Serialized Form
-
Package chemaxon.calculations
-
Class chemaxon.calculations.CalculationException extends RuntimeException implements Serializable
- serialVersionUID:
- 1L
-
-
Package chemaxon.calculations.clean
-
Class chemaxon.calculations.clean.AtomChangeEvent extends EventObject implements Serializable
-
-
Package chemaxon.calculator
-
Class chemaxon.calculator.CalculatorException extends Exception implements Serializable
- serialVersionUID:
- 1L
-
-
Package chemaxon.clustering
-
Class chemaxon.clustering.ChemicalSpace extends Vector implements Serializable
-
Class chemaxon.clustering.ClusteringException extends Exception implements Serializable
-
Class chemaxon.clustering.Heap.HeapException extends RuntimeException implements Serializable
-
Class chemaxon.clustering.InvalidLicenseKeyException extends Exception implements Serializable
-
-
Package chemaxon.common.util
-
Class chemaxon.common.util.ByteVector extends Object implements Serializable
- serialVersionUID:
- -1393815508326465236L
-
Serialized Fields
-
data
byte[] data
-
size
int size
-
-
Class chemaxon.common.util.DoubleVector extends Object implements Serializable
- serialVersionUID:
- -5138497375635267024L
-
Serialized Fields
-
data
double[] data
-
size
int size
-
-
Class chemaxon.common.util.FloatVector extends Object implements Serializable
- serialVersionUID:
- -2327634131748729635L
-
Serialized Fields
-
data
float[] data
-
size
int size
-
-
Class chemaxon.common.util.GeomCalc.GeomCalcException extends RuntimeException implements Serializable
- serialVersionUID:
- -1705490613297709773L
-
Class chemaxon.common.util.GeomCalc.Queue.Overflow extends Exception implements Serializable
- serialVersionUID:
- -6957894135268794743L
-
Class chemaxon.common.util.GeomCalc.Queue.Underflow extends Exception implements Serializable
- serialVersionUID:
- -1972826041963082169L
-
Class chemaxon.common.util.IntMap extends HashMap<K extends Object,Integer> implements Serializable
- serialVersionUID:
- 4318465509620546463L
-
Class chemaxon.common.util.IntPair extends Object implements Serializable
- serialVersionUID:
- 1961353781713733629L
-
Serialized Fields
-
left
int left
-
right
int right
-
-
Class chemaxon.common.util.IntVector extends Object implements Serializable
- serialVersionUID:
- -9011852065319440166L
-
Serialized Fields
-
data
int[] data
-
size
int size
-
-
Class chemaxon.common.util.LongVector extends Object implements Serializable
- serialVersionUID:
- 8437448887389765952L
-
Serialized Fields
-
data
long[] data
-
size
int size
-
-
Class chemaxon.common.util.ShortVector extends Object implements Serializable
- serialVersionUID:
- 8407562362886825374L
-
Serialized Fields
-
data
short[] data
-
size
int size
-
-
-
Package chemaxon.core
-
Class chemaxon.core.SequenceBuildingException extends RuntimeException implements Serializable
-
Serialized Fields
-
errorKey
String errorKey
-
-
-
-
Package chemaxon.core.calculations.valencecheck
-
Class chemaxon.core.calculations.valencecheck.ValenceCheckOptions extends Object implements Serializable
- serialVersionUID:
- 568843891825099500L
-
Serialized Fields
-
localAromatic
boolean localAromatic
-
traditionalNallowed
boolean traditionalNallowed
-
-
Class chemaxon.core.calculations.valencecheck.ValenceColumnException extends chemaxon.core.calculations.valencecheck.ValenceException implements Serializable
-
Class chemaxon.core.calculations.valencecheck.ValenceException extends Exception implements Serializable
-
Class chemaxon.core.calculations.valencecheck.ValenceTypeException extends chemaxon.core.calculations.valencecheck.ValenceException implements Serializable
-
-
Package chemaxon.core.util
-
Class chemaxon.core.util.BondTable extends Object implements Serializable
- serialVersionUID:
- -8372436801118701137L
-
Serialized Fields
-
atomCount
int atomCount
The size of the matrix, the number of atoms in the molecule it represents.
-
-
-
Package chemaxon.descriptors
-
Class chemaxon.descriptors.MDGeneratorException extends Exception implements Serializable
-
Class chemaxon.descriptors.MDParametersException extends RuntimeException implements Serializable
-
Class chemaxon.descriptors.MDReaderException extends Exception implements Serializable
-
Class chemaxon.descriptors.MDWriterException extends Exception implements Serializable
-
Class chemaxon.descriptors.SimilarityException extends Exception implements Serializable
-
-
Package chemaxon.formats
-
Class chemaxon.formats.MolFormatException extends IOException implements Serializable
-
Serialized Fields
-
lineNumberInFile
int lineNumberInFile
-
lineNumberInRecord
int lineNumberInRecord
-
-
-
-
Package chemaxon.formats.documents.jchemoffice
-
Class chemaxon.formats.documents.jchemoffice.BatchProcessingException extends IOException implements Serializable
- serialVersionUID:
- 1L
-
Class chemaxon.formats.documents.jchemoffice.InvalidSizeScaleArgumentException extends chemaxon.util.ArgumentException implements Serializable
- serialVersionUID:
- 1L
-
-
Package chemaxon.jchem.db
-
Class chemaxon.jchem.db.DatabaseSearchException extends Exception implements Serializable
-
Class chemaxon.jchem.db.MaxSearchFrequencyExceededException extends DatabaseSearchException implements Serializable
-
Class chemaxon.jchem.db.RecalculationException extends Exception implements Serializable
- serialVersionUID:
- -2767058042924323545L
-
Class chemaxon.jchem.db.TransferException extends Exception implements Serializable
- serialVersionUID:
- -5241498055624956036L
-
Class chemaxon.jchem.db.UpdateHandler.RowData extends Object implements Serializable
- serialVersionUID:
- -4040824446004135801L
-
Serialized Fields
-
chemTermColValues
Map<String,Object> chemTermColValues
-
descriptorData
byte[][] descriptorData
-
fingerprint
int[] fingerprint
-
flags
String flags
-
formula
String formula
-
hashCode
int hashCode
-
markushData
byte[] markushData
-
molecule
Molecule molecule
-
molName
String molName
-
molString
byte[] molString
-
molWeight
Double molWeight
-
noRingInfoInFP
boolean noRingInfoInFP
-
reactionMappingIncomplete
boolean reactionMappingIncomplete
-
screenDescriptor
byte[] screenDescriptor
-
smiles
String smiles
-
sortableFormula
String sortableFormula
-
tautomer
Molecule tautomer
-
tautomerFragmentHashCode
int[] tautomerFragmentHashCode
-
tautomerHashCode
int tautomerHashCode
-
-
Class chemaxon.jchem.db.UpdateHandlerException extends Exception implements Serializable
- serialVersionUID:
- -8755169336283449997L
-
Class chemaxon.jchem.db.UpdateHandlerMetaData extends Object implements Serializable
- serialVersionUID:
- -6512295793385774884L
-
Serialized Fields
-
chemTermColumns
String[] chemTermColumns
-
chemTermForColumn
Map<String,String> chemTermForColumn
-
collectionType
chemaxon.jchem.base.storage.StructureCollectionType collectionType
-
compressedStructureFieldSupported
boolean compressedStructureFieldSupported
-
descriptorSettings
Map<String,String> descriptorSettings
-
descriptorTypes
Map<String,String> descriptorTypes
-
duplicateFilteringOption
boolean duplicateFilteringOption
-
insertDescriptorNames
List<String> insertDescriptorNames
-
numberOfCombinedFPColumns
int numberOfCombinedFPColumns
-
numberOfEdges
int numberOfEdges
-
numberOfOnes
int numberOfOnes
-
numberOfStructuralFPColumns
int numberOfStructuralFPColumns
-
standardizerConfig
String standardizerConfig
-
structuralKeys
String structuralKeys
-
tableType
int tableType
-
tautomerDuplicateFilteringEnabled
boolean tautomerDuplicateFilteringEnabled
-
tautomerEqualityMode
chemaxon.sss.search.options.TautomerTransformationMode tautomerEqualityMode
-
updateDescriptorNames
List<String> updateDescriptorNames
-
-
Class chemaxon.jchem.db.UpdateHandlerRowDataException extends UpdateHandlerException implements Serializable
- serialVersionUID:
- -7274357064259684370L
-
Serialized Fields
-
rowData
UpdateHandler.RowData rowData
-
-
Class chemaxon.jchem.db.Updater.UpdateInfo extends Object implements Serializable
- serialVersionUID:
- 4160146885445230514L
-
Serialized Fields
-
additionalInformation
String[] additionalInformation
Additional information for the entities in same order, if needed.- Since:
- JChem 6.0
-
entityList
String[] entityList
The names of entities (e.g. table names) to be updated, 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.since 5.1.2 useUpdater.UpdateInfo.isProgressMonitoringSupported
instead.Indicates if the update process is the regeneration of all tables. Since this can be a lengthy process, progress monitoring may be needed. In this case the table names 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 extends Object implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
cacheHash
Hashtable<String,chemaxon.jchem.db.cache.JChemCache> cacheHash
-
cacheRemovalMethod
chemaxon.jchem.db.cache.CacheRemovalMethod cacheRemovalMethod
-
expirationTime
double expirationTime
-
maxCacheMemory
long maxCacheMemory
-
maxCacheMemoryCalculated
boolean maxCacheMemoryCalculated
-
maxCacheSizeMB
int maxCacheSizeMB
-
minFreeMemMB
int minFreeMemMB
-
-
Class chemaxon.jchem.db.cache.CacheRegistrationException extends RuntimeException implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
reason
chemaxon.jchem.db.cache.CacheRegistrationException.Reason reason
-
-
-
Package chemaxon.jep
-
Class chemaxon.jep.ChemFunction extends chemaxon.nfunk.jep.function.PostfixMathCommand implements Serializable
- serialVersionUID:
- -3446599636099344973L
-
Serialized Fields
-
cached
boolean cached
-
jep
ChemJEP jep
-
-
Class chemaxon.jep.ChemJEP extends chemaxon.nfunk.jep.JEP implements Serializable
-
Serialized Fields
-
context
ChemContext context
The evaluation context object. -
contextClass
Class contextClass
The evaluation context class.
-
-
-
Class chemaxon.jep.ConditionException extends Exception implements Serializable
-
Class chemaxon.jep.ContextFunction extends chemaxon.nfunk.jep.function.PostfixMathCommand implements Serializable
- serialVersionUID:
- 6471101129584627604L
-
Class chemaxon.jep.DissimilarityFunction extends chemaxon.jep.ChemFunction implements Serializable
-
Class chemaxon.jep.Evaluator extends Object implements Serializable
-
Serialized Fields
-
builtInConfig
chemaxon.jep.EvaluatorConfiguration builtInConfig
The configuration object containing default function/plugin declarations. -
config
chemaxon.jep.EvaluatorConfiguration config
The configuration object. -
externalConfig
chemaxon.jep.EvaluatorConfiguration externalConfig
The configuration object containing external function/plugin declarations. -
functionalGroupDisplayMolTable
Hashtable<String,String> functionalGroupDisplayMolTable
|functional group name| -> |displayable molecule representation| -
licenseEnvironment
String licenseEnvironment
-
servicesConfigurationPath
String servicesConfigurationPath
services configuration path- Since:
- 5.10
-
servicesFunctionTable
Hashtable<String,chemaxon.nfunk.jep.function.PostfixMathCommandI> servicesFunctionTable
Function table for services. -
symtab
chemaxon.nfunk.jep.SymbolTable symtab
The base symbol table. -
userConfig
chemaxon.jep.EvaluatorConfiguration userConfig
The configuration object containing user defined function/plugin declarations. -
verbose
boolean verbose
True if verbose output.
-
-
-
Class chemaxon.jep.EvaluatorFunction extends chemaxon.jep.ChemFunction implements Serializable
-
Serialized Fields
-
evaluator
Evaluator evaluator
-
-
-
Class chemaxon.jep.MatchFunction extends chemaxon.jep.ChemFunction implements Serializable
-
-
Package chemaxon.jep.context
-
Class chemaxon.jep.context.AtomContext extends MolContext implements Serializable
-
Serialized Fields
-
atom
int atom
The input atom index.
-
-
-
Class chemaxon.jep.context.MolContext extends Object implements Serializable
-
Serialized Fields
-
fingerprint
int[] fingerprint
Fingerprint of the input molecule. -
init
boolean init
-
reactionContext
ReactionContext reactionContext
reaction wrapped in this context -
supplier
com.google.common.base.Supplier<Molecule> supplier
The molecule supplier.
-
-
-
Class chemaxon.jep.context.ReactionContext extends Object implements Serializable
- serialVersionUID:
- -9162272287141708299L
-
Serialized Fields
-
agentAtomMapping
Map<Integer,MolAtom> agentAtomMapping
mapping of AtomMap -> Agent Atom -
productAtomMapping
Map<Integer,MolAtom> productAtomMapping
mapping of AtomMap -> Product Atom -
reactantAtomMapping
Map<Integer,MolAtom> reactantAtomMapping
mapping of AtomMap -> Reactant Atom -
reaction
RxnMolecule reaction
reaction wrapped in this context
-
-
Class chemaxon.jep.context.SearchContext extends MolContext implements Serializable
-
-
Package chemaxon.license
-
Class chemaxon.license.LicenseException extends RuntimeException implements Serializable
-
Serialized Fields
-
product
String product
-
-
-
Class chemaxon.license.LicenseProcessingException extends Exception implements Serializable
-
-
Package chemaxon.marvin
-
Class chemaxon.marvin.SketchApplication extends chemaxon.marvin.AbstractApplication implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
exitAction
Action exitAction
-
newWindowAction
Action newWindowAction
-
outSerName
String outSerName
-
sketchPane
MSketchPane sketchPane
-
-
Class chemaxon.marvin.ViewApplication extends chemaxon.marvin.AbstractApplication implements Serializable
- serialVersionUID:
- 1L
-
-
Package chemaxon.marvin.alignment
-
Class chemaxon.marvin.alignment.AlignmentException extends Exception implements Serializable
-
Class chemaxon.marvin.alignment.NoConstraintException extends chemaxon.marvin.alignment.AlignmentException implements Serializable
-
Class chemaxon.marvin.alignment.OptimizationException extends RuntimeException implements Serializable
- serialVersionUID:
- 1L
-
Class chemaxon.marvin.alignment.ShapeData extends Object implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
atoms
chemaxon.marvin.alignment.ShapeData.Atom[] atoms
-
bonds
chemaxon.marvin.alignment.ShapeData.Bond[] bonds
-
coloringScheme
AlignmentProperties.ColoringScheme coloringScheme
-
maxs
double[] maxs
-
mins
double[] mins
-
shapeEnabledAtoms
BitSet shapeEnabledAtoms
-
-
Class chemaxon.marvin.alignment.TooDissimilarException extends chemaxon.marvin.alignment.AlignmentException implements Serializable
-
-
Package chemaxon.marvin.beans
-
Class chemaxon.marvin.beans.MarvinPane extends JRootPane implements Serializable
- serialVersionUID:
- -9042549845769941129L
-
Serialized Fields
-
actionListener
chemaxon.marvin.beans.MarvinPane.MarvinActionListener actionListener
-
molPanel
chemaxon.marvin.common.swing.MolPanel molPanel
Underlying panel. -
params
String params
Parameter string.
-
-
Class chemaxon.marvin.beans.MolRenderer extends JPanel implements Serializable
- serialVersionUID:
- 7229361698115302929L
-
Serialized Fields
-
printer
MolPrinter printer
-
-
Class chemaxon.marvin.beans.MSketch extends Object implements Serializable
- serialVersionUID:
- 0L
-
Serialization Methods
-
readExternal
public void readExternal(ObjectInput in) throws IOException, ClassNotFoundException
Restores the sketcher's state.- Throws:
IOException
- if I/O errors occurClassNotFoundException
- If the class for an object being restored cannot be found.
-
writeExternal
public void writeExternal(ObjectOutput out) throws IOException
Saves the sketcher's state.- Throws:
IOException
- Includes any I/O exceptions that may occur
-
-
Class chemaxon.marvin.beans.MSketchPane extends MarvinPane implements Serializable
- serialVersionUID:
- 602496692422927170L
-
Serialized Fields
-
commonActions
chemaxon.marvin.common.swing.action.CommonActions commonActions
-
-
Class chemaxon.marvin.beans.MView extends Object implements Serializable
- serialVersionUID:
- 0L
-
Serialization Methods
-
readExternal
public void readExternal(ObjectInput in) throws IOException, ClassNotFoundException
Restores the viewer's state.- Throws:
IOException
- if I/O errors occurClassNotFoundException
- If the class for an object being restored cannot be found.
-
writeExternal
public void writeExternal(ObjectOutput out) throws IOException
Saves the viewer's state.- Throws:
IOException
- Includes any I/O exceptions that may occur
-
-
Class chemaxon.marvin.beans.MViewEditor extends AbstractCellEditor implements Serializable
- serialVersionUID:
- 1549621132660875966L
-
Serialized Fields
-
editorComponent
MViewPane editorComponent
-
-
Class chemaxon.marvin.beans.MViewPane extends MarvinPane implements Serializable
- serialVersionUID:
- -4430811090653077262L
-
Serialized Fields
-
delayedRepainter
chemaxon.marvin.beans.MViewPane.DelayedRepainter delayedRepainter
-
preferredSizeSet
boolean preferredSizeSet
-
tableSupport
TableSupport tableSupport
-
-
Class chemaxon.marvin.beans.MViewRenderer extends MViewPane implements Serializable
- serialVersionUID:
- 5566509759455312369L
-
-
Package chemaxon.marvin.calculations
-
Class chemaxon.marvin.calculations.BitPattern extends BitSet implements Serializable
-
-
Package chemaxon.marvin.io
-
Class chemaxon.marvin.io.Encoding extends Object implements Serializable
-
Serialization Methods
-
readExternal
public void readExternal(ObjectInput arg0) throws IOException
- Throws:
IOException
-
writeExternal
public void writeExternal(ObjectOutput arg0) throws IOException
- Throws:
IOException
-
-
-
Class chemaxon.marvin.io.MolExportException extends IOException implements Serializable
-
Serialized Fields
-
molIndex
int molIndex
-
-
-
Class chemaxon.marvin.io.MRecordParseException extends Exception implements Serializable
-
Serialized Fields
-
position
MRecordReader.Position position
-
-
-
-
Package chemaxon.marvin.modules.datatransfer
-
Class chemaxon.marvin.modules.datatransfer.CopyAsDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable
- serialVersionUID:
- -4564761584830399025L
-
Serialized Fields
-
bundle
ResourceBundle bundle
-
defaultFormat
String defaultFormat
-
formats
List<String> formats
-
prevSelectedIdx
int prevSelectedIdx
-
selectorList
JList selectorList
-
-
-
Package chemaxon.marvin.plugin
-
Class chemaxon.marvin.plugin.PluginException extends Exception implements Serializable
-
Serialized Fields
-
level
int level
Deprecated, for removal: This API element is subject to removal in a future version.Error level.
-
-
-
Class chemaxon.marvin.plugin.PluginInputCheckerException extends PluginException implements Serializable
-
-
Package chemaxon.marvin.plugin.concurrent
-
Class chemaxon.marvin.plugin.concurrent.PluginExecutionException extends ExecutionException implements Serializable
-
Serialized Fields
-
plugin
CalculatorPlugin plugin
-
-
-
-
Package chemaxon.marvin.plugin.gui
-
Class chemaxon.marvin.plugin.gui.CheckList extends JPanel implements Serializable
-
Serialized Fields
-
checkboxes
chemaxon.marvin.plugin.gui.CheckList.MCheckBox[] checkboxes
-
-
-
Class chemaxon.marvin.plugin.gui.OptionsPane extends JDialog implements Serializable
-
Serialized Fields
-
cancel
chemaxon.marvin.swing.ActionButton cancel
-
key
String key
-
ok
chemaxon.marvin.swing.ActionButton ok
-
okActionListener
ActionListener okActionListener
-
parameterPanel
ParameterPanelHandler parameterPanel
-
restoreDefaults
chemaxon.marvin.swing.ActionButton restoreDefaults
-
title
String title
-
-
-
Class chemaxon.marvin.plugin.gui.ParameterPanel extends JPanel implements Serializable
-
Serialized Fields
-
items
chemaxon.marvin.plugin.gui.ParameterItem[] items
-
-
-
Class chemaxon.marvin.plugin.gui.ResultView extends JDialog implements Serializable
- serialVersionUID:
- -5728800883025815500L
-
Serialized Fields
-
bottomComponent
JComponent bottomComponent
-
bottomTextArea
JTextArea bottomTextArea
-
chart
chemaxon.marvin.util.MarvinModule chart
-
chartPanel
JPanel chartPanel
-
copymi
JMenuItem copymi
-
detachmi
JMenuItem detachmi
-
imageFormat
String imageFormat
-
mpan
chemaxon.marvin.common.swing.MolPanel mpan
-
popup
JPopupMenu popup
-
popupcopymi
JMenuItem popupcopymi
-
resetmi
JMenuItem resetmi
-
topComponent
JComponent topComponent
-
topTextArea
JTextArea topTextArea
-
viewMenu
JMenu viewMenu
-
viewMol
Molecule viewMol
-
viewMols
Molecule[] viewMols
-
viewPanel
chemaxon.marvin.view.swing.ViewPanel viewPanel
-
viewText
String viewText
-
viewTexts
String[] viewTexts
-
-
-
Package chemaxon.marvin.services
-
Class chemaxon.marvin.services.ServiceException extends Exception implements Serializable
- serialVersionUID:
- 328496720368460819L
-
-
Package chemaxon.marvin.sketch
-
Class chemaxon.marvin.sketch.History extends Object implements Serializable
-
Serialized Fields
-
autoHydrogenizeHist
int[] autoHydrogenizeHist
-
changeSupport
PropertyChangeSupport changeSupport
-
cornerHist
Point[] cornerHist
-
historyOverflow
boolean historyOverflow
-
molgToZoomHist
MoleculeGraph[][] molgToZoomHist
-
molHist
MDocument[] molHist
-
molHistCur
int molHistCur
-
molHistLen
int molHistLen
-
molHistMax
int molHistMax
-
rotateMatrHist
CTransform3D[] rotateMatrHist
-
scaleHist
double[] scaleHist
-
scrollBarHist
int[][] scrollBarHist
-
selectionToZoomHist
boolean[] selectionToZoomHist
-
-
-
Class chemaxon.marvin.sketch.MolEditor extends Object implements Serializable
- serialVersionUID:
- 2463379690025911142L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream arg0) throws ClassNotFoundException, IOException
- Throws:
ClassNotFoundException
IOException
-
-
Serialized Fields
-
atomBranchPiece
Molecule atomBranchPiece
-
atomSelectionMode
int atomSelectionMode
-
atomStrings
Set<Integer> atomStrings
-
bondDraggedAlong
boolean bondDraggedAlong
-
bondDrawMode
boolean bondDrawMode
-
canMovCurfrag
boolean canMovCurfrag
-
canRotCurfrag
boolean canRotCurfrag
-
curfrag
MDocument curfrag
-
curfragJoin
com.chemaxon.marvin.editor.molecule.fusion.MolJoin curfragJoin
-
curfragMoved
boolean curfragMoved
-
curfragR
double curfragR
-
currentTool
chemaxon.marvin.sketch.tool.EditorTool currentTool
-
dataSgroupObject
DataSgroup dataSgroupObject
-
deleteRemovesTerminalAtoms
boolean deleteRemovesTerminalAtoms
-
disabledAliases
Set<String> disabledAliases
-
document
MDocument document
-
documentEdited
boolean documentEdited
-
elements
List<Integer> elements
-
extraBonds
Set<Integer> extraBonds
-
flyingBondMol
MoleculeGraph flyingBondMol
-
hadSelection
boolean hadSelection
-
historizeEnabled
boolean historizeEnabled
-
historizeUnSelection
boolean historizeUnSelection
-
history
chemaxon.marvin.sketch.History history
-
isAxisSet
boolean isAxisSet
-
isDataSgroupLabelPointed
boolean isDataSgroupLabelPointed
-
isProbablyDotNetApplication
boolean isProbablyDotNetApplication
-
isSketchApplication
boolean isSketchApplication
-
jointAtom
MolAtom jointAtom
-
lastBondFlags
int lastBondFlags
-
lastQueryBondString
String lastQueryBondString
-
lastSelectionCorner
Point lastSelectionCorner
-
lastSelectionDoc
MDocument lastSelectionDoc
-
lastSelectionScale
double lastSelectionScale
-
lpEnabled
boolean lpEnabled
-
mergedst
double mergedst
-
moveMode
int moveMode
-
newKeyboardMotion
boolean newKeyboardMotion
-
painter
chemaxon.marvin.paint.internal.MolPainter painter
-
persistentMoveMode
boolean persistentMoveMode
-
piece
Molecule piece
-
pieceOriginalObject
Molecule pieceOriginalObject
-
prevCurfrag
MDocument prevCurfrag
-
queryAtoms
Set<Integer> queryAtoms
-
reactionSupported
boolean reactionSupported
-
rotate3direction
int rotate3direction
-
rotate3dPhi
double rotate3dPhi
-
rotate3dPhiX
double rotate3dPhiX
-
rotate3dPhiY
double rotate3dPhiY
-
rotate3dx
double rotate3dx
-
rotate3dy
double rotate3dy
-
rotateZPhi
double rotateZPhi
-
rotation3DMode
int rotation3DMode
-
rotAxisPoint
DPoint3 rotAxisPoint
-
rotO
DPoint3 rotO
-
scrollBarVals
int[] scrollBarVals
-
selectionDoc
MSelectionDocument selectionDoc
-
selectionHistorized
boolean selectionHistorized
-
selectionHPoints
DPoint3[] selectionHPoints
-
showMolecule
Molecule showMolecule
-
starEnabled
boolean starEnabled
-
stickdst
double stickdst
-
-
-
Package chemaxon.marvin.space
-
Class chemaxon.marvin.space.EventQueue extends Vector implements Serializable
-
Class chemaxon.marvin.space.GraphicScene extends JPanel implements Serializable
-
Serialized Fields
-
_glListsToDelete
ArrayList<Integer> _glListsToDelete
-
activeCell
int activeCell
index of the active cell: cells are numbered line-by-line -
antialias
boolean antialias
-
backgroundColor
float[] backgroundColor
we use java.awt.Color in the following cases - when the color does not change too often - when the user can change the given color - when we don't have to give it to OGL2 too often (like color of an atom, etc) These are e.g. : background color, constant component colors -
backgroundColorChanged
boolean backgroundColorChanged
-
canvas
Component canvas
-
cellCount
int cellCount
number of cells (there might be fewer cells than cells.length()) -
cells
GraphicCell[] cells
components per cells, line-by-line 0 is the top-left corner -
columnCount
int columnCount
layout of the graphic view: number of cells per column -
defaultDrawProperties
Map<Object,Object> defaultDrawProperties
-
eventHandler
chemaxon.marvin.space.MSpaceEventHandler eventHandler
-
gl
javax.media.opengl.GL2 gl
-
glAutoDrawable
javax.media.opengl.GLAutoDrawable glAutoDrawable
-
globalDrawProperties
Properties globalDrawProperties
-
gltext
chemaxon.marvin.space.util.GLText gltext
this is used to display warning about unregistered product -
glu
javax.media.opengl.glu.GLU glu
-
height
int height
physical height of the entire scene (in pixels) -
initialized
boolean initialized
-
motionmode
int motionmode
standing or moving mode -
needsRefresh
int needsRefresh
Indicates with internal index which cell needs redraw. -1 means none, cellCount means all cells. -
needsReset
int needsReset
-
progressBar
chemaxon.marvin.space.gui.JMSpaceProgressBar progressBar
-
renderTargets
chemaxon.marvin.space.gl.shader.RenderTargets renderTargets
-
rowCount
int rowCount
layout of the graphic view: number of cells per row -
rx
double rx
rotation around x-y-z axises -
ry
double ry
rotation around x-y-z axises -
rz
double rz
rotation around x-y-z axises -
smoothBackground
boolean smoothBackground
-
synchronousMode
boolean synchronousMode
-
transparentBackground
int transparentBackground
-
userSettings
UserSettings userSettings
-
verboseLevel
int verboseLevel
-
width
int width
physical width of the entire scene (in pixels)
-
-
-
-
Package chemaxon.marvin.uif.dialog
-
Class chemaxon.marvin.uif.dialog.CategoriesDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable
-
Serialized Fields
-
bundle
ResourceBundle bundle
-
model
chemaxon.marvin.uif.dialog.model.CategoriesModel model
-
-
-
Class chemaxon.marvin.uif.dialog.ConfigurationDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable
-
Serialized Fields
-
module
chemaxon.marvin.uif.module.GUIModule module
-
-
-
Class chemaxon.marvin.uif.dialog.CustomizeDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable
-
Serialized Fields
-
bundle
ResourceBundle bundle
-
guiRegistryClone
chemaxon.marvin.uif.model.GUIRegistry guiRegistryClone
-
model
chemaxon.marvin.uif.dialog.model.CustomizeGUIModel model
-
moduleConf
chemaxon.marvin.uif.module.ModuleConfiguration moduleConf
-
-
-
Class chemaxon.marvin.uif.dialog.LicenseDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable
-
Class chemaxon.marvin.uif.dialog.MenuDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable
-
Serialized Fields
-
bundle
ResourceBundle bundle
-
model
chemaxon.marvin.uif.dialog.model.MenuManagerModel model
-
-
-
Class chemaxon.marvin.uif.dialog.MenuMoveDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable
-
Serialized Fields
-
bundle
ResourceBundle bundle
-
model
chemaxon.marvin.uif.dialog.model.ItemGroupModel model
-
-
-
Class chemaxon.marvin.uif.dialog.PopupDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable
-
Serialized Fields
-
bundle
ResourceBundle bundle
-
model
chemaxon.marvin.uif.dialog.model.PopupManagerModel model
-
-
-
Class chemaxon.marvin.uif.dialog.ShortcutEditorDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable
-
Serialized Fields
-
bundle
ResourceBundle bundle
-
model
chemaxon.marvin.uif.dialog.model.ShortcutModel model
-
-
-
Class chemaxon.marvin.uif.dialog.ToolBarDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable
-
Serialized Fields
-
bundle
ResourceBundle bundle
-
model
chemaxon.marvin.uif.dialog.model.ToolBarManagerModel model
-
-
-
-
Package chemaxon.marvin.util
-
Class chemaxon.marvin.util.CancelPrintException extends Exception implements Serializable
- serialVersionUID:
- 7380116746554005158L
-
Class chemaxon.marvin.util.MarvinModule extends Object implements Serializable
- serialVersionUID:
- 2763330874643316763L
-
Class chemaxon.marvin.util.MarvinOLEFrame extends JFrame implements Serializable
- serialVersionUID:
- 7801720334170069726L
-
Serialized Fields
-
sp
Semaphore sp
-
-
Class chemaxon.marvin.util.MarvinOLEPanel extends JPanel implements Serializable
- serialVersionUID:
- -6975415959061110410L
-
Serialized Fields
-
emfExportOptions
String emfExportOptions
-
importExceptionCaught
boolean importExceptionCaught
-
msketch
MSketchPane msketch
-
retainGUIPropertiesOnPanel
boolean retainGUIPropertiesOnPanel
-
semaphore
Semaphore semaphore
-
sketchPanel
chemaxon.marvin.sketch.swing.SketchPanel sketchPanel
-
structureGUIProperties
MPropertyContainer structureGUIProperties
-
-
Class chemaxon.marvin.util.SwingUtil extends Object implements Serializable
- serialVersionUID:
- -1600625160321014724L
-
-
Package chemaxon.marvin.util.codeassist
-
Class chemaxon.marvin.util.codeassist.ChemTermDocument extends DefaultStyledDocument implements Serializable
- serialVersionUID:
- -5894946790409031807L
-
Serialized Fields
-
comment
MutableAttributeSet comment
-
constant
MutableAttributeSet constant
-
constants
Map<String,AttributeSet> constants
-
currentElementIndex
int currentElementIndex
-
doc
DefaultStyledDocument doc
-
fontName
String fontName
-
fontSize
int fontSize
-
function
MutableAttributeSet function
-
functions
Map<String,AttributeSet> functions
-
HIGHLIGHT_TIMER
Timer HIGHLIGHT_TIMER
-
keyword
MutableAttributeSet keyword
-
keywords
Map<String,AttributeSet> keywords
-
lastPrefixState
boolean lastPrefixState
-
multiLineComment
boolean multiLineComment
-
normal
MutableAttributeSet normal
-
parenLength
int parenLength
-
parenOffset
int parenOffset
-
parenthesis
MutableAttributeSet parenthesis
-
prefix
String prefix
-
quote
MutableAttributeSet quote
-
rootElement
Element rootElement
-
-
Class chemaxon.marvin.util.codeassist.CompletionItemCellRenderer extends DefaultListCellRenderer implements Serializable
- serialVersionUID:
- 6746125418422903808L
-
Class chemaxon.marvin.util.codeassist.MacroManagerPanel extends JPanel implements Serializable
- serialVersionUID:
- -4703035835623320688L
-
Serialized Fields
-
ACCEPT_ACTION
Action ACCEPT_ACTION
-
acceptButton
JButton acceptButton
-
acceptEditButton
JButton acceptEditButton
-
addButton
JButton addButton
-
CANCEL_ACTION
Action CANCEL_ACTION
-
cancelButton
JButton cancelButton
-
cancelEditButton
JButton cancelEditButton
-
deleteButton
JButton deleteButton
-
descPane
JTextPane descPane
-
descScrollPane
JScrollPane descScrollPane
-
editButton
JButton editButton
-
editedItem
int editedItem
-
editPanel
JPanel editPanel
-
helper
chemaxon.marvin.util.codeassist.CodeAssistMacrosHelper helper
-
layout
CardLayout layout
-
listPanel
JPanel listPanel
-
macroList
JList macroList
-
macroListScroll
JScrollPane macroListScroll
-
macroPane
JTextPane macroPane
-
macroScrollPane
JScrollPane macroScrollPane
-
nameField
JTextField nameField
-
-
-
Package chemaxon.marvin.view
-
Class chemaxon.marvin.view.MDocStorage.CancellationException extends Exception implements Serializable
-
Class chemaxon.marvin.view.MDocStorage.RecordUnavailableException extends Exception implements Serializable
-
Serialized Fields
-
recordIndex
int recordIndex
-
-
-
-
Package chemaxon.marvin.view.swing
-
Class chemaxon.marvin.view.swing.TwoLists extends JPanel implements Serializable
-
Class chemaxon.marvin.view.swing.ViewCanvas extends chemaxon.marvin.common.swing.MolCanvas implements Serializable
- serialVersionUID:
- 3979819797881974530L
-
Serialization Methods
-
writeObject
private void writeObject(ObjectOutputStream arg0) throws IOException
- Throws:
IOException
-
-
Serialized Fields
-
cellIndex
int cellIndex
-
document
MDocument document
-
error
boolean error
-
highlightedAtom
int highlightedAtom
-
inZoomWindow
boolean inZoomWindow
-
markedAtom
int markedAtom
-
moleculeBackground
Color moleculeBackground
-
moleculeCenter
DPoint3 moleculeCenter
-
nextV
Vector<Object[]> nextV
-
painter
chemaxon.marvin.paint.internal.MolPainter painter
-
preferredSize1
Dimension preferredSize1
-
rescaleNeeded
boolean rescaleNeeded
-
rsize
Dimension rsize
-
viewFrame
chemaxon.marvin.view.swing.modules.MViewFrame viewFrame
-
viewPanel
chemaxon.marvin.view.swing.ViewPanel viewPanel
-
windowAction
chemaxon.marvin.swing.MAction windowAction
-
winScale
double winScale
-
-
Class chemaxon.marvin.view.swing.ViewHandler extends Object implements Serializable
-
Serialized Fields
-
cellFiller
chemaxon.marvin.view.swing.CellFiller cellFiller
-
debug
boolean debug
-
visibleDocs
chemaxon.marvin.view.swing.VisibleDocuments visibleDocs
-
-
-
Class chemaxon.marvin.view.swing.ViewPanel extends chemaxon.marvin.common.swing.MolPanel implements Serializable
- serialVersionUID:
- 802342314015862847L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream arg0) throws ClassNotFoundException, IOException
- Throws:
ClassNotFoundException
IOException
-
-
Serialized Fields
-
animator
chemaxon.marvin.view.swing.modules.MViewAnimator animator
-
animSynchronized
boolean animSynchronized
-
atomMarkAndHighlightEnabled
boolean atomMarkAndHighlightEnabled
-
autoTabScale
boolean autoTabScale
-
borderColor
Color borderColor
-
borderWidth
int borderWidth
-
clearStateOnOpenAction
Action clearStateOnOpenAction
-
cols
int cols
-
commonActions
chemaxon.marvin.common.swing.action.CommonActions commonActions
-
defaultFieldFont
Font defaultFieldFont
-
detachable
boolean detachable
-
draggable
boolean draggable
-
editable
int editable
-
fieldFontMap
Map<String,Font> fieldFontMap
-
findAction
Action findAction
-
findAgainAction
Action findAgainAction
-
findTextModule
chemaxon.marvin.view.swing.modules.FindText findTextModule
-
importEnabled
boolean importEnabled
-
molbgMap
Map<Integer,Color> molbgMap
-
moleculeSelections
chemaxon.marvin.common.AtomSelectionHandler[] moleculeSelections
-
molEdited
boolean molEdited
-
molFrame0
Window molFrame0
-
molString
String molString
-
molStrings
String[] molStrings
-
navigationActions
chemaxon.marvin.swing.MAction[] navigationActions
-
oldMarkedAtom
int oldMarkedAtom
-
oldMarkedCell
int oldMarkedCell
-
rasmolScripts
String[] rasmolScripts
-
rows
int rows
-
selectable
boolean selectable
-
selected
int selected
-
skbridge
chemaxon.marvin.view.modules.sketchbridge.MViewSketch skbridge
-
startLoad
boolean startLoad
-
tableSupport
TableSupport tableSupport
-
tabScale
double tabScale
-
tabScaleCalcInProgress
int tabScaleCalcInProgress
-
tabScaleCalcNeeded
boolean tabScaleCalcNeeded
-
viewActions
chemaxon.marvin.view.swing.ViewActions viewActions
-
viewHandler
chemaxon.marvin.view.swing.ViewHandler viewHandler
-
winScale
double winScale
-
-
Class chemaxon.marvin.view.swing.WholeNumberField extends JTextField implements Serializable
-
Serialized Fields
-
integerFormatter
NumberFormat integerFormatter
-
options
int options
-
toolkit
Toolkit toolkit
-
-
-
Class chemaxon.marvin.view.swing.WholeNumberField.WholeNumberDocument extends PlainDocument implements Serializable
-
-
Package chemaxon.naming
-
Class chemaxon.naming.NameFormatException extends MolFormatException implements Serializable
-
Serialized Fields
-
prefix
String prefix
-
-
-
Class chemaxon.naming.NameFormatException.FilteredCase extends NameFormatException implements Serializable
-
Class chemaxon.naming.NamePrefixException extends NameFormatException implements Serializable
-
Serialized Fields
-
token
String token
-
-
-
-
Package chemaxon.naming.document
-
Class chemaxon.naming.document.D2SOptionsParser.UnknownOptionException extends Exception implements Serializable
-
Class chemaxon.naming.document.D2SPdfParser extends org.apache.tika.parser.pdf.ExtendablePdfParser implements Serializable
-
Class chemaxon.naming.document.D2STextParser extends Object implements Serializable
-
Class chemaxon.naming.document.EncryptedDocumentException extends IOException implements Serializable
-
Class chemaxon.naming.document.OsrParser extends org.apache.tika.parser.AbstractParser implements Serializable
-
Class chemaxon.naming.document.SafeOfficeParser extends org.apache.tika.parser.microsoft.OfficeParser implements Serializable
-
Class chemaxon.naming.document.TimeoutException extends IOException implements Serializable
-
Serialized Fields
-
timeoutMS
long timeoutMS
-
-
-
Class chemaxon.naming.document.TrivialXmlParser extends org.apache.tika.parser.AbstractParser implements Serializable
-
-
Package chemaxon.naming.document.annotate
-
Class chemaxon.naming.document.annotate.AnnotationException extends IOException implements Serializable
-
-
Package chemaxon.reaction
-
Class chemaxon.reaction.PatternProperty extends Object implements Serializable
- serialVersionUID:
- -3617253669859174882L
-
Serialized Fields
-
representation
String representation
-
-
Class chemaxon.reaction.ReactionException extends Exception implements Serializable
- serialVersionUID:
- 1L
-
-
Package chemaxon.sss.search
-
Class chemaxon.sss.search.JChemSearchOptions extends SearchOptions implements Serializable
- serialVersionUID:
- -6025435983286725061L
-
Serialized Fields
-
absoluteStereo
int absoluteStereo
-
cacheRegistrationNeeded
boolean cacheRegistrationNeeded
Can be set to false in case of readonly databases and jcsearch. Only for internal use! -
descriptorConfig
String descriptorConfig
configuration for descriptor dissim. calculations -
descriptorName
String descriptorName
the identifier of stored descriptor used for dissim. calculations,null
means pure fingerprint similarity is performed -
dissimilarityMetric
String dissimilarityMetric
Dissimilarity metric name, 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:
HaltOnErrorOption
-
markushScreeningOptions
Set<chemaxon.sss.search.options.MarkushScreeningType> markushScreeningOptions
Set containing all enabled Markush screen methods -
matchCountOptions
MatchCountOptions matchCountOptions
-
maxResultCount
int maxResultCount
-
optimizeQueries
boolean optimizeQueries
Shows whether the query should be enumerated to improve search -
returnsNonHits
boolean returnsNonHits
-
totalSearchTimeoutLimitMilliseconds
int totalSearchTimeoutLimitMilliseconds
The search on a database timeouts reaching this number of milliseconds.
-
-
Class chemaxon.sss.search.MarkushFeature extends Object implements Serializable
- serialVersionUID:
- 8770437891053649928L
-
Serialized Fields
-
data
int[] data
Reference data to expanded object. Different for each type:MarkushFeature.RGROUP
: {R-atom union index, R-group definition index}MarkushFeature.LINKNODE
: {link atom union index}MarkushFeature.REPUNIT
: {RepeatingUnitSgroup sgroup index in markush}MarkushFeature.ATOMLIST
: {list atom union index}MarkushFeature.BONDLIST
: {list bond union bond index}MarkushFeature.MULTIBOND
: {union bond index, MulticenterSgroup sgroup index in markush}
RgMolecule.findRgroupIndex(int)
. -
hashCode
int hashCode
-
type
int type
Expansion type.
-
-
Class chemaxon.sss.search.MatchCountOptions extends Object implements Serializable
- serialVersionUID:
- 6422092438307828424L
-
Serialized Fields
-
matchCountHighLimit
int matchCountHighLimit
-
matchCountHighLimitInclusive
boolean matchCountHighLimitInclusive
-
matchCounthitLimit
int matchCounthitLimit
-
matchCountIncludesZero
boolean matchCountIncludesZero
-
matchCountLowLimit
int matchCountLowLimit
-
matchCountLowLimitInclusive
boolean matchCountLowLimitInclusive
-
matchCountRelation
String matchCountRelation
-
mode
int mode
-
-
Class chemaxon.sss.search.MolSearchOptions extends SearchOptions implements Serializable
- serialVersionUID:
- -6364233804214700841L
-
Serialized Fields
-
hitIncludesRNodes
boolean hitIncludesRNodes
If true, the result hit will contain R-nodes with dummy indexes -
hitIndexType
int hitIndexType
In case of Markush search specifies the representation of the Markush structure on which the hit indexes are retrieved. (default MARKUSH_HIT_ORIGINAL) -
ignoreChiralityForAtoms
chemaxon.common.util.IntVector ignoreChiralityForAtoms
Contains query atom numbers which should be ignored at the chirality check in case of exact stereo searching. It has a package visibility. -
markushEnabled
boolean markushEnabled
Decides whether targets with Markush features should be treated as Markush libraries (true) or just "strange" molecules (false) (default value: false). -
queryAbsoluteStereo
boolean queryAbsoluteStereo
If true, chiral centers in the query molecules are regarded as absolute stereo, ignoring the chiral flag. If the molecule contains any enhanced stereo labels, this flag has no effect. -
recursiveSMARTSMode
boolean recursiveSMARTSMode
true: at findAll searches only hits are retrieved where the first atom differs as well. -
switchOffAllProtectsForTDF
boolean switchOffAllProtectsForTDF
If true, all protect features are switched of during generic tautomer creation -
targetAbsoluteStereo
boolean targetAbsoluteStereo
If true, chiral centers in the target molecules are regarded as absolute stereo, ignoring the chiral flag. If the molecule contains any enhanced stereo labels, this flag has no effect. -
tautomerEqualityMode
chemaxon.sss.search.options.TautomerTransformationMode tautomerEqualityMode
-
-
Class chemaxon.sss.search.SearchException extends Exception implements Serializable
- serialVersionUID:
- 1698586463587833734L
-
Class chemaxon.sss.search.SearchOptions extends Object implements Serializable
- serialVersionUID:
- -6845044337680993338L
-
Serialized Fields
-
attachedDataMatch
int attachedDataMatch
Specifies attached data match type Default 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:
SearchOptions.setDoubleBondStereoMatchingMode(int)
-
endGroupMatching
boolean endGroupMatching
True: polymer endgroups must match (default: false) -
exactBondMatching
boolean exactBondMatching
true, if query bonds match only the same query bonds -
exactQueryAtomMatching
boolean exactQueryAtomMatching
If true, query information (eg atom list, any atom, number of hydrogens, aromaticity, etc) in atoms will not be evaluated, but rather exact matching of these information is required. It is useful for searching in query databases. Default is false.- Since:
- JChem 2.2
-
exactSpecialAtomMatching
String exactSpecialAtomMatching
-
exhaustiveModeLimit
int exhaustiveModeLimit
Upon reaching this number of steps, the search switches to exhaustive mode from fast mode. -
hCountMatching
int hCountMatching
Defines the interpretation of H count in the query. Default is HCOUNT_MATCHING_AUTO. -
hitOrdering
int hitOrdering
Specifies hit ordering, currently used in ordering undefined R-atom group matchings Default 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:
SearchOptions.setStereoSearchType(int)
-
targetHomologyMatchingMode
TargetHomologyMatchingMode targetHomologyMatchingMode
-
tautomerSearch
boolean tautomerSearch
True: tautomer searching is enabled (default value: false). -
tautomerSearchOption
int tautomerSearchOption
Specifies the tautomer searching behavior. Default: non-tautomer search, except: duplicate search in tautomer duplicate table -
tautomerSearchOptionLeftDefault
boolean tautomerSearchOptionLeftDefault
Shows that tautomerSearch value has not been set. -
throwExceptionOnTimeout
boolean throwExceptionOnTimeout
If the search should throw exception upon timeout. -
timeoutLimitMilliseconds
int timeoutLimitMilliseconds
The search on a single target timeouts reaching this number of milliseconds. -
transformMonomer
boolean transformMonomer
True: monomers are transformed to structural repeating units. (default: true) -
undefinedRAtom
int undefinedRAtom
Specifies match of undefined r-atom in query Default 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.
-
-
Class chemaxon.sss.search.SearchTimeoutException extends SearchException implements Serializable
- serialVersionUID:
- -78126823565453833L
-
Class chemaxon.sss.search.UnsupportedQueryException extends IllegalArgumentException implements Serializable
- serialVersionUID:
- 6255906179820229430L
-
-
Package chemaxon.sss.search.options
-
Package chemaxon.standardizer.advancedactions
-
Class chemaxon.standardizer.advancedactions.GroupList extends ArrayList<GroupDefinition> implements Serializable
-
-
Package chemaxon.struc
-
Class chemaxon.struc.CTransform3D extends Object implements Serializable
- serialVersionUID:
- 0L
-
Serialization Methods
-
readExternal
public void readExternal(ObjectInput in) throws IOException
Deserializes a transformation matrix.- Throws:
IOException
- Since:
- 3.5, 11/02/2004
-
writeExternal
public void writeExternal(ObjectOutput out) throws IOException
Serializes a transformation matrix.- Throws:
IOException
- Since:
- 3.5, 11/02/2004
-
-
Class chemaxon.struc.DefaultDictionary extends HashMap<String,SuperatomSgroup> implements Serializable
- serialVersionUID:
- 8013155936541949713L
-
Class chemaxon.struc.DPoint3 extends Object implements Serializable
- serialVersionUID:
- 0L
-
Serialization Methods
-
readExternal
public void readExternal(ObjectInput in) throws IOException, ClassNotFoundException
Deserializes a 3D point.- Throws:
IOException
ClassNotFoundException
-
writeExternal
public void writeExternal(ObjectOutput out) throws IOException
Serializes a 3D point.- Throws:
IOException
-
-
Class chemaxon.struc.ExtraAtomProperties extends Object implements Serializable
- serialVersionUID:
- -1980229820290558380L
-
Serialized Fields
-
aliasstr
String aliasstr
-
attachParentSgroup
Sgroup attachParentSgroup
-
countFlags
int countFlags
-
electronProp
int electronProp
-
extrargbs
long extrargbs
-
extrastr
String extrastr
-
flags
int flags
-
linkNodeOuterBonds
int linkNodeOuterBonds
-
list
int[] list
-
order
int order
-
qprops
Map<String,Object> qprops
-
querystr
String querystr
-
repetitionBits
int repetitionBits
-
rgroupId
short rgroupId
-
temporaryObjects
Map<String,Object> temporaryObjects
-
valence1
short valence1
-
-
Class chemaxon.struc.MacroMolecule.BadMoleculeException extends Exception implements Serializable
- serialVersionUID:
- 9037472982065239933L
-
Class chemaxon.struc.MDocument extends Object implements Serializable
- serialVersionUID:
- 553557622036381832L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
Deserializes a document. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
ClassNotFoundException
IOException
-
writeObject
private void writeObject(ObjectOutputStream oos) throws IOException
Serializes a document. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
IOException
-
-
Class chemaxon.struc.MDocument.Prop extends MProp implements Serializable
-
Class chemaxon.struc.MDocumentUtil extends Object implements Serializable
- serialVersionUID:
- 12600100100892L
-
Serialized Fields
-
doc
MDocument doc
-
-
Class chemaxon.struc.MObject extends Object implements Serializable
- serialVersionUID:
- 2435517510938087080L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream ois) throws IOException
Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
IOException
-
writeObject
private void writeObject(ObjectOutputStream oos) throws IOException
Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
IOException
-
-
Class chemaxon.struc.MolAtom extends Object implements Serializable
- serialVersionUID:
- -3974070468228529467L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
Deserializes an atom. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
ClassNotFoundException
IOException
-
writeObject
private void writeObject(ObjectOutputStream oos) throws IOException
Serializes an atom. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
IOException
-
-
Serialized Fields
-
angle
double angle
-
isValenceCheckNeeded
boolean isValenceCheckNeeded
-
-
Class chemaxon.struc.MolBond extends Object implements Serializable
- serialVersionUID:
- 3656012871856958335L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
Deserializes a bond. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
ClassNotFoundException
IOException
-
writeObject
private void writeObject(ObjectOutputStream oos) throws IOException
Serializes a bond. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
IOException
-
-
Class chemaxon.struc.Molecule extends MoleculeGraph implements Serializable
- serialVersionUID:
- 7275486436840296305L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
Deserializes a molecule. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
ClassNotFoundException
IOException
-
writeObject
private void writeObject(ObjectOutputStream oos) throws IOException
Serializes a molecule. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
IOException
-
-
Serialized Fields
-
id
String id
-
-
Class chemaxon.struc.MoleculeGraph extends Object implements Serializable
- serialVersionUID:
- -2053719583816270190L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
Deserializes a molecule graph. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
ClassNotFoundException
IOException
-
writeObject
private void writeObject(ObjectOutputStream oos) throws IOException
Serializes a molecule graph. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
IOException
-
-
Serialized Fields
-
fragmentTracker
chemaxon.struc.MoleculeGraph.FragmentTracker fragmentTracker
-
hasBicycloStereo
boolean hasBicycloStereo
Molecule has bicyclo stereo information. Can be set byMolAtom.setBicycloStereo(BicycloStereoDescriptor[])
. -
valenceCheckOptions
ValenceCheckOptions valenceCheckOptions
Valence check options for the molecule.
-
-
Class chemaxon.struc.MPoint extends MObject implements Serializable
- serialVersionUID:
- -3067277054033050963L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
ClassNotFoundException
IOException
-
writeObject
private void writeObject(ObjectOutputStream oos) throws IOException
Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
IOException
-
-
Class chemaxon.struc.MProp extends Object implements Serializable
- serialVersionUID:
- -5699803671884637223L
-
Serialized Fields
-
coordDependent
boolean coordDependent
-
grinvCC
long grinvCC
-
-
Class chemaxon.struc.MPropertyContainer extends Object implements Serializable
- serialVersionUID:
- -2575268570438177098L
-
Serialization Methods
-
readExternal
public void readExternal(ObjectInput in) throws IOException, ClassNotFoundException
Restores the property container's state.- Throws:
IOException
- if I/O errors occurClassNotFoundException
- If the class for an object being restored cannot be found.
-
writeExternal
public void writeExternal(ObjectOutput out) throws IOException
Saves the property container's state.- Throws:
IOException
- Includes any I/O exceptions that may occur
-
-
Class chemaxon.struc.MSelectionDocument extends MDocument implements Serializable
- serialVersionUID:
- 2379294894434293119L
-
Class chemaxon.struc.PageSettings extends Object implements Serializable
- serialVersionUID:
- -7674028514396457694L
-
Serialization Methods
-
readExternal
public void readExternal(ObjectInput arg0) throws IOException, ClassNotFoundException
- Throws:
IOException
ClassNotFoundException
-
writeExternal
public void writeExternal(ObjectOutput arg0) throws IOException
- Throws:
IOException
-
-
Class chemaxon.struc.QueryBond extends MolBond implements Serializable
- serialVersionUID:
- -5025485107616067648L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
Deserializes a bond. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
ClassNotFoundException
IOException
-
writeObject
private void writeObject(ObjectOutputStream oos) throws IOException
Serializes a bond. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
IOException
-
-
Class chemaxon.struc.RgMolecule extends Molecule implements Serializable
- serialVersionUID:
- -939153732283455787L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
Deserializes an RgMolecule. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
ClassNotFoundException
IOException
-
writeObject
private void writeObject(ObjectOutputStream oos) throws IOException
Serializes an RgMolecule. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
IOException
-
-
Class chemaxon.struc.RxnMolecule extends Molecule implements Serializable
- serialVersionUID:
- -2863036104564183121L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
Deserializes a reaction. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
ClassNotFoundException
IOException
-
writeObject
private void writeObject(ObjectOutputStream oos) throws IOException
Serializes a reaction. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
IOException
-
-
Class chemaxon.struc.SelectionMolecule extends MoleculeGraph implements Serializable
- serialVersionUID:
- 234062772192819675L
-
Class chemaxon.struc.SelectionRgMolecule extends SelectionMolecule implements Serializable
-
Class chemaxon.struc.Sgroup extends Object implements Serializable
- serialVersionUID:
- -6209766549185582411L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
Deserializes an Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
ClassNotFoundException
IOException
-
writeObject
private void writeObject(ObjectOutputStream oos) throws IOException
Serializes an Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
IOException
-
-
Serialized Fields
-
Class chemaxon.struc.StaticMolecule extends Object implements Serializable
- serialVersionUID:
- -6974806277329432018L
-
Serialized Fields
-
arrayFlags
int arrayFlags
-
atomCount
int atomCount
-
atomLists
byte[][] atomLists
-
atomMap
short[] atomMap
-
atomStereo
byte[] atomStereo
-
atomType
short[] atomType
-
bondAtom1
short[] bondAtom1
-
bondAtom2
short[] bondAtom2
-
bondCount
int bondCount
-
bondFlags
int[] bondFlags
-
charge
byte[] charge
-
connectionTable
short[] connectionTable
-
explicitHcount
byte[] explicitHcount
-
extendedAtomType
int[] extendedAtomType
-
hybridization
byte[] hybridization
-
implicitHcount
byte[] implicitHcount
-
massno
byte[] massno
-
name
String name
-
neighborCount
byte[] neighborCount
-
nodeEdgeList
short[][] nodeEdgeList
-
queryProperty
byte[][] queryProperty
-
radical
byte[] radical
-
rgroupId
short[] rgroupId
-
ringPerception
boolean ringPerception
-
sgroupId
String[] sgroupId
-
valence
byte[] valence
-
-
-
Package chemaxon.struc.graphics
-
Class chemaxon.struc.graphics.MAnalysisBox extends MTextBox implements Serializable
- serialVersionUID:
- -7630363128405095856L
-
Class chemaxon.struc.graphics.MAssigner extends MPolyline implements Serializable
-
Serialized Fields
-
order
int order
-
-
-
Class chemaxon.struc.graphics.MAtomSetPoint extends MPoint implements Serializable
- serialVersionUID:
- 5932389976054063500L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
ClassNotFoundException
IOException
-
writeObject
private void writeObject(ObjectOutputStream oos) throws IOException
Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
IOException
-
-
Class chemaxon.struc.graphics.MBracket extends MRectangle implements Serializable
- serialVersionUID:
- -5775562691065011181L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream ois) throws IOException
Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
IOException
-
writeObject
private void writeObject(ObjectOutputStream oos) throws IOException
Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
IOException
-
-
Serialized Fields
-
bracketOrientation
int bracketOrientation
Bracket orientation, bracket can have two sides (T_DOUBLE) or just one (T_SINGLE). Possible values: T_SINGLE, T_DOUBLE -
bracketType
int bracketType
-
-
Class chemaxon.struc.graphics.MChemicalStruct extends MObject implements Serializable
- serialVersionUID:
- 7098670860634457343L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
ClassNotFoundException
IOException
-
writeObject
private void writeObject(ObjectOutputStream oos) throws IOException
Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
IOException
-
-
Class chemaxon.struc.graphics.MEFlow extends MPolyline implements Serializable
- serialVersionUID:
- 891769518407563834L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream ois) throws IOException
Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
IOException
-
writeObject
private void writeObject(ObjectOutputStream oos) throws IOException
Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
IOException
-
-
Serialized Fields
-
baseElectronContainerIndex
int baseElectronContainerIndex
-
baseElectronIndexInContainer
int baseElectronIndexInContainer
-
-
Class chemaxon.struc.graphics.MEFlowBasePoint extends MPoint implements Serializable
- serialVersionUID:
- 1053944912020926984L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
ClassNotFoundException
IOException
-
writeObject
private void writeObject(ObjectOutputStream oos) throws IOException
Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
IOException
-
-
Serialized Fields
-
electronIndex
int electronIndex
-
electronLabel
String electronLabel
-
-
Class chemaxon.struc.graphics.MElectron extends MAtomSetPoint implements Serializable
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream arg0) throws IOException
- Throws:
IOException
-
writeObject
private void writeObject(ObjectOutputStream arg0) throws IOException
- Throws:
IOException
-
-
Serialized Fields
-
difLoc
DPoint3 difLoc
-
isPointed
boolean isPointed
-
-
-
Class chemaxon.struc.graphics.MElectronContainer extends MObject implements Serializable
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream arg0) throws IOException, ClassNotFoundException
- Throws:
IOException
ClassNotFoundException
-
writeObject
private void writeObject(ObjectOutputStream arg0) throws IOException
- Throws:
IOException
-
-
Serialized Fields
-
electronOccupation
boolean[] electronOccupation
-
electrons
chemaxon.struc.graphics.MElectron[] electrons
-
radical
boolean radical
-
-
-
Class chemaxon.struc.graphics.MEllipse extends MRectangle implements Serializable
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
ClassNotFoundException
IOException
-
writeObject
private void writeObject(ObjectOutputStream oos) throws IOException
Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
IOException
-
-
-
Class chemaxon.struc.graphics.MFont extends Object implements Serializable
- serialVersionUID:
- -7769715209509613515L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
ClassNotFoundException
IOException
-
writeObject
private void writeObject(ObjectOutputStream oos) throws IOException
Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
IOException
-
-
Class chemaxon.struc.graphics.MMidPoint extends MPoint implements Serializable
- serialVersionUID:
- 5307361876930807239L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
ClassNotFoundException
IOException
-
writeObject
private void writeObject(ObjectOutputStream oos) throws IOException
Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
IOException
-
-
Class chemaxon.struc.graphics.MMidPoint.Sticky extends MMidPoint implements Serializable
- serialVersionUID:
- 3223068581543532992L
-
Class chemaxon.struc.graphics.MMoleculeMovie extends MObject implements Serializable
- serialVersionUID:
- 6476041884742537582L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream arg0) throws ClassNotFoundException, IOException
- Throws:
ClassNotFoundException
IOException
-
writeObject
private void writeObject(ObjectOutputStream arg0) throws IOException
- Throws:
IOException
-
-
Class chemaxon.struc.graphics.MNameTextBox extends MTextBox implements Serializable
- serialVersionUID:
- 6302424343157644471L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream arg0) throws ClassNotFoundException, IOException
- Throws:
ClassNotFoundException
IOException
-
writeObject
private void writeObject(ObjectOutputStream arg0) throws IOException
- Throws:
IOException
-
-
Class chemaxon.struc.graphics.MPolyline extends MObject implements Serializable
- serialVersionUID:
- 4958026600768388648L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
ClassNotFoundException
IOException
-
writeObject
private void writeObject(ObjectOutputStream oos) throws IOException
Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
IOException
-
-
Serialized Fields
-
internalPointAddCount
int internalPointAddCount
-
internalPointPos
int internalPointPos
-
-
Class chemaxon.struc.graphics.MRArrow extends MPolyline implements Serializable
- serialVersionUID:
- 8638690394107448092L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream arg0) throws ClassNotFoundException, IOException
- Throws:
ClassNotFoundException
IOException
-
writeObject
private void writeObject(ObjectOutputStream arg0) throws IOException
- Throws:
IOException
-
-
Class chemaxon.struc.graphics.MReactionSign extends MTextBox implements Serializable
- serialVersionUID:
- -7025949002857142442L
-
Class chemaxon.struc.graphics.MRectangle extends MPolyline implements Serializable
- serialVersionUID:
- 2948229815278089239L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
ClassNotFoundException
IOException
-
writeObject
private void writeObject(ObjectOutputStream oos) throws IOException
Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
IOException
-
-
Class chemaxon.struc.graphics.MRectanglePoint extends MPoint implements Serializable
- serialVersionUID:
- -3067277054033050963L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
ClassNotFoundException
IOException
-
writeObject
private void writeObject(ObjectOutputStream oos) throws IOException
Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
IOException
-
-
Class chemaxon.struc.graphics.MRectanglePoint.Sticky extends MRectanglePoint implements Serializable
- serialVersionUID:
- 3364078480306200948L
-
Class chemaxon.struc.graphics.MRoundedRectangle extends MRectangle implements Serializable
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
ClassNotFoundException
IOException
-
writeObject
private void writeObject(ObjectOutputStream oos) throws IOException
Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
IOException
-
-
Serialized Fields
-
arcHeight
double arcHeight
-
arcWidth
double arcWidth
-
-
-
Class chemaxon.struc.graphics.MTextAttributes extends Object implements Serializable
- serialVersionUID:
- 6561552003080652755L
-
Serialization Methods
-
readExternal
public void readExternal(ObjectInput in) throws IOException, ClassNotFoundException
- Throws:
IOException
ClassNotFoundException
-
writeExternal
public void writeExternal(ObjectOutput out) throws IOException
- Throws:
IOException
-
-
Class chemaxon.struc.graphics.MTextBox extends MRectangle implements Serializable
- serialVersionUID:
- -7272723232157967384L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
ClassNotFoundException
IOException
-
writeObject
private void writeObject(ObjectOutputStream oos) throws IOException
Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
IOException
-
-
Serialized Fields
-
actionMap
ActionMap actionMap
-
-
Class chemaxon.struc.graphics.MTextDocument extends Object implements Serializable
- serialVersionUID:
- 6305880304790247656L
-
Serialization Methods
-
readExternal
public void readExternal(ObjectInput in) throws IOException, ClassNotFoundException
Restores the document.- Throws:
IOException
- if I/O errors occurClassNotFoundException
- If the class for an object being restored cannot be found.
-
writeExternal
public void writeExternal(ObjectOutput out) throws IOException
Saves the document.- Throws:
IOException
- Includes any I/O exceptions that may occur
-
-
-
Package chemaxon.struc.prop
-
Class chemaxon.struc.prop.MBooleanProp extends MProp implements Serializable
- serialVersionUID:
- -5366978422380739811L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
Restores the property's state.- Throws:
IOException
- if I/O errors occurClassNotFoundException
- If the class for an object being restored cannot be found.
-
writeObject
private void writeObject(ObjectOutputStream out) throws IOException
Saves the property's state.- Throws:
IOException
- Includes any I/O exceptions that may occur
-
-
Class chemaxon.struc.prop.MByteArrayProp extends MProp implements Serializable
- serialVersionUID:
- -4046371792715339701L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream arg0) throws IOException, ClassNotFoundException
- Throws:
IOException
ClassNotFoundException
-
writeObject
private void writeObject(ObjectOutputStream arg0) throws IOException
- Throws:
IOException
-
-
Class chemaxon.struc.prop.MCollectionProp extends MProp implements Serializable
- serialVersionUID:
- -7479938988131387052L
-
Class chemaxon.struc.prop.MDoubleArrayProp extends MProp implements Serializable
- serialVersionUID:
- -5670039985685584647L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
Restores the property's state.- Throws:
IOException
- if I/O errors occurClassNotFoundException
- If the class for an object being restored cannot be found.
-
writeObject
private void writeObject(ObjectOutputStream out) throws IOException
Saves the property's state.- Throws:
IOException
- Includes any I/O exceptions that may occur
-
-
Class chemaxon.struc.prop.MDoubleProp extends MProp implements Serializable
- serialVersionUID:
- -1221776439131689653L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
Restores the property's state.- Throws:
IOException
- if I/O errors occurClassNotFoundException
- If the class for an object being restored cannot be found.
-
writeObject
private void writeObject(ObjectOutputStream out) throws IOException
Saves the property's state.- Throws:
IOException
- Includes any I/O exceptions that may occur
-
-
Class chemaxon.struc.prop.MFontProp extends MProp implements Serializable
- serialVersionUID:
- 2369581307328116455L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream arg0) throws IOException, ClassNotFoundException
- Throws:
IOException
ClassNotFoundException
-
writeObject
private void writeObject(ObjectOutputStream arg0) throws IOException
- Throws:
IOException
-
-
Class chemaxon.struc.prop.MHashProp extends MCollectionProp implements Serializable
- serialVersionUID:
- 5457649877894058447L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
Restores the property's state.- Throws:
IOException
- if I/O errors occurClassNotFoundException
- If the class for an object being restored cannot be found.
-
writeObject
private void writeObject(ObjectOutputStream out) throws IOException
Saves the property's state.- Throws:
IOException
- Includes any I/O exceptions that may occur
-
-
Class chemaxon.struc.prop.MHCoords3DProp extends MProp implements Serializable
- serialVersionUID:
- 6646271128663088908L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
Restores the property's state.- Throws:
IOException
- if I/O errors occurClassNotFoundException
- If the class for an object being restored cannot be found.
-
writeObject
private void writeObject(ObjectOutputStream out) throws IOException
Saves the property's state.- Throws:
IOException
- Includes any I/O exceptions that may occur
-
-
Class chemaxon.struc.prop.MIntegerArrayProp extends MProp implements Serializable
- serialVersionUID:
- 6651869314046996057L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
Restores the property's state.- Throws:
IOException
- if I/O errors occurClassNotFoundException
- If the class for an object being restored cannot be found.
-
writeObject
private void writeObject(ObjectOutputStream out) throws IOException
Saves the property's state.- Throws:
IOException
- Includes any I/O exceptions that may occur
-
-
Class chemaxon.struc.prop.MIntegerProp extends MProp implements Serializable
- serialVersionUID:
- -7179550727198941747L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
Restores the property's state.- Throws:
IOException
- if I/O errors occurClassNotFoundException
- If the class for an object being restored cannot be found.
-
writeObject
private void writeObject(ObjectOutputStream out) throws IOException
Saves the property's state.- Throws:
IOException
- Includes any I/O exceptions that may occur
-
-
Class chemaxon.struc.prop.MListProp extends MCollectionProp implements Serializable
- serialVersionUID:
- 5360371881677476960L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
Restores the property's state.- Throws:
IOException
- if I/O errors occurClassNotFoundException
- If the class for an object being restored cannot be found.
-
writeObject
private void writeObject(ObjectOutputStream out) throws IOException
Saves the property's state.- Throws:
IOException
- Includes any I/O exceptions that may occur
-
-
Class chemaxon.struc.prop.MMoleculeProp extends MProp implements Serializable
- serialVersionUID:
- -7687559780023024273L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
Restores the property's state.- Throws:
IOException
- if I/O errors occurClassNotFoundException
- If the class for an object being restored cannot be found.
-
writeObject
private void writeObject(ObjectOutputStream out) throws IOException
Saves the property's state.- Throws:
IOException
- Includes any I/O exceptions that may occur
-
-
Class chemaxon.struc.prop.MMoleculeStringProp extends MStringProp implements Serializable
- serialVersionUID:
- -1005074014113755196L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream arg0) throws IOException, ClassNotFoundException
- Throws:
IOException
ClassNotFoundException
-
writeObject
private void writeObject(ObjectOutputStream arg0) throws IOException
- Throws:
IOException
-
-
Serialized Fields
-
format
String format
-
-
Class chemaxon.struc.prop.MObjectProp extends MProp implements Serializable
- serialVersionUID:
- 4005646748655675692L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
Restores the property's state.- Throws:
IOException
- if I/O errors occurClassNotFoundException
- If the class for an object being restored cannot be found.
-
writeObject
private void writeObject(ObjectOutputStream out) throws IOException
Saves the property's state.- Throws:
IOException
- Includes any I/O exceptions that may occur
-
-
Class chemaxon.struc.prop.MStringProp extends MProp implements Serializable
- serialVersionUID:
- 1373831606368751112L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
Restores the property's state.- Throws:
IOException
- if I/O errors occurClassNotFoundException
- If the class for an object being restored cannot be found.
-
writeObject
private void writeObject(ObjectOutputStream out) throws IOException
Saves the property's state.- Throws:
IOException
- Includes any I/O exceptions that may occur
-
-
-
Package chemaxon.struc.sgroup
-
Class chemaxon.struc.sgroup.AminoAcidSgroup extends SuperatomSgroup implements Serializable
- serialVersionUID:
- -4078870750580716173L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream arg0) throws ClassNotFoundException, IOException
- Throws:
ClassNotFoundException
IOException
-
writeObject
private void writeObject(ObjectOutputStream arg0) throws IOException
- Throws:
IOException
-
-
Serialized Fields
-
Class chemaxon.struc.sgroup.AttachmentPoint extends Object implements Serializable
- serialVersionUID:
- -7484860308765339862L
-
Class chemaxon.struc.sgroup.DataSgroup extends Sgroup implements Serializable
- serialVersionUID:
- -3132191586564122343L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
Deserializes a data Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
ClassNotFoundException
IOException
-
writeObject
private void writeObject(ObjectOutputStream oos) throws IOException
Serializes a data Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
IOException
-
-
Serialized Fields
-
labelPosition
chemaxon.struc.sgroup.DataSgroup.AbstractPosition labelPosition
-
sb
StringBuffer sb
temporary variable for getLineOnScreen
-
-
Class chemaxon.struc.sgroup.LeavingGroupAtom extends MolAtom implements Serializable
- serialVersionUID:
- 8591241919498353308L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream arg0) throws ClassNotFoundException, IOException
Deprecated.- Throws:
ClassNotFoundException
IOException
-
writeObject
private void writeObject(ObjectOutputStream arg0) throws IOException
Deprecated.- Throws:
IOException
-
-
Serialized Fields
-
alternativeName
String alternativeName
Deprecated.
-
-
Class chemaxon.struc.sgroup.MulticenterSgroup extends Sgroup implements Serializable
- serialVersionUID:
- -7213879722783498112L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
Deserializes a Multicenter Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
ClassNotFoundException
IOException
-
writeObject
private void writeObject(ObjectOutputStream oos) throws IOException
Serializes a Multicenter Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
IOException
-
-
Class chemaxon.struc.sgroup.MultipleSgroup extends Sgroup implements Serializable
- serialVersionUID:
- -1146464131016252826L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
Deserializes a multiple Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
ClassNotFoundException
IOException
-
writeObject
private void writeObject(ObjectOutputStream oos) throws IOException
Serializes a multiple Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
IOException
-
-
Class chemaxon.struc.sgroup.NoFreeAttachmentPointException extends RuntimeException implements Serializable
- serialVersionUID:
- 2226630752133341633L
-
Serialized Fields
-
sga
SgroupAtom sga
-
-
Class chemaxon.struc.sgroup.RepeatingUnitSgroup extends Sgroup implements Serializable
- serialVersionUID:
- -3209611525734625009L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
Deserializes an SRU Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
ClassNotFoundException
IOException
-
writeObject
private void writeObject(ObjectOutputStream oos) throws IOException
Serializes an SRU Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
IOException
-
-
Class chemaxon.struc.sgroup.SgroupAtom extends MolAtom implements Serializable
- serialVersionUID:
- -3185634359981637075L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
Deserializes an Sgroup superatom. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
ClassNotFoundException
IOException
-
writeObject
private void writeObject(ObjectOutputStream oos) throws IOException
Serializes an Sgroup superatom. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
IOException
-
-
Serialized Fields
-
labelCenter
int labelCenter
-
-
Class chemaxon.struc.sgroup.SuperatomSgroup extends Sgroup implements Serializable
- serialVersionUID:
- 2968529752634209305L
-
Serialization Methods
-
readObject
private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
Deserializes a superatom Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
ClassNotFoundException
IOException
-
writeObject
private void writeObject(ObjectOutputStream oos) throws IOException
Serializes a superatom Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.- Throws:
IOException
-
-
Serialized Fields
-
apContainer
chemaxon.struc.sgroup.AttachmentPointContainer apContainer
Attachment Point container object
-
-
-
Package chemaxon.util
-
Class chemaxon.util.ArgumentException extends Exception implements Serializable
- serialVersionUID:
- -8949782741678573705L
-
Class chemaxon.util.CmdLine.CmdLineException extends RuntimeException implements Serializable
- serialVersionUID:
- -895875464082822299L
-
Class chemaxon.util.Heap.HeapException extends RuntimeException implements Serializable
-
Class chemaxon.util.SearchAttributes extends chemaxon.jep.util.SearchAttributes implements Serializable
-
Class chemaxon.util.SupplierException extends RuntimeException implements Serializable
-
-
Package com.chemaxon.calculations.gui
-
Package com.chemaxon.calculations.io
-
Class com.chemaxon.calculations.io.OrderedInputProcessingException extends IllegalArgumentException implements Serializable
-
Serialized Fields
-
inputIndex
int inputIndex
-
-
-
-
Package com.chemaxon.calculations.util
-
Class com.chemaxon.calculations.util.CmdlineContext.ExitWithNonZeroStatus extends RuntimeException implements Serializable
-
Class com.chemaxon.calculations.util.CmdlineContext.ExitWithZeroStatus extends RuntimeException implements Serializable
-
-
Package com.chemaxon.clustering.framework
-
Class com.chemaxon.clustering.framework.RemoveSidechainsMolwalk extends Object implements Serializable
-
Class com.chemaxon.clustering.framework.RemoveSidechainsSc extends Object implements Serializable
-
Serialized Fields
-
keepUnsaturatedConnections
boolean keepUnsaturatedConnections
-
-
-
Class com.chemaxon.clustering.framework.SimpleFrameworkAssociation extends Object implements Serializable
-
-
Package com.chemaxon.descriptors.alignment
-
Class com.chemaxon.descriptors.alignment.AbstractShapeComparator extends Object implements Serializable
-
Serialized Fields
-
generator
DescriptorGenerator<T extends ShapeDescriptor> generator
-
-
-
Class com.chemaxon.descriptors.alignment.AbstractShapeGenerator extends Object implements Serializable
-
Serialized Fields
-
parameters
P extends AbstractShapeGeneratorParameter parameters
-
-
-
Class com.chemaxon.descriptors.alignment.AbstractShapeGeneratorParameter extends Object implements Serializable
-
Serialized Fields
-
atomTyping
AtomTyping atomTyping
The setting for available shape coloring methods.
-
-
-
Class com.chemaxon.descriptors.alignment.BaseShapeComparatorParameter extends Object implements Serializable
-
Serialized Fields
-
flexibilityMode
AlignmentProperties.FlexibilityMode flexibilityMode
-
shapeFunction
ShapeFunction shapeFunction
-
tryCount
com.google.common.base.Optional<Integer> tryCount
-
-
-
Class com.chemaxon.descriptors.alignment.ShapeComparatorException extends RuntimeException implements Serializable
- serialVersionUID:
- 1L
-
Class com.chemaxon.descriptors.alignment.ShapeGeneratorException extends RuntimeException implements Serializable
- serialVersionUID:
- 1L
-
-
Package com.chemaxon.descriptors.common
-
Package com.chemaxon.descriptors.fingerprints.cfp
-
Class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters extends Object implements Serializable
- serialVersionUID:
- 0L
-
Serialized Fields
-
bitsPerPattern
int bitsPerPattern
Bits set for each pattern. -
bondCount
int bondCount
Max pattern length considered (bond count). -
length
int length
Fingerprint length (bit count). -
rings
boolean rings
Consider rings in fingerprint generation.
-
-
-
Package com.chemaxon.descriptors.fingerprints.ecfp
-
Class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters extends Object implements Serializable
- serialVersionUID:
- 0L
-
Serialized Fields
-
atomTypizer
EcfpAtomTypizers atomTypizer
Atom typizer to use. -
diameter
int diameter
Diameter parameter. -
identifierConfigurationXml
com.google.common.base.Optional<String> identifierConfigurationXml
Identifier configuration for custom XML mode. -
length
int length
Fingerprint length (bit count).
-
-
Class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpParameters extends Object implements Serializable
- serialVersionUID:
- 0L
-
Serialized Fields
-
params
EcfpParameters params
-
-
-
Package com.chemaxon.descriptors.fingerprints.maccs
-
Class com.chemaxon.descriptors.fingerprints.maccs.GenerateMaccsFp extends Object implements Serializable
-
Serialized Fields
-
bit1
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit1
-
bit100
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit100
-
bit101
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit101
-
bit102
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit102
-
bit104
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit104
-
bit105
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit105
-
bit106
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit106
-
bit107
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit107
-
bit108
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit108
-
bit109
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit109
-
bit11
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit11
-
bit110
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit110
-
bit111
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit111
-
bit112
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit112
-
bit113
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit113
-
bit114
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit114
-
bit115
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit115
-
bit116
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit116
-
bit117
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit117
-
bit118
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit118
-
bit119
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit119
-
bit120
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit120
-
bit121
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit121
-
bit122
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit122
-
bit123
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit123
-
bit124
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit124
-
bit126
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit126
-
bit127
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit127
-
bit128
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit128
-
bit129
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit129
-
bit13
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit13
-
bit131
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit131
-
bit132
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit132
-
bit133
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit133
-
bit135
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit135
-
bit136
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit136
-
bit138
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit138
-
bit139
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit139
-
bit14
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit14
-
bit140
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit140
-
bit141
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit141
-
bit142
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit142
-
bit144
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit144
-
bit145
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit145
-
bit147
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit147
-
bit148
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit148
-
bit149
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit149
-
bit15
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit15
-
bit150
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit150
-
bit151
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit151
-
bit152
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit152
-
bit154
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit154
-
bit155
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit155
-
bit156
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit156
-
bit157
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit157
-
bit158
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit158
-
bit16
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit16
-
bit162
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit162
-
bit163
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit163
-
bit165
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit165
-
bit17
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit17
-
bit19
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit19
-
bit2
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit2
-
bit21
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit21
-
bit22
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit22
-
bit23
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit23
-
bit24
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit24
-
bit25
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit25
-
bit26
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit26
-
bit28
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit28
-
bit30
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit30
-
bit31
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit31
-
bit32
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit32
-
bit33
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit33
-
bit34
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit34
-
bit36
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit36
-
bit37
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit37
-
bit38
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit38
-
bit39
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit39
-
bit40
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit40
-
bit41
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit41
-
bit43
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit43
-
bit44
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit44
-
bit45
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit45
-
bit47
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit47
-
bit48
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit48
-
bit49
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit49
-
bit50
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit50
-
bit51
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit51
-
bit52
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit52
-
bit53
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit53
-
bit54
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit54
-
bit55
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit55
-
bit56
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit56
-
bit57
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit57
-
bit58
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit58
-
bit59
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit59
-
bit60
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit60
-
bit61
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit61
-
bit62
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit62
-
bit63
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit63
-
bit64
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit64
-
bit65
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit65
-
bit66
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit66
-
bit67
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit67
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bit68
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit68
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bit69
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit69
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bit70
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit70
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bit71
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit71
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bit72
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit72
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bit73
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit73
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bit74
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit74
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bit75
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit75
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bit76
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit76
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bit77
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit77
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bit78
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit78
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bit79
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit79
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bit8
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit8
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bit80
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit80
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bit81
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit81
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bit82
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit82
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bit83
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit83
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bit84
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit84
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bit85
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit85
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bit86
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit86
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bit87
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit87
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bit89
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit89
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bit90
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit90
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bit91
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit91
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bit92
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit92
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bit93
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit93
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bit94
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit94
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bit95
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit95
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bit96
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit96
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bit97
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit97
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bit98
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit98
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bit99
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit99
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-
-
Class com.chemaxon.descriptors.fingerprints.maccs.GsSearch extends Object implements Serializable
- serialVersionUID:
- 0L
-
Class com.chemaxon.descriptors.fingerprints.maccs.MaccsParameters extends Object implements Serializable
-
Class com.chemaxon.descriptors.fingerprints.maccs.RingAtomBs extends BitSet implements Serializable
- serialVersionUID:
- 0L
-
Class com.chemaxon.descriptors.fingerprints.maccs.RingBondBs extends BitSet implements Serializable
- serialVersionUID:
- 0L
-
-
Package com.chemaxon.descriptors.fingerprints.pf2d
-
Class com.chemaxon.descriptors.fingerprints.pf2d.PfComparatorImpl extends Object implements Serializable
-
Class com.chemaxon.descriptors.fingerprints.pf2d.PfParameters extends Object implements Serializable
- serialVersionUID:
- 0L
-
Serialized Fields
-
xmlConfig
com.google.common.base.Optional<String> xmlConfig
XML configuration string.
-
-
Class com.chemaxon.descriptors.fingerprints.pf2d.PharmacophoreFPImpl extends com.chemaxon.descriptors.common.realvector.FloatVectorDescriptorImpl implements Serializable
-
Serialized Fields
-
fingerprint
PharmacophoreFingerprint fingerprint
-
-
-
Class com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfParameters extends Object implements Serializable
- serialVersionUID:
- 0L
-
Serialized Fields
-
xmlConfig
com.google.common.base.Optional<String> xmlConfig
-
-
-
Package com.chemaxon.descriptors.metrics
-
Class com.chemaxon.descriptors.metrics.TverskyParameters extends Object implements Serializable
- serialVersionUID:
- 0L
-
Serialized Fields
-
coeffQuery
double coeffQuery
Coefficient for query only part. -
coeffTarget
double coeffTarget
Coefficient for target only part.
-
-
-
Package com.chemaxon.descriptors.vectors.binary
-
Class com.chemaxon.descriptors.vectors.binary.BvGeneratorImpl extends Object implements Serializable
- serialVersionUID:
- 0L
-
Serialized Fields
-
parameters
BvParameters parameters
-
-
Class com.chemaxon.descriptors.vectors.binary.BvParameters extends Object implements Serializable
- serialVersionUID:
- 0L
-
Serialized Fields
-
endianness
BinaryVectors.Endianness endianness
Endianness of long-int-byte-binary packing operations. -
length
int length
Fingerprint length (bit count). -
stringFormat
BvParameters.StringFormat stringFormat
String format to use.
-
-
-
Package com.chemaxon.descriptors.vectors.floats
-
Class com.chemaxon.descriptors.vectors.floats.FvGeneratorImpl extends Object implements Serializable
- serialVersionUID:
- 0L
-
Serialized Fields
-
parameters
FvParameters parameters
-
-
Class com.chemaxon.descriptors.vectors.floats.FvParameters extends Object implements Serializable
- serialVersionUID:
- 0L
-
Serialized Fields
-
length
int length
Fingerprint length (bit count). -
numericRepresentation
FvParameters.NumericRepresentation numericRepresentation
Numeric representation. -
scaledMax
double scaledMax
Maximum value for scaling. -
scaledMin
double scaledMin
Minimum value for scaling. -
sparseCompression
FvParameters.SparseCompression sparseCompression
Optimization for sparse vectors.
-
-
-
Package com.chemaxon.overlap.io
-
Class com.chemaxon.overlap.io.AllAbsentMasterMoleculeStorage extends Object implements Serializable
-
Serialized Fields
-
size
long size
-
-
-
Class com.chemaxon.overlap.io.ArraysBackedStorageTools.Builder extends Object implements Serializable
-
Serialized Fields
-
builtPages
List<C extends Serializable> builtPages
-
currentPage
List<E extends Serializable> currentPage
-
elementType
Class<E extends Serializable> elementType
-
getFromPage
com.chemaxon.descriptors.common.reflect.SerializableBiFunction<C extends Serializable,Integer,E extends Serializable> getFromPage
-
initialSkips
long initialSkips
-
listToPage
com.chemaxon.descriptors.common.reflect.SerializableFunction<List<E extends Serializable>,C extends Serializable> listToPage
-
pageSize
int pageSize
-
totalAbsents
long totalAbsents
-
totalSize
long totalSize
-
-
-
Class com.chemaxon.overlap.io.ArraysBackedStorageTools.Storage extends Object implements Serializable
-
Serialized Fields
-
elementType
Class<E extends Object> elementType
-
getFromPage
com.chemaxon.descriptors.common.reflect.SerializableBiFunction<C extends Object,Integer,E extends Object> getFromPage
-
initialSkips
long initialSkips
-
pages
List<C extends Object> pages
-
pageSize
int pageSize
-
totalAbsents
long totalAbsents
-
totalSize
long totalSize
-
-
-
Class com.chemaxon.overlap.io.CompactStringStorage extends Object implements Serializable
- serialVersionUID:
- 0L
-
Serialized Fields
-
absentCount
long absentCount
-
pagesize
int pagesize
-
size
long size
-
skips
long skips
-
starts
int[][] starts
-
storage
byte[][] storage
-
storedByteCount
long storedByteCount
-
-
Class com.chemaxon.overlap.io.CompactStringStorage.Metadata extends Object implements Serializable
-
Serialized Fields
-
absentCount
long absentCount
-
bytes
long bytes
-
lastPageSize
int lastPageSize
-
pageCount
int pageCount
-
pageSize
int pageSize
-
size
long size
-
skips
long skips
-
storeSizes
int[] storeSizes
-
storeStart
long storeStart
-
-
-
Class com.chemaxon.overlap.io.MasterMoleculeStorageImpl extends Object implements Serializable
- serialVersionUID:
- 0L
-
Serialized Fields
-
importOptsOrNull
String importOptsOrNull
-
sources
com.chemaxon.overlap.io.CompactStringStorage sources
-
-
-
Package com.chemaxon.search.transformation
-
Class com.chemaxon.search.transformation.TransformationException extends Exception implements Serializable
-