Serialized Form (JChem Base API documentation (c) 1998-2023 Chemaxon Ltd.)

Package chemaxon.calculations
- Class chemaxon.calculations.CalculationException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  1L
Package chemaxon.calculations.clean
- Class chemaxon.calculations.clean.AtomChangeEvent extends EventObject implements Serializable
Package chemaxon.calculator
- Class chemaxon.calculator.CalculatorException extends Exception implements Serializable
  
  serialVersionUID:
  
  1L
Package chemaxon.clustering
- Class chemaxon.clustering.ChemicalSpace extends Vector implements Serializable
  - Serialized Fields
    - checked
      
      BitSet checked
    - dimensions
      
      int dimensions
    - emptyset
      
      BitSet emptyset
    - fpsize
      
      int fpsize
    - inv
      
      chemaxon.clustering.ChemicalSpace.InvertedFile inv
    - weights
      
      float[] weights
    - willett
      
      boolean willett
- Class chemaxon.clustering.ClusteringException extends Exception implements Serializable
- Class chemaxon.clustering.Heap.HeapException extends RuntimeException implements Serializable
- Class chemaxon.clustering.InvalidLicenseKeyException extends Exception implements Serializable
Package chemaxon.common.util
- Class chemaxon.common.util.ByteVector extends Object implements Serializable
  
  serialVersionUID:
  
  -1393815508326465236L
  - Serialized Fields
    - data
      
      byte[] data
    - size
      
      int size
- Class chemaxon.common.util.DoubleVector extends Object implements Serializable
  
  serialVersionUID:
  
  -5138497375635267024L
  - Serialized Fields
    - data
      
      double[] data
    - size
      
      int size
- Class chemaxon.common.util.FloatVector extends Object implements Serializable
  
  serialVersionUID:
  
  -2327634131748729635L
  - Serialized Fields
    - data
      
      float[] data
    - size
      
      int size
- Class chemaxon.common.util.GeomCalc.GeomCalcException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  -1705490613297709773L
- Class chemaxon.common.util.GeomCalc.Queue.Overflow extends Exception implements Serializable
  
  serialVersionUID:
  
  -6957894135268794743L
- Class chemaxon.common.util.GeomCalc.Queue.Underflow extends Exception implements Serializable
  
  serialVersionUID:
  
  -1972826041963082169L
- Class chemaxon.common.util.IntMap extends HashMap<K extends Object,Integer> implements Serializable
  
  serialVersionUID:
  
  4318465509620546463L
- Class chemaxon.common.util.IntPair extends Object implements Serializable
  
  serialVersionUID:
  
  1961353781713733629L
  - Serialized Fields
    - left
      
      int left
    - right
      
      int right
- Class chemaxon.common.util.IntVector extends Object implements Serializable
  
  serialVersionUID:
  
  -9011852065319440166L
  - Serialized Fields
    - data
      
      int[] data
    - size
      
      int size
- Class chemaxon.common.util.LongVector extends Object implements Serializable
  
  serialVersionUID:
  
  8437448887389765952L
  - Serialized Fields
    - data
      
      long[] data
    - size
      
      int size
- Class chemaxon.common.util.ShortVector extends Object implements Serializable
  
  serialVersionUID:
  
  8407562362886825374L
  - Serialized Fields
    - data
      
      short[] data
    - size
      
      int size
Package chemaxon.core
- Class chemaxon.core.SequenceBuildingException extends RuntimeException implements Serializable
  - Serialized Fields
    - errorKey
      
      String errorKey
Package chemaxon.core.calculations.valencecheck
- Class chemaxon.core.calculations.valencecheck.ValenceCheckOptions extends Object implements Serializable
  
  serialVersionUID:
  
  568843891825099500L
  - Serialized Fields
    - localAromatic
      
      boolean localAromatic
    - traditionalNallowed
      
      boolean traditionalNallowed
- Class chemaxon.core.calculations.valencecheck.ValenceColumnException extends chemaxon.core.calculations.valencecheck.ValenceException implements Serializable
- Class chemaxon.core.calculations.valencecheck.ValenceException extends Exception implements Serializable
- Class chemaxon.core.calculations.valencecheck.ValenceTypeException extends chemaxon.core.calculations.valencecheck.ValenceException implements Serializable
Package chemaxon.core.util
- Class chemaxon.core.util.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
- Class chemaxon.descriptors.MDGeneratorException extends Exception implements Serializable
- Class chemaxon.descriptors.MDParametersException extends RuntimeException implements Serializable
- Class chemaxon.descriptors.MDReaderException extends Exception implements Serializable
- Class chemaxon.descriptors.MDWriterException extends Exception implements Serializable
- Class chemaxon.descriptors.SimilarityException extends Exception implements Serializable
Package chemaxon.formats
- Class chemaxon.formats.MolFormatException extends IOException implements Serializable
  - Serialized Fields
    - lineNumberInFile
      
      int lineNumberInFile
    - lineNumberInRecord
      
      int lineNumberInRecord
Package chemaxon.formats.documents.jchemoffice
- Class chemaxon.formats.documents.jchemoffice.BatchProcessingException extends IOException implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - _exceptions
      
      List<Throwable> _exceptions
- Class chemaxon.formats.documents.jchemoffice.InvalidSizeScaleArgumentException extends chemaxon.util.ArgumentException implements Serializable
  
  serialVersionUID:
  
  1L
Package chemaxon.jchem.db
- Class chemaxon.jchem.db.DatabaseSearchException extends Exception implements Serializable
- Class chemaxon.jchem.db.MaxSearchFrequencyExceededException extends DatabaseSearchException implements Serializable
- Class chemaxon.jchem.db.RecalculationException extends Exception implements Serializable
  
  serialVersionUID:
  
  -2767058042924323545L
- Class chemaxon.jchem.db.TransferException extends Exception implements Serializable
  
  serialVersionUID:
  
  -5241498055624956036L
- Class chemaxon.jchem.db.UpdateHandler.RowData extends Object implements Serializable
  
  serialVersionUID:
  
  -4040824446004135801L
  - Serialized Fields
    - chemTermColValues
      
      Map<String,Object> chemTermColValues
    - descriptorData
      
      byte[][] descriptorData
    - fingerprint
      
      int[] fingerprint
    - flags
      
      String flags
    - formula
      
      String formula
    - hashCode
      
      int hashCode
    - markushData
      
      byte[] markushData
    - molecule
      
      Molecule molecule
    - molName
      
      String molName
    - molString
      
      byte[] molString
    - molWeight
      
      Double molWeight
    - noRingInfoInFP
      
      boolean noRingInfoInFP
    - reactionMappingIncomplete
      
      boolean reactionMappingIncomplete
    - screenDescriptor
      
      byte[] screenDescriptor
    - smiles
      
      String smiles
    - sortableFormula
      
      String sortableFormula
    - tautomer
      
      Molecule tautomer
    - tautomerFragmentHashCode
      
      int[] tautomerFragmentHashCode
    - tautomerHashCode
      
      int tautomerHashCode
- Class chemaxon.jchem.db.UpdateHandlerException extends Exception implements Serializable
  
  serialVersionUID:
  
  -8755169336283449997L
- Class chemaxon.jchem.db.UpdateHandlerMetaData extends Object implements Serializable
  
  serialVersionUID:
  
  -6512295793385774884L
  - Serialized Fields
    - chemTermColumns
      
      String[] chemTermColumns
    - chemTermForColumn
      
      Map<String,String> chemTermForColumn
    - collectionType
      
      chemaxon.jchem.base.storage.StructureCollectionType collectionType
    - compressedStructureFieldSupported
      
      boolean compressedStructureFieldSupported
    - descriptorSettings
      
      Map<String,String> descriptorSettings
    - descriptorTypes
      
      Map<String,String> descriptorTypes
    - duplicateFilteringOption
      
      boolean duplicateFilteringOption
    - insertDescriptorNames
      
      List<String> insertDescriptorNames
    - numberOfCombinedFPColumns
      
      int numberOfCombinedFPColumns
    - numberOfEdges
      
      int numberOfEdges
    - numberOfOnes
      
      int numberOfOnes
    - numberOfStructuralFPColumns
      
      int numberOfStructuralFPColumns
    - standardizerConfig
      
      String standardizerConfig
    - structuralKeys
      
      String structuralKeys
    - tableType
      
      int tableType
    - tautomerDuplicateFilteringEnabled
      
      boolean tautomerDuplicateFilteringEnabled
    - tautomerEqualityMode
      
      chemaxon.sss.search.options.TautomerTransformationMode tautomerEqualityMode
    - updateDescriptorNames
      
      List<String> updateDescriptorNames
- Class chemaxon.jchem.db.UpdateHandlerRowDataException extends UpdateHandlerException implements Serializable
  
  serialVersionUID:
  
  -7274357064259684370L
  - Serialized Fields
    - rowData
      
      UpdateHandler.RowData rowData
- Class chemaxon.jchem.db.Updater.UpdateInfo extends Object implements Serializable
  
  serialVersionUID:
  
  4160146885445230514L
  - Serialized Fields
    - additionalInformation
      
      String[] additionalInformation
      
      Additional information for the entities in same order, if needed.
      
      Since:
      
      JChem 6.0
    - entityList
      
      String[] entityList
      
      The names of entities (e.g. table names) to be updated, or null.
    - isOperationRequired
      
      boolean isOperationRequired
      
      Indicates whether the operation is required or not.
      
      Since:
      
      JChem 5.3
    - isProgressMonitoringSupported
      
      boolean isProgressMonitoringSupported
      
      Indicates whether update process supports progress monitoring.
      
      Since:
      
      JChem 5.1.2
    - isRegeneration
      
      boolean isRegeneration
      
      Deprecated.
      since 5.1.2 use Updater.UpdateInfo.isProgressMonitoringSupported instead.
      
      Indicates if the update process is the regeneration of all tables. Since this can be a lengthy process, progress monitoring may be needed. In this case the table names in Updater.UpdateInfo.entityList can be used directly for UpdateHandler.recalculateTable(chemaxon.util.ConnectionHandler, String, boolean, String, java.util.Map, Boolean, chemaxon.jchem.file.ProgressWriter)
    - isStructuralChange
      
      boolean isStructuralChange
      
      Indicates whether the operation is required or not.
      
      Since:
      
      JChem 5.8
    - message
      
      String message
      
      Massage describing what update is necessary and why.
    - processingMessage
      
      String processingMessage
      
      A message that can be displayed during the update, e.g. "Recalculating tables"
    - regenerationType
      
      int regenerationType
      
      Indicates the regeneration type.
      
      Since:
      
      JChem 5.2.4
Package chemaxon.jchem.db.cache
- Class chemaxon.jchem.db.cache.CachePool extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - cacheHash
      
      Hashtable<String,chemaxon.jchem.db.cache.JChemCache> cacheHash
    - cacheRemovalMethod
      
      chemaxon.jchem.db.cache.CacheRemovalMethod cacheRemovalMethod
    - expirationTime
      
      double expirationTime
    - maxCacheMemory
      
      long maxCacheMemory
    - maxCacheMemoryCalculated
      
      boolean maxCacheMemoryCalculated
    - maxCacheSizeMB
      
      int maxCacheSizeMB
    - minFreeMemMB
      
      int minFreeMemMB
- Class chemaxon.jchem.db.cache.CacheRegistrationException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - reason
      
      chemaxon.jchem.db.cache.CacheRegistrationException.Reason reason
Package chemaxon.jep
- Class chemaxon.jep.ChemFunction extends chemaxon.nfunk.jep.function.PostfixMathCommand implements Serializable
  
  serialVersionUID:
  
  -3446599636099344973L
  - Serialized Fields
    - cached
      
      boolean cached
    - jep
      
      ChemJEP jep
- Class chemaxon.jep.ChemJEP extends chemaxon.nfunk.jep.JEP implements Serializable
  - Serialized Fields
    - context
      
      ChemContext context
      
      The evaluation context object.
    - contextClass
      
      Class contextClass
      
      The evaluation context class.
- Class chemaxon.jep.ConditionException extends Exception implements Serializable
- Class chemaxon.jep.ContextFunction extends chemaxon.nfunk.jep.function.PostfixMathCommand implements Serializable
  
  serialVersionUID:
  
  6471101129584627604L
  - Serialized Fields
    - jep
      
      ChemJEP jep
    - name
      
      String name
- Class chemaxon.jep.DissimilarityFunction extends chemaxon.jep.ChemFunction implements Serializable
  - Serialized Fields
    - className
      
      String className
    - descriptors
      
      String[] descriptors
- Class chemaxon.jep.Evaluator extends Object implements Serializable
  - Serialized Fields
    - builtInConfig
      
      chemaxon.jep.EvaluatorConfiguration builtInConfig
      
      The configuration object containing default function/plugin declarations.
    - config
      
      chemaxon.jep.EvaluatorConfiguration config
      
      The configuration object.
    - externalConfig
      
      chemaxon.jep.EvaluatorConfiguration externalConfig
      
      The configuration object containing external function/plugin declarations.
    - functionalGroupDisplayMolTable
      
      Hashtable<String,String> functionalGroupDisplayMolTable
      
      |functional group name| -> |displayable molecule representation|
    - licenseEnvironment
      
      String licenseEnvironment
    - servicesConfigurationPath
      
      String servicesConfigurationPath
      
      services configuration path
      
      Since:
      
      5.10
    - servicesFunctionTable
      
      Hashtable<String,chemaxon.nfunk.jep.function.PostfixMathCommandI> servicesFunctionTable
      
      Function table for services.
    - symtab
      
      chemaxon.nfunk.jep.SymbolTable symtab
      
      The base symbol table.
    - userConfig
      
      chemaxon.jep.EvaluatorConfiguration userConfig
      
      The configuration object containing user defined function/plugin declarations.
    - verbose
      
      boolean verbose
      
      True if verbose output.
- Class chemaxon.jep.EvaluatorFunction extends chemaxon.jep.ChemFunction implements Serializable
  - Serialized Fields
    - evaluator
      
      Evaluator evaluator
- Class chemaxon.jep.MatchFunction extends chemaxon.jep.ChemFunction implements Serializable
  - Serialized Fields
    - attributes
      
      chemaxon.jep.util.SearchAttributes attributes
    - className
      
      String className
    - dir
      
      String dir
    - licenseEnvironment
      
      String licenseEnvironment
    - standardizer
      
      chemaxon.jep.Standardizer standardizer
    - subMatches
      
      Hashtable subMatches
    - type
      
      int type
Package chemaxon.jep.context
- Class chemaxon.jep.context.AtomContext extends MolContext implements Serializable
  - Serialized Fields
    - atom
      
      int atom
      
      The input atom index.
- Class chemaxon.jep.context.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
      
      com.google.common.base.Supplier<Molecule> supplier
      
      The molecule supplier.
- Class chemaxon.jep.context.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 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
- Class chemaxon.license.LicenseException extends RuntimeException implements Serializable
  - Serialized Fields
    - product
      
      String product
- Class chemaxon.license.LicenseProcessingException extends Exception implements Serializable
Package chemaxon.marvin
- Class chemaxon.marvin.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 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
- Class chemaxon.marvin.alignment.AlignmentException extends Exception implements Serializable
- Class chemaxon.marvin.alignment.NoConstraintException extends chemaxon.marvin.alignment.AlignmentException implements Serializable
- Class chemaxon.marvin.alignment.OptimizationException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  1L
- Class chemaxon.marvin.alignment.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
- Class chemaxon.marvin.alignment.TooDissimilarException extends chemaxon.marvin.alignment.AlignmentException implements Serializable
Package chemaxon.marvin.beans
- Class chemaxon.marvin.beans.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 extends JPanel implements Serializable
  
  serialVersionUID:
  
  7229361698115302929L
  - Serialized Fields
    - printer
      
      MolPrinter printer
- Class chemaxon.marvin.beans.MSketch extends Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialization Methods
    - readExternal
      
      public void readExternal(ObjectInput in) throws IOException, ClassNotFoundException
      
      Restores the sketcher's state.
      
      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.
      
      Throws:
      
      IOException - Includes any I/O exceptions that may occur
- Class chemaxon.marvin.beans.MSketchPane extends MarvinPane implements Serializable
  
  serialVersionUID:
  
  602496692422927170L
  - Serialized Fields
    - commonActions
      
      chemaxon.marvin.common.swing.action.CommonActions commonActions
- Class chemaxon.marvin.beans.MView extends Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialization Methods
    - readExternal
      
      public void readExternal(ObjectInput in) throws IOException, ClassNotFoundException
      
      Restores the viewer's state.
      
      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.
      
      Throws:
      
      IOException - Includes any I/O exceptions that may occur
- Class chemaxon.marvin.beans.MViewEditor extends AbstractCellEditor implements Serializable
  
  serialVersionUID:
  
  1549621132660875966L
  - Serialized Fields
    - editorComponent
      
      MViewPane editorComponent
- Class chemaxon.marvin.beans.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 extends MViewPane implements Serializable
  
  serialVersionUID:
  
  5566509759455312369L
Package chemaxon.marvin.calculations
- Class chemaxon.marvin.calculations.BitPattern extends BitSet implements Serializable
Package chemaxon.marvin.io
- Class chemaxon.marvin.io.Encoding extends Object implements Serializable
  - Serialization Methods
    - readExternal
      
      public void readExternal(ObjectInput arg0) throws IOException
      
      Throws:
      
      IOException
    - writeExternal
      
      public void writeExternal(ObjectOutput arg0) throws IOException
      
      Throws:
      
      IOException
- Class chemaxon.marvin.io.MolExportException extends IOException implements Serializable
  - Serialized Fields
    - molIndex
      
      int molIndex
- Class chemaxon.marvin.io.MRecordParseException extends Exception implements Serializable
  - Serialized Fields
    - position
      
      MRecordReader.Position position
Package chemaxon.marvin.modules.datatransfer
- Class chemaxon.marvin.modules.datatransfer.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 selectorList
Package chemaxon.marvin.plugin
- Class chemaxon.marvin.plugin.PluginException extends Exception implements Serializable
  - Serialized Fields
    - level
      
      int level
      
      Deprecated, for removal: This API element is subject to removal in a future version.
      
      Error level.
- Class chemaxon.marvin.plugin.PluginInputCheckerException extends PluginException implements Serializable
Package chemaxon.marvin.plugin.concurrent
- Class chemaxon.marvin.plugin.concurrent.PluginExecutionException extends ExecutionException implements Serializable
  - Serialized Fields
    - plugin
      
      CalculatorPlugin plugin

Package chemaxon.marvin.plugin.gui

Class chemaxon.marvin.plugin.gui.CheckList extends JPanel implements Serializable
- Serialized Fields
  - checkboxes
```
chemaxon.marvin.plugin.gui.CheckList.MCheckBox[] checkboxes
```

Class chemaxon.marvin.plugin.gui.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

title
```
String title
```

Class chemaxon.marvin.plugin.gui.ParameterPanel extends JPanel implements Serializable
- Serialized Fields
  - items
```
chemaxon.marvin.plugin.gui.ParameterItem[] items
```

Class chemaxon.marvin.plugin.gui.ResultView extends JDialog implements Serializable

serialVersionUID:: -5728800883025815500L

Serialized Fields

bottomComponent
```
JComponent bottomComponent
```
bottomTextArea
```
JTextArea bottomTextArea
```
chart
```
chemaxon.marvin.util.MarvinModule 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
- Class chemaxon.marvin.services.ServiceException extends Exception implements Serializable
  
  serialVersionUID:
  
  328496720368460819L

Package chemaxon.marvin.sketch

Class chemaxon.marvin.sketch.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 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.space
- Class chemaxon.marvin.space.EventQueue extends Vector implements Serializable
- Class chemaxon.marvin.space.GraphicScene extends JPanel implements Serializable
  - Serialized Fields
    - _glListsToDelete
      
      ArrayList<Integer> _glListsToDelete
    - activeCell
      
      int activeCell
      
      index of the active cell: cells are numbered line-by-line
    - antialias
      
      boolean antialias
    - backgroundColor
      
      float[] backgroundColor
      
      we use java.awt.Color in the following cases - when the color does not change too often - when the user can change the given color - when we don't have to give it to OGL2 too often (like color of an atom, etc) These are e.g. : background color, constant component colors
    - backgroundColorChanged
      
      boolean backgroundColorChanged
    - canvas
      
      Component canvas
    - cellCount
      
      int cellCount
      
      number of cells (there might be fewer cells than cells.length())
    - cells
      
      GraphicCell[] cells
      
      components per cells, line-by-line 0 is the top-left corner
    - columnCount
      
      int columnCount
      
      layout of the graphic view: number of cells per column
    - defaultDrawProperties
      
      Map<Object,Object> defaultDrawProperties
    - eventHandler
      
      chemaxon.marvin.space.MSpaceEventHandler eventHandler
    - gl
      
      javax.media.opengl.GL2 gl
    - glAutoDrawable
      
      javax.media.opengl.GLAutoDrawable glAutoDrawable
    - globalDrawProperties
      
      Properties globalDrawProperties
    - gltext
      
      chemaxon.marvin.space.util.GLText gltext
      
      this is used to display warning about unregistered product
    - glu
      
      javax.media.opengl.glu.GLU glu
    - height
      
      int height
      
      physical height of the entire scene (in pixels)
    - initialized
      
      boolean initialized
    - motionmode
      
      int motionmode
      
      standing or moving mode
    - needsRefresh
      
      int needsRefresh
      
      Indicates with internal index which cell needs redraw. -1 means none, cellCount means all cells.
    - needsReset
      
      int needsReset
    - progressBar
      
      chemaxon.marvin.space.gui.JMSpaceProgressBar progressBar
    - renderTargets
      
      chemaxon.marvin.space.gl.shader.RenderTargets renderTargets
    - rowCount
      
      int rowCount
      
      layout of the graphic view: number of cells per row
    - rx
      
      double rx
      
      rotation around x-y-z axises
    - ry
      
      double ry
      
      rotation around x-y-z axises
    - rz
      
      double rz
      
      rotation around x-y-z axises
    - smoothBackground
      
      boolean smoothBackground
    - synchronousMode
      
      boolean synchronousMode
    - transparentBackground
      
      int transparentBackground
    - userSettings
      
      UserSettings userSettings
    - verboseLevel
      
      int verboseLevel
    - width
      
      int width
      
      physical width of the entire scene (in pixels)
Package chemaxon.marvin.uif.dialog
- Class chemaxon.marvin.uif.dialog.CategoriesDialog 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 extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable
  - Serialized Fields
    - module
      
      chemaxon.marvin.uif.module.GUIModule module
- Class chemaxon.marvin.uif.dialog.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 extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable
- Class chemaxon.marvin.uif.dialog.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 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 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 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 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
- Class chemaxon.marvin.util.CancelPrintException extends Exception implements Serializable
  
  serialVersionUID:
  
  7380116746554005158L
- Class chemaxon.marvin.util.MarvinModule extends Object implements Serializable
  
  serialVersionUID:
  
  2763330874643316763L
- Class chemaxon.marvin.util.MarvinOLEFrame extends JFrame implements Serializable
  
  serialVersionUID:
  
  7801720334170069726L
  - Serialized Fields
    - sp
      
      Semaphore sp
- Class chemaxon.marvin.util.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 extends Object implements Serializable
  
  serialVersionUID:
  
  -1600625160321014724L

Package chemaxon.marvin.util.codeassist

Class chemaxon.marvin.util.codeassist.ChemTermDocument extends DefaultStyledDocument implements Serializable

serialVersionUID:: -5894946790409031807L

Serialized Fields

comment
```
MutableAttributeSet comment
```
constant
```
MutableAttributeSet constant
```
constants
```
Map<String,AttributeSet> constants
```
currentElementIndex
```
int currentElementIndex
```
doc
```
DefaultStyledDocument doc
```
fontName
```
String fontName
```
fontSize
```
int fontSize
```
function
```
MutableAttributeSet function
```
functions
```
Map<String,AttributeSet> functions
```
HIGHLIGHT_TIMER
```
Timer HIGHLIGHT_TIMER
```
keyword
```
MutableAttributeSet keyword
```
keywords
```
Map<String,AttributeSet> keywords
```
lastPrefixState
```
boolean lastPrefixState
```
multiLineComment
```
boolean multiLineComment
```
normal
```
MutableAttributeSet normal
```
parenLength
```
int parenLength
```
parenOffset
```
int parenOffset
```
parenthesis
```
MutableAttributeSet parenthesis
```
prefix
```
String prefix
```
quote
```
MutableAttributeSet quote
```
rootElement
```
Element rootElement
```

Class chemaxon.marvin.util.codeassist.CompletionItemCellRenderer extends DefaultListCellRenderer implements Serializable

serialVersionUID:

6746125418422903808L

Class chemaxon.marvin.util.codeassist.MacroManagerPanel extends JPanel implements Serializable

serialVersionUID:: -4703035835623320688L

Serialized Fields

ACCEPT_ACTION
```
Action ACCEPT_ACTION
```
acceptButton
```
JButton acceptButton
```
acceptEditButton
```
JButton acceptEditButton
```
addButton
```
JButton addButton
```
CANCEL_ACTION
```
Action CANCEL_ACTION
```
cancelButton
```
JButton cancelButton
```
cancelEditButton
```
JButton cancelEditButton
```
deleteButton
```
JButton deleteButton
```
descPane
```
JTextPane descPane
```
descScrollPane
```
JScrollPane descScrollPane
```
editButton
```
JButton editButton
```
editedItem
```
int editedItem
```
editPanel
```
JPanel editPanel
```

helper

chemaxon.marvin.util.codeassist.CodeAssistMacrosHelper helper

layout
```
CardLayout layout
```
listPanel
```
JPanel listPanel
```
macroList
```
JList macroList
```
macroListScroll
```
JScrollPane macroListScroll
```
macroPane
```
JTextPane macroPane
```
macroScrollPane
```
JScrollPane macroScrollPane
```
nameField
```
JTextField nameField
```

Package chemaxon.marvin.view
- Class chemaxon.marvin.view.MDocStorage.CancellationException extends Exception implements Serializable
- Class chemaxon.marvin.view.MDocStorage.RecordUnavailableException extends Exception implements Serializable
  - Serialized Fields
    - recordIndex
      
      int recordIndex

Package chemaxon.marvin.view.swing

Class chemaxon.marvin.view.swing.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 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

chemaxon.marvin.swing.MAction windowAction

winScale
```
double winScale
```

Class chemaxon.marvin.view.swing.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 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

chemaxon.marvin.swing.MAction[] navigationActions

oldMarkedAtom
```
int oldMarkedAtom
```
oldMarkedCell
```
int oldMarkedCell
```
rasmolScripts
```
String[] rasmolScripts
```
rows
```
int rows
```
selectable
```
boolean selectable
```
selected
```
int selected
```

skbridge

chemaxon.marvin.view.modules.sketchbridge.MViewSketch skbridge

startLoad
```
boolean startLoad
```
tableSupport
```
TableSupport tableSupport
```
tabScale
```
double tabScale
```
tabScaleCalcInProgress
```
int tabScaleCalcInProgress
```
tabScaleCalcNeeded
```
boolean tabScaleCalcNeeded
```

viewActions

chemaxon.marvin.view.swing.ViewActions viewActions

viewHandler

chemaxon.marvin.view.swing.ViewHandler viewHandler

winScale
```
double winScale
```

Class chemaxon.marvin.view.swing.WholeNumberField extends JTextField implements Serializable
- Serialized Fields
  - integerFormatter
```
NumberFormat integerFormatter
```
  - options
```
int options
```
  - toolkit
```
Toolkit toolkit
```
Class chemaxon.marvin.view.swing.WholeNumberField.WholeNumberDocument extends PlainDocument implements Serializable

Package chemaxon.naming
- Class chemaxon.naming.NameFormatException extends MolFormatException implements Serializable
  - Serialized Fields
    - prefix
      
      String prefix
- Class chemaxon.naming.NameFormatException.FilteredCase extends NameFormatException implements Serializable
- Class chemaxon.naming.NamePrefixException extends NameFormatException implements Serializable
  - Serialized Fields
    - token
      
      String token
Package chemaxon.naming.document
- Class chemaxon.naming.document.D2SOptionsParser.UnknownOptionException extends Exception implements Serializable
- Class chemaxon.naming.document.D2SPdfParser extends org.apache.tika.parser.pdf.ExtendablePdfParser implements Serializable
- Class chemaxon.naming.document.D2STextParser extends Object implements Serializable
- Class chemaxon.naming.document.EncryptedDocumentException extends IOException implements Serializable
- Class chemaxon.naming.document.OsrParser extends org.apache.tika.parser.AbstractParser implements Serializable
- Class chemaxon.naming.document.SafeOfficeParser extends org.apache.tika.parser.microsoft.OfficeParser implements Serializable
- Class chemaxon.naming.document.TimeoutException extends IOException implements Serializable
  - Serialized Fields
    - timeoutMS
      
      long timeoutMS
- Class chemaxon.naming.document.TrivialXmlParser extends org.apache.tika.parser.AbstractParser implements Serializable
Package chemaxon.naming.document.annotate
- Class chemaxon.naming.document.annotate.AnnotationException extends IOException implements Serializable
Package chemaxon.reaction
- Class chemaxon.reaction.PatternProperty extends Object implements Serializable
  
  serialVersionUID:
  
  -3617253669859174882L
  - Serialized Fields
    - representation
      
      String representation
- Class chemaxon.reaction.ReactionException extends Exception implements Serializable
  
  serialVersionUID:
  
  1L
Package chemaxon.sss.search
- Class chemaxon.sss.search.JChemSearchOptions extends SearchOptions implements Serializable
  
  serialVersionUID:
  
  -6025435983286725061L
  - Serialized Fields
    - absoluteStereo
      
      int absoluteStereo
    - cacheRegistrationNeeded
      
      boolean cacheRegistrationNeeded
      
      Can be set to false in case of readonly databases and jcsearch. Only for internal use!
    - descriptorConfig
      
      String descriptorConfig
      
      configuration for descriptor dissim. calculations
    - descriptorName
      
      String descriptorName
      
      the identifier of stored descriptor used for dissim. calculations, null means pure fingerprint similarity is performed
    - dissimilarityMetric
      
      String dissimilarityMetric
      
      Dissimilarity metric name, or null for default.
    - dissimilarityMetricParameters
      
      String dissimilarityMetricParameters
      
      Dissimilarity metric parameters.
    - dissimilarityThreshold
      
      float dissimilarityThreshold
    - dissimilarityThresholdExcluded
      
      boolean dissimilarityThresholdExcluded
    - filterQuery
      
      String filterQuery
    - formulaSearchQuery
      
      String formulaSearchQuery
      
      Query of the formula search.
    - formulaSearchType
      
      int formulaSearchType
      
      Type of the formula search. See: chemaxon.sss.formula.FormulaSearch
    - haltOnError
      
      HaltOnErrorOption haltOnError
      
      Error handling of the search.
      
      See Also:
      
      HaltOnErrorOption
    - markushScreeningOptions
      
      Set<chemaxon.sss.search.options.MarkushScreeningType> markushScreeningOptions
      
      Set containing all enabled Markush screen methods
    - matchCountOptions
      
      MatchCountOptions matchCountOptions
    - maxResultCount
      
      int maxResultCount
    - optimizeQueries
      
      boolean optimizeQueries
      
      Shows whether the query should be enumerated to improve search
    - returnsNonHits
      
      boolean returnsNonHits
    - totalSearchTimeoutLimitMilliseconds
      
      int totalSearchTimeoutLimitMilliseconds
      
      The search on a database timeouts reaching this number of milliseconds.
- Class chemaxon.sss.search.MarkushFeature extends Object implements Serializable
  
  serialVersionUID:
  
  8770437891053649928L
  - Serialized Fields
    - data
      
      int[] data
      
      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
    - type
      
      int type
      
      Expansion type.
- Class chemaxon.sss.search.MatchCountOptions extends Object implements Serializable
  
  serialVersionUID:
  
  6422092438307828424L
  - Serialized Fields
    - matchCountHighLimit
      
      int matchCountHighLimit
    - matchCountHighLimitInclusive
      
      boolean matchCountHighLimitInclusive
    - matchCounthitLimit
      
      int matchCounthitLimit
    - matchCountIncludesZero
      
      boolean matchCountIncludesZero
    - matchCountLowLimit
      
      int matchCountLowLimit
    - matchCountLowLimitInclusive
      
      boolean matchCountLowLimitInclusive
    - matchCountRelation
      
      String matchCountRelation
    - mode
      
      int mode
- Class chemaxon.sss.search.MolSearchOptions extends SearchOptions implements Serializable
  
  serialVersionUID:
  
  -6364233804214700841L
  - Serialized Fields
    - hitIncludesRNodes
      
      boolean hitIncludesRNodes
      
      If true, the result hit will contain R-nodes with dummy indexes
    - hitIndexType
      
      int hitIndexType
      
      In case of Markush search specifies the representation of the Markush structure on which the hit indexes are retrieved. (default MARKUSH_HIT_ORIGINAL)
    - ignoreChiralityForAtoms
      
      chemaxon.common.util.IntVector ignoreChiralityForAtoms
      
      Contains query atom numbers which should be ignored at the chirality check in case of exact stereo searching. It has a package visibility.
    - markushEnabled
      
      boolean markushEnabled
      
      Decides whether targets with Markush features should be treated as Markush libraries (true) or just "strange" molecules (false) (default value: false).
    - queryAbsoluteStereo
      
      boolean queryAbsoluteStereo
      
      If true, chiral centers in the query molecules are regarded as absolute stereo, ignoring the chiral flag. If the molecule contains any enhanced stereo labels, this flag has no effect.
    - recursiveSMARTSMode
      
      boolean recursiveSMARTSMode
      
      true: at findAll searches only hits are retrieved where the first atom differs as well.
    - switchOffAllProtectsForTDF
      
      boolean switchOffAllProtectsForTDF
      
      If true, all protect features are switched of during generic tautomer creation
    - targetAbsoluteStereo
      
      boolean targetAbsoluteStereo
      
      If true, chiral centers in the target molecules are regarded as absolute stereo, ignoring the chiral flag. If the molecule contains any enhanced stereo labels, this flag has no effect.
    - tautomerEqualityMode
      
      chemaxon.sss.search.options.TautomerTransformationMode tautomerEqualityMode
- Class chemaxon.sss.search.SearchException extends Exception implements Serializable
  
  serialVersionUID:
  
  1698586463587833734L
- Class chemaxon.sss.search.SearchOptions extends Object implements Serializable
  
  serialVersionUID:
  
  -6845044337680993338L
  - Serialized Fields
    - attachedDataMatch
      
      int attachedDataMatch
      
      Specifies attached data match type Default is SearchConstants.ATTACHED_DATA_MATCH_IGNORE
    - attachedDataPrefixes
      
      String attachedDataPrefixes
      
      Data sgroup name prefixes that will be used for comparison When null, all data sgroups will be used.
    - bridgingRAllowed
      
      boolean bridgingRAllowed
      
      True: different undefined R-atoms can match the same group of atoms. Default value: false.
    - changedUserComparator
      
      boolean changedUserComparator
      
      true if user-defined comparators has changed
    - chargeMatching
      
      int chargeMatching
      
      Specifies the charge searching behaviour. Default is CHARGE_MATCHING_DEFAULT (charged query matches only charged target, noncharged query matches all)
    - checkSpHyb
      
      boolean checkSpHyb
      
      If we need to check the sp-hybridization state of the atoms. If used together with vagueBond-4 (SearchConstants.VAGUE_BOND_LEVEL4) option then the bond types are ignored, but the sp hybridization state is still calculated considering the bond types. Benzene matches cyclohexene with double bonds outside (O=C1C(=O)C(=O)C(=O)C(=O)C(=O)1), both planar but different bonds.
      
      Since:
      
      5.1
    - chemTermsFilterOption
      
      chemaxon.sss.search.options.ChemTermsFilterOption chemTermsFilterOption
    - completeHG
      
      boolean completeHG
      
      Specifies if only complete structures should match on target homology groups.
    - copolymerMatching
      
      boolean copolymerMatching
      
      True: Polymers in copolymers can only be matched by copolymers. (default: false)
    - dirty
      
      boolean dirty
      
      This flag is set to true whenever any of the options change. It can be used by Search objects to check whether options changed since the previous initialization. (They set the dirty flag to false during their own initialization.)
    - doubleBondStereoMatchingMode
      
      int doubleBondStereoMatchingMode
      
      Defines the double bond stereo matching mode. Default is DBS_MARKED.
      
      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 (eg atom list, any atom, number of hydrogens, aromaticity, etc) in atoms will not be evaluated, but rather exact matching of these information is required. It is useful for searching in query databases. Default is false.
      
      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 behaviour. Default is ISOTOPE_MATCHING_DEFAULT (isotope query matches only isotope target, nonisotope query matches all)
    - keepQueryOrder
      
      boolean keepQueryOrder
      
      True: instructs search to rearrange query atoms for better search performance.
    - markushAromHandling
      
      MarkushAromaticityHandlingOption markushAromHandling
      
      Specifies handling Markush aromatization information (ambiguous aromatic rings) during Markush search. Currently, the default is MarkushAromaticityHandlingOption.ALL_MATCH_AMBIG: consider Markush aromatization during Markush search, but do not check the hit afterwards.
    - mixSgroupMatching
      
      boolean mixSgroupMatching
      
      True: consider COM, MIX and FOR sgroups during search (default value: true).
    - orderSensitiveSearch
      
      boolean orderSensitiveSearch
      
      Specifies whether the same set of target atoms found in a different order should be considered as a different hit.
    - phaseShift
      
      boolean phaseShift
      
      True: the phase-shifted polymers are matching on each other. (default: true)
    - polymerMatching
      
      boolean polymerMatching
      
      True: consider polymer sgroups during search (default value: true).
    - radicalMatching
      
      int radicalMatching
      
      Specifies the radical searching behaviour. Default is RADICAL_MATCHING_DEFAULT (radical query matches only radical target, nonradical query matches all)
    - reactionUnpairedMapMatching
      
      boolean reactionUnpairedMapMatching
      
      True: in reaction search unpaired (orphan and widow) atom maps can match any atom map (default value: true).
    - rLigandEqualityCheck
      
      boolean rLigandEqualityCheck
      
      True: undefined R-atoms with the same R-group ID should match the same structure. Default value: true.
    - searchType
      
      int searchType
      
      Search type: global mode of search.
    - ssrOption
      
      SetOfSmallestRingsOption ssrOption
      
      Which set of smallest rings to use for property calculations.
    - stereoModel
      
      int stereoModel
      
      Specifies the used stereo model.
    - stereoSearchType
      
      int stereoSearchType
      
      The way stereo information is considered in searching. Default is SearchConstants.STEREO_SPECIFIC.
      
      See Also:
      
      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.
- Class chemaxon.sss.search.SearchTimeoutException extends SearchException implements Serializable
  
  serialVersionUID:
  
  -78126823565453833L
- Class chemaxon.sss.search.UnsupportedQueryException extends IllegalArgumentException implements Serializable
  
  serialVersionUID:
  
  6255906179820229430L
Package chemaxon.sss.search.options
- Class chemaxon.sss.search.options.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 extends ArrayList<GroupDefinition> implements Serializable
Package chemaxon.struc
- Class chemaxon.struc.CTransform3D extends Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialization Methods
    - readExternal
      
      public void readExternal(ObjectInput in) throws IOException
      
      Deserializes a transformation matrix.
      
      Throws:
      
      IOException
      
      Since:
      
      3.5, 11/02/2004
    - writeExternal
      
      public void writeExternal(ObjectOutput out) throws IOException
      
      Serializes a transformation matrix.
      
      Throws:
      
      IOException
      
      Since:
      
      3.5, 11/02/2004
- Class chemaxon.struc.DefaultDictionary extends HashMap<String,SuperatomSgroup> implements Serializable
  
  serialVersionUID:
  
  8013155936541949713L
- Class chemaxon.struc.DPoint3 extends Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialization Methods
    - readExternal
      
      public void readExternal(ObjectInput in) throws IOException, ClassNotFoundException
      
      Deserializes a 3D point.
      
      Throws:
      
      IOException
      
      ClassNotFoundException
    - writeExternal
      
      public void writeExternal(ObjectOutput out) throws IOException
      
      Serializes a 3D point.
      
      Throws:
      
      IOException
- Class chemaxon.struc.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
- Class chemaxon.struc.MacroMolecule.BadMoleculeException extends Exception implements Serializable
  
  serialVersionUID:
  
  9037472982065239933L
- Class chemaxon.struc.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.
      
      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.
      
      Throws:
      
      IOException
- Class chemaxon.struc.MDocument.Prop extends MProp implements Serializable
- Class chemaxon.struc.MDocumentUtil extends Object implements Serializable
  
  serialVersionUID:
  
  12600100100892L
  - Serialized Fields
    - doc
      
      MDocument doc
- Class chemaxon.struc.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.
      
      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.
      
      Throws:
      
      IOException
- Class chemaxon.struc.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.
      
      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.
      
      Throws:
      
      IOException
  - Serialized Fields
    - angle
      
      double angle
    - isValenceCheckNeeded
      
      boolean isValenceCheckNeeded
- Class chemaxon.struc.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.
      
      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.
      
      Throws:
      
      IOException
- Class chemaxon.struc.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.
      
      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.
      
      Throws:
      
      IOException
  - Serialized Fields
    - id
      
      String id
- Class chemaxon.struc.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.
      
      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.
      
      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 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.
      
      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.
      
      Throws:
      
      IOException
- Class chemaxon.struc.MProp extends Object implements Serializable
  
  serialVersionUID:
  
  -5699803671884637223L
  - Serialized Fields
    - coordDependent
      
      boolean coordDependent
    - grinvCC
      
      long grinvCC
- Class chemaxon.struc.MPropertyContainer extends Object implements Serializable
  
  serialVersionUID:
  
  -2575268570438177098L
  - Serialization Methods
    - readExternal
      
      public void readExternal(ObjectInput in) throws IOException, ClassNotFoundException
      
      Restores the property container's state.
      
      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.
      
      Throws:
      
      IOException - Includes any I/O exceptions that may occur
- Class chemaxon.struc.MSelectionDocument extends MDocument implements Serializable
  
  serialVersionUID:
  
  2379294894434293119L
- Class chemaxon.struc.PageSettings extends Object implements Serializable
  
  serialVersionUID:
  
  -7674028514396457694L
  - Serialization Methods
    - readExternal
      
      public void readExternal(ObjectInput arg0) throws IOException, ClassNotFoundException
      
      Throws:
      
      IOException
      
      ClassNotFoundException
    - writeExternal
      
      public void writeExternal(ObjectOutput arg0) throws IOException
      
      Throws:
      
      IOException
- Class chemaxon.struc.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.
      
      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.
      
      Throws:
      
      IOException
- Class chemaxon.struc.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.
      
      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.
      
      Throws:
      
      IOException
- Class chemaxon.struc.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.
      
      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.
      
      Throws:
      
      IOException
- Class chemaxon.struc.SelectionMolecule extends MoleculeGraph implements Serializable
  
  serialVersionUID:
  
  234062772192819675L
- Class chemaxon.struc.SelectionRgMolecule extends SelectionMolecule implements Serializable
- Class chemaxon.struc.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.
      
      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.
      
      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 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 extends MTextBox implements Serializable
  
  serialVersionUID:
  
  -7630363128405095856L
  - Serialized Fields
    - mol
      
      Molecule mol
    - terms
      
      List<chemaxon.struc.graphics.analysis.MAnalysisBoxTerm> terms
- Class chemaxon.struc.graphics.MAssigner extends MPolyline implements Serializable
  - Serialized Fields
    - order
      
      int order
- Class chemaxon.struc.graphics.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.
      
      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.
      
      Throws:
      
      IOException
- Class chemaxon.struc.graphics.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.
      
      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.
      
      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 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.
      
      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.
      
      Throws:
      
      IOException
- Class chemaxon.struc.graphics.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.
      
      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.
      
      Throws:
      
      IOException
  - Serialized Fields
    - baseElectronContainerIndex
      
      int baseElectronContainerIndex
    - baseElectronIndexInContainer
      
      int baseElectronIndexInContainer
- Class chemaxon.struc.graphics.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.
      
      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.
      
      Throws:
      
      IOException
  - Serialized Fields
    - electronIndex
      
      int electronIndex
    - electronLabel
      
      String electronLabel
- Class chemaxon.struc.graphics.MElectron extends MAtomSetPoint implements Serializable
  - Serialization Methods
    - readObject
      
      private void readObject(ObjectInputStream arg0) throws IOException
      
      Throws:
      
      IOException
    - writeObject
      
      private void writeObject(ObjectOutputStream arg0) throws IOException
      
      Throws:
      
      IOException
  - Serialized Fields
    - difLoc
      
      DPoint3 difLoc
    - isPointed
      
      boolean isPointed
- Class chemaxon.struc.graphics.MElectronContainer extends MObject implements Serializable
  - Serialization Methods
    - readObject
      
      private void readObject(ObjectInputStream arg0) throws IOException, ClassNotFoundException
      
      Throws:
      
      IOException
      
      ClassNotFoundException
    - writeObject
      
      private void writeObject(ObjectOutputStream arg0) throws IOException
      
      Throws:
      
      IOException
  - Serialized Fields
    - electronOccupation
      
      boolean[] electronOccupation
    - electrons
      
      chemaxon.struc.graphics.MElectron[] electrons
    - radical
      
      boolean radical
- Class chemaxon.struc.graphics.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.
      
      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.
      
      Throws:
      
      IOException
- Class chemaxon.struc.graphics.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.
      
      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.
      
      Throws:
      
      IOException
- Class chemaxon.struc.graphics.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.
      
      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.
      
      Throws:
      
      IOException
- Class chemaxon.struc.graphics.MMidPoint.Sticky extends MMidPoint implements Serializable
  
  serialVersionUID:
  
  3223068581543532992L
- Class chemaxon.struc.graphics.MMoleculeMovie extends MObject implements Serializable
  
  serialVersionUID:
  
  6476041884742537582L
  - 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.struc.graphics.MNameTextBox extends MTextBox implements Serializable
  
  serialVersionUID:
  
  6302424343157644471L
  - 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.struc.graphics.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.
      
      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.
      
      Throws:
      
      IOException
  - Serialized Fields
    - internalPointAddCount
      
      int internalPointAddCount
    - internalPointPos
      
      int internalPointPos
- Class chemaxon.struc.graphics.MRArrow extends MPolyline implements Serializable
  
  serialVersionUID:
  
  8638690394107448092L
  - 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.struc.graphics.MReactionSign extends MTextBox implements Serializable
  
  serialVersionUID:
  
  -7025949002857142442L
- Class chemaxon.struc.graphics.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.
      
      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.
      
      Throws:
      
      IOException
- Class chemaxon.struc.graphics.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.
      
      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.
      
      Throws:
      
      IOException
- Class chemaxon.struc.graphics.MRectanglePoint.Sticky extends MRectanglePoint implements Serializable
  
  serialVersionUID:
  
  3364078480306200948L
- Class chemaxon.struc.graphics.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.
      
      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.
      
      Throws:
      
      IOException
  - Serialized Fields
    - arcHeight
      
      double arcHeight
    - arcWidth
      
      double arcWidth
- Class chemaxon.struc.graphics.MTextAttributes extends Object implements Serializable
  
  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 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.
      
      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.
      
      Throws:
      
      IOException
  - Serialized Fields
    - actionMap
      
      ActionMap actionMap
- Class chemaxon.struc.graphics.MTextDocument extends Object implements Serializable
  
  serialVersionUID:
  
  6305880304790247656L
  - Serialization Methods
    - readExternal
      
      public void readExternal(ObjectInput in) throws IOException, ClassNotFoundException
      
      Restores the document.
      
      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.
      
      Throws:
      
      IOException - Includes any I/O exceptions that may occur
Package chemaxon.struc.prop
- Class chemaxon.struc.prop.MBooleanProp extends MProp implements Serializable
  
  serialVersionUID:
  
  -5366978422380739811L
  - Serialization Methods
    - readObject
      
      private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
      
      Restores the property's state.
      
      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.
      
      Throws:
      
      IOException - Includes any I/O exceptions that may occur
- Class chemaxon.struc.prop.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 extends MProp implements Serializable
  
  serialVersionUID:
  
  -7479938988131387052L
- Class chemaxon.struc.prop.MDoubleArrayProp extends MProp implements Serializable
  
  serialVersionUID:
  
  -5670039985685584647L
  - Serialization Methods
    - readObject
      
      private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
      
      Restores the property's state.
      
      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.
      
      Throws:
      
      IOException - Includes any I/O exceptions that may occur
- Class chemaxon.struc.prop.MDoubleProp extends MProp implements Serializable
  
  serialVersionUID:
  
  -1221776439131689653L
  - Serialization Methods
    - readObject
      
      private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
      
      Restores the property's state.
      
      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.
      
      Throws:
      
      IOException - Includes any I/O exceptions that may occur
- Class chemaxon.struc.prop.MFontProp extends MProp implements Serializable
  
  serialVersionUID:
  
  2369581307328116455L
  - 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.MHashProp extends MCollectionProp implements Serializable
  
  serialVersionUID:
  
  5457649877894058447L
  - Serialization Methods
    - readObject
      
      private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
      
      Restores the property's state.
      
      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.
      
      Throws:
      
      IOException - Includes any I/O exceptions that may occur
- Class chemaxon.struc.prop.MHCoords3DProp extends MProp implements Serializable
  
  serialVersionUID:
  
  6646271128663088908L
  - Serialization Methods
    - readObject
      
      private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
      
      Restores the property's state.
      
      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.
      
      Throws:
      
      IOException - Includes any I/O exceptions that may occur
- Class chemaxon.struc.prop.MIntegerArrayProp extends MProp implements Serializable
  
  serialVersionUID:
  
  6651869314046996057L
  - Serialization Methods
    - readObject
      
      private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
      
      Restores the property's state.
      
      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.
      
      Throws:
      
      IOException - Includes any I/O exceptions that may occur
- Class chemaxon.struc.prop.MIntegerProp extends MProp implements Serializable
  
  serialVersionUID:
  
  -7179550727198941747L
  - Serialization Methods
    - readObject
      
      private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
      
      Restores the property's state.
      
      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.
      
      Throws:
      
      IOException - Includes any I/O exceptions that may occur
- Class chemaxon.struc.prop.MListProp extends MCollectionProp implements Serializable
  
  serialVersionUID:
  
  5360371881677476960L
  - Serialization Methods
    - readObject
      
      private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
      
      Restores the property's state.
      
      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.
      
      Throws:
      
      IOException - Includes any I/O exceptions that may occur
- Class chemaxon.struc.prop.MMoleculeProp extends MProp implements Serializable
  
  serialVersionUID:
  
  -7687559780023024273L
  - Serialization Methods
    - readObject
      
      private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
      
      Restores the property's state.
      
      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.
      
      Throws:
      
      IOException - Includes any I/O exceptions that may occur
- Class chemaxon.struc.prop.MMoleculeStringProp extends MStringProp implements Serializable
  
  serialVersionUID:
  
  -1005074014113755196L
  - Serialization Methods
    - readObject
      
      private void readObject(ObjectInputStream arg0) throws IOException, ClassNotFoundException
      
      Throws:
      
      IOException
      
      ClassNotFoundException
    - writeObject
      
      private void writeObject(ObjectOutputStream arg0) throws IOException
      
      Throws:
      
      IOException
  - Serialized Fields
    - format
      
      String format
- Class chemaxon.struc.prop.MObjectProp extends MProp implements Serializable
  
  serialVersionUID:
  
  4005646748655675692L
  - Serialization Methods
    - readObject
      
      private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
      
      Restores the property's state.
      
      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.
      
      Throws:
      
      IOException - Includes any I/O exceptions that may occur
- Class chemaxon.struc.prop.MStringProp extends MProp implements Serializable
  
  serialVersionUID:
  
  1373831606368751112L
  - Serialization Methods
    - readObject
      
      private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
      
      Restores the property's state.
      
      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.
      
      Throws:
      
      IOException - Includes any I/O exceptions that may occur
Package chemaxon.struc.sgroup
- Class chemaxon.struc.sgroup.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 extends Object implements Serializable
  
  serialVersionUID:
  
  -7484860308765339862L
  - Serialized Fields
    - atom
      
      MolAtom atom
    - bond
      
      MolBond bond
    - crossingBondType
      
      int crossingBondType
    - leavingAtom
      
      chemaxon.struc.sgroup.LeavingGroupAtom leavingAtom
    - order
      
      int order
- Class chemaxon.struc.sgroup.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.
      
      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.
      
      Throws:
      
      IOException
  - Serialized Fields
    - labelPosition
      
      chemaxon.struc.sgroup.DataSgroup.AbstractPosition labelPosition
    - sb
      
      StringBuffer sb
      
      temporary variable for getLineOnScreen
- Class chemaxon.struc.sgroup.LeavingGroupAtom extends MolAtom implements Serializable
  
  serialVersionUID:
  
  8591241919498353308L
  - Serialization Methods
    - readObject
      
      private void readObject(ObjectInputStream arg0) throws ClassNotFoundException, IOException
      
      Deprecated.
      
      Throws:
      
      ClassNotFoundException
      
      IOException
    - writeObject
      
      private void writeObject(ObjectOutputStream arg0) throws IOException
      
      Deprecated.
      
      Throws:
      
      IOException
  - Serialized Fields
    - alternativeName
      
      String alternativeName
      
      Deprecated.
- Class chemaxon.struc.sgroup.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.
      
      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.
      
      Throws:
      
      IOException
- Class chemaxon.struc.sgroup.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.
      
      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.
      
      Throws:
      
      IOException
- Class chemaxon.struc.sgroup.NoFreeAttachmentPointException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  2226630752133341633L
  - Serialized Fields
    - sga
      
      SgroupAtom sga
- Class chemaxon.struc.sgroup.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.
      
      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.
      
      Throws:
      
      IOException
- Class chemaxon.struc.sgroup.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.
      
      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.
      
      Throws:
      
      IOException
  - Serialized Fields
    - labelCenter
      
      int labelCenter
- Class chemaxon.struc.sgroup.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.
      
      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.
      
      Throws:
      
      IOException
  - Serialized Fields
    - apContainer
      
      chemaxon.struc.sgroup.AttachmentPointContainer apContainer
      
      Attachment Point container object
Package chemaxon.util
- Class chemaxon.util.ArgumentException extends Exception implements Serializable
  
  serialVersionUID:
  
  -8949782741678573705L
- Class chemaxon.util.CmdLine.CmdLineException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  -895875464082822299L
- Class chemaxon.util.Heap.HeapException extends RuntimeException implements Serializable
- Class chemaxon.util.SearchAttributes extends chemaxon.jep.util.SearchAttributes implements Serializable
- Class chemaxon.util.SupplierException extends RuntimeException implements Serializable
Package com.chemaxon.calculations.gui
- Class com.chemaxon.calculations.gui.MChart extends chemaxon.marvin.util.MarvinModule implements Serializable
  - Serialized Fields
    - chart
      
      com.objectplanet.chart.LineChart chart
    - colors
      
      Color[] colors
    - legendMols
      
      Molecule[] legendMols
    - legendTexts
      
      String[] legendTexts
    - precision
      
      int precision
Package com.chemaxon.calculations.io
- Class com.chemaxon.calculations.io.OrderedInputProcessingException extends IllegalArgumentException implements Serializable
  - Serialized Fields
    - inputIndex
      
      int inputIndex
Package com.chemaxon.calculations.util
- Class com.chemaxon.calculations.util.CmdlineContext.ExitWithNonZeroStatus extends RuntimeException implements Serializable
- Class com.chemaxon.calculations.util.CmdlineContext.ExitWithZeroStatus extends RuntimeException implements Serializable
Package com.chemaxon.clustering.framework
- Class com.chemaxon.clustering.framework.RemoveSidechainsMolwalk extends Object implements Serializable
- Class com.chemaxon.clustering.framework.RemoveSidechainsSc extends Object implements Serializable
  - Serialized Fields
    - keepUnsaturatedConnections
      
      boolean keepUnsaturatedConnections
- Class com.chemaxon.clustering.framework.SimpleFrameworkAssociation extends Object implements Serializable
  - Serialized Fields
    - indexToFramework
      
      List<T extends Object> indexToFramework
Package com.chemaxon.descriptors.alignment
- Class com.chemaxon.descriptors.alignment.AbstractShapeComparator extends Object implements Serializable
  - Serialized Fields
    - generator
      
      DescriptorGenerator<T extends ShapeDescriptor> generator
- Class com.chemaxon.descriptors.alignment.AbstractShapeGenerator extends Object implements Serializable
  - Serialized Fields
    - parameters
      
      P extends AbstractShapeGeneratorParameter parameters
- Class com.chemaxon.descriptors.alignment.AbstractShapeGeneratorParameter extends Object implements Serializable
  - Serialized Fields
    - atomTyping
      
      AtomTyping atomTyping
      
      The setting for available shape coloring methods.
- Class com.chemaxon.descriptors.alignment.BaseShapeComparatorParameter extends Object implements Serializable
  - Serialized Fields
    - flexibilityMode
      
      AlignmentProperties.FlexibilityMode flexibilityMode
    - shapeFunction
      
      ShapeFunction shapeFunction
    - tryCount
      
      com.google.common.base.Optional<Integer> tryCount
- Class com.chemaxon.descriptors.alignment.ShapeComparatorException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  1L
- Class com.chemaxon.descriptors.alignment.ShapeGeneratorException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  1L
Package com.chemaxon.descriptors.common
Package com.chemaxon.descriptors.fingerprints.cfp
- Class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters extends Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - bitsPerPattern
      
      int bitsPerPattern
      
      Bits set for each pattern.
    - bondCount
      
      int bondCount
      
      Max pattern length considered (bond count).
    - length
      
      int length
      
      Fingerprint length (bit count).
    - rings
      
      boolean rings
      
      Consider rings in fingerprint generation.
Package com.chemaxon.descriptors.fingerprints.ecfp
- Class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters extends Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - atomTypizer
      
      EcfpAtomTypizers atomTypizer
      
      Atom typizer to use.
    - diameter
      
      int diameter
      
      Diameter parameter.
    - identifierConfigurationXml
      
      com.google.common.base.Optional<String> identifierConfigurationXml
      
      Identifier configuration for custom XML mode.
    - length
      
      int length
      
      Fingerprint length (bit count).
- Class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpParameters extends Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - params
      
      EcfpParameters params

Package com.chemaxon.descriptors.fingerprints.maccs

Class com.chemaxon.descriptors.fingerprints.maccs.GenerateMaccsFp extends Object implements Serializable

Serialized Fields

bit1

com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit1

bit100

com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit100

bit101

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bit102

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bit104

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bit105

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bit106

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bit107

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bit108

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bit109

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bit11

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bit110

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bit111

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bit112

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bit113

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bit114

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bit115

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bit116

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bit117

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bit118

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bit119

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bit120

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bit121

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bit122

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bit123

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bit124

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bit126

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bit128

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bit13

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bit131

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bit132

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bit133

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bit135

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bit136

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bit138

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bit139

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bit14

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bit140

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bit141

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bit144

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bit147

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bit148

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bit149

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bit15

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bit150

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bit151

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bit152

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bit154

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bit155

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bit157

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bit16

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bit162

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bit163

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bit165

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bit17

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bit19

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bit2

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bit21

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bit22

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bit23

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bit25

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bit26

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bit28

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bit30

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bit31

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bit32

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bit33

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bit34

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bit36

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bit39

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bit64

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bit70

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bit8

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bit80

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bit96

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bit97

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bit98

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bit99

com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit99

Class com.chemaxon.descriptors.fingerprints.maccs.GsSearch extends Object implements Serializable

serialVersionUID:

0L
- Serialized Fields
  - log
```
org.apache.commons.logging.Log log
```
  - queries
```
Molecule[] queries
```
  - sma
```
String sma
```
Class com.chemaxon.descriptors.fingerprints.maccs.MaccsParameters extends Object implements Serializable
Class com.chemaxon.descriptors.fingerprints.maccs.RingAtomBs extends BitSet implements Serializable

serialVersionUID:

0L
- Serialized Fields
  - mol
```
Molecule mol
```
  - ringAtoms
```
BitSet ringAtoms
```
Class com.chemaxon.descriptors.fingerprints.maccs.RingBondBs extends BitSet implements Serializable

serialVersionUID:

0L
- Serialized Fields
  - mol
```
Molecule mol
```
  - ringBonds
```
BitSet ringBonds
```

Package com.chemaxon.descriptors.fingerprints.pf2d
- Class com.chemaxon.descriptors.fingerprints.pf2d.PfComparatorImpl extends Object implements Serializable
- Class com.chemaxon.descriptors.fingerprints.pf2d.PfParameters extends Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - xmlConfig
      
      com.google.common.base.Optional<String> xmlConfig
      
      XML configuration string.
- Class com.chemaxon.descriptors.fingerprints.pf2d.PharmacophoreFPImpl extends com.chemaxon.descriptors.common.realvector.FloatVectorDescriptorImpl implements Serializable
  - Serialized Fields
    - fingerprint
      
      PharmacophoreFingerprint fingerprint
- Class com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfParameters extends Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - xmlConfig
      
      com.google.common.base.Optional<String> xmlConfig
Package com.chemaxon.descriptors.metrics
- Class com.chemaxon.descriptors.metrics.TverskyParameters extends Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - coeffQuery
      
      double coeffQuery
      
      Coefficient for query only part.
    - coeffTarget
      
      double coeffTarget
      
      Coefficient for target only part.
Package com.chemaxon.descriptors.vectors.binary
- Class com.chemaxon.descriptors.vectors.binary.BvGeneratorImpl extends Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - parameters
      
      BvParameters parameters
- Class com.chemaxon.descriptors.vectors.binary.BvParameters extends Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - endianness
      
      BinaryVectors.Endianness endianness
      
      Endianness of long-int-byte-binary packing operations.
    - length
      
      int length
      
      Fingerprint length (bit count).
    - stringFormat
      
      BvParameters.StringFormat stringFormat
      
      String format to use.
Package com.chemaxon.descriptors.vectors.floats
- Class com.chemaxon.descriptors.vectors.floats.FvGeneratorImpl extends Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - parameters
      
      FvParameters parameters
- Class com.chemaxon.descriptors.vectors.floats.FvParameters extends Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - length
      
      int length
      
      Fingerprint length (bit count).
    - numericRepresentation
      
      FvParameters.NumericRepresentation numericRepresentation
      
      Numeric representation.
    - scaledMax
      
      double scaledMax
      
      Maximum value for scaling.
    - scaledMin
      
      double scaledMin
      
      Minimum value for scaling.
    - sparseCompression
      
      FvParameters.SparseCompression sparseCompression
      
      Optimization for sparse vectors.
Package com.chemaxon.overlap.io
- Class com.chemaxon.overlap.io.AllAbsentMasterMoleculeStorage extends Object implements Serializable
  - Serialized Fields
    - size
      
      long size
- Class com.chemaxon.overlap.io.ArraysBackedStorageTools.Builder extends Object implements Serializable
  - Serialized Fields
    - builtPages
      
      List<C extends Serializable> builtPages
    - currentPage
      
      List<E extends Serializable> currentPage
    - elementType
      
      Class<E extends Serializable> elementType
    - getFromPage
      
      com.chemaxon.descriptors.common.reflect.SerializableBiFunction<C extends Serializable,Integer,E extends Serializable> getFromPage
    - initialSkips
      
      long initialSkips
    - listToPage
      
      com.chemaxon.descriptors.common.reflect.SerializableFunction<List<E extends Serializable>,C extends Serializable> listToPage
    - pageSize
      
      int pageSize
    - totalAbsents
      
      long totalAbsents
    - totalSize
      
      long totalSize
- Class com.chemaxon.overlap.io.ArraysBackedStorageTools.Storage extends Object implements Serializable
  - Serialized Fields
    - elementType
      
      Class<E extends Object> elementType
    - getFromPage
      
      com.chemaxon.descriptors.common.reflect.SerializableBiFunction<C extends Object,Integer,E extends Object> getFromPage
    - initialSkips
      
      long initialSkips
    - pages
      
      List<C extends Object> pages
    - pageSize
      
      int pageSize
    - totalAbsents
      
      long totalAbsents
    - totalSize
      
      long totalSize
- Class com.chemaxon.overlap.io.CompactStringStorage extends Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - absentCount
      
      long absentCount
    - pagesize
      
      int pagesize
    - size
      
      long size
    - skips
      
      long skips
    - starts
      
      int[][] starts
    - storage
      
      byte[][] storage
    - storedByteCount
      
      long storedByteCount
- Class com.chemaxon.overlap.io.CompactStringStorage.Metadata extends Object implements Serializable
  - Serialized Fields
    - absentCount
      
      long absentCount
    - bytes
      
      long bytes
    - lastPageSize
      
      int lastPageSize
    - pageCount
      
      int pageCount
    - pageSize
      
      int pageSize
    - size
      
      long size
    - skips
      
      long skips
    - storeSizes
      
      int[] storeSizes
    - storeStart
      
      long storeStart
- Class com.chemaxon.overlap.io.MasterMoleculeStorageImpl extends Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - importOptsOrNull
      
      String importOptsOrNull
    - sources
      
      com.chemaxon.overlap.io.CompactStringStorage sources
Package com.chemaxon.search.transformation
- Class com.chemaxon.search.transformation.TransformationException extends Exception implements Serializable

Serialized Form

Package chemaxon.calculations

Class chemaxon.calculations.CalculationException extends RuntimeException implements Serializable

Package chemaxon.calculations.clean

Class chemaxon.calculations.clean.AtomChangeEvent extends EventObject implements Serializable

Package chemaxon.calculator

Class chemaxon.calculator.CalculatorException extends Exception implements Serializable

Package chemaxon.clustering

Class chemaxon.clustering.ChemicalSpace extends Vector implements Serializable

Serialized Fields

checked

dimensions

emptyset

fpsize

inv

weights

willett

Class chemaxon.clustering.ClusteringException extends Exception implements Serializable

Class chemaxon.clustering.Heap.HeapException extends RuntimeException implements Serializable

Class chemaxon.clustering.InvalidLicenseKeyException extends Exception implements Serializable

Package chemaxon.common.util

Class chemaxon.common.util.ByteVector extends Object implements Serializable

Serialized Fields

data

size

Class chemaxon.common.util.DoubleVector extends Object implements Serializable

Serialized Fields

data

size

Class chemaxon.common.util.FloatVector extends Object implements Serializable

Serialized Fields

data

size

Class chemaxon.common.util.GeomCalc.GeomCalcException extends RuntimeException implements Serializable

Class chemaxon.common.util.GeomCalc.Queue.Overflow extends Exception implements Serializable

Class chemaxon.common.util.GeomCalc.Queue.Underflow extends Exception implements Serializable

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

Class chemaxon.common.util.IntPair extends Object implements Serializable

Serialized Fields

left

right

Class chemaxon.common.util.IntVector extends Object implements Serializable

Serialized Fields

data

size

Class chemaxon.common.util.LongVector extends Object implements Serializable

Serialized Fields

data

size

Class chemaxon.common.util.ShortVector extends Object implements Serializable

Serialized Fields

data

size

Package chemaxon.core

Class chemaxon.core.SequenceBuildingException extends RuntimeException implements Serializable

Serialized Fields

errorKey

Package chemaxon.core.calculations.valencecheck

Class chemaxon.core.calculations.valencecheck.ValenceCheckOptions extends Object implements Serializable

Serialized Fields

localAromatic

traditionalNallowed

Class chemaxon.core.calculations.valencecheck.ValenceColumnException extends chemaxon.core.calculations.valencecheck.ValenceException implements Serializable

Class chemaxon.core.calculations.valencecheck.ValenceException extends Exception implements Serializable

Class chemaxon.core.calculations.valencecheck.ValenceTypeException extends chemaxon.core.calculations.valencecheck.ValenceException implements Serializable

Package chemaxon.core.util

Class chemaxon.core.util.BondTable extends Object implements Serializable

Serialized Fields

atomCount

Package chemaxon.descriptors

Class chemaxon.descriptors.MDGeneratorException extends Exception implements Serializable

Class chemaxon.descriptors.MDParametersException extends RuntimeException implements Serializable

Class chemaxon.descriptors.MDReaderException extends Exception implements Serializable

Class chemaxon.descriptors.MDWriterException extends Exception implements Serializable

Class chemaxon.descriptors.SimilarityException extends Exception implements Serializable

Package chemaxon.formats

Class chemaxon.formats.MolFormatException extends IOException implements Serializable

Serialized Fields

lineNumberInFile

lineNumberInRecord

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