002857142442L
- Class chemaxon.struc.graphics.MRectangle
  
  class MRectangle extends MPolyline implements Serializable
  
  serialVersionUID:
  
  2948229815278089239L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
    
    Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    ois - the object input stream
    
    Throws:
    
    ClassNotFoundException
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream oos) throws IOException
    
    Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    oos - the object output stream
    
    Throws:
    
    IOException
- Class chemaxon.struc.graphics.MRectanglePoint
  
  class MRectanglePoint extends MPoint implements Serializable
  
  serialVersionUID:
  
  -3067277054033050963L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
    
    Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    ois - the object input stream
    
    Throws:
    
    ClassNotFoundException
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream oos) throws IOException
    
    Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    oos - the object output stream
    
    Throws:
    
    IOException
- Class chemaxon.struc.graphics.MRectanglePoint.Sticky
  
  class Sticky extends MRectanglePoint implements Serializable
  
  serialVersionUID:
  
  3364078480306200948L
- Class chemaxon.struc.graphics.MRoundedRectangle
  
  class MRoundedRectangle extends MRectangle implements Serializable
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
    
    Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    ois - the object input stream
    
    Throws:
    
    ClassNotFoundException
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream oos) throws IOException
    
    Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    oos - the object output stream
    
    Throws:
    
    IOException
  - Serialized Fields
    
    arcHeight
    
    double arcHeight
    
    arcWidth
    
    double arcWidth
- Class chemaxon.struc.graphics.MTextAttributes
  
  class MTextAttributes extends Object implements Externalizable
  
  serialVersionUID:
  
  6561552003080652755L
  - Serialization Methods
    
    readExternal
    
    public void readExternal(ObjectInput in) throws IOException, ClassNotFoundException
    
    Throws:
    
    IOException
    
    ClassNotFoundException
    
    writeExternal
    
    public void writeExternal(ObjectOutput out) throws IOException
    
    Throws:
    
    IOException
- Class chemaxon.struc.graphics.MTextBox
  
  class MTextBox extends MRectangle implements Serializable
  
  serialVersionUID:
  
  -7272723232157967384L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
    
    Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    ois - the object input stream
    
    Throws:
    
    ClassNotFoundException
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream oos) throws IOException
    
    Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    oos - the object output stream
    
    Throws:
    
    IOException
  - Serialized Fields
    
    actionMap
    
    ActionMap actionMap
- Class chemaxon.struc.graphics.MTextDocument
  
  class MTextDocument extends Object implements Externalizable
  
  serialVersionUID:
  
  6305880304790247656L
  - Serialization Methods
    
    readExternal
    
    public void readExternal(ObjectInput in) throws IOException, ClassNotFoundException
    
    Restores the document.
    
    Parameters:
    
    in - the stream to read data from in order to restore the object
    
    Throws:
    
    IOException - if I/O errors occur
    
    ClassNotFoundException - If the class for an object being restored cannot be found.
    
    writeExternal
    
    public void writeExternal(ObjectOutput out) throws IOException
    
    Saves the document.
    
    Parameters:
    
    out - the stream to write the object to
    
    Throws:
    
    IOException - Includes any I/O exceptions that may occur
Package chemaxon.struc.prop
- Class chemaxon.struc.prop.MBooleanProp
  
  class MBooleanProp extends MProp implements Serializable
  
  serialVersionUID:
  
  -5366978422380739811L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Restores the property's state.
    
    Parameters:
    
    in - the stream to read data from in order to restore the object
    
    Throws:
    
    IOException - if I/O errors occur
    
    ClassNotFoundException - If the class for an object being restored cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Saves the property's state.
    
    Parameters:
    
    out - the stream to write the object to
    
    Throws:
    
    IOException - Includes any I/O exceptions that may occur
- Class chemaxon.struc.prop.MByteArrayProp
  
  class MByteArrayProp extends MProp implements Serializable
  
  serialVersionUID:
  
  -4046371792715339701L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream arg0) throws IOException, ClassNotFoundException
    
    Throws:
    
    IOException
    
    ClassNotFoundException
    
    writeObject
    
    private void writeObject(ObjectOutputStream arg0) throws IOException
    
    Throws:
    
    IOException
- Class chemaxon.struc.prop.MCollectionProp
  
  class MCollectionProp extends MProp implements Serializable
  
  serialVersionUID:
  
  -7479938988131387052L
- Class chemaxon.struc.prop.MDoubleArrayProp
  
  class MDoubleArrayProp extends MProp implements Serializable
  
  serialVersionUID:
  
  -5670039985685584647L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Restores the property's state.
    
    Parameters:
    
    in - the stream to read data from in order to restore the object
    
    Throws:
    
    IOException - if I/O errors occur
    
    ClassNotFoundException - If the class for an object being restored cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Saves the property's state.
    
    Parameters:
    
    out - the stream to write the object to
    
    Throws:
    
    IOException - Includes any I/O exceptions that may occur
- Class chemaxon.struc.prop.MDoubleProp
  
  class MDoubleProp extends MProp implements Serializable
  
  serialVersionUID:
  
  -1221776439131689653L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Restores the property's state.
    
    Parameters:
    
    in - the stream to read data from in order to restore the object
    
    Throws:
    
    IOException - if I/O errors occur
    
    ClassNotFoundException - If the class for an object being restored cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Saves the property's state.
    
    Parameters:
    
    out - the stream to write the object to
    
    Throws:
    
    IOException - Includes any I/O exceptions that may occur
- Class chemaxon.struc.prop.MFontProp
  
  class MFontProp extends MProp implements Serializable
  
  serialVersionUID:
  
  2369581307328116455L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Throws:
    
    IOException
    
    ClassNotFoundException
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Throws:
    
    IOException
- Class chemaxon.struc.prop.MHashProp
  
  class MHashProp extends MCollectionProp implements Serializable
  
  serialVersionUID:
  
  5457649877894058447L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Restores the property's state.
    
    Parameters:
    
    in - the stream to read data from in order to restore the object
    
    Throws:
    
    IOException - if I/O errors occur
    
    ClassNotFoundException - If the class for an object being restored cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Saves the property's state.
    
    Parameters:
    
    out - the stream to write the object to
    
    Throws:
    
    IOException - Includes any I/O exceptions that may occur
- Class chemaxon.struc.prop.MHCoords3DProp
  
  class MHCoords3DProp extends MProp implements Serializable
  
  serialVersionUID:
  
  6646271128663088908L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Restores the property's state.
    
    Parameters:
    
    in - the stream to read data from in order to restore the object
    
    Throws:
    
    IOException - if I/O errors occur
    
    ClassNotFoundException - If the class for an object being restored cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Saves the property's state.
    
    Parameters:
    
    out - the stream to write the object to
    
    Throws:
    
    IOException - Includes any I/O exceptions that may occur
- Class chemaxon.struc.prop.MIntegerArrayProp
  
  class MIntegerArrayProp extends MProp implements Serializable
  
  serialVersionUID:
  
  6651869314046996057L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Restores the property's state.
    
    Parameters:
    
    in - the stream to read data from in order to restore the object
    
    Throws:
    
    IOException - if I/O errors occur
    
    ClassNotFoundException - If the class for an object being restored cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Saves the property's state.
    
    Parameters:
    
    out - the stream to write the object to
    
    Throws:
    
    IOException - Includes any I/O exceptions that may occur
- Class chemaxon.struc.prop.MIntegerProp
  
  class MIntegerProp extends MProp implements Serializable
  
  serialVersionUID:
  
  -7179550727198941747L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Restores the property's state.
    
    Parameters:
    
    in - the stream to read data from in order to restore the object
    
    Throws:
    
    IOException - if I/O errors occur
    
    ClassNotFoundException - If the class for an object being restored cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Saves the property's state.
    
    Parameters:
    
    out - the stream to write the object to
    
    Throws:
    
    IOException - Includes any I/O exceptions that may occur
- Class chemaxon.struc.prop.MListProp
  
  class MListProp extends MCollectionProp implements Serializable
  
  serialVersionUID:
  
  5360371881677476960L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Restores the property's state.
    
    Parameters:
    
    in - the stream to read data from in order to restore the object
    
    Throws:
    
    IOException - if I/O errors occur
    
    ClassNotFoundException - If the class for an object being restored cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Saves the property's state.
    
    Parameters:
    
    out - the stream to write the object to
    
    Throws:
    
    IOException - Includes any I/O exceptions that may occur
- Class chemaxon.struc.prop.MMoleculeProp
  
  class MMoleculeProp extends MProp implements Serializable
  
  serialVersionUID:
  
  -7687559780023024273L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Restores the property's state.
    
    Parameters:
    
    in - the stream to read data from in order to restore the object
    
    Throws:
    
    IOException - if I/O errors occur
    
    ClassNotFoundException - If the class for an object being restored cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Saves the property's state.
    
    Parameters:
    
    out - the stream to write the object to
    
    Throws:
    
    IOException - Includes any I/O exceptions that may occur
- Class chemaxon.struc.prop.MMoleculeStringProp
  
  class MMoleculeStringProp extends MStringProp implements Serializable
  
  serialVersionUID:
  
  -1005074014113755196L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Restores the property's state.
    
    Parameters:
    
    in - the stream to read data from in order to restore the object
    
    Throws:
    
    IOException - if I/O errors occur
    
    ClassNotFoundException - If the class for an object being restored cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Saves the property's state.
    
    Parameters:
    
    out - the stream to write the object to
    
    Throws:
    
    IOException - Includes any I/O exceptions that may occur
  - Serialized Fields
    
    format
    
    String format
- Class chemaxon.struc.prop.MObjectProp
  
  class MObjectProp extends MProp implements Serializable
  
  serialVersionUID:
  
  4005646748655675692L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Restores the property's state.
    
    Parameters:
    
    in - the stream to read data from in order to restore the object
    
    Throws:
    
    IOException - if I/O errors occur
    
    ClassNotFoundException - If the class for an object being restored cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Saves the property's state.
    
    Parameters:
    
    out - the stream to write the object to
    
    Throws:
    
    IOException - Includes any I/O exceptions that may occur
- Class chemaxon.struc.prop.MStringProp
  
  class MStringProp extends MProp implements Serializable
  
  serialVersionUID:
  
  1373831606368751112L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Restores the property's state.
    
    Parameters:
    
    in - the stream to read data from in order to restore the object
    
    Throws:
    
    IOException - if I/O errors occur
    
    ClassNotFoundException - If the class for an object being restored cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Saves the property's state.
    
    Parameters:
    
    out - the stream to write the object to
    
    Throws:
    
    IOException - Includes any I/O exceptions that may occur
Package chemaxon.struc.sgroup
- Class chemaxon.struc.sgroup.AminoAcidSgroup
  
  class AminoAcidSgroup extends SuperatomSgroup implements Serializable
  
  serialVersionUID:
  
  -4078870750580716173L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream arg0) throws ClassNotFoundException, IOException
    
    Throws:
    
    ClassNotFoundException
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream arg0) throws IOException
    
    Throws:
    
    IOException
  - Serialized Fields
    
    modified
    
    boolean modified
    
    oneLetterName
    
    String oneLetterName
    
    threeLetterName
    
    String threeLetterName
- Class chemaxon.struc.sgroup.AttachmentPoint
  
  class AttachmentPoint extends Object implements Serializable
  
  serialVersionUID:
  
  -7484860308765339862L
  - Serialized Fields
    
    atom
    
    MolAtom atom
    
    bond
    
    MolBond bond
    
    order
    
    int order
- Class chemaxon.struc.sgroup.DataSgroup
  
  class DataSgroup extends Sgroup implements Serializable
  
  serialVersionUID:
  
  -3132191586564122343L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
    
    Deserializes a data Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    ois - the object input stream
    
    Throws:
    
    ClassNotFoundException
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream oos) throws IOException
    
    Serializes a data Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    oos - the object output stream
    
    Throws:
    
    IOException
  - Serialized Fields
    
    labelPosition
    
    chemaxon.struc.sgroup.DataSgroup.AbstractPosition labelPosition
    
    sb
    
    StringBuffer sb
    
    temporary variable for getLineOnScreen
- Class chemaxon.struc.sgroup.MulticenterSgroup
  
  class MulticenterSgroup extends Sgroup implements Serializable
  
  serialVersionUID:
  
  -7213879722783498112L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
    
    Deserializes a Multicenter Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    ois - the object input stream
    
    Throws:
    
    ClassNotFoundException
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream oos) throws IOException
    
    Serializes a Multicenter Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    oos - the object output stream
    
    Throws:
    
    IOException
- Class chemaxon.struc.sgroup.MultipleSgroup
  
  class MultipleSgroup extends Sgroup implements Serializable
  
  serialVersionUID:
  
  -1146464131016252826L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
    
    Deserializes a multiple Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    ois - the object input stream
    
    Throws:
    
    ClassNotFoundException
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream oos) throws IOException
    
    Serializes a multiple Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    oos - the object output stream
    
    Throws:
    
    IOException
- Exception chemaxon.struc.sgroup.NoFreeAttachmentPointException
  
  class NoFreeAttachmentPointException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  2226630752133341633L
  - Serialized Fields
    
    sga
    
    SgroupAtom sga
- Class chemaxon.struc.sgroup.RepeatingUnitSgroup
  
  class RepeatingUnitSgroup extends Sgroup implements Serializable
  
  serialVersionUID:
  
  -3209611525734625009L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
    
    Deserializes an SRU Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    ois - the object input stream
    
    Throws:
    
    ClassNotFoundException
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream oos) throws IOException
    
    Serializes an SRU Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    oos - the object output stream
    
    Throws:
    
    IOException
- Class chemaxon.struc.sgroup.SgroupAtom
  
  class SgroupAtom extends MolAtom implements Serializable
  
  serialVersionUID:
  
  -3185634359981637075L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
    
    Deserializes an Sgroup superatom. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    ois - the object input stream
    
    Throws:
    
    ClassNotFoundException
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream oos) throws IOException
    
    Serializes an Sgroup superatom. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    oos - the object output stream
    
    Throws:
    
    IOException
  - Serialized Fields
    
    labelCenter
    
    int labelCenter
- Class chemaxon.struc.sgroup.SuperatomSgroup
  
  class SuperatomSgroup extends Sgroup implements Serializable
  
  serialVersionUID:
  
  2968529752634209305L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
    
    Deserializes a superatom Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    ois - the object input stream
    
    Throws:
    
    ClassNotFoundException
    
    IOException
    
    writeObject
    
    private void writeObject(ObjectOutputStream oos) throws IOException
    
    Serializes a superatom Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.
    
    Parameters:
    
    oos - the object output stream
    
    Throws:
    
    IOException
  - Serialized Fields
    
    apContainer
    
    chemaxon.struc.sgroup.AttachmentPointContainer apContainer
    
    Attachment Point container object
Package com.chemaxon.search.transformation
- Exception com.chemaxon.search.transformation.TransformationException
  
  class TransformationException extends Exception implements Serializable

Serialized Form

Package chemaxon.calculations

Exception chemaxon.calculations.CalculationException

Package chemaxon.calculations.clean

Class chemaxon.calculations.clean.AtomChangeEvent

Package chemaxon.calculator

Exception chemaxon.calculator.CalculatorException

Package chemaxon.common.util

Exception chemaxon.common.util.ArgumentException

Class chemaxon.common.util.ByteVector

Serialized Fields

data

size

Class chemaxon.common.util.DoubleVector

Serialized Fields

data

size

Class chemaxon.common.util.FloatVector

Serialized Fields

data

size

Class chemaxon.common.util.IntVector

Serialized Fields

data

size

Exception chemaxon.common.util.LazyCalculationAlreadyFailedException

Class chemaxon.common.util.LongVector

Serialized Fields

data

size

Exception chemaxon.common.util.ResourceCleaner.ResourceClosingException

Exception chemaxon.common.util.ServiceNotFoundException

Class chemaxon.common.util.ShortVector

Serialized Fields

data

size

Package chemaxon.core

Exception chemaxon.core.SequenceBuildingException

Serialized Fields

errorKey

Package chemaxon.core.calculations.valencecheck

Class chemaxon.core.calculations.valencecheck.ValenceCheckOptions

Serialized Fields

localAromatic

traditionalNAllowed

Exception chemaxon.core.calculations.valencecheck.ValenceColumnException

Exception chemaxon.core.calculations.valencecheck.ValenceException

Exception chemaxon.core.calculations.valencecheck.ValenceTypeException

Package chemaxon.core.util

Class chemaxon.core.util.BondTable

Serialized Fields

atomCount

Package chemaxon.descriptors

Exception chemaxon.descriptors.MDGeneratorException

Exception chemaxon.descriptors.MDParametersException

Exception chemaxon.descriptors.SimilarityException

Package chemaxon.formats

Exception chemaxon.formats.MolFormatException

Serialized Fields

lineNumberInFile

lineNumberInRecord

Package chemaxon.jep

Class chemaxon.jep.ChemFunction

Serialized Fields

context

Class chemaxon.jep.ChemJEP

Serialized Fields

allowUndeclared

context

contextClass

errorList

evaluator

expression

funTab

implicitMul

legacyMode

symTab

traverse

Exception chemaxon.jep.ConditionException

Class chemaxon.jep.Evaluator