Serialized Form
-
Package chemaxon.calculations
-
Exception chemaxon.calculations.CalculationException
class CalculationException extends RuntimeException implements Serializable- serialVersionUID:
- 1L
-
-
Package chemaxon.calculations.clean
-
Class chemaxon.calculations.clean.AtomChangeEvent
class AtomChangeEvent extends EventObject implements Serializable
-
-
Package chemaxon.calculator
-
Exception chemaxon.calculator.CalculatorException
class CalculatorException extends Exception implements Serializable- serialVersionUID:
- 1L
-
-
Package chemaxon.clustering
-
Class chemaxon.clustering.ChemicalSpace
class ChemicalSpace extends Vector implements Serializable-
Serialized Fields
-
dimensions
int dimensions
-
fpsize
int fpsize
-
weights
float[] weights
-
-
-
Exception chemaxon.clustering.ClusteringException
class ClusteringException extends Exception implements Serializable -
Exception chemaxon.clustering.InvalidLicenseKeyException
class InvalidLicenseKeyException extends Exception implements Serializable
-
-
Package chemaxon.clustering.libmcs
-
Exception chemaxon.clustering.libmcs.Heap.HeapException
class HeapException extends RuntimeException implements Serializable
-
-
Package chemaxon.common.util
-
Class chemaxon.common.util.ByteVector
class ByteVector extends Object implements Serializable- serialVersionUID:
- -1393815508326465236L
-
Serialized Fields
-
data
byte[] data
-
size
int size
-
-
Class chemaxon.common.util.DoubleVector
class DoubleVector extends Object implements Serializable- serialVersionUID:
- -5138497375635267024L
-
Serialized Fields
-
data
double[] data
-
size
int size
-
-
Class chemaxon.common.util.FloatVector
class FloatVector extends Object implements Serializable- serialVersionUID:
- -2327634131748729635L
-
Serialized Fields
-
data
float[] data
-
size
int size
-
-
Exception chemaxon.common.util.GeomCalc.GeomCalcException
class GeomCalcException extends RuntimeException implements Serializable- serialVersionUID:
- -1705490613297709773L
-
Exception chemaxon.common.util.GeomCalc.Queue.Overflow
class Overflow extends Exception implements Serializable- serialVersionUID:
- -6957894135268794743L
-
Exception chemaxon.common.util.GeomCalc.Queue.Underflow
class Underflow extends Exception implements Serializable- serialVersionUID:
- -1972826041963082169L
-
Class chemaxon.common.util.IntMap
- serialVersionUID:
- 4318465509620546463L
-
Record Class chemaxon.common.util.IntPair
class IntPair extends Record implements Serializable- serialVersionUID:
- 1961353781713733629L
-
Serialized Fields
-
left
int left
Deprecated, for removal: This API element is subject to removal in a future version. -
right
int right
Deprecated, for removal: This API element is subject to removal in a future version.
-
-
Class chemaxon.common.util.IntVector
class IntVector extends Object implements Serializable- serialVersionUID:
- -9011852065319440166L
-
Serialized Fields
-
data
int[] data
-
size
int size
-
-
Exception chemaxon.common.util.LazyCalculationAlreadyFailedException
class LazyCalculationAlreadyFailedException extends RuntimeException implements Serializable -
Class chemaxon.common.util.LongVector
class LongVector extends Object implements Serializable- serialVersionUID:
- 8437448887389765952L
-
Serialized Fields
-
data
long[] data
-
size
int size
-
-
Exception chemaxon.common.util.ResourceCleaner.ResourceClosingException
class ResourceClosingException extends RuntimeException implements Serializable -
Exception chemaxon.common.util.ServiceNotFoundException
class ServiceNotFoundException extends RuntimeException implements Serializable-
Serialized Fields
-
serviceType
Class<?> serviceType
-
-
-
Class chemaxon.common.util.ShortVector
class ShortVector extends Object implements Serializable- serialVersionUID:
- 8407562362886825374L
-
Serialized Fields
-
data
short[] data
-
size
int size
-
-
-
Package chemaxon.core
-
Exception chemaxon.core.SequenceBuildingException
class SequenceBuildingException extends RuntimeException implements Serializable-
Serialized Fields
-
errorKey
String errorKey
-
-
-
-
Package chemaxon.core.calculations.valencecheck
-
Class chemaxon.core.calculations.valencecheck.ValenceCheckOptions
class ValenceCheckOptions extends Object implements Serializable- serialVersionUID:
- 568843891825099500L
-
Serialized Fields
-
localAromatic
boolean localAromatic
-
traditionalNallowed
boolean traditionalNallowed
-
-
Exception chemaxon.core.calculations.valencecheck.ValenceColumnException
class ValenceColumnException extends chemaxon.core.calculations.valencecheck.ValenceException implements Serializable -
Exception chemaxon.core.calculations.valencecheck.ValenceException
class ValenceException extends Exception implements Serializable -
Exception chemaxon.core.calculations.valencecheck.ValenceTypeException
class ValenceTypeException extends chemaxon.core.calculations.valencecheck.ValenceException implements Serializable
-
-
Package chemaxon.core.util
-
Class chemaxon.core.util.BondTable
class BondTable extends Object implements Serializable- serialVersionUID:
- -8372436801118701137L
-
Serialized Fields
-
atomCount
int atomCount
The size of the matrix, the number of atoms in the molecule it represents.
-
-
-
Package chemaxon.descriptors
-
Exception chemaxon.descriptors.MDGeneratorException
class MDGeneratorException extends Exception implements Serializable -
Exception chemaxon.descriptors.MDParametersException
class MDParametersException extends RuntimeException implements Serializable -
Exception chemaxon.descriptors.MDReaderException
class MDReaderException extends Exception implements Serializable -
Exception chemaxon.descriptors.MDWriterException
class MDWriterException extends Exception implements Serializable -
Exception chemaxon.descriptors.SimilarityException
class SimilarityException extends Exception implements Serializable
-
-
Package chemaxon.formats
-
Exception chemaxon.formats.MolFormatException
class MolFormatException extends IOException implements Serializable-
Serialized Fields
-
lineNumberInFile
int lineNumberInFile
-
lineNumberInRecord
int lineNumberInRecord
-
-
-
-
Package chemaxon.formats.documents.jchemoffice
-
Exception chemaxon.formats.documents.jchemoffice.BatchProcessingException
class BatchProcessingException extends IOException implements Serializable- serialVersionUID:
- 1L
-
Exception chemaxon.formats.documents.jchemoffice.InvalidSizeScaleArgumentException
class InvalidSizeScaleArgumentException extends chemaxon.util.ArgumentException implements Serializable- serialVersionUID:
- 1L
-
-
Package chemaxon.jchem.db
-
Exception chemaxon.jchem.db.DatabaseSearchException
class DatabaseSearchException extends Exception implements Serializable -
Exception chemaxon.jchem.db.MaxSearchFrequencyExceededException
class MaxSearchFrequencyExceededException extends DatabaseSearchException implements Serializable -
Exception chemaxon.jchem.db.RecalculationException
class RecalculationException extends Exception implements Serializable- serialVersionUID:
- -2767058042924323545L
-
Exception chemaxon.jchem.db.TransferException
class TransferException extends Exception implements Serializable- serialVersionUID:
- -5241498055624956036L
-
Class chemaxon.jchem.db.UpdateHandler.RowData
class RowData extends Object implements Serializable- serialVersionUID:
- -4040824446004135801L
-
Serialized Fields
-
chemTermColValues
Map<String,
Object> chemTermColValues -
descriptorData
byte[][] descriptorData
-
fingerprint
int[] fingerprint
-
flags
String flags
-
formula
String formula
-
hashCode
int hashCode
-
markushData
byte[] markushData
-
molecule
Molecule molecule
-
molName
String molName
-
molString
byte[] molString
-
molWeight
Double molWeight
-
noRingInfoInFP
boolean noRingInfoInFP
-
reactionMappingIncomplete
boolean reactionMappingIncomplete
-
screenDescriptor
byte[] screenDescriptor
-
smiles
String smiles
-
sortableFormula
String sortableFormula
-
tautomer
Molecule tautomer
-
tautomerFragmentHashCode
int[] tautomerFragmentHashCode
-
tautomerHashCode
int tautomerHashCode
-
-
Exception chemaxon.jchem.db.UpdateHandlerException
class UpdateHandlerException extends Exception implements Serializable- serialVersionUID:
- -8755169336283449997L
-
Class chemaxon.jchem.db.UpdateHandlerMetaData
class UpdateHandlerMetaData extends Object implements Serializable- serialVersionUID:
- -6512295793385774884L
-
Serialized Fields
-
chemTermColumns
String[] chemTermColumns
-
chemTermForColumn
Map<String,
String> chemTermForColumn -
collectionType
chemaxon.jchem.base.storage.StructureCollectionType collectionType
-
compressedStructureFieldSupported
boolean compressedStructureFieldSupported
-
descriptorSettings
Map<String,
String> descriptorSettings -
descriptorTypes
Map<String,
String> descriptorTypes -
duplicateFilteringOption
boolean duplicateFilteringOption
-
insertDescriptorNames
List<String> insertDescriptorNames
-
numberOfCombinedFPColumns
int numberOfCombinedFPColumns
-
numberOfEdges
int numberOfEdges
-
numberOfOnes
int numberOfOnes
-
numberOfStructuralFPColumns
int numberOfStructuralFPColumns
-
standardizerConfig
String standardizerConfig
-
structuralKeys
String structuralKeys
-
tableType
int tableType
-
tautomerDuplicateFilteringEnabled
boolean tautomerDuplicateFilteringEnabled
-
tautomerEqualityMode
chemaxon.sss.search.options.TautomerEqualityMode tautomerEqualityMode
-
updateDescriptorNames
List<String> updateDescriptorNames
-
-
Exception chemaxon.jchem.db.UpdateHandlerRowDataException
class UpdateHandlerRowDataException extends UpdateHandlerException implements Serializable- serialVersionUID:
- -7274357064259684370L
-
Serialized Fields
-
rowData
UpdateHandler.RowData rowData
-
-
Class chemaxon.jchem.db.Updater.UpdateInfo
class UpdateInfo extends Object implements Serializable- serialVersionUID:
- 4160146885445230514L
-
Serialized Fields
-
additionalInformation
String[] additionalInformation
Additional information for the entities in same order, if needed.- Since:
- JChem 6.0
-
entityList
String[] entityList
The names of entities (e.g. table names) to be updated, ornull
. -
isOperationRequired
boolean isOperationRequired
Indicates whether the operation is required or not.- Since:
- JChem 5.3
-
isProgressMonitoringSupported
boolean isProgressMonitoringSupported
Indicates whether update process supports progress monitoring.- Since:
- JChem 5.1.2
-
isRegeneration
boolean isRegeneration
Deprecated.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 inUpdater.UpdateInfo.entityList
can be used directly forUpdateHandler.recalculateTable(chemaxon.util.ConnectionHandler, String, boolean, String, java.util.Map, Boolean, chemaxon.jchem.file.ProgressWriter)
-
isStructuralChange
boolean isStructuralChange
Indicates whether the operation is required or not.- Since:
- JChem 5.8
-
message
String message
Massage describing what update is necessary and why. -
processingMessage
String processingMessage
A message that can be displayed during the update, e.g. "Recalculating tables" -
regenerationType
int regenerationType
Indicates the regeneration type.- Since:
- JChem 5.2.4
-
-
-
Package chemaxon.jchem.db.cache
-
Class chemaxon.jchem.db.cache.CachePool
class CachePool extends Object implements Serializable- serialVersionUID:
- 1L
-
Serialized Fields
-
cacheHash
Hashtable<String,
chemaxon.jchem.db.cache.JChemCache> cacheHash -
cacheRemovalMethod
chemaxon.jchem.db.cache.CacheRemovalMethod cacheRemovalMethod
-
expirationTime
double expirationTime
-
maxCacheMemory
long maxCacheMemory
-
maxCacheMemoryCalculated
boolean maxCacheMemoryCalculated
-
maxCacheSizeMB
int maxCacheSizeMB
-
minFreeMemMB
int minFreeMemMB
-
-
Exception chemaxon.jchem.db.cache.CacheRegistrationException
class CacheRegistrationException extends RuntimeException implements Serializable- serialVersionUID:
- 1L
-
Serialized Fields
-
reason
chemaxon.jchem.db.cache.CacheRegistrationException.Reason reason
-
-
-
Package chemaxon.jep
-
Class chemaxon.jep.ChemFunction
class ChemFunction extends chemaxon.nfunk.jep.function.PostfixMathCommand implements Serializable- serialVersionUID:
- -3446599636099344973L
-
Serialized Fields
-
cached
boolean cached
-
jep
ChemJEP jep
-
-
Class chemaxon.jep.ChemJEP
class ChemJEP extends chemaxon.nfunk.jep.JEP implements Serializable-
Serialized Fields
-
context
ChemContext context
The evaluation context object.
-
-
-
Exception chemaxon.jep.ConditionException
class ConditionException extends Exception implements Serializable -
Class chemaxon.jep.ContextFunction
class ContextFunction extends chemaxon.nfunk.jep.function.PostfixMathCommand implements Serializable- serialVersionUID:
- 6471101129584627604L
-
Class chemaxon.jep.DissimilarityFunction
class DissimilarityFunction extends chemaxon.jep.ChemFunction implements Serializable -
Class chemaxon.jep.Evaluator
class Evaluator extends Object implements Serializable-
Serialized Fields
-
builtInConfig
chemaxon.jep.EvaluatorConfiguration builtInConfig
The configuration object containing default function/plugin declarations. -
config
chemaxon.jep.EvaluatorConfiguration config
The configuration object. -
externalConfig
chemaxon.jep.EvaluatorConfiguration externalConfig
The configuration object containing external function/plugin declarations. -
functionalGroupDisplayMolTable
Hashtable<String,
String> functionalGroupDisplayMolTable |functional group name| -> |displayable molecule representation| -
licenseEnvironment
String licenseEnvironment
-
servicesConfigurationPath
String servicesConfigurationPath
services configuration path- Since:
- 5.10
-
servicesFunctionTable
Hashtable<String,
chemaxon.nfunk.jep.function.PostfixMathCommandI> servicesFunctionTable Function table for services. -
symtab
chemaxon.nfunk.jep.SymbolTable symtab
The base symbol table. -
userConfig
chemaxon.jep.EvaluatorConfiguration userConfig
The configuration object containing user defined function/plugin declarations. -
verbose
boolean verbose
True if verbose output.
-
-
-
Class chemaxon.jep.EvaluatorFunction
class EvaluatorFunction extends chemaxon.jep.ChemFunction implements Serializable-
Serialized Fields
-
evaluator
Evaluator evaluator
-
-
-
Class chemaxon.jep.MatchFunction
class MatchFunction extends chemaxon.jep.ChemFunction implements Serializable
-
-
Package chemaxon.jep.context
-
Class chemaxon.jep.context.AtomContext
class AtomContext extends MolContext implements Serializable-
Serialized Fields
-
atom
int atom
The input atom index.
-
-
-
Class chemaxon.jep.context.MolContext
class MolContext extends Object implements Serializable-
Serialized Fields
-
fingerprint
int[] fingerprint
Fingerprint of the input molecule. -
init
boolean init
-
reactionContext
ReactionContext reactionContext
reaction wrapped in this context -
supplier
Supplier<Molecule> supplier
The molecule supplier.
-
-
-
Class chemaxon.jep.context.ReactionContext
class ReactionContext extends Object implements Serializable- serialVersionUID:
- -9162272287141708299L
-
Serialized Fields
-
agentAtomMapping
Map<Integer,
MolAtom> agentAtomMapping mapping of AtomMap -> Agent Atom -
productAtomMapping
Map<Integer,
MolAtom> productAtomMapping mapping of AtomMap -> Product Atom -
reactantAtomMapping
Map<Integer,
MolAtom> reactantAtomMapping mapping of AtomMap -> Reactant Atom -
reaction
RxnMolecule reaction
reaction wrapped in this context
-
-
Class chemaxon.jep.context.SearchContext
class SearchContext extends MolContext implements Serializable
-
-
Package chemaxon.license
-
Exception chemaxon.license.LicenseException
class LicenseException extends RuntimeException implements Serializable-
Serialized Fields
-
product
String product
-
-
-
Exception chemaxon.license.LicenseProcessingException
class LicenseProcessingException extends Exception implements Serializable
-
-
Package chemaxon.marvin
-
Class chemaxon.marvin.SketchApplication
class SketchApplication extends chemaxon.marvin.AbstractApplication implements Serializable- serialVersionUID:
- 1L
-
Serialized Fields
-
exitAction
Action exitAction
-
newWindowAction
Action newWindowAction
-
outSerName
String outSerName
-
sketchPane
MSketchPane sketchPane
-
-
Class chemaxon.marvin.ViewApplication
class ViewApplication extends chemaxon.marvin.AbstractApplication implements Serializable- serialVersionUID:
- 1L
-
-
Package chemaxon.marvin.alignment
-
Exception chemaxon.marvin.alignment.AlignmentException
class AlignmentException extends Exception implements Serializable -
Exception chemaxon.marvin.alignment.NoConstraintException
class NoConstraintException extends chemaxon.marvin.alignment.AlignmentException implements Serializable -
Exception chemaxon.marvin.alignment.OptimizationException
class OptimizationException extends RuntimeException implements Serializable- serialVersionUID:
- 1L
-
Class chemaxon.marvin.alignment.ShapeData
class ShapeData extends Object implements Serializable- serialVersionUID:
- 1L
-
Serialized Fields
-
atoms
chemaxon.marvin.alignment.ShapeData.Atom[] atoms
-
bonds
chemaxon.marvin.alignment.ShapeData.Bond[] bonds
-
coloringScheme
AlignmentProperties.ColoringScheme coloringScheme
-
maxs
double[] maxs
-
mins
double[] mins
-
shapeEnabledAtoms
BitSet shapeEnabledAtoms
-
-
Exception chemaxon.marvin.alignment.TooDissimilarException
class TooDissimilarException extends chemaxon.marvin.alignment.AlignmentException implements Serializable
-
-
Package chemaxon.marvin.beans
-
Class chemaxon.marvin.beans.MarvinPane
class MarvinPane extends JRootPane implements Serializable- serialVersionUID:
- -9042549845769941129L
-
Serialized Fields
-
actionListener
chemaxon.marvin.beans.MarvinPane.MarvinActionListener actionListener
-
molPanel
chemaxon.marvin.common.swing.MolPanel molPanel
Underlying panel. -
params
String params
Parameter string.
-
-
Class chemaxon.marvin.beans.MolRenderer
class MolRenderer extends JPanel implements Serializable- serialVersionUID:
- 7229361698115302929L
-
Serialized Fields
-
printer
MolPrinter printer
-
-
Class chemaxon.marvin.beans.MSketch
class MSketch extends Object implements Externalizable- serialVersionUID:
- 0L
-
Serialization Methods
-
readExternal
Restores the sketcher's state.- Parameters:
in
- the stream to read data from in order to restore the object- Throws:
IOException
- if I/O errors occurClassNotFoundException
- If the class for an object being restored cannot be found.
-
writeExternal
Saves the sketcher's state.- Parameters:
out
- the stream to write the object to- Throws:
IOException
- Includes any I/O exceptions that may occur
-
-
Class chemaxon.marvin.beans.MSketchPane
class MSketchPane extends MarvinPane implements Serializable- serialVersionUID:
- 602496692422927170L
-
Serialized Fields
-
commonActions
chemaxon.marvin.common.swing.action.CommonActions commonActions
-
-
Class chemaxon.marvin.beans.MView
class MView extends Object implements Externalizable- serialVersionUID:
- 0L
-
Serialization Methods
-
readExternal
Restores the viewer's state.- Parameters:
in
- the stream to read data from in order to restore the object- Throws:
IOException
- if I/O errors occurClassNotFoundException
- If the class for an object being restored cannot be found.
-
writeExternal
Saves the viewer's state.- Parameters:
out
- the stream to write the object to- Throws:
IOException
- Includes any I/O exceptions that may occur
-
-
Class chemaxon.marvin.beans.MViewEditor
class MViewEditor extends AbstractCellEditor implements Serializable- serialVersionUID:
- 1549621132660875966L
-
Serialized Fields
-
editorComponent
MViewPane editorComponent
-
-
Class chemaxon.marvin.beans.MViewPane
class MViewPane extends MarvinPane implements Serializable- serialVersionUID:
- -4430811090653077262L
-
Serialized Fields
-
delayedRepainter
chemaxon.marvin.beans.MViewPane.DelayedRepainter delayedRepainter
-
preferredSizeSet
boolean preferredSizeSet
-
tableSupport
TableSupport tableSupport
-
-
Class chemaxon.marvin.beans.MViewRenderer
class MViewRenderer extends MViewPane implements Serializable- serialVersionUID:
- 5566509759455312369L
-
-
Package chemaxon.marvin.calculations
-
Class chemaxon.marvin.calculations.BitPattern
class BitPattern extends BitSet implements Serializable
-
-
Package chemaxon.marvin.io
-
Class chemaxon.marvin.io.Encoding
class Encoding extends Object implements Externalizable-
Serialization Methods
-
readExternal
- Throws:
IOException
-
writeExternal
- Throws:
IOException
-
-
-
Exception chemaxon.marvin.io.MolExportException
class MolExportException extends IOException implements Serializable-
Serialized Fields
-
molIndex
int molIndex
-
-
-
Exception chemaxon.marvin.io.MRecordParseException
class MRecordParseException extends Exception implements Serializable-
Serialized Fields
-
position
MRecordReader.Position position
-
-
-
-
Package chemaxon.marvin.modules.datatransfer
-
Class chemaxon.marvin.modules.datatransfer.CopyAsDialog
class CopyAsDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable- serialVersionUID:
- -4564761584830399025L
-
-
Package chemaxon.marvin.plugin
-
Exception chemaxon.marvin.plugin.PluginException
class PluginException extends Exception implements Serializable -
Exception chemaxon.marvin.plugin.PluginInputCheckerException
class PluginInputCheckerException extends PluginException implements Serializable
-
-
Package chemaxon.marvin.plugin.concurrent
-
Exception chemaxon.marvin.plugin.concurrent.PluginExecutionException
class PluginExecutionException extends ExecutionException implements Serializable-
Serialized Fields
-
plugin
CalculatorPlugin plugin
-
-
-
-
Package chemaxon.marvin.plugin.gui
-
Class chemaxon.marvin.plugin.gui.CheckList
class CheckList extends JPanel implements Serializable-
Serialized Fields
-
checkboxes
chemaxon.marvin.plugin.gui.CheckList.MCheckBox[] checkboxes
-
-
-
Class chemaxon.marvin.plugin.gui.OptionsPane
class OptionsPane extends JDialog implements Serializable-
Serialized Fields
-
cancel
chemaxon.marvin.swing.ActionButton cancel
-
key
String key
-
ok
chemaxon.marvin.swing.ActionButton ok
-
okActionListener
ActionListener okActionListener
-
parameterPanel
ParameterPanelHandler parameterPanel
-
restoreDefaults
chemaxon.marvin.swing.ActionButton restoreDefaults
-
-
-
Class chemaxon.marvin.plugin.gui.ParameterPanel
class ParameterPanel extends JPanel implements Serializable-
Serialized Fields
-
items
chemaxon.marvin.plugin.gui.ParameterItem[] items
-
-
-
Class chemaxon.marvin.plugin.gui.ResultView
class ResultView extends JDialog implements Serializable- serialVersionUID:
- -5728800883025815500L
-
Serialized Fields
-
bottomComponent
JComponent bottomComponent
-
bottomTextArea
JTextArea bottomTextArea
-
chart
com.chemaxon.calculations.gui.MChart chart
-
chartPanel
JPanel chartPanel
-
copymi
JMenuItem copymi
-
detachmi
JMenuItem detachmi
-
imageFormat
String imageFormat
-
mpan
chemaxon.marvin.common.swing.MolPanel mpan
-
popup
JPopupMenu popup
-
popupcopymi
JMenuItem popupcopymi
-
resetmi
JMenuItem resetmi
-
topComponent
JComponent topComponent
-
topTextArea
JTextArea topTextArea
-
viewMenu
JMenu viewMenu
-
viewMol
Molecule viewMol
-
viewMols
Molecule[] viewMols
-
viewPanel
chemaxon.marvin.view.swing.ViewPanel viewPanel
-
viewText
String viewText
-
viewTexts
String[] viewTexts
-
-
-
Package chemaxon.marvin.services
-
Exception chemaxon.marvin.services.ServiceException
class ServiceException extends Exception implements Serializable- serialVersionUID:
- 328496720368460819L
-
-
Package chemaxon.marvin.sketch
-
Class chemaxon.marvin.sketch.History
class History extends Object implements Serializable-
Serialized Fields
-
autoHydrogenizeHist
int[] autoHydrogenizeHist
-
changeSupport
PropertyChangeSupport changeSupport
-
cornerHist
Point[] cornerHist
-
historyOverflow
boolean historyOverflow
-
molgToZoomHist
MoleculeGraph[][] molgToZoomHist
-
molHist
MDocument[] molHist
-
molHistCur
int molHistCur
-
molHistLen
int molHistLen
-
molHistMax
int molHistMax
-
rotateMatrHist
CTransform3D[] rotateMatrHist
-
scaleHist
double[] scaleHist
-
scrollBarHist
int[][] scrollBarHist
-
selectionToZoomHist
boolean[] selectionToZoomHist
-
-
-
Class chemaxon.marvin.sketch.MolEditor
class MolEditor extends Object implements Serializable- serialVersionUID:
- 2463379690025911142L
-
Serialization Methods
-
readObject
- Throws:
ClassNotFoundException
IOException
-
-
Serialized Fields
-
atomBranchPiece
Molecule atomBranchPiece
-
atomSelectionMode
int atomSelectionMode
-
atomStrings
Set<Integer> atomStrings
-
bondDraggedAlong
boolean bondDraggedAlong
-
bondDrawMode
boolean bondDrawMode
-
canMovCurfrag
boolean canMovCurfrag
-
canRotCurfrag
boolean canRotCurfrag
-
curfrag
MDocument curfrag
-
curfragJoin
com.chemaxon.marvin.editor.molecule.fusion.MolJoin curfragJoin
-
curfragMoved
boolean curfragMoved
-
curfragR
double curfragR
-
currentTool
chemaxon.marvin.sketch.tool.EditorTool currentTool
-
dataSgroupObject
DataSgroup dataSgroupObject
-
deleteRemovesTerminalAtoms
boolean deleteRemovesTerminalAtoms
-
disabledAliases
Set<String> disabledAliases
-
document
MDocument document
-
documentEdited
boolean documentEdited
-
elements
List<Integer> elements
-
extraBonds
Set<Integer> extraBonds
-
flyingBondMol
MoleculeGraph flyingBondMol
-
hadSelection
boolean hadSelection
-
historizeEnabled
boolean historizeEnabled
-
historizeUnSelection
boolean historizeUnSelection
-
history
chemaxon.marvin.sketch.History history
-
isAxisSet
boolean isAxisSet
-
isDataSgroupLabelPointed
boolean isDataSgroupLabelPointed
-
isProbablyDotNetApplication
boolean isProbablyDotNetApplication
-
isSketchApplication
boolean isSketchApplication
-
jointAtom
MolAtom jointAtom
-
lastBondFlags
int lastBondFlags
-
lastQueryBondString
String lastQueryBondString
-
lastSelectionCorner
Point lastSelectionCorner
-
lastSelectionDoc
MDocument lastSelectionDoc
-
lastSelectionScale
double lastSelectionScale
-
lpEnabled
boolean lpEnabled
-
mergedst
double mergedst
-
moveMode
int moveMode
-
newKeyboardMotion
boolean newKeyboardMotion
-
painter
chemaxon.marvin.paint.internal.MolPainter painter
-
persistentMoveMode
boolean persistentMoveMode
-
piece
Molecule piece
-
pieceOriginalObject
Molecule pieceOriginalObject
-
prevCurfrag
MDocument prevCurfrag
-
queryAtoms
Set<Integer> queryAtoms
-
reactionSupported
boolean reactionSupported
-
rotate3direction
int rotate3direction
-
rotate3dPhi
double rotate3dPhi
-
rotate3dPhiX
double rotate3dPhiX
-
rotate3dPhiY
double rotate3dPhiY
-
rotate3dx
double rotate3dx
-
rotate3dy
double rotate3dy
-
rotateZPhi
double rotateZPhi
-
rotation3DMode
int rotation3DMode
-
rotAxisPoint
DPoint3 rotAxisPoint
-
rotO
DPoint3 rotO
-
scrollBarVals
int[] scrollBarVals
-
selectionDoc
MSelectionDocument selectionDoc
-
selectionHistorized
boolean selectionHistorized
-
selectionHPoints
DPoint3[] selectionHPoints
-
showMolecule
Molecule showMolecule
-
starEnabled
boolean starEnabled
-
stickdst
double stickdst
-
-
-
Package chemaxon.marvin.space
-
Class chemaxon.marvin.space.EventQueue
-
Class chemaxon.marvin.space.GraphicScene
class GraphicScene extends JPanel implements Serializable-
Serialized Fields
-
_glListsToDelete
ArrayList<Integer> _glListsToDelete
-
activeCell
int activeCell
index of the active cell: cells are numbered line-by-line -
antialias
boolean antialias
-
backgroundColor
float[] backgroundColor
we use java.awt.Color in the following cases - when the color does not change too often - when the user can change the given color - when we don't have to give it to OGL2 too often (like color of an atom, etc) These are e.g. : background color, constant component colors -
backgroundColorChanged
boolean backgroundColorChanged
-
canvas
Component canvas
-
cellCount
int cellCount
number of cells (there might be fewer cells than cells.length()) -
cells
GraphicCell[] cells
components per cells, line-by-line 0 is the top-left corner -
columnCount
int columnCount
layout of the graphic view: number of cells per column -
defaultDrawProperties
Map<Object,
Object> defaultDrawProperties -
eventHandler
chemaxon.marvin.space.MSpaceEventHandler eventHandler
-
gl
javax.media.opengl.GL2 gl
-
glAutoDrawable
javax.media.opengl.GLAutoDrawable glAutoDrawable
-
globalDrawProperties
Properties globalDrawProperties
-
glu
javax.media.opengl.glu.GLU glu
-
height
int height
physical height of the entire scene (in pixels) -
initialized
boolean initialized
-
motionmode
int motionmode
standing or moving mode -
needsRefresh
int needsRefresh
Indicates with internal index which cell needs redraw. -1 means none, cellCount means all cells. -
needsReset
int needsReset
-
progressBar
chemaxon.marvin.space.gui.JMSpaceProgressBar progressBar
-
renderTargets
chemaxon.marvin.space.gl.shader.RenderTargets renderTargets
-
rowCount
int rowCount
layout of the graphic view: number of cells per row -
rx
double rx
rotation around x-y-z axises -
ry
double ry
rotation around x-y-z axises -
rz
double rz
rotation around x-y-z axises -
smoothBackground
boolean smoothBackground
-
synchronousMode
boolean synchronousMode
-
transparentBackground
int transparentBackground
-
userSettings
UserSettings userSettings
-
verboseLevel
int verboseLevel
-
width
int width
physical width of the entire scene (in pixels)
-
-
-
-
Package chemaxon.marvin.uif.dialog
-
Class chemaxon.marvin.uif.dialog.CategoriesDialog
class CategoriesDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable-
Serialized Fields
-
bundle
ResourceBundle bundle
-
model
chemaxon.marvin.uif.dialog.model.CategoriesModel model
-
-
-
Class chemaxon.marvin.uif.dialog.ConfigurationDialog
class ConfigurationDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable-
Serialized Fields
-
module
chemaxon.marvin.uif.module.GUIModule module
-
-
-
Class chemaxon.marvin.uif.dialog.CustomizeDialog
class CustomizeDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable-
Serialized Fields
-
bundle
ResourceBundle bundle
-
guiRegistryClone
chemaxon.marvin.uif.model.GUIRegistry guiRegistryClone
-
model
chemaxon.marvin.uif.dialog.model.CustomizeGUIModel model
-
moduleConf
chemaxon.marvin.uif.module.ModuleConfiguration moduleConf
-
-
-
Class chemaxon.marvin.uif.dialog.LicenseDialog
class LicenseDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable -
Class chemaxon.marvin.uif.dialog.MenuDialog
class MenuDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable-
Serialized Fields
-
bundle
ResourceBundle bundle
-
model
chemaxon.marvin.uif.dialog.model.MenuManagerModel model
-
-
-
Class chemaxon.marvin.uif.dialog.MenuMoveDialog
class MenuMoveDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable-
Serialized Fields
-
bundle
ResourceBundle bundle
-
model
chemaxon.marvin.uif.dialog.model.ItemGroupModel model
-
-
-
Class chemaxon.marvin.uif.dialog.PopupDialog
class PopupDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable-
Serialized Fields
-
bundle
ResourceBundle bundle
-
model
chemaxon.marvin.uif.dialog.model.PopupManagerModel model
-
-
-
Class chemaxon.marvin.uif.dialog.ShortcutEditorDialog
class ShortcutEditorDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable-
Serialized Fields
-
bundle
ResourceBundle bundle
-
model
chemaxon.marvin.uif.dialog.model.ShortcutModel model
-
-
-
Class chemaxon.marvin.uif.dialog.ToolBarDialog
class ToolBarDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable-
Serialized Fields
-
bundle
ResourceBundle bundle
-
model
chemaxon.marvin.uif.dialog.model.ToolBarManagerModel model
-
-
-
-
Package chemaxon.marvin.util
-
Exception chemaxon.marvin.util.CancelPrintException
class CancelPrintException extends Exception implements Serializable- serialVersionUID:
- 7380116746554005158L
-
Class chemaxon.marvin.util.MarvinModule
class MarvinModule extends Object implements Serializable- serialVersionUID:
- 2763330874643316763L
-
Class chemaxon.marvin.util.MarvinOLEFrame
class MarvinOLEFrame extends JFrame implements Serializable- serialVersionUID:
- 7801720334170069726L
-
Serialized Fields
-
sp
Semaphore sp
-
-
Class chemaxon.marvin.util.MarvinOLEPanel
class MarvinOLEPanel extends JPanel implements Serializable- serialVersionUID:
- -6975415959061110410L
-
Serialized Fields
-
emfExportOptions
String emfExportOptions
-
importExceptionCaught
boolean importExceptionCaught
-
msketch
MSketchPane msketch
-
retainGUIPropertiesOnPanel
boolean retainGUIPropertiesOnPanel
-
semaphore
Semaphore semaphore
-
sketchPanel
chemaxon.marvin.sketch.swing.SketchPanel sketchPanel
-
structureGUIProperties
MPropertyContainer structureGUIProperties
-
-
Class chemaxon.marvin.util.SwingUtil
class SwingUtil extends Object implements Serializable- serialVersionUID:
- -1600625160321014724L
-
-
Package chemaxon.marvin.util.codeassist
-
Class chemaxon.marvin.util.codeassist.ChemTermDocument
class ChemTermDocument extends DefaultStyledDocument implements Serializable- serialVersionUID:
- -5894946790409031807L
-
Serialized Fields
-
comment
MutableAttributeSet comment
-
constant
MutableAttributeSet constant
-
constants
Map<String,
AttributeSet> constants -
currentElementIndex
int currentElementIndex
-
doc
DefaultStyledDocument doc
-
fontName
String fontName
-
fontSize
int fontSize
-
function
MutableAttributeSet function
-
functions
Map<String,
AttributeSet> functions -
HIGHLIGHT_TIMER
Timer HIGHLIGHT_TIMER
-
keyword
MutableAttributeSet keyword
-
keywords
Map<String,
AttributeSet> keywords -
lastPrefixState
boolean lastPrefixState
-
multiLineComment
boolean multiLineComment
-
normal
MutableAttributeSet normal
-
parenLength
int parenLength
-
parenOffset
int parenOffset
-
parenthesis
MutableAttributeSet parenthesis
-
prefix
String prefix
-
quote
MutableAttributeSet quote
-
rootElement
Element rootElement
-
-
Class chemaxon.marvin.util.codeassist.CompletionItemCellRenderer
class CompletionItemCellRenderer extends DefaultListCellRenderer implements Serializable- serialVersionUID:
- 6746125418422903808L
-
Class chemaxon.marvin.util.codeassist.MacroManagerPanel
class MacroManagerPanel extends JPanel implements Serializable- serialVersionUID:
- -4703035835623320688L
-
Serialized Fields
-
ACCEPT_ACTION
Action ACCEPT_ACTION
-
acceptButton
JButton acceptButton
-
acceptEditButton
JButton acceptEditButton
-
addButton
JButton addButton
-
CANCEL_ACTION
Action CANCEL_ACTION
-
cancelButton
JButton cancelButton
-
cancelEditButton
JButton cancelEditButton
-
deleteButton
JButton deleteButton
-
descPane
JTextPane descPane
-
descScrollPane
JScrollPane descScrollPane
-
editButton
JButton editButton
-
editedItem
int editedItem
-
editPanel
JPanel editPanel
-
helper
chemaxon.marvin.util.codeassist.CodeAssistMacrosHelper helper
-
layout
CardLayout layout
-
listPanel
JPanel listPanel
-
macroList
JList macroList
-
macroListScroll
JScrollPane macroListScroll
-
macroPane
JTextPane macroPane
-
macroScrollPane
JScrollPane macroScrollPane
-
nameField
JTextField nameField
-
-
-
Package chemaxon.marvin.view
-
Exception chemaxon.marvin.view.MDocStorage.CancellationException
class CancellationException extends Exception implements Serializable
-
-
Package chemaxon.marvin.view.swing
-
Class chemaxon.marvin.view.swing.TwoLists
class TwoLists extends JPanel implements Serializable -
Class chemaxon.marvin.view.swing.ViewCanvas
class ViewCanvas extends chemaxon.marvin.common.swing.MolCanvas implements Serializable- serialVersionUID:
- 3979819797881974530L
-
Serialization Methods
-
writeObject
- Throws:
IOException
-
-
Serialized Fields
-
cellIndex
int cellIndex
-
document
MDocument document
-
error
boolean error
-
highlightedAtom
int highlightedAtom
-
inZoomWindow
boolean inZoomWindow
-
markedAtom
int markedAtom
-
moleculeBackground
Color moleculeBackground
-
moleculeCenter
DPoint3 moleculeCenter
-
nextV
Vector<Object[]> nextV
-
painter
chemaxon.marvin.paint.internal.MolPainter painter
-
preferredSize1
Dimension preferredSize1
-
rescaleNeeded
boolean rescaleNeeded
-
rsize
Dimension rsize
-
viewFrame
chemaxon.marvin.view.swing.modules.MViewFrame viewFrame
-
viewPanel
chemaxon.marvin.view.swing.ViewPanel viewPanel
-
windowAction
chemaxon.marvin.swing.MAction windowAction
-
winScale
double winScale
-
-
Class chemaxon.marvin.view.swing.ViewHandler
class ViewHandler extends Object implements Serializable-
Serialized Fields
-
cellFiller
chemaxon.marvin.view.swing.CellFiller cellFiller
-
debug
boolean debug
-
visibleDocs
chemaxon.marvin.view.swing.VisibleDocuments visibleDocs
-
-
-
Class chemaxon.marvin.view.swing.ViewPanel
class ViewPanel extends chemaxon.marvin.common.swing.MolPanel implements Serializable- serialVersionUID:
- 802342314015862847L
-
Serialization Methods
-
readObject
- Throws:
ClassNotFoundException
IOException
-
-
Serialized Fields
-
animator
chemaxon.marvin.view.swing.modules.MViewAnimator animator
-
animSynchronized
boolean animSynchronized
-
atomMarkAndHighlightEnabled
boolean atomMarkAndHighlightEnabled
-
autoTabScale
boolean autoTabScale
-
borderColor
Color borderColor
-
borderWidth
int borderWidth
-
clearStateOnOpenAction
Action clearStateOnOpenAction
-
cols
int cols
-
commonActions
chemaxon.marvin.common.swing.action.CommonActions commonActions
-
defaultFieldFont
Font defaultFieldFont
-
detachable
boolean detachable
-
draggable
boolean draggable
-
editable
int editable
-
fieldFontMap
Map<String,
Font> fieldFontMap -
findAction
Action findAction
-
findAgainAction
Action findAgainAction
-
findTextModule
chemaxon.marvin.view.swing.modules.FindText findTextModule
-
importEnabled
boolean importEnabled
-
molbgMap
Map<Integer,
Color> molbgMap -
moleculeSelections
chemaxon.marvin.common.AtomSelectionHandler[] moleculeSelections
-
molEdited
boolean molEdited
-
molFrame0
Window molFrame0
-
molString
String molString
-
molStrings
String[] molStrings
-
navigationActions
chemaxon.marvin.swing.MAction[] navigationActions
-
oldMarkedAtom
int oldMarkedAtom
-
oldMarkedCell
int oldMarkedCell
-
rasmolScripts
String[] rasmolScripts
-
rows
int rows
-
selectable
boolean selectable
-
selected
int selected
-
skbridge
chemaxon.marvin.view.modules.sketchbridge.MViewSketch skbridge
-
startLoad
boolean startLoad
-
tableSupport
TableSupport tableSupport
-
tabScale
double tabScale
-
tabScaleCalcInProgress
int tabScaleCalcInProgress
-
tabScaleCalcNeeded
boolean tabScaleCalcNeeded
-
viewActions
chemaxon.marvin.view.swing.ViewActions viewActions
-
viewHandler
chemaxon.marvin.view.swing.ViewHandler viewHandler
-
winScale
double winScale
-
-
Class chemaxon.marvin.view.swing.WholeNumberField
class WholeNumberField extends JTextField implements Serializable-
Serialized Fields
-
integerFormatter
NumberFormat integerFormatter
-
options
int options
-
toolkit
Toolkit toolkit
-
-
-
Class chemaxon.marvin.view.swing.WholeNumberField.WholeNumberDocument
class WholeNumberDocument extends PlainDocument implements Serializable
-
-
Package chemaxon.naming
-
Exception chemaxon.naming.NameFormatException
class NameFormatException extends MolFormatException implements Serializable-
Serialized Fields
-
prefix
String prefix
-
-
-
Exception chemaxon.naming.NameFormatException.FilteredCase
class FilteredCase extends NameFormatException implements Serializable -
Exception chemaxon.naming.NamePrefixException
class NamePrefixException extends NameFormatException implements Serializable-
Serialized Fields
-
token
String token
-
-
-
-
Package chemaxon.naming.document
-
Exception chemaxon.naming.document.D2SOptionsParser.UnknownOptionException
class UnknownOptionException extends Exception implements Serializable -
Class chemaxon.naming.document.D2SPdfParser
class D2SPdfParser extends org.apache.tika.parser.pdf.ExtendablePdfParser implements Serializable -
Class chemaxon.naming.document.D2STextParser
class D2STextParser extends Object implements Serializable -
Exception chemaxon.naming.document.EncryptedDocumentException
class EncryptedDocumentException extends IOException implements Serializable -
Class chemaxon.naming.document.OsrParser
class OsrParser extends org.apache.tika.parser.AbstractParser implements Serializable -
Class chemaxon.naming.document.SafeOfficeParser
class SafeOfficeParser extends org.apache.tika.parser.microsoft.OfficeParser implements Serializable -
Exception chemaxon.naming.document.TimeoutException
class TimeoutException extends IOException implements Serializable-
Serialized Fields
-
timeoutMS
long timeoutMS
-
-
-
Class chemaxon.naming.document.TrivialXmlParser
class TrivialXmlParser extends org.apache.tika.parser.AbstractParser implements Serializable
-
-
Package chemaxon.naming.document.annotate
-
Exception chemaxon.naming.document.annotate.AnnotationException
class AnnotationException extends IOException implements Serializable
-
-
Package chemaxon.reaction
-
Class chemaxon.reaction.PatternProperty
class PatternProperty extends Object implements Serializable- serialVersionUID:
- -3617253669859174882L
-
Serialized Fields
-
representation
String representation
-
-
Exception chemaxon.reaction.ReactionException
class ReactionException extends Exception implements Serializable- serialVersionUID:
- 1L
-
-
Package chemaxon.sss.search
-
Class chemaxon.sss.search.JChemSearchOptions
class JChemSearchOptions extends SearchOptions implements Serializable- serialVersionUID:
- -6025435983286725061L
-
Serialized Fields
-
absoluteStereo
int absoluteStereo
-
cacheRegistrationNeeded
boolean cacheRegistrationNeeded
Can be set to false in case of readonly databases and jcsearch. Only for internal use! -
descriptorConfig
String descriptorConfig
configuration for descriptor dissim. calculations -
descriptorName
String descriptorName
the identifier of stored descriptor used for dissim. calculations,null
means pure fingerprint similarity is performed -
dissimilarityMetric
String dissimilarityMetric
Dissimilarity metric name, ornull
for default. -
dissimilarityMetricParameters
String dissimilarityMetricParameters
Dissimilarity metric parameters. -
dissimilarityThreshold
float dissimilarityThreshold
-
dissimilarityThresholdExcluded
boolean dissimilarityThresholdExcluded
-
filterQuery
String filterQuery
-
formulaSearchQuery
String formulaSearchQuery
Query of the formula search. -
formulaSearchType
int formulaSearchType
Type of the formula search. See: chemaxon.sss.formula.FormulaSearch -
haltOnError
HaltOnErrorOption haltOnError
Error handling of the search.- See Also:
-
markushScreeningOptions
Set<chemaxon.sss.search.options.MarkushScreeningType> markushScreeningOptions
Set containing all enabled Markush screen methods -
matchCountOptions
MatchCountOptions matchCountOptions
-
maxResultCount
int maxResultCount
-
optimizeQueries
boolean optimizeQueries
Shows whether the query should be enumerated to improve search -
returnsNonHits
boolean returnsNonHits
-
totalSearchTimeoutLimitMilliseconds
int totalSearchTimeoutLimitMilliseconds
The search on a database timeouts reaching this number of milliseconds.
-
-
Class chemaxon.sss.search.MarkushFeature
class MarkushFeature extends Object implements Serializable- serialVersionUID:
- 8770437891053649928L
-
Serialized Fields
-
data
int[] data
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}
RgMolecule.findRgroupIndex(int)
. -
hashCode
int hashCode
-
type
int type
Expansion type.
-
-
Class chemaxon.sss.search.MatchCountOptions
class MatchCountOptions extends Object implements Serializable- serialVersionUID:
- 6422092438307828424L
-
Serialized Fields
-
matchCountHighLimit
int matchCountHighLimit
-
matchCountHighLimitInclusive
boolean matchCountHighLimitInclusive
-
matchCounthitLimit
int matchCounthitLimit
-
matchCountIncludesZero
boolean matchCountIncludesZero
-
matchCountLowLimit
int matchCountLowLimit
-
matchCountLowLimitInclusive
boolean matchCountLowLimitInclusive
-
matchCountRelation
String matchCountRelation
-
mode
int mode
-
-
Class chemaxon.sss.search.MolSearchOptions
class MolSearchOptions extends SearchOptions implements Serializable- serialVersionUID:
- -6364233804214700841L
-
Serialized Fields
-
hitIncludesRNodes
boolean hitIncludesRNodes
If true, the result hit will contain R-nodes with dummy indexes -
hitIndexType
int hitIndexType
In case of Markush search specifies the representation of the Markush structure on which the hit indexes are retrieved. (default MARKUSH_HIT_ORIGINAL) -
ignoreChiralityForAtoms
chemaxon.common.util.IntVector ignoreChiralityForAtoms
Contains query atom numbers which should be ignored at the chirality check in case of exact stereo searching. It has a package visibility. -
markushEnabled
boolean markushEnabled
Decides whether targets with Markush features should be treated as Markush libraries (true) or just "strange" molecules (false) (default value: false). -
queryAbsoluteStereo
boolean queryAbsoluteStereo
If true, chiral centers in the query molecules are regarded as absolute stereo, ignoring the chiral flag. If the molecule contains any enhanced stereo labels, this flag has no effect. -
recursiveSMARTSMode
boolean recursiveSMARTSMode
true: at findAll searches only hits are retrieved where the first atom differs as well. -
switchOffAllProtectsForTDF
boolean switchOffAllProtectsForTDF
If true, all protect features are switched of during generic tautomer creation -
targetAbsoluteStereo
boolean targetAbsoluteStereo
If true, chiral centers in the target molecules are regarded as absolute stereo, ignoring the chiral flag. If the molecule contains any enhanced stereo labels, this flag has no effect. -
tautomerEqualityMode
chemaxon.sss.search.options.TautomerEqualityMode tautomerEqualityMode
The way tautomer duplication is checked. Used only at duplicate, full and full fragment searches. Internal use only.
-
-
Exception chemaxon.sss.search.SearchException
class SearchException extends Exception implements Serializable- serialVersionUID:
- 1698586463587833734L
-
Class chemaxon.sss.search.SearchOptions
class SearchOptions extends Object implements Serializable- serialVersionUID:
- -6845044337680993338L
-
Serialized Fields
-
attachedDataMatch
int attachedDataMatch
Specifies attached data match type Default isSearchConstants.ATTACHED_DATA_MATCH_IGNORE
-
attachedDataPrefixes
String attachedDataPrefixes
Data sgroup name prefixes that will be used for comparison When null, all data sgroups will be used. -
bridgingRAllowed
boolean bridgingRAllowed
True: different undefined R-atoms can match the same group of atoms. Default value: false. -
changedUserComparator
boolean changedUserComparator
true if user-defined comparators has changed -
chargeMatching
int chargeMatching
Specifies the charge searching behaviour. Default is CHARGE_MATCHING_DEFAULT (charged query matches only charged target, noncharged query matches all) -
checkSpHyb
boolean checkSpHyb
If we need to check the sp-hybridization state of the atoms. If used together with vagueBond-4 (SearchConstants.VAGUE_BOND_LEVEL4
) option then the bond types are ignored, but the sp hybridization state is still calculated considering the bond types. Benzene matches cyclohexene with double bonds outside (O=C1C(=O)C(=O)C(=O)C(=O)C(=O)1), both planar but different bonds.- Since:
- 5.1
-
chemTermsFilterOption
chemaxon.sss.search.options.ChemTermsFilterOption chemTermsFilterOption
-
completeHG
boolean completeHG
Specifies if only complete structures should match on target homology groups. -
copolymerMatching
boolean copolymerMatching
True: Polymers in copolymers can only be matched by copolymers. (default: false) -
dirty
boolean dirty
This flag is set to true whenever any of the options change. It can be used by Search objects to check whether options changed since the previous initialization. (They set the dirty flag to false during their own initialization.) -
doubleBondStereoMatchingMode
int doubleBondStereoMatchingMode
Defines the double bond stereo matching mode. Default is DBS_MARKED.- Since:
- JChem 2.2
- See Also:
-
endGroupMatching
boolean endGroupMatching
True: polymer endgroups must match (default: false) -
exactBondMatching
boolean exactBondMatching
true, if query bonds match only the same query bonds -
exactQueryAtomMatching
boolean exactQueryAtomMatching
If true, query information (eg atom list, any atom, number of hydrogens, aromaticity, etc) in atoms will not be evaluated, but rather exact matching of these information is required. It is useful for searching in query databases. Default is false.- Since:
- JChem 2.2
-
exactSpecialAtomMatching
String exactSpecialAtomMatching
-
exhaustiveModeLimit
int exhaustiveModeLimit
Upon reaching this number of steps, the search switches to exhaustive mode from fast mode. -
hCountMatching
int hCountMatching
Defines the interpretation of H count in the query. Default is HCOUNT_MATCHING_AUTO. -
hitOrdering
int hitOrdering
Specifies hit ordering, currently used in ordering undefined R-atom group matchings Default isSearchConstants.HIT_ORDERING_NONE
. -
homologyBroadTranslation
HomologyTranslationOption homologyBroadTranslation
If pseudo atoms with homology names are present in the target, they should be handled as homology group not as pseudo atoms. false - handle as pseudo atoms. -
homologyNarrowTranslation
HomologyTranslationOption homologyNarrowTranslation
If pseudo atoms with homology names are present in the query, they should be handled as homology group not as pseudo atoms. false - handle as pseudo atoms. -
ignoreAxialStereo
boolean ignoreAxialStereo
-
ignoreCumuleneCisTransStereo
boolean ignoreCumuleneCisTransStereo
-
ignoreDoubleBondStereo
boolean ignoreDoubleBondStereo
-
ignoreSynAntiStereo
boolean ignoreSynAntiStereo
-
ignoreTetrahedralStereo
boolean ignoreTetrahedralStereo
-
implicitHMatching
int implicitHMatching
Specifies match between explicit and implicit hydrogens. Default is IMPLICIT_H_MATCHING_DEFAULT (matching depends on the circumstances of search) -
isotopeMatching
int isotopeMatching
Specifies the isotope searching behaviour. Default is ISOTOPE_MATCHING_DEFAULT (isotope query matches only isotope target, nonisotope query matches all) -
keepQueryOrder
boolean keepQueryOrder
True: instructs search to rearrange query atoms for better search performance. -
markushAromHandling
MarkushAromaticityHandlingOption markushAromHandling
Specifies handling Markush aromatization information (ambiguous aromatic rings) during Markush search. Currently, the default isMarkushAromaticityHandlingOption.ALL_MATCH_AMBIG
: consider Markush aromatization during Markush search, but do not check the hit afterwards. -
mixSgroupMatching
boolean mixSgroupMatching
True: consider COM, MIX and FOR sgroups during search (default value: true). -
orderSensitiveSearch
boolean orderSensitiveSearch
Specifies whether the same set of target atoms found in a different order should be considered as a different hit. -
phaseShift
boolean phaseShift
True: the phase-shifted polymers are matching on each other. (default: true) -
polymerMatching
boolean polymerMatching
True: consider polymer sgroups during search (default value: true). -
radicalMatching
int radicalMatching
Specifies the radical searching behaviour. Default is RADICAL_MATCHING_DEFAULT (radical query matches only radical target, nonradical query matches all) -
reactionUnpairedMapMatching
boolean reactionUnpairedMapMatching
True: in reaction search unpaired (orphan and widow) atom maps can match any atom map (default value: true). -
rLigandEqualityCheck
boolean rLigandEqualityCheck
True: undefined R-atoms with the same R-group ID should match the same structure. Default value: true. -
searchType
int searchType
Search type: global mode of search. -
ssrOption
SetOfSmallestRingsOption ssrOption
Which set of smallest rings to use for property calculations. -
stereoModel
int stereoModel
Specifies the used stereo model. -
stereoSearchType
int stereoSearchType
The way stereo information is considered in searching. Default isSearchConstants.STEREO_SPECIFIC
.- See Also:
-
targetHomologyMatchingMode
TargetHomologyMatchingMode targetHomologyMatchingMode
-
tautomerSearch
boolean tautomerSearch
True: tautomer searching is enabled (default value: false). -
tautomerSearchOption
int tautomerSearchOption
Specifies the tautomer searching behavior. Default: non-tautomer search, except: duplicate search in tautomer duplicate table -
tautomerSearchOptionLeftDefault
boolean tautomerSearchOptionLeftDefault
Shows that tautomerSearch value has not been set. -
throwExceptionOnTimeout
boolean throwExceptionOnTimeout
If the search should throw exception upon timeout. -
timeoutLimitMilliseconds
int timeoutLimitMilliseconds
The search on a single target timeouts reaching this number of milliseconds. -
transformMonomer
boolean transformMonomer
True: monomers are transformed to structural repeating units. (default: true) -
undefinedRAtom
int undefinedRAtom
Specifies match of undefined r-atom in query Default isSearchConstants.UNDEF_R_MATCHING_GROUP
. -
undefinedRAtomUserDefined
boolean undefinedRAtomUserDefined
True if undefinedRAtom option is user defined, false if automatically set by RGroupDecomposition depending on whether the original query has undefined R-atoms. Used in RGroupDecomposition only. -
userComparators
ArrayList<MolComparator> userComparators
User defined MolComparators -
vagueBondLevel
int vagueBondLevel
Option for less strict evaluation of query bonds (e.g. ambiguious aromaticity). Default value isSearchConstants.VAGUE_BOND_LEVEL_HALF
-
valenceMatching
boolean valenceMatching
True: valence is checked during search (default value: true). -
verbose
boolean verbose
For debugging purposes. Public, because it does not count for the dirty flag.
-
-
Exception chemaxon.sss.search.SearchTimeoutException
class SearchTimeoutException extends SearchException implements Serializable- serialVersionUID:
- -78126823565453833L
-
Exception chemaxon.sss.search.UnsupportedQueryException
class UnsupportedQueryException extends IllegalArgumentException implements Serializable- serialVersionUID:
- 6255906179820229430L
-
-
Package chemaxon.sss.search.options
-
Class chemaxon.sss.search.options.ChemTermsFilterOption
class ChemTermsFilterOption extends Object implements Serializable- serialVersionUID:
- 8226348996476285704L
-
-
Package chemaxon.standardizer.advancedactions
-
Class chemaxon.standardizer.advancedactions.GroupList
-
-
Package chemaxon.struc
-
Class chemaxon.struc.CTransform3D
class CTransform3D extends Object implements Externalizable- serialVersionUID:
- 0L
-
Serialization Methods
-
readExternal
Deserializes a transformation matrix.- Parameters:
in
- the object input stream- Throws:
IOException
- Since:
- 3.5, 11/02/2004
-
writeExternal
Serializes a transformation matrix.- Parameters:
out
- the object output stream- Throws:
IOException
- Since:
- 3.5, 11/02/2004
-
-
Class chemaxon.struc.DefaultDictionary
- serialVersionUID:
- 8013155936541949713L
-
Class chemaxon.struc.DPoint3
class DPoint3 extends Object implements Externalizable- serialVersionUID:
- 0L
-
Serialization Methods
-
readExternal
Deserializes a 3D point.- Parameters:
in
- the object input stream- Throws:
IOException
ClassNotFoundException
-
writeExternal
Serializes a 3D point.- Parameters:
out
- the object output stream- Throws:
IOException
-
-
Class chemaxon.struc.ExtraAtomProperties
class ExtraAtomProperties extends Object implements Serializable- serialVersionUID:
- -1980229820290558380L
-
Serialized Fields
-
aliasstr
String aliasstr
-
attachParentSgroup
Sgroup attachParentSgroup
-
countFlags
int countFlags
-
electronProp
int electronProp
-
extrargbs
long extrargbs
-
extrastr
String extrastr
-
flags
int flags
-
linkNodeOuterBonds
int linkNodeOuterBonds
-
list
int[] list
-
order
int order
-
qprops
Map<String,
Object> qprops -
querystr
String querystr
-
repetitionBits
int repetitionBits
-
rgroupId
short rgroupId
-
temporaryObjects
Map<String,
Object> temporaryObjects -
valence1
short valence1
-
-
Exception chemaxon.struc.MacroMolecule.BadMoleculeException
class BadMoleculeException extends Exception implements Serializable- serialVersionUID:
- 9037472982065239933L
-
Class chemaxon.struc.MDocument
class MDocument extends Object implements Serializable- serialVersionUID:
- 553557622036381832L
-
Serialization Methods
-
readObject
Deserializes a document. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
ois
- the object input stream- Throws:
ClassNotFoundException
IOException
-
writeObject
Serializes a document. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
oos
- the object output stream- Throws:
IOException
-
-
Class chemaxon.struc.MDocument.Prop
class Prop extends MProp implements Serializable -
Class chemaxon.struc.MDocumentUtil
class MDocumentUtil extends Object implements Serializable- serialVersionUID:
- 12600100100892L
-
Serialized Fields
-
doc
MDocument doc
-
-
Class chemaxon.struc.MObject
class MObject extends Object implements Serializable- serialVersionUID:
- 2435517510938087080L
-
Serialization Methods
-
readObject
Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
ois
- the object input stream- Throws:
IOException
-
writeObject
Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
oos
- the object output stream- Throws:
IOException
-
-
Class chemaxon.struc.MolAtom
class MolAtom extends Object implements Serializable- serialVersionUID:
- -3974070468228529467L
-
Serialization Methods
-
readObject
Deserializes an atom. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
ois
- the object input stream- Throws:
ClassNotFoundException
IOException
-
writeObject
Serializes an atom. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
oos
- the object output stream- Throws:
IOException
-
-
Serialized Fields
-
angle
double angle
-
isValenceCheckNeeded
boolean isValenceCheckNeeded
-
-
Class chemaxon.struc.MolBond
class MolBond extends Object implements Serializable- serialVersionUID:
- 3656012871856958335L
-
Serialization Methods
-
readObject
Deserializes a bond. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
ois
- the object input stream- Throws:
ClassNotFoundException
IOException
-
writeObject
Serializes a bond. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
oos
- the object output stream- Throws:
IOException
-
-
Class chemaxon.struc.Molecule
class Molecule extends MoleculeGraph implements Serializable- serialVersionUID:
- 7275486436840296305L
-
Serialization Methods
-
readObject
Deserializes a molecule. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
ois
- the object input stream- Throws:
ClassNotFoundException
IOException
-
writeObject
Serializes a molecule. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
oos
- the object output stream- Throws:
IOException
-
-
Serialized Fields
-
id
String id
-
-
Class chemaxon.struc.MoleculeGraph
class MoleculeGraph extends Object implements Serializable- serialVersionUID:
- -2053719583816270190L
-
Serialization Methods
-
readObject
Deserializes a molecule graph. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
ois
- the object input stream- Throws:
ClassNotFoundException
IOException
-
writeObject
Serializes a molecule graph. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
oos
- the object output stream- Throws:
IOException
-
-
Serialized Fields
-
fragmentTracker
chemaxon.struc.MoleculeGraph.FragmentTracker fragmentTracker
-
hasBicycloStereo
boolean hasBicycloStereo
Molecule has bicyclo stereo information. Can be set byMolAtom.setBicycloStereo(BicycloStereoDescriptor[])
. -
valenceCheckOptions
ValenceCheckOptions valenceCheckOptions
Valence check options for the molecule.
-
-
Class chemaxon.struc.MPoint
class MPoint extends MObject implements Serializable- serialVersionUID:
- -3067277054033050963L
-
Serialization Methods
-
readObject
Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
ois
- the object input stream- Throws:
ClassNotFoundException
IOException
-
writeObject
Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
oos
- the object output stream- Throws:
IOException
-
-
Class chemaxon.struc.MProp
class MProp extends Object implements Serializable- serialVersionUID:
- -5699803671884637223L
-
Serialized Fields
-
coordDependent
boolean coordDependent
-
grinvCC
long grinvCC
-
-
Class chemaxon.struc.MPropertyContainer
class MPropertyContainer extends Object implements Externalizable- serialVersionUID:
- -2575268570438177098L
-
Serialization Methods
-
readExternal
Restores the property container's state.- Parameters:
in
- the stream to read data from in order to restore the object- Throws:
IOException
- if I/O errors occurClassNotFoundException
- If the class for an object being restored cannot be found.
-
writeExternal
Saves the property container's state.- Parameters:
out
- the stream to write the object to- Throws:
IOException
- Includes any I/O exceptions that may occur
-
-
Class chemaxon.struc.MSelectionDocument
class MSelectionDocument extends MDocument implements Serializable- serialVersionUID:
- 2379294894434293119L
-
Class chemaxon.struc.PageSettings
class PageSettings extends Object implements Externalizable- serialVersionUID:
- -7674028514396457694L
-
Serialization Methods
-
readExternal
- Throws:
IOException
ClassNotFoundException
-
writeExternal
- Throws:
IOException
-
-
Class chemaxon.struc.QueryBond
class QueryBond extends MolBond implements Serializable- serialVersionUID:
- -5025485107616067648L
-
Serialization Methods
-
readObject
Deserializes a bond. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
ois
- the object input stream- Throws:
ClassNotFoundException
IOException
-
writeObject
Serializes a bond. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
oos
- the object output stream- Throws:
IOException
-
-
Class chemaxon.struc.RgMolecule
class RgMolecule extends Molecule implements Serializable- serialVersionUID:
- -939153732283455787L
-
Serialization Methods
-
readObject
Deserializes an RgMolecule. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
ois
- the object input stream- Throws:
ClassNotFoundException
IOException
-
writeObject
Serializes an RgMolecule. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
oos
- the object output stream- Throws:
IOException
-
-
Class chemaxon.struc.RxnMolecule
class RxnMolecule extends Molecule implements Serializable- serialVersionUID:
- -2863036104564183121L
-
Serialization Methods
-
readObject
Deserializes a reaction. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
ois
- the object input stream- Throws:
ClassNotFoundException
IOException
-
writeObject
Serializes a reaction. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
oos
- the object output stream- Throws:
IOException
-
-
Class chemaxon.struc.SelectionMolecule
class SelectionMolecule extends MoleculeGraph implements Serializable- serialVersionUID:
- 234062772192819675L
-
Class chemaxon.struc.SelectionRgMolecule
class SelectionRgMolecule extends SelectionMolecule implements Serializable -
Class chemaxon.struc.Sgroup
class Sgroup extends Object implements Serializable- serialVersionUID:
- -6209766549185582411L
-
Serialization Methods
-
readObject
Deserializes an Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
ois
- the object input stream- Throws:
ClassNotFoundException
IOException
-
writeObject
Serializes an Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
oos
- the object output stream- Throws:
IOException
-
-
Serialized Fields
-
Class chemaxon.struc.StaticMolecule
class StaticMolecule extends Object implements Serializable- serialVersionUID:
- -6974806277329432018L
-
Serialized Fields
-
arrayFlags
int arrayFlags
-
atomCount
int atomCount
-
atomLists
byte[][] atomLists
-
atomMap
short[] atomMap
-
atomStereo
byte[] atomStereo
-
atomType
short[] atomType
-
bondAtom1
short[] bondAtom1
-
bondAtom2
short[] bondAtom2
-
bondCount
int bondCount
-
bondFlags
int[] bondFlags
-
charge
byte[] charge
-
connectionTable
short[] connectionTable
-
explicitHcount
byte[] explicitHcount
-
extendedAtomType
int[] extendedAtomType
-
hybridization
byte[] hybridization
-
implicitHcount
byte[] implicitHcount
-
massno
byte[] massno
-
name
String name
-
neighborCount
byte[] neighborCount
-
nodeEdgeList
short[][] nodeEdgeList
-
queryProperty
byte[][] queryProperty
-
radical
byte[] radical
-
rgroupId
short[] rgroupId
-
ringPerception
boolean ringPerception
-
sgroupId
String[] sgroupId
-
valence
byte[] valence
-
-
-
Package chemaxon.struc.graphics
-
Class chemaxon.struc.graphics.MAnalysisBox
class MAnalysisBox extends MTextBox implements Serializable- serialVersionUID:
- -7630363128405095856L
-
Class chemaxon.struc.graphics.MAssigner
class MAssigner extends MPolyline implements Serializable-
Serialized Fields
-
order
int order
-
-
-
Class chemaxon.struc.graphics.MAtomSetPoint
class MAtomSetPoint extends MPoint implements Serializable- serialVersionUID:
- 5932389976054063500L
-
Serialization Methods
-
readObject
Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
ois
- the object input stream- Throws:
ClassNotFoundException
IOException
-
writeObject
Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
oos
- the object output stream- Throws:
IOException
-
-
Class chemaxon.struc.graphics.MBracket
class MBracket extends MRectangle implements Serializable- serialVersionUID:
- -5775562691065011181L
-
Serialization Methods
-
readObject
Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
ois
- the object input stream- Throws:
IOException
-
writeObject
Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
oos
- the object output stream- Throws:
IOException
-
-
Serialized Fields
-
bracketOrientation
int bracketOrientation
Bracket orientation, bracket can have two sides (T_DOUBLE) or just one (T_SINGLE). Possible values: T_SINGLE, T_DOUBLE -
bracketType
int bracketType
-
-
Class chemaxon.struc.graphics.MChemicalStruct
class MChemicalStruct extends MObject implements Serializable- serialVersionUID:
- 7098670860634457343L
-
Serialization Methods
-
readObject
Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
ois
- the object input stream- Throws:
ClassNotFoundException
IOException
-
writeObject
Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
oos
- the object output stream- Throws:
IOException
-
-
Class chemaxon.struc.graphics.MEFlow
class MEFlow extends MPolyline implements Serializable- serialVersionUID:
- 891769518407563834L
-
Serialization Methods
-
readObject
Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
ois
- the object input stream- Throws:
IOException
-
writeObject
Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
oos
- the object output stream- Throws:
IOException
-
-
Serialized Fields
-
baseElectronContainerIndex
int baseElectronContainerIndex
-
baseElectronIndexInContainer
int baseElectronIndexInContainer
-
-
Class chemaxon.struc.graphics.MEFlowBasePoint
class MEFlowBasePoint extends MPoint implements Serializable- serialVersionUID:
- 1053944912020926984L
-
Serialization Methods
-
readObject
Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
ois
- the object input stream- Throws:
ClassNotFoundException
IOException
-
writeObject
Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
oos
- the object output stream- Throws:
IOException
-
-
Serialized Fields
-
electronIndex
int electronIndex
-
electronLabel
String electronLabel
-
-
Class chemaxon.struc.graphics.MElectron
class MElectron extends MAtomSetPoint implements Serializable-
Serialization Methods
-
readObject
- Throws:
IOException
-
writeObject
- Throws:
IOException
-
-
Serialized Fields
-
difLoc
DPoint3 difLoc
-
isPointed
boolean isPointed
-
-
-
Class chemaxon.struc.graphics.MElectronContainer
class MElectronContainer extends MObject implements Serializable-
Serialization Methods
-
readObject
- Throws:
IOException
ClassNotFoundException
-
writeObject
- Throws:
IOException
-
-
Serialized Fields
-
electronOccupation
boolean[] electronOccupation
-
electrons
chemaxon.struc.graphics.MElectron[] electrons
-
radical
boolean radical
-
-
-
Class chemaxon.struc.graphics.MEllipse
class MEllipse extends MRectangle implements Serializable-
Serialization Methods
-
readObject
Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
ois
- the object input stream- Throws:
ClassNotFoundException
IOException
-
writeObject
Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
oos
- the object output stream- Throws:
IOException
-
-
-
Class chemaxon.struc.graphics.MFont
class MFont extends Object implements Serializable- serialVersionUID:
- -7769715209509613515L
-
Serialization Methods
-
readObject
Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
ois
- the object input stream- Throws:
ClassNotFoundException
IOException
-
writeObject
Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
oos
- the object output stream- Throws:
IOException
-
-
Class chemaxon.struc.graphics.MMidPoint
class MMidPoint extends MPoint implements Serializable- serialVersionUID:
- 5307361876930807239L
-
Serialization Methods
-
readObject
Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
ois
- the object input stream- Throws:
ClassNotFoundException
IOException
-
writeObject
Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
oos
- the object output stream- Throws:
IOException
-
-
Class chemaxon.struc.graphics.MMidPoint.Sticky
class Sticky extends MMidPoint implements Serializable- serialVersionUID:
- 3223068581543532992L
-
Class chemaxon.struc.graphics.MMoleculeMovie
class MMoleculeMovie extends MObject implements Serializable- serialVersionUID:
- 6476041884742537582L
-
Serialization Methods
-
readObject
- Throws:
ClassNotFoundException
IOException
-
writeObject
- Throws:
IOException
-
-
Class chemaxon.struc.graphics.MNameTextBox
class MNameTextBox extends MTextBox implements Serializable- serialVersionUID:
- 6302424343157644471L
-
Serialization Methods
-
readObject
- Throws:
ClassNotFoundException
IOException
-
writeObject
- Throws:
IOException
-
-
Class chemaxon.struc.graphics.MPolyline
class MPolyline extends MObject implements Serializable- serialVersionUID:
- 4958026600768388648L
-
Serialization Methods
-
readObject
Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
ois
- the object input stream- Throws:
ClassNotFoundException
IOException
-
writeObject
Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
oos
- the object output stream- Throws:
IOException
-
-
Serialized Fields
-
internalPointAddCount
int internalPointAddCount
-
internalPointPos
int internalPointPos
-
-
Class chemaxon.struc.graphics.MRArrow
class MRArrow extends MPolyline implements Serializable- serialVersionUID:
- 8638690394107448092L
-
Serialization Methods
-
readObject
- Throws:
ClassNotFoundException
IOException
-
writeObject
- Throws:
IOException
-
-
Class chemaxon.struc.graphics.MReactionSign
class MReactionSign extends MTextBox implements Serializable- serialVersionUID:
- -7025949002857142442L
-
Class chemaxon.struc.graphics.MRectangle
class MRectangle extends MPolyline implements Serializable- serialVersionUID:
- 2948229815278089239L
-
Serialization Methods
-
readObject
Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
ois
- the object input stream- Throws:
ClassNotFoundException
IOException
-
writeObject
Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
oos
- the object output stream- Throws:
IOException
-
-
Class chemaxon.struc.graphics.MRectanglePoint
class MRectanglePoint extends MPoint implements Serializable- serialVersionUID:
- -3067277054033050963L
-
Serialization Methods
-
readObject
Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
ois
- the object input stream- Throws:
ClassNotFoundException
IOException
-
writeObject
Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
oos
- the object output stream- Throws:
IOException
-
-
Class chemaxon.struc.graphics.MRectanglePoint.Sticky
class Sticky extends MRectanglePoint implements Serializable- serialVersionUID:
- 3364078480306200948L
-
Class chemaxon.struc.graphics.MRoundedRectangle
class MRoundedRectangle extends MRectangle implements Serializable-
Serialization Methods
-
readObject
Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
ois
- the object input stream- Throws:
ClassNotFoundException
IOException
-
writeObject
Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
oos
- the object output stream- Throws:
IOException
-
-
Serialized Fields
-
arcHeight
double arcHeight
-
arcWidth
double arcWidth
-
-
-
Class chemaxon.struc.graphics.MTextAttributes
class MTextAttributes extends Object implements Externalizable- serialVersionUID:
- 6561552003080652755L
-
Serialization Methods
-
readExternal
- Throws:
IOException
ClassNotFoundException
-
writeExternal
- Throws:
IOException
-
-
Class chemaxon.struc.graphics.MTextBox
class MTextBox extends MRectangle implements Serializable- serialVersionUID:
- -7272723232157967384L
-
Serialization Methods
-
readObject
Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
ois
- the object input stream- Throws:
ClassNotFoundException
IOException
-
writeObject
Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
oos
- the object output stream- Throws:
IOException
-
-
Serialized Fields
-
actionMap
ActionMap actionMap
-
-
Class chemaxon.struc.graphics.MTextDocument
class MTextDocument extends Object implements Externalizable- serialVersionUID:
- 6305880304790247656L
-
Serialization Methods
-
readExternal
Restores the document.- Parameters:
in
- the stream to read data from in order to restore the object- Throws:
IOException
- if I/O errors occurClassNotFoundException
- If the class for an object being restored cannot be found.
-
writeExternal
Saves the document.- Parameters:
out
- the stream to write the object to- Throws:
IOException
- Includes any I/O exceptions that may occur
-
-
-
Package chemaxon.struc.prop
-
Class chemaxon.struc.prop.MBooleanProp
class MBooleanProp extends MProp implements Serializable- serialVersionUID:
- -5366978422380739811L
-
Serialization Methods
-
readObject
Restores the property's state.- Parameters:
in
- the stream to read data from in order to restore the object- Throws:
IOException
- if I/O errors occurClassNotFoundException
- If the class for an object being restored cannot be found.
-
writeObject
Saves the property's state.- Parameters:
out
- the stream to write the object to- Throws:
IOException
- Includes any I/O exceptions that may occur
-
-
Class chemaxon.struc.prop.MByteArrayProp
class MByteArrayProp extends MProp implements Serializable- serialVersionUID:
- -4046371792715339701L
-
Serialization Methods
-
readObject
- Throws:
IOException
ClassNotFoundException
-
writeObject
- Throws:
IOException
-
-
Class chemaxon.struc.prop.MCollectionProp
class MCollectionProp extends MProp implements Serializable- serialVersionUID:
- -7479938988131387052L
-
Class chemaxon.struc.prop.MDoubleArrayProp
class MDoubleArrayProp extends MProp implements Serializable- serialVersionUID:
- -5670039985685584647L
-
Serialization Methods
-
readObject
Restores the property's state.- Parameters:
in
- the stream to read data from in order to restore the object- Throws:
IOException
- if I/O errors occurClassNotFoundException
- If the class for an object being restored cannot be found.
-
writeObject
Saves the property's state.- Parameters:
out
- the stream to write the object to- Throws:
IOException
- Includes any I/O exceptions that may occur
-
-
Class chemaxon.struc.prop.MDoubleProp
class MDoubleProp extends MProp implements Serializable- serialVersionUID:
- -1221776439131689653L
-
Serialization Methods
-
readObject
Restores the property's state.- Parameters:
in
- the stream to read data from in order to restore the object- Throws:
IOException
- if I/O errors occurClassNotFoundException
- If the class for an object being restored cannot be found.
-
writeObject
Saves the property's state.- Parameters:
out
- the stream to write the object to- Throws:
IOException
- Includes any I/O exceptions that may occur
-
-
Class chemaxon.struc.prop.MFontProp
class MFontProp extends MProp implements Serializable- serialVersionUID:
- 2369581307328116455L
-
Serialization Methods
-
readObject
- Throws:
IOException
ClassNotFoundException
-
writeObject
- Throws:
IOException
-
-
Class chemaxon.struc.prop.MHashProp
class MHashProp extends MCollectionProp implements Serializable- serialVersionUID:
- 5457649877894058447L
-
Serialization Methods
-
readObject
Restores the property's state.- Parameters:
in
- the stream to read data from in order to restore the object- Throws:
IOException
- if I/O errors occurClassNotFoundException
- If the class for an object being restored cannot be found.
-
writeObject
Saves the property's state.- Parameters:
out
- the stream to write the object to- Throws:
IOException
- Includes any I/O exceptions that may occur
-
-
Class chemaxon.struc.prop.MHCoords3DProp
class MHCoords3DProp extends MProp implements Serializable- serialVersionUID:
- 6646271128663088908L
-
Serialization Methods
-
readObject
Restores the property's state.- Parameters:
in
- the stream to read data from in order to restore the object- Throws:
IOException
- if I/O errors occurClassNotFoundException
- If the class for an object being restored cannot be found.
-
writeObject
Saves the property's state.- Parameters:
out
- the stream to write the object to- Throws:
IOException
- Includes any I/O exceptions that may occur
-
-
Class chemaxon.struc.prop.MIntegerArrayProp
class MIntegerArrayProp extends MProp implements Serializable- serialVersionUID:
- 6651869314046996057L
-
Serialization Methods
-
readObject
Restores the property's state.- Parameters:
in
- the stream to read data from in order to restore the object- Throws:
IOException
- if I/O errors occurClassNotFoundException
- If the class for an object being restored cannot be found.
-
writeObject
Saves the property's state.- Parameters:
out
- the stream to write the object to- Throws:
IOException
- Includes any I/O exceptions that may occur
-
-
Class chemaxon.struc.prop.MIntegerProp
class MIntegerProp extends MProp implements Serializable- serialVersionUID:
- -7179550727198941747L
-
Serialization Methods
-
readObject
Restores the property's state.- Parameters:
in
- the stream to read data from in order to restore the object- Throws:
IOException
- if I/O errors occurClassNotFoundException
- If the class for an object being restored cannot be found.
-
writeObject
Saves the property's state.- Parameters:
out
- the stream to write the object to- Throws:
IOException
- Includes any I/O exceptions that may occur
-
-
Class chemaxon.struc.prop.MListProp
class MListProp extends MCollectionProp implements Serializable- serialVersionUID:
- 5360371881677476960L
-
Serialization Methods
-
readObject
Restores the property's state.- Parameters:
in
- the stream to read data from in order to restore the object- Throws:
IOException
- if I/O errors occurClassNotFoundException
- If the class for an object being restored cannot be found.
-
writeObject
Saves the property's state.- Parameters:
out
- the stream to write the object to- Throws:
IOException
- Includes any I/O exceptions that may occur
-
-
Class chemaxon.struc.prop.MMoleculeProp
class MMoleculeProp extends MProp implements Serializable- serialVersionUID:
- -7687559780023024273L
-
Serialization Methods
-
readObject
Restores the property's state.- Parameters:
in
- the stream to read data from in order to restore the object- Throws:
IOException
- if I/O errors occurClassNotFoundException
- If the class for an object being restored cannot be found.
-
writeObject
Saves the property's state.- Parameters:
out
- the stream to write the object to- Throws:
IOException
- Includes any I/O exceptions that may occur
-
-
Class chemaxon.struc.prop.MMoleculeStringProp
class MMoleculeStringProp extends MStringProp implements Serializable- serialVersionUID:
- -1005074014113755196L
-
Serialization Methods
-
readObject
- Throws:
IOException
ClassNotFoundException
-
writeObject
- Throws:
IOException
-
-
Serialized Fields
-
format
String format
-
-
Class chemaxon.struc.prop.MObjectProp
class MObjectProp extends MProp implements Serializable- serialVersionUID:
- 4005646748655675692L
-
Serialization Methods
-
readObject
Restores the property's state.- Parameters:
in
- the stream to read data from in order to restore the object- Throws:
IOException
- if I/O errors occurClassNotFoundException
- If the class for an object being restored cannot be found.
-
writeObject
Saves the property's state.- Parameters:
out
- the stream to write the object to- Throws:
IOException
- Includes any I/O exceptions that may occur
-
-
Class chemaxon.struc.prop.MStringProp
class MStringProp extends MProp implements Serializable- serialVersionUID:
- 1373831606368751112L
-
Serialization Methods
-
readObject
Restores the property's state.- Parameters:
in
- the stream to read data from in order to restore the object- Throws:
IOException
- if I/O errors occurClassNotFoundException
- If the class for an object being restored cannot be found.
-
writeObject
Saves the property's state.- Parameters:
out
- the stream to write the object to- Throws:
IOException
- Includes any I/O exceptions that may occur
-
-
-
Package chemaxon.struc.sgroup
-
Class chemaxon.struc.sgroup.AminoAcidSgroup
class AminoAcidSgroup extends SuperatomSgroup implements Serializable- serialVersionUID:
- -4078870750580716173L
-
Serialization Methods
-
readObject
- Throws:
ClassNotFoundException
IOException
-
writeObject
- Throws:
IOException
-
-
Serialized Fields
-
Class chemaxon.struc.sgroup.AttachmentPoint
class AttachmentPoint extends Object implements Serializable- serialVersionUID:
- -7484860308765339862L
-
Class chemaxon.struc.sgroup.DataSgroup
class DataSgroup extends Sgroup implements Serializable- serialVersionUID:
- -3132191586564122343L
-
Serialization Methods
-
readObject
Deserializes a data Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
ois
- the object input stream- Throws:
ClassNotFoundException
IOException
-
writeObject
Serializes a data Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
oos
- the object output stream- Throws:
IOException
-
-
Serialized Fields
-
labelPosition
chemaxon.struc.sgroup.DataSgroup.AbstractPosition labelPosition
-
sb
StringBuffer sb
temporary variable for getLineOnScreen
-
-
Class chemaxon.struc.sgroup.MulticenterSgroup
class MulticenterSgroup extends Sgroup implements Serializable- serialVersionUID:
- -7213879722783498112L
-
Serialization Methods
-
readObject
Deserializes a Multicenter Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
ois
- the object input stream- Throws:
ClassNotFoundException
IOException
-
writeObject
Serializes a Multicenter Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
oos
- the object output stream- Throws:
IOException
-
-
Class chemaxon.struc.sgroup.MultipleSgroup
class MultipleSgroup extends Sgroup implements Serializable- serialVersionUID:
- -1146464131016252826L
-
Serialization Methods
-
readObject
Deserializes a multiple Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
ois
- the object input stream- Throws:
ClassNotFoundException
IOException
-
writeObject
Serializes a multiple Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
oos
- the object output stream- Throws:
IOException
-
-
Exception chemaxon.struc.sgroup.NoFreeAttachmentPointException
class NoFreeAttachmentPointException extends RuntimeException implements Serializable- serialVersionUID:
- 2226630752133341633L
-
Serialized Fields
-
sga
SgroupAtom sga
-
-
Class chemaxon.struc.sgroup.RepeatingUnitSgroup
class RepeatingUnitSgroup extends Sgroup implements Serializable- serialVersionUID:
- -3209611525734625009L
-
Serialization Methods
-
readObject
Deserializes an SRU Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
ois
- the object input stream- Throws:
ClassNotFoundException
IOException
-
writeObject
Serializes an SRU Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
oos
- the object output stream- Throws:
IOException
-
-
Class chemaxon.struc.sgroup.SgroupAtom
class SgroupAtom extends MolAtom implements Serializable- serialVersionUID:
- -3185634359981637075L
-
Serialization Methods
-
readObject
Deserializes an Sgroup superatom. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
ois
- the object input stream- Throws:
ClassNotFoundException
IOException
-
writeObject
Serializes an Sgroup superatom. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
oos
- the object output stream- Throws:
IOException
-
-
Serialized Fields
-
labelCenter
int labelCenter
-
-
Class chemaxon.struc.sgroup.SuperatomSgroup
class SuperatomSgroup extends Sgroup implements Serializable- serialVersionUID:
- 2968529752634209305L
-
Serialization Methods
-
readObject
Deserializes a superatom Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
ois
- the object input stream- Throws:
ClassNotFoundException
IOException
-
writeObject
Serializes a superatom Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Parameters:
oos
- the object output stream- Throws:
IOException
-
-
Serialized Fields
-
apContainer
chemaxon.struc.sgroup.AttachmentPointContainer apContainer
Attachment Point container object
-
-
-
Package chemaxon.util
-
Exception chemaxon.util.ArgumentException
class ArgumentException extends Exception implements Serializable- serialVersionUID:
- -8949782741678573705L
-
Exception chemaxon.util.Heap.HeapException
class HeapException extends RuntimeException implements Serializable -
Class chemaxon.util.SearchAttributes
class SearchAttributes extends chemaxon.jep.util.SearchAttributes implements Serializable -
Exception chemaxon.util.SupplierException
class SupplierException extends RuntimeException implements Serializable
-
-
Package com.chemaxon.calculations.gui
-
Class com.chemaxon.calculations.gui.MChart
class MChart extends chemaxon.marvin.util.MarvinModule implements Serializable
-
-
Package com.chemaxon.calculations.io
-
Exception com.chemaxon.calculations.io.OrderedInputProcessingException
class OrderedInputProcessingException extends IllegalArgumentException implements Serializable-
Serialized Fields
-
inputIndex
int inputIndex
Deprecated, for removal: This API element is subject to removal in a future version.
-
-
-
-
Package com.chemaxon.clustering.framework
-
Class com.chemaxon.clustering.framework.RemoveSidechainsMolwalk
class RemoveSidechainsMolwalk extends Object implements Serializable -
Class com.chemaxon.clustering.framework.RemoveSidechainsSc
class RemoveSidechainsSc extends Object implements Serializable-
Serialized Fields
-
keepUnsaturatedConnections
boolean keepUnsaturatedConnections
-
-
-
Class com.chemaxon.clustering.framework.SimpleFrameworkAssociation
class SimpleFrameworkAssociation extends Object implements Serializable
-
-
Package com.chemaxon.descriptors.alignment
-
Class com.chemaxon.descriptors.alignment.AbstractShapeComparator
class AbstractShapeComparator extends Object implements Serializable-
Serialized Fields
-
generator
DescriptorGenerator<T extends ShapeDescriptor> generator
-
-
-
Class com.chemaxon.descriptors.alignment.AbstractShapeGenerator
class AbstractShapeGenerator extends Object implements Serializable-
Serialized Fields
-
parameters
P extends AbstractShapeGeneratorParameter parameters
-
-
-
Class com.chemaxon.descriptors.alignment.AbstractShapeGeneratorParameter
class AbstractShapeGeneratorParameter extends Object implements Serializable-
Serialized Fields
-
atomTyping
AtomTyping atomTyping
The setting for available shape coloring methods.
-
-
-
Class com.chemaxon.descriptors.alignment.BaseShapeComparatorParameter
class BaseShapeComparatorParameter extends Object implements Serializable-
Serialized Fields
-
flexibilityMode
AlignmentProperties.FlexibilityMode flexibilityMode
-
shapeFunction
ShapeFunction shapeFunction
-
tryCount
com.google.common.base.Optional<Integer> tryCount
-
-
-
Exception com.chemaxon.descriptors.alignment.ShapeComparatorException
class ShapeComparatorException extends RuntimeException implements Serializable- serialVersionUID:
- 1L
-
Exception com.chemaxon.descriptors.alignment.ShapeGeneratorException
class ShapeGeneratorException extends RuntimeException implements Serializable- serialVersionUID:
- 1L
-
-
Package com.chemaxon.descriptors.common
-
Package com.chemaxon.descriptors.fingerprints.cfp
-
Class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters
class CfpParameters extends Object implements Serializable- serialVersionUID:
- 0L
-
Serialized Fields
-
bitsPerPattern
int bitsPerPattern
Bits set for each pattern. -
bondCount
int bondCount
Max pattern length considered (bond count). -
length
int length
Fingerprint length (bit count). -
rings
boolean rings
Consider rings in fingerprint generation.
-
-
-
Package com.chemaxon.descriptors.fingerprints.ecfp
-
Class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters
class EcfpParameters extends Object implements Serializable- serialVersionUID:
- 0L
-
Serialized Fields
-
atomTypizer
EcfpAtomTypizers atomTypizer
Atom typizer to use. -
diameter
int diameter
Diameter parameter. -
identifierConfigurationXml
com.google.common.base.Optional<String> identifierConfigurationXml
Identifier configuration for custom XML mode. -
length
int length
Fingerprint length (bit count).
-
-
Class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpParameters
class ThreadLocalizedEcfpParameters extends Object implements Serializable- serialVersionUID:
- 0L
-
Serialized Fields
-
params
EcfpParameters params
-
-
-
Package com.chemaxon.descriptors.fingerprints.maccs
-
Class com.chemaxon.descriptors.fingerprints.maccs.MaccsParameters
class MaccsParameters extends Object implements Serializable
-
-
Package com.chemaxon.descriptors.fingerprints.pf2d
-
Class com.chemaxon.descriptors.fingerprints.pf2d.PfComparatorImpl
class PfComparatorImpl extends Object implements Serializable -
Class com.chemaxon.descriptors.fingerprints.pf2d.PfParameters
class PfParameters extends Object implements Serializable- serialVersionUID:
- 0L
-
Serialized Fields
-
xmlConfig
com.google.common.base.Optional<String> xmlConfig
XML configuration string.
-
-
Class com.chemaxon.descriptors.fingerprints.pf2d.PharmacophoreFPImpl
class PharmacophoreFPImpl extends com.chemaxon.descriptors.common.realvector.FloatVectorDescriptorImpl implements Serializable-
Serialized Fields
-
fingerprint
PharmacophoreFingerprint fingerprint
-
-
-
Class com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfParameters
class ThreadLocalizedPfParameters extends Object implements Serializable- serialVersionUID:
- 0L
-
Serialized Fields
-
xmlConfig
com.google.common.base.Optional<String> xmlConfig
-
-
-
Package com.chemaxon.descriptors.metrics
-
Class com.chemaxon.descriptors.metrics.TverskyParameters
class TverskyParameters extends Object implements Serializable- serialVersionUID:
- 0L
-
Serialized Fields
-
coeffQuery
double coeffQuery
Coefficient for query only part. -
coeffTarget
double coeffTarget
Coefficient for target only part.
-
-
-
Package com.chemaxon.descriptors.vectors.binary
-
Class com.chemaxon.descriptors.vectors.binary.BvGeneratorImpl
class BvGeneratorImpl extends Object implements Serializable- serialVersionUID:
- 0L
-
Serialized Fields
-
parameters
BvParameters parameters
-
-
Class com.chemaxon.descriptors.vectors.binary.BvParameters
class BvParameters extends Object implements Serializable- serialVersionUID:
- 0L
-
Serialized Fields
-
endianness
BinaryVectors.Endianness endianness
Endianness of long-int-byte-binary packing operations. -
length
int length
Fingerprint length (bit count). -
stringFormat
BvParameters.StringFormat stringFormat
String format to use.
-
-
-
Package com.chemaxon.descriptors.vectors.floats
-
Class com.chemaxon.descriptors.vectors.floats.FvGeneratorImpl
class FvGeneratorImpl extends Object implements Serializable- serialVersionUID:
- 0L
-
Serialized Fields
-
parameters
FvParameters parameters
-
-
Class com.chemaxon.descriptors.vectors.floats.FvParameters
class FvParameters extends Object implements Serializable- serialVersionUID:
- 0L
-
Serialized Fields
-
length
int length
Fingerprint length (bit count). -
numericRepresentation
FvParameters.NumericRepresentation numericRepresentation
Numeric representation. -
scaledMax
double scaledMax
Maximum value for scaling. -
scaledMin
double scaledMin
Minimum value for scaling. -
sparseCompression
FvParameters.SparseCompression sparseCompression
Optimization for sparse vectors.
-
-
-
Package com.chemaxon.overlap.io
-
Class com.chemaxon.overlap.io.AllAbsentMasterMoleculeStorage
class AllAbsentMasterMoleculeStorage extends Object implements Serializable-
Serialized Fields
-
size
long size
Deprecated, for removal: This API element is subject to removal in a future version.
-
-
-
Class com.chemaxon.overlap.io.ArraysBackedStorageTools.Builder
class Builder extends Object implements Serializable-
Serialized Fields
-
builtPages
List<C extends Serializable> builtPages
-
currentPage
List<E extends Serializable> currentPage
-
elementType
Class<E extends Serializable> elementType
-
getFromPage
com.chemaxon.descriptors.common.reflect.SerializableBiFunction<C extends Serializable,
Integer, E extends Serializable> getFromPage -
initialSkips
long initialSkips
-
listToPage
com.chemaxon.descriptors.common.reflect.SerializableFunction<List<E extends Serializable>,
C extends Serializable> listToPage -
pageSize
int pageSize
-
totalAbsents
long totalAbsents
-
totalSize
long totalSize
-
-
-
Class com.chemaxon.overlap.io.ArraysBackedStorageTools.Storage
class Storage extends Object implements Serializable-
Serialized Fields
-
elementType
Class<E extends Object> elementType
-
getFromPage
com.chemaxon.descriptors.common.reflect.SerializableBiFunction<C extends Object,
Integer, E extends Object> getFromPage -
initialSkips
long initialSkips
-
pages
List<C extends Object> pages
-
pageSize
int pageSize
-
totalAbsents
long totalAbsents
-
totalSize
long totalSize
-
-
-
Class com.chemaxon.overlap.io.CompactStringStorage
class CompactStringStorage extends Object implements Serializable- serialVersionUID:
- 0L
-
Serialized Fields
-
absentCount
long absentCount
Deprecated, for removal: This API element is subject to removal in a future version. -
pagesize
int pagesize
Deprecated, for removal: This API element is subject to removal in a future version. -
size
long size
Deprecated, for removal: This API element is subject to removal in a future version. -
skips
long skips
Deprecated, for removal: This API element is subject to removal in a future version. -
starts
int[][] starts
Deprecated, for removal: This API element is subject to removal in a future version. -
storage
byte[][] storage
Deprecated, for removal: This API element is subject to removal in a future version. -
storedByteCount
long storedByteCount
Deprecated, for removal: This API element is subject to removal in a future version.
-
-
Class com.chemaxon.overlap.io.CompactStringStorage.Metadata
class Metadata extends Object implements Serializable-
Serialized Fields
-
absentCount
long absentCount
-
bytes
long bytes
-
lastPageSize
int lastPageSize
-
pageCount
int pageCount
-
pageSize
int pageSize
-
size
long size
-
skips
long skips
-
storeSizes
int[] storeSizes
-
storeStart
long storeStart
-
-
-
Class com.chemaxon.overlap.io.MasterMoleculeStorageImpl
class MasterMoleculeStorageImpl extends Object implements Serializable- serialVersionUID:
- 0L
-
Serialized Fields
-
importOptsOrNull
String importOptsOrNull
Deprecated, for removal: This API element is subject to removal in a future version. -
sources
com.chemaxon.overlap.io.CompactStringStorage sources
Deprecated, for removal: This API element is subject to removal in a future version.
-
-
-
Package com.chemaxon.search.transformation
-
Exception com.chemaxon.search.transformation.TransformationException
class TransformationException extends Exception implements Serializable
-
Updater.UpdateInfo.isProgressMonitoringSupported
instead.