Serialized Form (JChem Base API documentation (c) 1998-2021 ChemAxon Ltd.)

Package chemaxon.calculations
- Class chemaxon.calculations.CalculationException extends java.lang.RuntimeException implements Serializable
  
  serialVersionUID:
  
  1L
Package chemaxon.clustering
- Class chemaxon.clustering.ChemicalSpace extends java.util.Vector implements Serializable
  - Serialized Fields
    - weights
```
float[] weights
```
    - inv
```
chemaxon.clustering.ChemicalSpace.InvertedFile inv
```
    - dimensions
```
int dimensions
```
    - fpsize
```
int fpsize
```
    - emptyset
```
java.util.BitSet emptyset
```
    - checked
```
java.util.BitSet checked
```
    - willett
```
boolean willett
```
- Class chemaxon.clustering.ClusteringException extends java.lang.Exception implements Serializable
- Class chemaxon.clustering.InvalidLicenseKeyException extends java.lang.Exception implements Serializable
Package chemaxon.common.util
- Class chemaxon.common.util.ByteVector extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -1393815508326465236L
  - Serialized Fields
    - data
```
byte[] data
```
    - size
```
int size
```
- Class chemaxon.common.util.DoubleVector extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -5138497375635267024L
  - Serialized Fields
    - data
```
double[] data
```
    - size
```
int size
```
- Class chemaxon.common.util.FloatVector extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -2327634131748729635L
  - Serialized Fields
    - data
```
float[] data
```
    - size
```
int size
```
- Class chemaxon.common.util.GeomCalc.GeomCalcException extends java.lang.RuntimeException implements Serializable
  
  serialVersionUID:
  
  -1705490613297709773L
- Class chemaxon.common.util.GeomCalc.Queue.Overflow extends java.lang.Exception implements Serializable
  
  serialVersionUID:
  
  -6957894135268794743L
- Class chemaxon.common.util.GeomCalc.Queue.Underflow extends java.lang.Exception implements Serializable
  
  serialVersionUID:
  
  -1972826041963082169L
- Class chemaxon.common.util.IntMap extends java.util.HashMap<K,java.lang.Integer> implements Serializable
  
  serialVersionUID:
  
  4318465509620546463L
- Class chemaxon.common.util.IntPair extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1961353781713733629L
  - Serialized Fields
    - left
```
int left
```
    - right
```
int right
```
- Class chemaxon.common.util.IntVector extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -9011852065319440166L
  - Serialized Fields
    - data
```
int[] data
```
    - size
```
int size
```
- Class chemaxon.common.util.LongVector extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  8437448887389765952L
  - Serialized Fields
    - data
```
long[] data
```
    - size
```
int size
```
- Class chemaxon.common.util.ShortVector extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  8407562362886825374L
  - Serialized Fields
    - data
```
short[] data
```
    - size
```
int size
```
Package chemaxon.core
- Class chemaxon.core.SequenceBuildingException extends java.lang.RuntimeException implements Serializable
  - Serialized Fields
    - errorKey
```
java.lang.String errorKey
```
Package chemaxon.core.calculations.valencecheck
- Class chemaxon.core.calculations.valencecheck.ValenceCheckOptions extends java.lang.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 java.lang.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 java.lang.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 java.lang.Exception implements Serializable
- Class chemaxon.descriptors.MDParametersException extends java.lang.RuntimeException implements Serializable
- Class chemaxon.descriptors.MDReaderException extends java.lang.Exception implements Serializable
- Class chemaxon.descriptors.MDWriterException extends java.lang.Exception implements Serializable
- Class chemaxon.descriptors.SimilarityException extends java.lang.Exception implements Serializable
Package chemaxon.formats
- Class chemaxon.formats.MolFormatException extends java.io.IOException implements Serializable
  - Serialized Fields
    - lineNumberInRecord
```
int lineNumberInRecord
```
    - lineNumberInFile
```
int lineNumberInFile
```
Package chemaxon.formats.documents.jchemoffice
- Class chemaxon.formats.documents.jchemoffice.BatchProcessingException extends java.io.IOException implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - _exceptions
```
java.util.List<E> _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 java.lang.Exception implements Serializable
- Class chemaxon.jchem.db.MaxSearchFrequencyExceededException extends DatabaseSearchException implements Serializable
- Class chemaxon.jchem.db.RecalculationException extends java.lang.Exception implements Serializable
  
  serialVersionUID:
  
  -2767058042924323545L
- Class chemaxon.jchem.db.TransferException extends java.lang.Exception implements Serializable
  
  serialVersionUID:
  
  -5241498055624956036L
- Class chemaxon.jchem.db.UpdateHandler.RowData extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -4040824446004135801L
  - Serialized Fields
    - molString
```
byte[] molString
```
    - fingerprint
```
int[] fingerprint
```
    - hashCode
```
int hashCode
```
    - molWeight
```
java.lang.Double molWeight
```
    - formula
```
java.lang.String formula
```
    - sortableFormula
```
java.lang.String sortableFormula
```
    - smiles
```
java.lang.String smiles
```
    - noRingInfoInFP
```
boolean noRingInfoInFP
```
    - reactionMappingIncomplete
```
boolean reactionMappingIncomplete
```
    - markushData
```
byte[] markushData
```
    - molecule
```
Molecule molecule
```
    - chemTermColValues
```
java.util.Map<K,V> chemTermColValues
```
    - tautomer
```
Molecule tautomer
```
    - flags
```
java.lang.String flags
```
    - molName
```
java.lang.String molName
```
    - tautomerHashCode
```
int tautomerHashCode
```
    - tautomerFragmentHashCode
```
int[] tautomerFragmentHashCode
```
    - screenDescriptor
```
byte[] screenDescriptor
```
    - descriptorData
```
byte[][] descriptorData
```
- Class chemaxon.jchem.db.UpdateHandlerException extends java.lang.Exception implements Serializable
  
  serialVersionUID:
  
  -8755169336283449997L
- Class chemaxon.jchem.db.UpdateHandlerMetaData extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -6512295793385774884L
  - Serialized Fields
    - tableType
```
int tableType
```
    - collectionType
```
chemaxon.jchem.base.storage.StructureCollectionType collectionType
```
    - tautomerDuplicateFilteringEnabled
```
boolean tautomerDuplicateFilteringEnabled
```
    - tautomerEqualityMode
```
chemaxon.sss.search.options.TautomerTransformationMode tautomerEqualityMode
```
    - duplicateFilteringOption
```
boolean duplicateFilteringOption
```
    - standardizerConfig
```
java.lang.String standardizerConfig
```
    - numberOfStructuralFPColumns
```
int numberOfStructuralFPColumns
```
    - numberOfCombinedFPColumns
```
int numberOfCombinedFPColumns
```
    - structuralKeys
```
java.lang.String structuralKeys
```
    - numberOfEdges
```
int numberOfEdges
```
    - numberOfOnes
```
int numberOfOnes
```
    - chemTermColumns
```
java.lang.String[] chemTermColumns
```
    - chemTermForColumn
```
java.util.Map<K,V> chemTermForColumn
```
    - compressedStructureFieldSupported
```
boolean compressedStructureFieldSupported
```
    - insertDescriptorNames
```
java.util.List<E> insertDescriptorNames
```
    - updateDescriptorNames
```
java.util.List<E> updateDescriptorNames
```
    - descriptorTypes
```
java.util.Map<K,V> descriptorTypes
```
    - descriptorSettings
```
java.util.Map<K,V> descriptorSettings
```
- Class chemaxon.jchem.db.UpdateHandlerRowDataException extends UpdateHandlerException implements Serializable
  
  serialVersionUID:
  
  -7274357064259684370L
  - Serialized Fields
    - rowData
```
UpdateHandler.RowData rowData
```
- Class chemaxon.jchem.db.Updater.UpdateInfo extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  4160146885445230514L
  - Serialized Fields
    - message
```
java.lang.String message
```
      Massage describing what update is necessary and why.
    - entityList
```
java.lang.String[] entityList
```
      The names of entities (e.g. table names) to be updated, or null.
    - processingMessage
```
java.lang.String processingMessage
```
      A message that can be displayed during the update, e.g. "Recalculating tables"
    - 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)
    - isProgressMonitoringSupported
```
boolean isProgressMonitoringSupported
```
      Indicates whether update process supports progress monitoring.
      
      Since:
      
      JChem 5.1.2
    - regenerationType
```
int regenerationType
```
      Indicates the regeneration type.
      
      Since:
      
      JChem 5.2.4
    - isOperationRequired
```
boolean isOperationRequired
```
      Indicates whether the operation is required or not.
      
      Since:
      
      JChem 5.3
    - isStructuralChange
```
boolean isStructuralChange
```
      Indicates whether the operation is required or not.
      
      Since:
      
      JChem 5.8
    - additionalInformation
```
java.lang.String[] additionalInformation
```
      Additional information for the entities in same order, if needed.
      
      Since:
      
      JChem 6.0
Package chemaxon.jchem.db.cache
- Class chemaxon.jchem.db.cache.CachePool extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - cacheHash
```
java.util.Hashtable<K,V> cacheHash
```
    - maxCacheSizeMB
```
int maxCacheSizeMB
```
    - minFreeMemMB
```
int minFreeMemMB
```
    - maxCacheMemory
```
long maxCacheMemory
```
    - maxCacheMemoryCalculated
```
boolean maxCacheMemoryCalculated
```
    - expirationTime
```
double expirationTime
```
    - cacheRemovalMethod
```
chemaxon.jchem.db.cache.CacheRemovalMethod cacheRemovalMethod
```
- Class chemaxon.jchem.db.cache.CacheRegistrationException extends java.lang.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
    - jep
```
ChemJEP jep
```
    - cached
```
boolean cached
```
- Class chemaxon.jep.ChemJEP extends chemaxon.nfunk.jep.JEP implements Serializable
  - Serialized Fields
    - contextClass
```
java.lang.Class<T> contextClass
```
      The evaluation context class.
    - context
```
ChemContext context
```
      The evaluation context object.
- Class chemaxon.jep.ConditionException extends java.lang.Exception implements Serializable
- Class chemaxon.jep.ContextFunction extends chemaxon.nfunk.jep.function.PostfixMathCommand implements Serializable
  
  serialVersionUID:
  
  6471101129584627604L
  - Serialized Fields
    - name
```
java.lang.String name
```
    - jep
```
ChemJEP jep
```
- Class chemaxon.jep.DissimilarityFunction extends chemaxon.jep.ChemFunction implements Serializable
  - Serialized Fields
    - className
```
java.lang.String className
```
    - descriptors
```
java.lang.String[] descriptors
```
- Class chemaxon.jep.Evaluator extends java.lang.Object implements Serializable
  - Serialized Fields
    - builtInConfig
```
chemaxon.jep.EvaluatorConfiguration builtInConfig
```
      The configuration object containing default function/plugin declarations.
    - externalConfig
```
chemaxon.jep.EvaluatorConfiguration externalConfig
```
      The configuration object containing external function/plugin declarations.
    - userConfig
```
chemaxon.jep.EvaluatorConfiguration userConfig
```
      The configuration object containing user defined function/plugin declarations.
    - config
```
chemaxon.jep.EvaluatorConfiguration config
```
      The configuration object.
    - servicesFunctionTable
```
java.util.Hashtable<K,V> servicesFunctionTable
```
      Function table for services.
    - symtab
```
chemaxon.nfunk.jep.SymbolTable symtab
```
      The base symbol table.
    - functionalGroupDisplayMolTable
```
java.util.Hashtable<K,V> functionalGroupDisplayMolTable
```
      |functional group name| -> |displayable molecule representation|
    - verbose
```
boolean verbose
```
      True if verbose output.
    - licenseEnvironment
```
java.lang.String licenseEnvironment
```
    - servicesConfigurationPath
```
java.lang.String servicesConfigurationPath
```
      services configuration path
      
      Since:
      
      5.10
- 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
    - className
```
java.lang.String className
```
    - subMatches
```
java.util.Hashtable<K,V> subMatches
```
    - type
```
int type
```
    - attributes
```
chemaxon.util.SearchAttributes attributes
```
    - dir
```
java.lang.String dir
```
    - standardizer
```
chemaxon.jep.Standardizer standardizer
```
    - licenseEnvironment
```
java.lang.String licenseEnvironment
```
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 java.lang.Object implements Serializable
  - Serialized Fields
    - supplier
```
com.google.common.base.Supplier<T> supplier
```
      The molecule supplier.
    - fingerprint
```
int[] fingerprint
```
      Fingerprint of the input molecule.
    - reactionContext
```
ReactionContext reactionContext
```
      reaction wrapped in this context
    - init
```
boolean init
```
- Class chemaxon.jep.context.ReactionContext extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -9162272287141708299L
  - Serialized Fields
    - reaction
```
RxnMolecule reaction
```
      reaction wrapped in this context
    - reactantAtomMapping
```
java.util.Map<K,V> reactantAtomMapping
```
      mapping of AtomMap -> Reactant Atom
    - productAtomMapping
```
java.util.Map<K,V> productAtomMapping
```
      mapping of AtomMap -> Product Atom
    - agentAtomMapping
```
java.util.Map<K,V> agentAtomMapping
```
      mapping of AtomMap -> Agent Atom
- Class chemaxon.jep.context.SearchContext extends MolContext implements Serializable
  - Serialized Fields
    - query
```
Molecule query
```
    - target
```
Molecule target
```
    - queryFingerprint
```
int[] queryFingerprint
```
    - targetFingerprint
```
int[] targetFingerprint
```
    - map
```
int[] map
```
    - hit
```
int[] hit
```
Package chemaxon.license
- Class chemaxon.license.LicenseException extends java.lang.RuntimeException implements Serializable
  - Serialized Fields
    - product
```
java.lang.String product
```
- Class chemaxon.license.LicenseProcessingException extends java.lang.Exception implements Serializable
Package chemaxon.marvin
- Class chemaxon.marvin.AbstractApplication extends javax.swing.JFrame implements Serializable
- Class chemaxon.marvin.SketchApplication extends chemaxon.marvin.AbstractApplication implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - sketchPane
```
MSketchPane sketchPane
```
    - outSerName
```
java.lang.String outSerName
```
    - newWindowAction
```
javax.swing.Action newWindowAction
```
    - exitAction
```
javax.swing.Action exitAction
```
- Class chemaxon.marvin.ViewApplication extends chemaxon.marvin.AbstractApplication implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - colorKeys
```
java.util.List<E> colorKeys
```
    - viewPane
```
MViewPane viewPane
```
    - openAction
```
javax.swing.Action openAction
```
    - printAction
```
javax.swing.Action printAction
```
    - exitAction
```
javax.swing.Action exitAction
```
    - hasInitalized
```
boolean hasInitalized
```
Package chemaxon.marvin.alignment
- Class chemaxon.marvin.alignment.AlignmentException extends java.lang.Exception implements Serializable
- Class chemaxon.marvin.alignment.NoConstraintException extends chemaxon.marvin.alignment.AlignmentException implements Serializable
- Class chemaxon.marvin.alignment.OptimizationException extends java.lang.RuntimeException implements Serializable
  
  serialVersionUID:
  
  1L
- Class chemaxon.marvin.alignment.ShapeData extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - shapeEnabledAtoms
```
java.util.BitSet shapeEnabledAtoms
```
    - atoms
```
chemaxon.marvin.alignment.ShapeData.Atom[] atoms
```
    - bonds
```
chemaxon.marvin.alignment.ShapeData.Bond[] bonds
```
    - coloringScheme
```
AlignmentProperties.ColoringScheme coloringScheme
```
    - mins
```
double[] mins
```
    - maxs
```
double[] maxs
```
- Class chemaxon.marvin.alignment.TooDissimilarException extends chemaxon.marvin.alignment.AlignmentException implements Serializable
Package chemaxon.marvin.beans
- Class chemaxon.marvin.beans.MarvinPane extends javax.swing.JRootPane implements Serializable
  
  serialVersionUID:
  
  -9042549845769941129L
  - Serialized Fields
    - molPanel
```
chemaxon.marvin.common.swing.MolPanel molPanel
```
      Underlying panel.
    - params
```
java.lang.String params
```
      Parameter string.
    - actionListener
```
chemaxon.marvin.beans.MarvinPane.MarvinActionListener actionListener
```
- Class chemaxon.marvin.beans.MolRenderer extends javax.swing.JPanel implements Serializable
  
  serialVersionUID:
  
  7229361698115302929L
  - Serialized Fields
    - printer
```
MolPrinter printer
```
- Class chemaxon.marvin.beans.MSketch extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialization Methods
    - readExternal
```
public void readExternal(java.io.ObjectInput in)
                  throws java.io.IOException,
                         java.lang.ClassNotFoundException
```
      Restores the sketcher's state.
      
      Throws:
      
      java.io.IOException - if I/O errors occur
      
      java.lang.ClassNotFoundException - If the class for an object being restored cannot be found.
    - writeExternal
```
public void writeExternal(java.io.ObjectOutput out)
                   throws java.io.IOException
```
      Saves the sketcher's state.
      
      Throws:
      
      java.io.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 java.lang.Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialization Methods
    - readExternal
```
public void readExternal(java.io.ObjectInput in)
                  throws java.io.IOException,
                         java.lang.ClassNotFoundException
```
      Restores the viewer's state.
      
      Throws:
      
      java.io.IOException - if I/O errors occur
      
      java.lang.ClassNotFoundException - If the class for an object being restored cannot be found.
    - writeExternal
```
public void writeExternal(java.io.ObjectOutput out)
                   throws java.io.IOException
```
      Saves the viewer's state.
      
      Throws:
      
      java.io.IOException - Includes any I/O exceptions that may occur
- Class chemaxon.marvin.beans.MViewEditor extends javax.swing.AbstractCellEditor implements Serializable
  
  serialVersionUID:
  
  1549621132660875966L
  - Serialized Fields
    - editorComponent
```
MViewPane editorComponent
```
- Class chemaxon.marvin.beans.MViewPane extends MarvinPane implements Serializable
  
  serialVersionUID:
  
  -4430811090653077262L
  - Serialized Fields
    - tableSupport
```
TableSupport tableSupport
```
    - preferredSizeSet
```
boolean preferredSizeSet
```
    - delayedRepainter
```
chemaxon.marvin.beans.MViewPane.DelayedRepainter delayedRepainter
```
- Class chemaxon.marvin.beans.MViewRenderer extends MViewPane implements Serializable
  
  serialVersionUID:
  
  5566509759455312369L
Package chemaxon.marvin.calculations
- Class chemaxon.marvin.calculations.BitPattern extends java.util.BitSet implements Serializable
Package chemaxon.marvin.io
- Class chemaxon.marvin.io.Encoding extends java.lang.Object implements Serializable
  - Serialization Methods
    - readExternal
```
public void readExternal(java.io.ObjectInput arg0)
                  throws java.io.IOException
```
      Throws:
      
      java.io.IOException
    - writeExternal
```
public void writeExternal(java.io.ObjectOutput arg0)
                   throws java.io.IOException
```
      Throws:
      
      java.io.IOException
- Class chemaxon.marvin.io.MolExportException extends java.io.IOException implements Serializable
  - Serialized Fields
    - molIndex
```
int molIndex
```
- Class chemaxon.marvin.io.MRecordParseException extends java.lang.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
```
java.util.ResourceBundle bundle
```
    - formats
```
java.util.List<E> formats
```
    - defaultFormat
```
java.lang.String defaultFormat
```
    - selectorList
```
javax.swing.JList<E> selectorList
```
    - prevSelectedIdx
```
int prevSelectedIdx
```
Package chemaxon.marvin.plugin
- Class chemaxon.marvin.plugin.PluginException extends java.lang.Exception implements Serializable
  - Serialized Fields
    - level
```
int level
```
      Error level.
Package chemaxon.marvin.plugin.concurrent
- Class chemaxon.marvin.plugin.concurrent.PluginExecutionException extends java.util.concurrent.ExecutionException implements Serializable
  - Serialized Fields
    - plugin
```
CalculatorPlugin plugin
```

Package chemaxon.marvin.plugin.gui

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

Class chemaxon.marvin.plugin.gui.OptionsPane extends javax.swing.JDialog implements Serializable

Serialized Fields

parameterPanel
```
ParameterPanelHandler parameterPanel
```

okActionListener

java.awt.event.ActionListener okActionListener

key
```
java.lang.String key
```
title
```
java.lang.String title
```
ok
```
chemaxon.marvin.swing.ActionButton ok
```

cancel

chemaxon.marvin.swing.ActionButton cancel

restoreDefaults

chemaxon.marvin.swing.ActionButton restoreDefaults

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

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

serialVersionUID:: -5728800883025815500L

Serialized Fields

mpan

chemaxon.marvin.common.swing.MolPanel mpan

bottomTextArea
```
javax.swing.JTextArea bottomTextArea
```
bottomComponent
```
javax.swing.JComponent bottomComponent
```
topTextArea
```
javax.swing.JTextArea topTextArea
```
topComponent
```
javax.swing.JComponent topComponent
```
chartPanel
```
javax.swing.JPanel chartPanel
```
chart
```
chemaxon.marvin.util.MarvinModule chart
```
viewMenu
```
javax.swing.JMenu viewMenu
```
copymi
```
javax.swing.JMenuItem copymi
```
popupcopymi
```
javax.swing.JMenuItem popupcopymi
```
resetmi
```
javax.swing.JMenuItem resetmi
```
popup
```
javax.swing.JPopupMenu popup
```
detachmi
```
javax.swing.JMenuItem detachmi
```
viewMols
```
Molecule[] viewMols
```
viewTexts
```
java.lang.String[] viewTexts
```

viewPanel

chemaxon.marvin.view.swing.ViewPanel viewPanel

viewMol
```
Molecule viewMol
```
viewText
```
java.lang.String viewText
```
imageFormat
```
java.lang.String imageFormat
```

Package chemaxon.marvin.services
- Class chemaxon.marvin.services.ServiceException extends java.lang.Exception implements Serializable
  
  serialVersionUID:
  
  328496720368460819L

Package chemaxon.marvin.sketch

Class chemaxon.marvin.sketch.History extends java.lang.Object implements Serializable

Serialized Fields

molHist
```
MDocument[] molHist
```
cornerHist
```
java.awt.Point[] cornerHist
```
scaleHist
```
double[] scaleHist
```
autoHydrogenizeHist
```
int[] autoHydrogenizeHist
```
scrollBarHist
```
int[][] scrollBarHist
```
selectionToZoomHist
```
boolean[] selectionToZoomHist
```
molgToZoomHist
```
MoleculeGraph[][] molgToZoomHist
```
rotateMatrHist
```
CTransform3D[] rotateMatrHist
```
molHistLen
```
int molHistLen
```
molHistCur
```
int molHistCur
```
molHistMax
```
int molHistMax
```
historyOverflow
```
boolean historyOverflow
```

changeSupport

java.beans.PropertyChangeSupport changeSupport

Class chemaxon.marvin.sketch.MolEditor extends java.lang.Object implements Serializable

serialVersionUID:: 2463379690025911142L

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream arg0)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException

Throws:: java.lang.ClassNotFoundException; java.io.IOException

Serialized Fields

currentTool

chemaxon.marvin.sketch.tool.EditorTool currentTool

moveMode
```
int moveMode
```
persistentMoveMode
```
boolean persistentMoveMode
```
document
```
MDocument document
```
selectionDoc
```
MSelectionDocument selectionDoc
```
elements
```
java.util.List<E> elements
```
queryAtoms
```
java.util.Set<E> queryAtoms
```
extraBonds
```
java.util.Set<E> extraBonds
```
atomStrings
```
java.util.Set<E> atomStrings
```
disabledAliases
```
java.util.Set<E> disabledAliases
```
lpEnabled
```
boolean lpEnabled
```
starEnabled
```
boolean starEnabled
```
reactionSupported
```
boolean reactionSupported
```
stickdst
```
double stickdst
```
mergedst
```
double mergedst
```
history
```
chemaxon.marvin.sketch.History history
```

painter

chemaxon.marvin.paint.internal.MolPainter painter

curfrag
```
MDocument curfrag
```
prevCurfrag
```
MDocument prevCurfrag
```
flyingBondMol
```
MoleculeGraph flyingBondMol
```
curfragMoved
```
boolean curfragMoved
```
canRotCurfrag
```
boolean canRotCurfrag
```
canMovCurfrag
```
boolean canMovCurfrag
```
atomSelectionMode
```
int atomSelectionMode
```
curfragR
```
double curfragR
```
rotO
```
DPoint3 rotO
```
rotAxisPoint
```
DPoint3 rotAxisPoint
```
isAxisSet
```
boolean isAxisSet
```
rotateZPhi
```
double rotateZPhi
```
rotate3dPhiX
```
double rotate3dPhiX
```
rotate3dPhiY
```
double rotate3dPhiY
```
rotate3dPhi
```
double rotate3dPhi
```
rotate3dx
```
double rotate3dx
```
rotate3dy
```
double rotate3dy
```
rotate3direction
```
int rotate3direction
```
atomBranchPiece
```
Molecule atomBranchPiece
```
piece
```
Molecule piece
```
pieceOriginalObject
```
Molecule pieceOriginalObject
```
showMolecule
```
Molecule showMolecule
```
bondDrawMode
```
boolean bondDrawMode
```
lastBondFlags
```
int lastBondFlags
```
lastQueryBondString
```
java.lang.String lastQueryBondString
```
jointAtom
```
MolAtom jointAtom
```

curfragJoin

com.chemaxon.marvin.editor.molecule.fusion.MolJoin curfragJoin

bondDraggedAlong
```
boolean bondDraggedAlong
```
historizeEnabled
```
boolean historizeEnabled
```
documentEdited
```
boolean documentEdited
```
isDataSgroupLabelPointed
```
boolean isDataSgroupLabelPointed
```
dataSgroupObject
```
DataSgroup dataSgroupObject
```
hadSelection
```
boolean hadSelection
```
scrollBarVals
```
int[] scrollBarVals
```
lastSelectionDoc
```
MDocument lastSelectionDoc
```
lastSelectionCorner
```
java.awt.Point lastSelectionCorner
```
lastSelectionScale
```
double lastSelectionScale
```
selectionHistorized
```
boolean selectionHistorized
```
historizeUnSelection
```
boolean historizeUnSelection
```
deleteRemovesTerminalAtoms
```
boolean deleteRemovesTerminalAtoms
```
rotation3DMode
```
int rotation3DMode
```
newKeyboardMotion
```
boolean newKeyboardMotion
```
selectionHPoints
```
DPoint3[] selectionHPoints
```

Package chemaxon.marvin.space
- Class chemaxon.marvin.space.EventQueue extends java.util.Vector implements Serializable
- Class chemaxon.marvin.space.GraphicScene extends javax.swing.JPanel implements Serializable
  - Serialized Fields
    - eventHandler
```
chemaxon.marvin.space.MSpaceEventHandler eventHandler
```
    - progressBar
```
chemaxon.marvin.space.gui.JMSpaceProgressBar progressBar
```
    - rowCount
```
int rowCount
```
      layout of the graphic view: number of cells per row
    - columnCount
```
int columnCount
```
      layout of the graphic view: number of cells per column
    - activeCell
```
int activeCell
```
      index of the active cell: cells are numbered line-by-line
    - cells
```
GraphicCell[] cells
```
      components per cells, line-by-line 0 is the top-left corner
    - cellCount
```
int cellCount
```
      number of cells (there might be fewer cells than cells.length())
    - needsRefresh
```
int needsRefresh
```
      Indicates with internal index which cell needs redraw. -1 means none, cellCount means all cells.
    - needsReset
```
int needsReset
```
    - initialized
```
boolean initialized
```
    - antialias
```
boolean antialias
```
    - synchronousMode
```
boolean synchronousMode
```
    - verboseLevel
```
int verboseLevel
```
    - motionmode
```
int motionmode
```
      standing or moving mode
    - width
```
int width
```
      physical width of the entire scene (in pixels)
    - height
```
int height
```
      physical height of the entire scene (in pixels)
    - 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
```
    - transparentBackground
```
int transparentBackground
```
    - smoothBackground
```
boolean smoothBackground
```
    - 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
    - gl
```
javax.media.opengl.GL2 gl
```
    - glu
```
javax.media.opengl.glu.GLU glu
```
    - glAutoDrawable
```
javax.media.opengl.GLAutoDrawable glAutoDrawable
```
    - canvas
```
java.awt.Component canvas
```
    - gltext
```
chemaxon.marvin.space.util.GLText gltext
```
      this is used to display warning about unregistered product
    - _glListsToDelete
```
java.util.ArrayList<E> _glListsToDelete
```
    - globalDrawProperties
```
java.util.Properties globalDrawProperties
```
    - defaultDrawProperties
```
java.util.Map<K,V> defaultDrawProperties
```
    - userSettings
```
UserSettings userSettings
```
    - renderTargets
```
chemaxon.marvin.space.gl.shader.RenderTargets renderTargets
```
Package chemaxon.marvin.uif.dialog
- Class chemaxon.marvin.uif.dialog.CategoriesDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable
  - Serialized Fields
    - model
```
chemaxon.marvin.uif.dialog.model.CategoriesModel model
```
    - bundle
```
java.util.ResourceBundle bundle
```
- 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
```
java.util.ResourceBundle bundle
```
    - model
```
chemaxon.marvin.uif.dialog.model.CustomizeGUIModel model
```
    - guiRegistryClone
```
chemaxon.marvin.uif.model.GUIRegistry guiRegistryClone
```
    - 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
    - model
```
chemaxon.marvin.uif.dialog.model.MenuManagerModel model
```
    - bundle
```
java.util.ResourceBundle bundle
```
- Class chemaxon.marvin.uif.dialog.MenuMoveDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable
  - Serialized Fields
    - bundle
```
java.util.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
    - model
```
chemaxon.marvin.uif.dialog.model.PopupManagerModel model
```
    - bundle
```
java.util.ResourceBundle bundle
```
- Class chemaxon.marvin.uif.dialog.ShortcutEditorDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable
  - Serialized Fields
    - model
```
chemaxon.marvin.uif.dialog.model.ShortcutModel model
```
    - bundle
```
java.util.ResourceBundle bundle
```
- Class chemaxon.marvin.uif.dialog.ToolBarDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable
  - Serialized Fields
    - bundle
```
java.util.ResourceBundle bundle
```
    - model
```
chemaxon.marvin.uif.dialog.model.ToolBarManagerModel model
```
Package chemaxon.marvin.util
- Class chemaxon.marvin.util.CancelPrintException extends java.lang.Exception implements Serializable
  
  serialVersionUID:
  
  7380116746554005158L
- Class chemaxon.marvin.util.MarvinModule extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  2763330874643316763L
- Class chemaxon.marvin.util.MarvinOLEFrame extends javax.swing.JFrame implements Serializable
  
  serialVersionUID:
  
  7801720334170069726L
  - Serialized Fields
    - sp
```
java.util.concurrent.Semaphore sp
```
- Class chemaxon.marvin.util.MarvinOLEPanel extends javax.swing.JPanel implements Serializable
  
  serialVersionUID:
  
  -6975415959061110410L
  - Serialized Fields
    - emfExportOptions
```
java.lang.String emfExportOptions
```
    - msketch
```
MSketchPane msketch
```
    - sketchPanel
```
chemaxon.marvin.sketch.swing.SketchPanel sketchPanel
```
    - semaphore
```
java.util.concurrent.Semaphore semaphore
```
    - importExceptionCaught
```
boolean importExceptionCaught
```
    - retainGUIPropertiesOnPanel
```
boolean retainGUIPropertiesOnPanel
```
    - structureGUIProperties
```
MPropertyContainer structureGUIProperties
```
- Class chemaxon.marvin.util.SwingUtil extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -1600625160321014724L

Package chemaxon.marvin.util.codeassist

Class chemaxon.marvin.util.codeassist.ChemTermDocument extends javax.swing.text.DefaultStyledDocument implements Serializable

serialVersionUID:: -5894946790409031807L

Serialized Fields

doc

javax.swing.text.DefaultStyledDocument doc

rootElement
```
javax.swing.text.Element rootElement
```
multiLineComment
```
boolean multiLineComment
```

normal

javax.swing.text.MutableAttributeSet normal

comment

javax.swing.text.MutableAttributeSet comment

quote

javax.swing.text.MutableAttributeSet quote

keyword

javax.swing.text.MutableAttributeSet keyword

function

javax.swing.text.MutableAttributeSet function

parenthesis

javax.swing.text.MutableAttributeSet parenthesis

constant

javax.swing.text.MutableAttributeSet constant

keywords
```
java.util.Map<K,V> keywords
```
functions
```
java.util.Map<K,V> functions
```
constants
```
java.util.Map<K,V> constants
```
fontSize
```
int fontSize
```
fontName
```
java.lang.String fontName
```
parenOffset
```
int parenOffset
```
parenLength
```
int parenLength
```
currentElementIndex
```
int currentElementIndex
```
prefix
```
java.lang.String prefix
```
lastPrefixState
```
boolean lastPrefixState
```
HIGHLIGHT_TIMER
```
javax.swing.Timer HIGHLIGHT_TIMER
```

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

serialVersionUID:

6746125418422903808L

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

serialVersionUID:: -4703035835623320688L

Serialized Fields

macroListScroll
```
javax.swing.JScrollPane macroListScroll
```
macroList
```
javax.swing.JList<E> macroList
```
addButton
```
javax.swing.JButton addButton
```
editButton
```
javax.swing.JButton editButton
```
deleteButton
```
javax.swing.JButton deleteButton
```
listPanel
```
javax.swing.JPanel listPanel
```
editPanel
```
javax.swing.JPanel editPanel
```
layout
```
java.awt.CardLayout layout
```
acceptButton
```
javax.swing.JButton acceptButton
```
cancelButton
```
javax.swing.JButton cancelButton
```
nameField
```
javax.swing.JTextField nameField
```
descScrollPane
```
javax.swing.JScrollPane descScrollPane
```
macroScrollPane
```
javax.swing.JScrollPane macroScrollPane
```
macroPane
```
javax.swing.JTextPane macroPane
```
descPane
```
javax.swing.JTextPane descPane
```
acceptEditButton
```
javax.swing.JButton acceptEditButton
```
cancelEditButton
```
javax.swing.JButton cancelEditButton
```
editedItem
```
int editedItem
```

helper

chemaxon.marvin.util.codeassist.CodeAssistMacrosHelper helper

ACCEPT_ACTION
```
javax.swing.Action ACCEPT_ACTION
```
CANCEL_ACTION
```
javax.swing.Action CANCEL_ACTION
```

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

Package chemaxon.marvin.view.swing

Class chemaxon.marvin.view.swing.TwoLists extends javax.swing.JPanel implements Serializable

Serialized Fields

listData1
```
java.lang.String[] listData1
```
listData2
```
java.lang.String[] listData2
```
list1
```
javax.swing.JList<E> list1
```
list2
```
javax.swing.JList<E> list2
```
addButton
```
javax.swing.JButton addButton
```
addAllButton
```
javax.swing.JButton addAllButton
```
removeButton
```
javax.swing.JButton removeButton
```
removeAllButton
```
javax.swing.JButton removeAllButton
```
allSelected
```
boolean allSelected
```

Class chemaxon.marvin.view.swing.ViewCanvas extends chemaxon.marvin.common.swing.MolCanvas implements Serializable

serialVersionUID:: 3979819797881974530L

Serialization Methods

writeObject

private void writeObject(java.io.ObjectOutputStream arg0)
                  throws java.io.IOException

Throws:: java.io.IOException

Serialized Fields

windowAction

chemaxon.marvin.swing.MAction windowAction

document
```
MDocument document
```
inZoomWindow
```
boolean inZoomWindow
```
markedAtom
```
int markedAtom
```
highlightedAtom
```
int highlightedAtom
```

viewPanel

chemaxon.marvin.view.swing.ViewPanel viewPanel

viewFrame

chemaxon.marvin.view.swing.modules.MViewFrame viewFrame

cellIndex
```
int cellIndex
```
winScale
```
double winScale
```
moleculeCenter
```
DPoint3 moleculeCenter
```
preferredSize1
```
java.awt.Dimension preferredSize1
```
rsize
```
java.awt.Dimension rsize
```
error
```
boolean error
```

painter

chemaxon.marvin.paint.internal.MolPainter painter

moleculeBackground
```
java.awt.Color moleculeBackground
```
nextV
```
java.util.Vector<E> nextV
```
rescaleNeeded
```
boolean rescaleNeeded
```

Class chemaxon.marvin.view.swing.ViewHandler extends java.lang.Object implements Serializable
- Serialized Fields
  - debug
```
boolean debug
```
  - visibleDocs
```
chemaxon.marvin.view.swing.VisibleDocuments visibleDocs
```
  - cellFiller
```
chemaxon.marvin.view.swing.CellFiller cellFiller
```

Class chemaxon.marvin.view.swing.ViewPanel extends chemaxon.marvin.common.swing.MolPanel implements Serializable

serialVersionUID:: 802342314015862847L

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream arg0)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException

Throws:: java.lang.ClassNotFoundException; java.io.IOException

Serialized Fields

molFrame0
```
java.awt.Window molFrame0
```

viewActions

chemaxon.marvin.view.swing.ViewActions viewActions

navigationActions

chemaxon.marvin.swing.MAction[] navigationActions

molStrings
```
java.lang.String[] molStrings
```
molString
```
java.lang.String molString
```
rasmolScripts
```
java.lang.String[] rasmolScripts
```

moleculeSelections

chemaxon.marvin.common.AtomSelectionHandler[] moleculeSelections

viewHandler

chemaxon.marvin.view.swing.ViewHandler viewHandler

defaultFieldFont
```
java.awt.Font defaultFieldFont
```
fieldFontMap
```
java.util.Map<K,V> fieldFontMap
```
findAction
```
javax.swing.Action findAction
```
findAgainAction
```
javax.swing.Action findAgainAction
```

clearStateOnOpenAction

javax.swing.Action clearStateOnOpenAction

winScale
```
double winScale
```
borderWidth
```
int borderWidth
```
borderColor
```
java.awt.Color borderColor
```
tabScale
```
double tabScale
```
autoTabScale
```
boolean autoTabScale
```
tabScaleCalcNeeded
```
boolean tabScaleCalcNeeded
```
animSynchronized
```
boolean animSynchronized
```
startLoad
```
boolean startLoad
```
rows
```
int rows
```
cols
```
int cols
```

animator

chemaxon.marvin.view.swing.modules.MViewAnimator animator

selectable
```
boolean selectable
```
editable
```
int editable
```
importEnabled
```
boolean importEnabled
```

skbridge

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

findTextModule

chemaxon.marvin.view.swing.modules.FindText findTextModule

selected
```
int selected
```
detachable
```
boolean detachable
```
tabScaleCalcInProgress
```
int tabScaleCalcInProgress
```
draggable
```
boolean draggable
```
molbgMap
```
java.util.Map<K,V> molbgMap
```
tableSupport
```
TableSupport tableSupport
```

commonActions

chemaxon.marvin.common.swing.action.CommonActions commonActions

molEdited
```
boolean molEdited
```
oldMarkedCell
```
int oldMarkedCell
```
oldMarkedAtom
```
int oldMarkedAtom
```
atomMarkAndHighlightEnabled
```
boolean atomMarkAndHighlightEnabled
```

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

Package chemaxon.naming
- Class chemaxon.naming.NameFormatException extends MolFormatException implements Serializable
  - Serialized Fields
    - tokens
```
chemaxon.naming.n2s.lex.data.Token[] tokens
```
    - prefix
```
java.lang.String prefix
```
- Class chemaxon.naming.NameFormatException.FilteredCase extends NameFormatException implements Serializable
- Class chemaxon.naming.NamePrefixException extends NameFormatException implements Serializable
  - Serialized Fields
    - token
```
java.lang.String token
```
Package chemaxon.naming.document
- Class chemaxon.naming.document.D2SOptionsParser.UnknownOptionException extends java.lang.Exception implements Serializable
- Class chemaxon.naming.document.D2SPDFParser extends ExtendablePDFParser implements Serializable
- Class chemaxon.naming.document.D2STextParser extends java.lang.Object implements Serializable
- Class chemaxon.naming.document.EncryptedDocumentException extends java.io.IOException implements Serializable
- Class chemaxon.naming.document.OSRParser extends AbstractParser implements Serializable
- Class chemaxon.naming.document.SafeOfficeParser extends OfficeParser implements Serializable
- Class chemaxon.naming.document.TimeoutException extends java.io.IOException implements Serializable
  - Serialized Fields
    - timeoutMS
```
long timeoutMS
```
- Class chemaxon.naming.document.TrivialXMLParser extends AbstractParser implements Serializable
- Class chemaxon.naming.document.XMLStaxParser extends AbstractParser implements Serializable
  
  serialVersionUID:
  
  -6028836725280212837L
Package chemaxon.naming.document.annotate
- Class chemaxon.naming.document.annotate.AnnotationException extends java.io.IOException implements Serializable
Package chemaxon.reaction
- Class chemaxon.reaction.EqualableMolecule extends Molecule implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - mol
```
Molecule mol
```
    - hashcode
```
int hashcode
```
- Class chemaxon.reaction.MoleculeData extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - grinvCC
```
long grinvCC
```
- Class chemaxon.reaction.PatternProperty extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -3617253669859174882L
  - Serialized Fields
    - representation
```
java.lang.String representation
```
- Class chemaxon.reaction.Reaction extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -3004308308384113541L
  - Serialized Fields
    - data
```
int data
```
    - id
```
java.lang.String id
```
    - rxn
```
RxnMolecule rxn
```
    - reactantMatchingRule
```
java.lang.String reactantMatchingRule
```
    - reactivityRule
```
java.lang.String reactivityRule
```
    - selectivityRule
```
java.lang.String selectivityRule
```
    - tolerances
```
double[] tolerances
```
    - map2nopar
```
int[] map2nopar
```
    - map2map
```
int[] map2map
```
    - smaps
```
int[] smaps
```
    - emaps
```
int[] emaps
```
    - rbondtypes
```
int[] rbondtypes
```
    - pbondtypes
```
int[] pbondtypes
```
    - bcount
```
int bcount
```
    - map2stereo
```
int[] map2stereo
```
    - rmaps
```
java.util.List<E>[] rmaps
```
    - pmaps
```
java.util.List<E>[] pmaps
```
    - map2raindex
```
int[] map2raindex
```
    - map2paindex
```
int[] map2paindex
```
    - map2rindex
```
int[] map2rindex
```
    - map2pindex
```
int[] map2pindex
```
    - rindex2map
```
int[] rindex2map
```
    - pindex2map
```
int[] pindex2map
```
    - rparities
```
java.util.ArrayList<E> rparities
```
    - pparities
```
java.util.ArrayList<E> pparities
```
    - rcistrans
```
java.util.ArrayList<E> rcistrans
```
    - pcistrans
```
java.util.ArrayList<E> pcistrans
```
    - reactants
```
Molecule[] reactants
```
    - products
```
Molecule[] products
```
- Class chemaxon.reaction.ReactionException extends java.lang.Exception implements Serializable
  
  serialVersionUID:
  
  1L
- Class chemaxon.reaction.ReactionPerformer extends java.lang.Object implements Serializable
  - Serialized Fields
    - reaction
```
chemaxon.reaction.Reaction reaction
```
    - searcher
```
chemaxon.reaction.ReactionSearcher searcher
```
    - context
```
ReactionContext context
```
    - origmaps
```
int[] origmaps
```
    - rligandsets
```
java.util.ArrayList<E> rligandsets
```
    - rcistranssets
```
java.util.ArrayList<E> rcistranssets
```
    - reactants
```
Molecule[] reactants
```
    - currentReactants
```
Molecule[] currentReactants
```
    - productsets
```
java.util.ArrayList<E> productsets
```
    - transformedProductSet
```
chemaxon.reaction.ProductSet transformedProductSet
```
    - absStereo
```
boolean absStereo
```
    - options
```
chemaxon.reaction.ReactorOptions options
```
    - baseProductID
```
java.lang.String baseProductID
```
    - globalProductIndex
```
int globalProductIndex
```
    - reactantProperties
```
java.util.Properties reactantProperties
```
    - stgrpMap
```
java.util.ArrayList<E> stgrpMap
```
    - reactionMap
```
java.util.Map<K,V> reactionMap
```
    - reactorLogger
```
chemaxon.reaction.ReactorLogger reactorLogger
```
- Class chemaxon.reaction.Reactor extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - licenseEnvironment
```
java.lang.String licenseEnvironment
```
    - rre
```
chemaxon.reaction.ReactionResultEnumerator rre
```
    - reaction
```
chemaxon.reaction.Reaction reaction
```
      The reaction scheme with rules
    - performer
```
chemaxon.reaction.ReactionPerformer performer
```
      The reaction performer.
    - explicitStandardizer
```
Standardizer explicitStandardizer
```
      The reactant standardizer object.
    - reactionDefinedStandardizer
```
Standardizer reactionDefinedStandardizer
```
      The reactant standardizer object defined by the reaction scheme.
    - ignoreReactionDefinedStandardizer
```
boolean ignoreReactionDefinedStandardizer
```
      Ignore standardizer defined in Reactor.reactionDefinedStandardizer.
    - outputReactionMappingStyle
```
int outputReactionMappingStyle
```
      Output reaction mapping style.
    - fakeResultType
```
int fakeResultType
```
      Fake result type. Can be Reactor.FUSED_REACTION_OUTPUT
    - originalInputReactants
```
Molecule[] originalInputReactants
```
      The original input reactants.
    - reactants
```
Molecule[] reactants
```
      The reactant array.
    - first
```
boolean first
```
      True if first hit is to be returned.
    - pieces
```
int pieces
```
      The number of result items to be returned for one reactant set
    - currentPieces
```
int currentPieces
```
    - options
```
chemaxon.reaction.ReactorOptions options
```
- Class chemaxon.reaction.ReactorOptions extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - resultType
```
int resultType
```
    - duplicateFilteringMethod
```
int duplicateFilteringMethod
```
    - ignoreRules
```
int ignoreRules
```
    - ratio
```
int[] ratio
```
    - pinds
```
int[] pinds
```
    - reverse
```
boolean reverse
```
    - excludeOverlappingHits
```
boolean excludeOverlappingHits
```
    - mapResult
```
boolean mapResult
```
    - single
```
boolean single
```
    - rmduprefs
```
boolean rmduprefs
```
    - cached
```
boolean cached
```
    - searchOptionsString
```
java.lang.String searchOptionsString
```
    - reactionIDProp
```
java.lang.String reactionIDProp
```
    - reactantIDProps
```
java.lang.String[] reactantIDProps
```
    - productIDProps
```
java.lang.String[] productIDProps
```
    - copyAllReactantProperties
```
boolean copyAllReactantProperties
```
    - sourceProperties
```
java.lang.String[][] sourceProperties
```
    - targetProperties
```
java.lang.String[][] targetProperties
```
    - patternBasedProperties
```
java.util.Map<K,V> patternBasedProperties
```
    - showUnsuccessfulReactions
```
boolean showUnsuccessfulReactions
```
    - generateMinorProducts
```
boolean generateMinorProducts
```
    - markReactionCenter
```
boolean markReactionCenter
```
- Class chemaxon.reaction.RxnException extends SearchException implements Serializable
  
  serialVersionUID:
  
  3156388646087913621L
- Class chemaxon.reaction.SearchData extends chemaxon.reaction.MoleculeData implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - hitDataList
```
java.util.ArrayList<E> hitDataList
```
    - complete
```
boolean complete
```
Package chemaxon.sss.search
- Class chemaxon.sss.search.JChemSearchOptions extends SearchOptions implements Serializable
  
  serialVersionUID:
  
  -6025435983286725061L
  - Serialized Fields
    - absoluteStereo
```
int absoluteStereo
```
    - filterQuery
```
java.lang.String filterQuery
```
    - dissimilarityThreshold
```
float dissimilarityThreshold
```
    - dissimilarityThresholdExcluded
```
boolean dissimilarityThresholdExcluded
```
    - maxResultCount
```
int maxResultCount
```
    - returnsNonHits
```
boolean returnsNonHits
```
    - dissimilarityMetric
```
java.lang.String dissimilarityMetric
```
      Dissimilarity metric name, or null for default.
    - dissimilarityMetricParameters
```
java.lang.String dissimilarityMetricParameters
```
      Dissimilarity metric parameters.
    - descriptorConfig
```
java.lang.String descriptorConfig
```
      configuration for descriptor dissim. calculations
    - descriptorName
```
java.lang.String descriptorName
```
      the identifier of stored descriptor used for dissim. calculations, null means pure fingerprint similarity is performed
    - formulaSearchType
```
int formulaSearchType
```
      Type of the formula search. See: chemaxon.sss.formula.FormulaSearch
    - formulaSearchQuery
```
java.lang.String formulaSearchQuery
```
      Query of the formula search.
    - matchCountOptions
```
MatchCountOptions matchCountOptions
```
    - optimizeQueries
```
boolean optimizeQueries
```
      Shows whether the query should be enumerated to improve search
    - cacheRegistrationNeeded
```
boolean cacheRegistrationNeeded
```
      Can be set to false in case of readonly databases and jcsearch. Only for internal use!
    - totalSearchTimeoutLimitMilliseconds
```
int totalSearchTimeoutLimitMilliseconds
```
      The search on a database timeouts reaching this number of milliseconds.
    - markushScreeningOptions
```
java.util.Set<E> markushScreeningOptions
```
      Set containing all enabled Markush screen methods
    - haltOnError
```
HaltOnErrorOption haltOnError
```
      Error handling of the search.
      
      See Also:
      
      HaltOnErrorOption
- Class chemaxon.sss.search.MarkushFeature extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  8770437891053649928L
  - Serialized Fields
    - type
```
int type
```
      Expansion type.
    - 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
```
- Class chemaxon.sss.search.MatchCountOptions extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  6422092438307828424L
  - Serialized Fields
    - matchCountIncludesZero
```
boolean matchCountIncludesZero
```
    - mode
```
int mode
```
    - matchCountLowLimit
```
int matchCountLowLimit
```
    - matchCountHighLimit
```
int matchCountHighLimit
```
    - matchCountLowLimitInclusive
```
boolean matchCountLowLimitInclusive
```
    - matchCountHighLimitInclusive
```
boolean matchCountHighLimitInclusive
```
    - matchCounthitLimit
```
int matchCounthitLimit
```
    - matchCountRelation
```
java.lang.String matchCountRelation
```
- Class chemaxon.sss.search.MolSearchOptions extends SearchOptions implements Serializable
  
  serialVersionUID:
  
  -6364233804214700841L
  - Serialized Fields
    - 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.
    - hitIncludesRNodes
```
boolean hitIncludesRNodes
```
      If true, the result hit will contain R-nodes with dummy indexes
    - 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.
    - 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.
    - 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)
    - markushEnabled
```
boolean markushEnabled
```
      Decides whether targets with Markush features should be treated as Markush libraries (true) or just "strange" molecules (false) (default value: false).
    - 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
    - tautomerEqualityMode
```
chemaxon.sss.search.options.TautomerTransformationMode tautomerEqualityMode
```
- Class chemaxon.sss.search.SearchException extends java.lang.Exception implements Serializable
  
  serialVersionUID:
  
  1698586463587833734L
- Class chemaxon.sss.search.SearchOptions extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -6845044337680993338L
  - Serialized Fields
    - 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.)
    - 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
    - doubleBondStereoMatchingMode
```
int doubleBondStereoMatchingMode
```
      Defines the double bond stereo matching mode. Default is DBS_MARKED.
      
      Since:
      
      JChem 2.2
      
      See Also:
      
      SearchOptions.setDoubleBondStereoMatchingMode(int)
    - hCountMatching
```
int hCountMatching
```
      Defines the interpretation of H count in the query. Default is HCOUNT_MATCHING_AUTO.
    - verbose
```
boolean verbose
```
      For debugging purposes. Public, because it does not count for the dirty flag.
    - searchType
```
int searchType
```
      Search type: global mode of search.
    - vagueBondLevel
```
int vagueBondLevel
```
      Option for less strict evaluation of query bonds (e.g. ambiguious aromaticity). Default value is SearchConstants.VAGUE_BOND_LEVEL_HALF
    - completeHG
```
boolean completeHG
```
      Specifies if only complete structures should match on target homology groups.
    - exactBondMatching
```
boolean exactBondMatching
```
      true, if query bonds match only the same query bonds
    - orderSensitiveSearch
```
boolean orderSensitiveSearch
```
      Specifies whether the same set of target atoms found in a different order should be considered as a different hit.
    - keepQueryOrder
```
boolean keepQueryOrder
```
      True: instructs search to rearrange query atoms for better search performance.
    - 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.
    - isotopeMatching
```
int isotopeMatching
```
      Specifies the isotope searching behaviour. Default is ISOTOPE_MATCHING_DEFAULT (isotope query matches only isotope target, nonisotope query matches all)
    - chargeMatching
```
int chargeMatching
```
      Specifies the charge searching behaviour. Default is CHARGE_MATCHING_DEFAULT (charged query matches only charged target, noncharged query matches all)
    - valenceMatching
```
boolean valenceMatching
```
      True: valence is checked 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)
    - mixSgroupMatching
```
boolean mixSgroupMatching
```
      True: consider COM, MIX and FOR sgroups during search (default value: true).
    - polymerMatching
```
boolean polymerMatching
```
      True: consider polymer sgroups during search (default value: true).
    - endGroupMatching
```
boolean endGroupMatching
```
      True: polymer endgroups must match (default: false)
    - transformMonomer
```
boolean transformMonomer
```
      True: monomers are transformed to structural repeating units. (default: true)
    - phaseShift
```
boolean phaseShift
```
      True: the phase-shifted polymers are matching on each other. (default: true)
    - copolymerMatching
```
boolean copolymerMatching
```
      True: Polymers in copolymers can only be matched by copolymers. (default: false)
    - 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.
    - 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.
    - 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)
    - ignoreTetrahedralStereo
```
boolean ignoreTetrahedralStereo
```
      See Also:
      
      SearchOptions.setIgnoreTetrahedralStereo(boolean)
    - ignoreDoubleBondStereo
```
boolean ignoreDoubleBondStereo
```
      See Also:
      
      SearchOptions.setIgnoreDoubleBondStereo(boolean)
    - ignoreAxialStereo
```
boolean ignoreAxialStereo
```
      See Also:
      
      SearchOptions.setIgnoreAxialStereo(boolean)
    - ignoreCumuleneCisTransStereo
```
boolean ignoreCumuleneCisTransStereo
```
      See Also:
      
      SearchOptions.setIgnoreCumuleneOrRingCisTransStereo(boolean)
    - ignoreSynAntiStereo
```
boolean ignoreSynAntiStereo
```
      See Also:
      
      SearchOptions.setIgnoreSynAntiStereo(boolean)
    - 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
    - implicitHMatching
```
int implicitHMatching
```
      Specifies match between explicit and implicit hydrogens. Default is IMPLICIT_H_MATCHING_DEFAULT (matching depends on the circumstances of search)
    - reactionUnpairedMapMatching
```
boolean reactionUnpairedMapMatching
```
      True: in reaction search unpaired (orphan and widow) atom maps can match any atom map (default value: 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.
    - bridgingRAllowed
```
boolean bridgingRAllowed
```
      True: different undefined R-atoms can match the same group of atoms. Default value: false.
    - rLigandEqualityCheck
```
boolean rLigandEqualityCheck
```
      True: undefined R-atoms with the same R-group ID should match the same structure. Default value: true.
    - hitOrdering
```
int hitOrdering
```
      Specifies hit ordering, currently used in ordering undefined R-atom group matchings Default is SearchConstants.HIT_ORDERING_NONE.
    - attachedDataMatch
```
int attachedDataMatch
```
      Specifies attached data match type Default is SearchConstants.ATTACHED_DATA_MATCH_IGNORE
    - attachedDataPrefixes
```
java.lang.String attachedDataPrefixes
```
      Data sgroup name prefixes that will be used for comparison When null, all data sgroups will be used.
    - exactSpecialAtomMatching
```
java.lang.String exactSpecialAtomMatching
```
    - chemTermsFilterOption
```
chemaxon.sss.search.options.ChemTermsFilterOption chemTermsFilterOption
```
    - changedUserComparator
```
boolean changedUserComparator
```
      true if user-defined comparators has changed
    - userComparators
```
java.util.ArrayList<E> userComparators
```
      User defined MolComparators
    - exhaustiveModeLimit
```
int exhaustiveModeLimit
```
      Upon reaching this number of steps, the search switches to exhaustive mode from fast mode.
    - timeoutLimitMilliseconds
```
int timeoutLimitMilliseconds
```
      The search on a single target timeouts reaching this number of milliseconds.
    - throwExceptionOnTimeout
```
boolean throwExceptionOnTimeout
```
      If the search should throw exception upon timeout.
    - 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.
    - targetHomologyMatchingMode
```
TargetHomologyMatchingMode targetHomologyMatchingMode
```
- Class chemaxon.sss.search.SearchTimeoutException extends SearchException implements Serializable
  
  serialVersionUID:
  
  -78126823565453833L
- Class chemaxon.sss.search.UnsupportedQueryException extends java.lang.IllegalArgumentException implements Serializable
  
  serialVersionUID:
  
  6255906179820229430L
Package chemaxon.sss.search.options
- Class chemaxon.sss.search.options.ChemTermsFilterOption extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  8226348996476285704L
  - Serialized Fields
    - chemTermsFilter
```
java.lang.String chemTermsFilter
```
    - chemTermsFilterConfig
```
java.lang.String chemTermsFilterConfig
```
    - ignoreCTExceptions
```
boolean ignoreCTExceptions
```
Package chemaxon.standardizer.advancedactions
- Class chemaxon.standardizer.advancedactions.GroupList extends java.util.ArrayList<GroupDefinition> implements Serializable
Package chemaxon.struc
- Class chemaxon.struc.CTransform3D extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialization Methods
    - readExternal
```
public void readExternal(java.io.ObjectInput in)
                  throws java.io.IOException
```
      Deserializes a transformation matrix.
      
      Throws:
      
      java.io.IOException
      
      Since:
      
      3.5, 11/02/2004
    - writeExternal
```
public void writeExternal(java.io.ObjectOutput out)
                   throws java.io.IOException
```
      Serializes a transformation matrix.
      
      Throws:
      
      java.io.IOException
      
      Since:
      
      3.5, 11/02/2004
- Class chemaxon.struc.DefaultDictionary extends java.util.HashMap<java.lang.String,SuperatomSgroup> implements Serializable
  
  serialVersionUID:
  
  8013155936541949713L
- Class chemaxon.struc.DPoint3 extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialization Methods
    - readExternal
```
public void readExternal(java.io.ObjectInput in)
                  throws java.io.IOException,
                         java.lang.ClassNotFoundException
```
      Deserializes a 3D point.
      
      Throws:
      
      java.io.IOException
      
      java.lang.ClassNotFoundException
    - writeExternal
```
public void writeExternal(java.io.ObjectOutput out)
                   throws java.io.IOException
```
      Serializes a 3D point.
      
      Throws:
      
      java.io.IOException
- Class chemaxon.struc.ExtraAtomProperties extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -1980229820290558380L
  - Serialized Fields
    - attachParentSgroup
```
Sgroup attachParentSgroup
```
    - valence1
```
short valence1
```
    - order
```
int order
```
    - qprops
```
java.util.Map<K,V> qprops
```
    - querystr
```
java.lang.String querystr
```
    - aliasstr
```
java.lang.String aliasstr
```
    - extrastr
```
java.lang.String extrastr
```
    - extrargbs
```
long extrargbs
```
    - list
```
int[] list
```
    - flags
```
int flags
```
    - rgroupId
```
short rgroupId
```
    - countFlags
```
int countFlags
```
    - repetitionBits
```
int repetitionBits
```
    - linkNodeOuterBonds
```
int linkNodeOuterBonds
```
    - electronProp
```
int electronProp
```
    - temporaryObjects
```
java.util.Map<K,V> temporaryObjects
```
- Class chemaxon.struc.MacroMolecule.BadMoleculeException extends java.lang.Exception implements Serializable
  
  serialVersionUID:
  
  9037472982065239933L
- Class chemaxon.struc.MDocument extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  553557622036381832L
  - Serialization Methods
    - readObject
```
private void readObject(java.io.ObjectInputStream ois)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException
```
      Deserializes a document. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.lang.ClassNotFoundException
      
      java.io.IOException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream oos)
                  throws java.io.IOException
```
      Serializes a document. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.io.IOException
- Class chemaxon.struc.MDocument.Prop extends MProp implements Serializable
- Class chemaxon.struc.MDocumentUtil extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  12600100100892L
  - Serialized Fields
    - doc
```
MDocument doc
```
- Class chemaxon.struc.MObject extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  2435517510938087080L
  - Serialization Methods
    - readObject
```
private void readObject(java.io.ObjectInputStream ois)
                 throws java.io.IOException
```
      Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.io.IOException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream oos)
                  throws java.io.IOException
```
      Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.io.IOException
- Class chemaxon.struc.MolAtom extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -3974070468228529467L
  - Serialization Methods
    - readObject
```
private void readObject(java.io.ObjectInputStream ois)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException
```
      Deserializes an atom. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.lang.ClassNotFoundException
      
      java.io.IOException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream oos)
                  throws java.io.IOException
```
      Serializes an atom. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.io.IOException
  - Serialized Fields
    - isValenceCheckNeeded
```
boolean isValenceCheckNeeded
```
    - angle
```
double angle
```
- Class chemaxon.struc.MolBond extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  3656012871856958335L
  - Serialization Methods
    - readObject
```
private void readObject(java.io.ObjectInputStream ois)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException
```
      Deserializes a bond. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.lang.ClassNotFoundException
      
      java.io.IOException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream oos)
                  throws java.io.IOException
```
      Serializes a bond. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.io.IOException
- Class chemaxon.struc.Molecule extends MoleculeGraph implements Serializable
  
  serialVersionUID:
  
  7275486436840296305L
  - Serialization Methods
    - readObject
```
private void readObject(java.io.ObjectInputStream ois)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException
```
      Deserializes a molecule. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.lang.ClassNotFoundException
      
      java.io.IOException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream oos)
                  throws java.io.IOException
```
      Serializes a molecule. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.io.IOException
  - Serialized Fields
    - id
```
java.lang.String id
```
- Class chemaxon.struc.MoleculeGraph extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -2053719583816270190L
  - Serialization Methods
    - readObject
```
private void readObject(java.io.ObjectInputStream ois)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException
```
      Deserializes a molecule graph. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.lang.ClassNotFoundException
      
      java.io.IOException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream oos)
                  throws java.io.IOException
```
      Serializes a molecule graph. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.io.IOException
  - Serialized Fields
    - hasBicycloStereo
```
boolean hasBicycloStereo
```
      Molecule has bicyclo stereo information. Can be set by MolAtom.setBicycloStereo(BicycloStereoDescriptor[]).
    - valenceCheckOptions
```
ValenceCheckOptions valenceCheckOptions
```
      Valence check options for the molecule.
    - fragmentTracker
```
chemaxon.struc.MoleculeGraph.FragmentTracker fragmentTracker
```
- Class chemaxon.struc.MPoint extends MObject implements Serializable
  
  serialVersionUID:
  
  -3067277054033050963L
  - Serialization Methods
    - readObject
```
private void readObject(java.io.ObjectInputStream ois)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException
```
      Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.lang.ClassNotFoundException
      
      java.io.IOException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream oos)
                  throws java.io.IOException
```
      Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.io.IOException
- Class chemaxon.struc.MProp extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -5699803671884637223L
  - Serialized Fields
    - grinvCC
```
long grinvCC
```
    - coordDependent
```
boolean coordDependent
```
- Class chemaxon.struc.MPropertyContainer extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -2575268570438177098L
  - Serialization Methods
    - readExternal
```
public void readExternal(java.io.ObjectInput in)
                  throws java.io.IOException,
                         java.lang.ClassNotFoundException
```
      Restores the property container's state.
      
      Throws:
      
      java.io.IOException - if I/O errors occur
      
      java.lang.ClassNotFoundException - If the class for an object being restored cannot be found.
    - writeExternal
```
public void writeExternal(java.io.ObjectOutput out)
                   throws java.io.IOException
```
      Saves the property container's state.
      
      Throws:
      
      java.io.IOException - Includes any I/O exceptions that may occur
- Class chemaxon.struc.MSelectionDocument extends MDocument implements Serializable
  
  serialVersionUID:
  
  2379294894434293119L
- Class chemaxon.struc.PageSettings extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -7674028514396457694L
  - Serialization Methods
    - readExternal
```
public void readExternal(java.io.ObjectInput arg0)
                  throws java.io.IOException,
                         java.lang.ClassNotFoundException
```
      Throws:
      
      java.io.IOException
      
      java.lang.ClassNotFoundException
    - writeExternal
```
public void writeExternal(java.io.ObjectOutput arg0)
                   throws java.io.IOException
```
      Throws:
      
      java.io.IOException
- Class chemaxon.struc.QueryBond extends MolBond implements Serializable
  
  serialVersionUID:
  
  -5025485107616067648L
  - Serialization Methods
    - readObject
```
private void readObject(java.io.ObjectInputStream ois)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException
```
      Deserializes a bond. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.lang.ClassNotFoundException
      
      java.io.IOException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream oos)
                  throws java.io.IOException
```
      Serializes a bond. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.io.IOException
- Class chemaxon.struc.RgMolecule extends Molecule implements Serializable
  
  serialVersionUID:
  
  -939153732283455787L
  - Serialization Methods
    - readObject
```
private void readObject(java.io.ObjectInputStream ois)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException
```
      Deserializes an RgMolecule. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.lang.ClassNotFoundException
      
      java.io.IOException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream oos)
                  throws java.io.IOException
```
      Serializes an RgMolecule. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.io.IOException
- Class chemaxon.struc.RxnMolecule extends Molecule implements Serializable
  
  serialVersionUID:
  
  -2863036104564183121L
  - Serialization Methods
    - readObject
```
private void readObject(java.io.ObjectInputStream ois)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException
```
      Deserializes a reaction. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.lang.ClassNotFoundException
      
      java.io.IOException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream oos)
                  throws java.io.IOException
```
      Serializes a reaction. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.io.IOException
- Class chemaxon.struc.SelectionMolecule extends MoleculeGraph implements Serializable
  
  serialVersionUID:
  
  234062772192819675L
- Class chemaxon.struc.SelectionRgMolecule extends SelectionMolecule implements Serializable
- Class chemaxon.struc.Sgroup extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -6209766549185582411L
  - Serialization Methods
    - readObject
```
private void readObject(java.io.ObjectInputStream ois)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException
```
      Deserializes an Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.lang.ClassNotFoundException
      
      java.io.IOException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream oos)
                  throws java.io.IOException
```
      Serializes an Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.io.IOException
  - Serialized Fields
    - id
```
java.lang.String id
```
    - atomSet
```
java.util.Set<E> atomSet
```
      Set for storing the atoms of the s-group's graph.
- Class chemaxon.struc.StaticMolecule extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -6974806277329432018L
  - Serialized Fields
    - ringPerception
```
boolean ringPerception
```
    - name
```
java.lang.String name
```
    - arrayFlags
```
int arrayFlags
```
    - atomCount
```
int atomCount
```
    - connectionTable
```
short[] connectionTable
```
    - neighborCount
```
byte[] neighborCount
```
    - nodeEdgeList
```
short[][] nodeEdgeList
```
    - bondCount
```
int bondCount
```
    - atomType
```
short[] atomType
```
    - bondAtom1
```
short[] bondAtom1
```
    - bondAtom2
```
short[] bondAtom2
```
    - bondFlags
```
int[] bondFlags
```
    - extendedAtomType
```
int[] extendedAtomType
```
    - atomLists
```
byte[][] atomLists
```
    - hybridization
```
byte[] hybridization
```
    - atomStereo
```
byte[] atomStereo
```
    - implicitHcount
```
byte[] implicitHcount
```
    - explicitHcount
```
byte[] explicitHcount
```
    - valence
```
byte[] valence
```
    - queryProperty
```
byte[][] queryProperty
```
    - radical
```
byte[] radical
```
    - charge
```
byte[] charge
```
    - massno
```
byte[] massno
```
    - atomMap
```
short[] atomMap
```
    - rgroupId
```
short[] rgroupId
```
    - sgroupId
```
java.lang.String[] sgroupId
```
Package chemaxon.struc.graphics
- Class chemaxon.struc.graphics.MAnalysisBox extends MTextBox implements Serializable
  
  serialVersionUID:
  
  -7630363128405095856L
  - Serialized Fields
    - mol
```
Molecule mol
```
    - terms
```
java.util.List<E> 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(java.io.ObjectInputStream ois)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException
```
      Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.lang.ClassNotFoundException
      
      java.io.IOException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream oos)
                  throws java.io.IOException
```
      Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.io.IOException
- Class chemaxon.struc.graphics.MBracket extends MRectangle implements Serializable
  
  serialVersionUID:
  
  -5775562691065011181L
  - Serialization Methods
    - readObject
```
private void readObject(java.io.ObjectInputStream ois)
                 throws java.io.IOException
```
      Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.io.IOException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream oos)
                  throws java.io.IOException
```
      Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.io.IOException
  - Serialized Fields
    - bracketType
```
int bracketType
```
    - bracketOrientation
```
int bracketOrientation
```
      Bracket orientation, bracket can have two sides (T_DOUBLE) or just one (T_SINGLE). Possible values: T_SINGLE, T_DOUBLE
- Class chemaxon.struc.graphics.MChemicalStruct extends MObject implements Serializable
  
  serialVersionUID:
  
  7098670860634457343L
  - Serialization Methods
    - readObject
```
private void readObject(java.io.ObjectInputStream ois)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException
```
      Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.lang.ClassNotFoundException
      
      java.io.IOException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream oos)
                  throws java.io.IOException
```
      Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.io.IOException
- Class chemaxon.struc.graphics.MEFlow extends MPolyline implements Serializable
  
  serialVersionUID:
  
  891769518407563834L
  - Serialization Methods
    - readObject
```
private void readObject(java.io.ObjectInputStream ois)
                 throws java.io.IOException
```
      Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.io.IOException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream oos)
                  throws java.io.IOException
```
      Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.io.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(java.io.ObjectInputStream ois)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException
```
      Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.lang.ClassNotFoundException
      
      java.io.IOException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream oos)
                  throws java.io.IOException
```
      Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.io.IOException
  - Serialized Fields
    - electronIndex
```
int electronIndex
```
    - electronLabel
```
java.lang.String electronLabel
```
- Class chemaxon.struc.graphics.MElectron extends MAtomSetPoint implements Serializable
  - Serialization Methods
    - readObject
```
private void readObject(java.io.ObjectInputStream arg0)
                 throws java.io.IOException
```
      Throws:
      
      java.io.IOException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream arg0)
                  throws java.io.IOException
```
      Throws:
      
      java.io.IOException
  - Serialized Fields
    - difLoc
```
DPoint3 difLoc
```
    - isPointed
```
boolean isPointed
```
- Class chemaxon.struc.graphics.MElectronContainer extends MObject implements Serializable
  - Serialization Methods
    - readObject
```
private void readObject(java.io.ObjectInputStream arg0)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException
```
      Throws:
      
      java.io.IOException
      
      java.lang.ClassNotFoundException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream arg0)
                  throws java.io.IOException
```
      Throws:
      
      java.io.IOException
  - Serialized Fields
    - electrons
```
chemaxon.struc.graphics.MElectron[] electrons
```
    - electronOccupation
```
boolean[] electronOccupation
```
    - radical
```
boolean radical
```
- Class chemaxon.struc.graphics.MEllipse extends MRectangle implements Serializable
  - Serialization Methods
    - readObject
```
private void readObject(java.io.ObjectInputStream ois)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException
```
      Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.lang.ClassNotFoundException
      
      java.io.IOException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream oos)
                  throws java.io.IOException
```
      Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.io.IOException
- Class chemaxon.struc.graphics.MFont extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -7769715209509613515L
  - Serialization Methods
    - readObject
```
private void readObject(java.io.ObjectInputStream ois)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException
```
      Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.lang.ClassNotFoundException
      
      java.io.IOException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream oos)
                  throws java.io.IOException
```
      Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.io.IOException
- Class chemaxon.struc.graphics.MMidPoint extends MPoint implements Serializable
  
  serialVersionUID:
  
  5307361876930807239L
  - Serialization Methods
    - readObject
```
private void readObject(java.io.ObjectInputStream ois)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException
```
      Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.lang.ClassNotFoundException
      
      java.io.IOException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream oos)
                  throws java.io.IOException
```
      Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.io.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(java.io.ObjectInputStream arg0)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException
```
      Throws:
      
      java.lang.ClassNotFoundException
      
      java.io.IOException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream arg0)
                  throws java.io.IOException
```
      Throws:
      
      java.io.IOException
- Class chemaxon.struc.graphics.MNameTextBox extends MTextBox implements Serializable
  
  serialVersionUID:
  
  6302424343157644471L
  - Serialization Methods
    - readObject
```
private void readObject(java.io.ObjectInputStream arg0)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException
```
      Throws:
      
      java.lang.ClassNotFoundException
      
      java.io.IOException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream arg0)
                  throws java.io.IOException
```
      Throws:
      
      java.io.IOException
- Class chemaxon.struc.graphics.MPolyline extends MObject implements Serializable
  
  serialVersionUID:
  
  4958026600768388648L
  - Serialization Methods
    - readObject
```
private void readObject(java.io.ObjectInputStream ois)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException
```
      Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.lang.ClassNotFoundException
      
      java.io.IOException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream oos)
                  throws java.io.IOException
```
      Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.io.IOException
  - Serialized Fields
    - internalPointPos
```
int internalPointPos
```
    - internalPointAddCount
```
int internalPointAddCount
```
- Class chemaxon.struc.graphics.MRArrow extends MPolyline implements Serializable
  
  serialVersionUID:
  
  8638690394107448092L
  - Serialization Methods
    - readObject
```
private void readObject(java.io.ObjectInputStream arg0)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException
```
      Throws:
      
      java.lang.ClassNotFoundException
      
      java.io.IOException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream arg0)
                  throws java.io.IOException
```
      Throws:
      
      java.io.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(java.io.ObjectInputStream ois)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException
```
      Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.lang.ClassNotFoundException
      
      java.io.IOException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream oos)
                  throws java.io.IOException
```
      Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.io.IOException
- Class chemaxon.struc.graphics.MRectanglePoint extends MPoint implements Serializable
  
  serialVersionUID:
  
  -3067277054033050963L
  - Serialization Methods
    - readObject
```
private void readObject(java.io.ObjectInputStream ois)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException
```
      Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.lang.ClassNotFoundException
      
      java.io.IOException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream oos)
                  throws java.io.IOException
```
      Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.io.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(java.io.ObjectInputStream ois)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException
```
      Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.lang.ClassNotFoundException
      
      java.io.IOException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream oos)
                  throws java.io.IOException
```
      Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.io.IOException
  - Serialized Fields
    - arcWidth
```
double arcWidth
```
    - arcHeight
```
double arcHeight
```
- Class chemaxon.struc.graphics.MTextAttributes extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  6561552003080652755L
  - Serialization Methods
    - readExternal
```
public void readExternal(java.io.ObjectInput in)
                  throws java.io.IOException,
                         java.lang.ClassNotFoundException
```
      Throws:
      
      java.io.IOException
      
      java.lang.ClassNotFoundException
    - writeExternal
```
public void writeExternal(java.io.ObjectOutput out)
                   throws java.io.IOException
```
      Throws:
      
      java.io.IOException
- Class chemaxon.struc.graphics.MTextBox extends MRectangle implements Serializable
  
  serialVersionUID:
  
  -7272723232157967384L
  - Serialization Methods
    - readObject
```
private void readObject(java.io.ObjectInputStream ois)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException
```
      Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.lang.ClassNotFoundException
      
      java.io.IOException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream oos)
                  throws java.io.IOException
```
      Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.io.IOException
  - Serialized Fields
    - actionMap
```
javax.swing.ActionMap actionMap
```
- Class chemaxon.struc.graphics.MTextDocument extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  6305880304790247656L
  - Serialization Methods
    - readExternal
```
public void readExternal(java.io.ObjectInput in)
                  throws java.io.IOException,
                         java.lang.ClassNotFoundException
```
      Restores the document.
      
      Throws:
      
      java.io.IOException - if I/O errors occur
      
      java.lang.ClassNotFoundException - If the class for an object being restored cannot be found.
    - writeExternal
```
public void writeExternal(java.io.ObjectOutput out)
                   throws java.io.IOException
```
      Saves the document.
      
      Throws:
      
      java.io.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(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException
```
      Restores the property's state.
      
      Throws:
      
      java.io.IOException - if I/O errors occur
      
      java.lang.ClassNotFoundException - If the class for an object being restored cannot be found.
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException
```
      Saves the property's state.
      
      Throws:
      
      java.io.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(java.io.ObjectInputStream arg0)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException
```
      Throws:
      
      java.io.IOException
      
      java.lang.ClassNotFoundException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream arg0)
                  throws java.io.IOException
```
      Throws:
      
      java.io.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(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException
```
      Restores the property's state.
      
      Throws:
      
      java.io.IOException - if I/O errors occur
      
      java.lang.ClassNotFoundException - If the class for an object being restored cannot be found.
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException
```
      Saves the property's state.
      
      Throws:
      
      java.io.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(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException
```
      Restores the property's state.
      
      Throws:
      
      java.io.IOException - if I/O errors occur
      
      java.lang.ClassNotFoundException - If the class for an object being restored cannot be found.
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException
```
      Saves the property's state.
      
      Throws:
      
      java.io.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(java.io.ObjectInputStream arg0)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException
```
      Throws:
      
      java.io.IOException
      
      java.lang.ClassNotFoundException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream arg0)
                  throws java.io.IOException
```
      Throws:
      
      java.io.IOException
- Class chemaxon.struc.prop.MHashProp extends MCollectionProp implements Serializable
  
  serialVersionUID:
  
  5457649877894058447L
  - Serialization Methods
    - readObject
```
private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException
```
      Restores the property's state.
      
      Throws:
      
      java.io.IOException - if I/O errors occur
      
      java.lang.ClassNotFoundException - If the class for an object being restored cannot be found.
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException
```
      Saves the property's state.
      
      Throws:
      
      java.io.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(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException
```
      Restores the property's state.
      
      Throws:
      
      java.io.IOException - if I/O errors occur
      
      java.lang.ClassNotFoundException - If the class for an object being restored cannot be found.
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException
```
      Saves the property's state.
      
      Throws:
      
      java.io.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(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException
```
      Restores the property's state.
      
      Throws:
      
      java.io.IOException - if I/O errors occur
      
      java.lang.ClassNotFoundException - If the class for an object being restored cannot be found.
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException
```
      Saves the property's state.
      
      Throws:
      
      java.io.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(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException
```
      Restores the property's state.
      
      Throws:
      
      java.io.IOException - if I/O errors occur
      
      java.lang.ClassNotFoundException - If the class for an object being restored cannot be found.
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException
```
      Saves the property's state.
      
      Throws:
      
      java.io.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(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException
```
      Restores the property's state.
      
      Throws:
      
      java.io.IOException - if I/O errors occur
      
      java.lang.ClassNotFoundException - If the class for an object being restored cannot be found.
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException
```
      Saves the property's state.
      
      Throws:
      
      java.io.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(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException
```
      Restores the property's state.
      
      Throws:
      
      java.io.IOException - if I/O errors occur
      
      java.lang.ClassNotFoundException - If the class for an object being restored cannot be found.
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException
```
      Saves the property's state.
      
      Throws:
      
      java.io.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(java.io.ObjectInputStream arg0)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException
```
      Throws:
      
      java.io.IOException
      
      java.lang.ClassNotFoundException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream arg0)
                  throws java.io.IOException
```
      Throws:
      
      java.io.IOException
  - Serialized Fields
    - format
```
java.lang.String format
```
- Class chemaxon.struc.prop.MObjectProp extends MProp implements Serializable
  
  serialVersionUID:
  
  4005646748655675692L
  - Serialization Methods
    - readObject
```
private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException
```
      Restores the property's state.
      
      Throws:
      
      java.io.IOException - if I/O errors occur
      
      java.lang.ClassNotFoundException - If the class for an object being restored cannot be found.
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException
```
      Saves the property's state.
      
      Throws:
      
      java.io.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(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException
```
      Restores the property's state.
      
      Throws:
      
      java.io.IOException - if I/O errors occur
      
      java.lang.ClassNotFoundException - If the class for an object being restored cannot be found.
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException
```
      Saves the property's state.
      
      Throws:
      
      java.io.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(java.io.ObjectInputStream arg0)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException
```
      Throws:
      
      java.lang.ClassNotFoundException
      
      java.io.IOException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream arg0)
                  throws java.io.IOException
```
      Throws:
      
      java.io.IOException
  - Serialized Fields
    - oneLetterName
```
java.lang.String oneLetterName
```
    - threeLetterName
```
java.lang.String threeLetterName
```
    - modified
```
boolean modified
```
- Class chemaxon.struc.sgroup.AttachmentPoint extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -7484860308765339862L
  - Serialized Fields
    - atom
```
MolAtom atom
```
    - order
```
int order
```
    - bond
```
MolBond bond
```
    - leavingAtom
```
chemaxon.struc.sgroup.LeavingGroupAtom leavingAtom
```
    - crossingBondType
```
int crossingBondType
```
- Class chemaxon.struc.sgroup.DataSgroup extends Sgroup implements Serializable
  
  serialVersionUID:
  
  -3132191586564122343L
  - Serialization Methods
    - readObject
```
private void readObject(java.io.ObjectInputStream ois)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException
```
      Deserializes a data Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.lang.ClassNotFoundException
      
      java.io.IOException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream oos)
                  throws java.io.IOException
```
      Serializes a data Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.io.IOException
  - Serialized Fields
    - sb
```
java.lang.StringBuffer sb
```
      temporary variable for getLineOnScreen
    - labelPosition
```
chemaxon.struc.sgroup.DataSgroup.AbstractPosition labelPosition
```
- Class chemaxon.struc.sgroup.LeavingGroupAtom extends MolAtom implements Serializable
  
  serialVersionUID:
  
  8591241919498353308L
  - Serialization Methods
    - readObject
```
private void readObject(java.io.ObjectInputStream arg0)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException
```
      Deprecated.
      
      Throws:
      
      java.lang.ClassNotFoundException
      
      java.io.IOException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream arg0)
                  throws java.io.IOException
```
      Deprecated.
      
      Throws:
      
      java.io.IOException
  - Serialized Fields
    - alternativeName
```
java.lang.String alternativeName
```
      Deprecated.
- Class chemaxon.struc.sgroup.MulticenterSgroup extends Sgroup implements Serializable
  
  serialVersionUID:
  
  -7213879722783498112L
  - Serialization Methods
    - readObject
```
private void readObject(java.io.ObjectInputStream ois)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException
```
      Deserializes a Multicenter Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.lang.ClassNotFoundException
      
      java.io.IOException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream oos)
                  throws java.io.IOException
```
      Serializes a Multicenter Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.io.IOException
- Class chemaxon.struc.sgroup.MultipleSgroup extends Sgroup implements Serializable
  
  serialVersionUID:
  
  -1146464131016252826L
  - Serialization Methods
    - readObject
```
private void readObject(java.io.ObjectInputStream ois)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException
```
      Deserializes a multiple Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.lang.ClassNotFoundException
      
      java.io.IOException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream oos)
                  throws java.io.IOException
```
      Serializes a multiple Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.io.IOException
- Class chemaxon.struc.sgroup.NoFreeAttachmentPointException extends java.lang.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(java.io.ObjectInputStream ois)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException
```
      Deserializes an SRU Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.lang.ClassNotFoundException
      
      java.io.IOException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream oos)
                  throws java.io.IOException
```
      Serializes an SRU Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.io.IOException
- Class chemaxon.struc.sgroup.SgroupAtom extends MolAtom implements Serializable
  
  serialVersionUID:
  
  -3185634359981637075L
  - Serialization Methods
    - readObject
```
private void readObject(java.io.ObjectInputStream ois)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException
```
      Deserializes an Sgroup superatom. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.lang.ClassNotFoundException
      
      java.io.IOException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream oos)
                  throws java.io.IOException
```
      Serializes an Sgroup superatom. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.io.IOException
  - Serialized Fields
    - labelCenter
```
int labelCenter
```
- Class chemaxon.struc.sgroup.SuperatomSgroup extends Sgroup implements Serializable
  
  serialVersionUID:
  
  2968529752634209305L
  - Serialization Methods
    - readObject
```
private void readObject(java.io.ObjectInputStream ois)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException
```
      Deserializes a superatom Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.lang.ClassNotFoundException
      
      java.io.IOException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream oos)
                  throws java.io.IOException
```
      Serializes a superatom Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.
      
      Throws:
      
      java.io.IOException
  - Serialized Fields
    - apContainer
```
chemaxon.struc.sgroup.AttachmentPointContainer apContainer
```
      Attachment Point container object
Package chemaxon.util
- Class chemaxon.util.ArgumentException extends java.lang.Exception implements Serializable
  
  serialVersionUID:
  
  -8949782741678573705L
- Class chemaxon.util.CmdLine.CmdLineException extends java.lang.RuntimeException implements Serializable
  
  serialVersionUID:
  
  -895875464082822299L
- Class chemaxon.util.Heap.HeapException extends java.lang.RuntimeException implements Serializable
- Class chemaxon.util.SearchAttributes extends java.lang.Object implements Serializable
  - Serialized Fields
    - stereoSearch
```
boolean stereoSearch
```
      Deprecated.
    - doubleBondStereoMatchingMode
```
int doubleBondStereoMatchingMode
```
      Deprecated.
    - subgraphSearch
```
boolean subgraphSearch
```
      Deprecated.
    - exactAtomMatching
```
boolean exactAtomMatching
```
      Deprecated.
    - exactStereoMatching
```
boolean exactStereoMatching
```
      Deprecated.
    - orderSensitiveSearch
```
boolean orderSensitiveSearch
```
      Deprecated.
- Class chemaxon.util.SupplierException extends java.lang.RuntimeException implements Serializable
Package chemaxon.util.concurrent.processors
- Class chemaxon.util.concurrent.processors.InputProducerException extends java.lang.Exception implements Serializable
- Class chemaxon.util.concurrent.processors.WorkUnitException extends java.lang.Exception implements Serializable
Package com.chemaxon.calculations.io
- Class com.chemaxon.calculations.io.OrderedInputProcessingException extends java.lang.IllegalArgumentException implements Serializable
  - Serialized Fields
    - inputIndex
```
int inputIndex
```
Package com.chemaxon.calculations.util
- Class com.chemaxon.calculations.util.CmdlineContext.ExitWithNonZeroStatus extends java.lang.RuntimeException implements Serializable
- Class com.chemaxon.calculations.util.CmdlineContext.ExitWithZeroStatus extends java.lang.RuntimeException implements Serializable
Package com.chemaxon.clustering.framework
- Class com.chemaxon.clustering.framework.RemoveSidechainsMolwalk extends java.lang.Object implements Serializable
- Class com.chemaxon.clustering.framework.RemoveSidechainsSc extends java.lang.Object implements Serializable
  - Serialized Fields
    - keepUnsaturatedConnections
```
boolean keepUnsaturatedConnections
```
- Class com.chemaxon.clustering.framework.SimpleFrameworkAssociation extends java.lang.Object implements Serializable
  - Serialized Fields
    - indexToFramework
```
java.util.List<E> indexToFramework
```
Package com.chemaxon.descriptors.alignment
- Class com.chemaxon.descriptors.alignment.AbstractShapeComparator extends java.lang.Object implements Serializable
  - Serialized Fields
    - generator
```
DescriptorGenerator<B extends Descriptor> generator
```
- Class com.chemaxon.descriptors.alignment.AbstractShapeGenerator extends java.lang.Object implements Serializable
  - Serialized Fields
    - parameters
```
AbstractShapeGeneratorParameter parameters
```
- Class com.chemaxon.descriptors.alignment.AbstractShapeGeneratorParameter extends java.lang.Object implements Serializable
  - Serialized Fields
    - atomTyping
```
AtomTyping atomTyping
```
      The setting for available shape coloring methods.
- Class com.chemaxon.descriptors.alignment.BaseShapeComparatorParameter extends java.lang.Object implements Serializable
  - Serialized Fields
    - flexibilityMode
```
AlignmentProperties.FlexibilityMode flexibilityMode
```
    - shapeFunction
```
ShapeFunction shapeFunction
```
    - tryCount
```
com.google.common.base.Optional<T> tryCount
```
- Class com.chemaxon.descriptors.alignment.ShapeComparatorException extends java.lang.RuntimeException implements Serializable
  
  serialVersionUID:
  
  1L
- Class com.chemaxon.descriptors.alignment.ShapeGeneratorException extends java.lang.RuntimeException implements Serializable
  
  serialVersionUID:
  
  1L
Package com.chemaxon.descriptors.common
Package com.chemaxon.descriptors.fingerprints.cfp
- Class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - bitsPerPattern
```
int bitsPerPattern
```
      Bits set for each pattern.
    - length
```
int length
```
      Fingerprint length (bit count).
    - bondCount
```
int bondCount
```
      Max pattern length considered (bond count).
    - rings
```
boolean rings
```
      Consider rings in fingerprint generation.
Package com.chemaxon.descriptors.fingerprints.ecfp
- Class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - diameter
```
int diameter
```
      Diameter parameter.
    - length
```
int length
```
      Fingerprint length (bit count).
    - atomTypizer
```
EcfpAtomTypizers atomTypizer
```
      Atom typizer to use.
    - identifierConfigurationXml
```
com.google.common.base.Optional<T> identifierConfigurationXml
```
      Identifier configuration for custom XML mode.
- Class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpParameters extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - params
```
EcfpParameters params
```

Package com.chemaxon.descriptors.fingerprints.maccs

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

Serialized Fields

bit1

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

bit2

com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit2

bit8

com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit8

bit11

com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit11

bit13

com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit13

bit14

com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit14

bit15

com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit15

bit16

com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit16

bit17

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

serialVersionUID:

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

serialVersionUID:

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

serialVersionUID:

0L
- Serialized Fields
  - mol
```
Molecule mol
```
  - ringBonds
```
java.util.BitSet ringBonds
```

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

Serialized Form

Package chemaxon.calculations

Class chemaxon.calculations.CalculationException extends java.lang.RuntimeException implements Serializable

Package chemaxon.clustering

Class chemaxon.clustering.ChemicalSpace extends java.util.Vector implements Serializable

Serialized Fields

weights

inv

dimensions

fpsize

emptyset

checked

willett

Class chemaxon.clustering.ClusteringException extends java.lang.Exception implements Serializable

Class chemaxon.clustering.InvalidLicenseKeyException extends java.lang.Exception implements Serializable

Package chemaxon.common.util

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

Serialized Fields

data

size

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

Serialized Fields

data

size

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

Serialized Fields

data

size

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

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

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

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

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

Serialized Fields

left

right

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

Serialized Fields

data

size

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

Serialized Fields

data

size

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

Serialized Fields

data

size

Package chemaxon.core

Class chemaxon.core.SequenceBuildingException extends java.lang.RuntimeException implements Serializable

Serialized Fields

errorKey

Package chemaxon.core.calculations.valencecheck

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

Serialized Fields

atomCount

Package chemaxon.descriptors

Class chemaxon.descriptors.MDGeneratorException extends java.lang.Exception implements Serializable

Class chemaxon.descriptors.MDParametersException extends java.lang.RuntimeException implements Serializable

Class chemaxon.descriptors.MDReaderException extends java.lang.Exception implements Serializable

Class chemaxon.descriptors.MDWriterException extends java.lang.Exception implements Serializable

Class chemaxon.descriptors.SimilarityException extends java.lang.Exception implements Serializable

Package chemaxon.formats

Class chemaxon.formats.MolFormatException extends java.io.IOException implements Serializable

Serialized Fields

lineNumberInRecord

lineNumberInFile

Package chemaxon.formats.documents.jchemoffice

Class chemaxon.formats.documents.jchemoffice.BatchProcessingException extends java.io.IOException implements Serializable

Serialized Fields

_exceptions

Class chemaxon.formats.documents.jchemoffice.InvalidSizeScaleArgumentException extends chemaxon.util.ArgumentException implements Serializable