Serialized Form

Package chemaxon.calculations

Exception chemaxon.calculations.CalculationException

class CalculationException extends RuntimeException implements Serializable

serialVersionUID:

1L

Package chemaxon.calculations.clean

Class chemaxon.calculations.clean.AtomChangeEvent

class AtomChangeEvent extends EventObject implements Serializable

Package chemaxon.calculator

Exception chemaxon.calculator.CalculatorException

class CalculatorException extends Exception implements Serializable

serialVersionUID:

1L

Package chemaxon.clustering

Class chemaxon.clustering.ChemicalSpace

class ChemicalSpace extends Vector implements Serializable

Serialized Fields

dimensions

int dimensions

fpsize

int fpsize

weights

float[] weights

Exception chemaxon.clustering.ClusteringException

class ClusteringException extends Exception implements Serializable

Exception chemaxon.clustering.InvalidLicenseKeyException

class InvalidLicenseKeyException extends Exception implements Serializable

Package chemaxon.clustering.libmcs

Exception chemaxon.clustering.libmcs.Heap.HeapException

class HeapException extends RuntimeException implements Serializable

Package chemaxon.common.util

Class chemaxon.common.util.ByteVector

class ByteVector extends Object implements Serializable

serialVersionUID:

-1393815508326465236L

Serialized Fields

data

byte[] data

size

int size

Class chemaxon.common.util.DoubleVector

class DoubleVector extends Object implements Serializable

serialVersionUID:

-5138497375635267024L

Serialized Fields

data

double[] data

size

int size

Class chemaxon.common.util.FloatVector

class FloatVector extends Object implements Serializable

serialVersionUID:

-2327634131748729635L

Serialized Fields

data

float[] data

size

int size

Exception chemaxon.common.util.GeomCalc.GeomCalcException

class GeomCalcException extends RuntimeException implements Serializable

serialVersionUID:

-1705490613297709773L

Exception chemaxon.common.util.GeomCalc.Queue.Overflow

class Overflow extends Exception implements Serializable

serialVersionUID:

-6957894135268794743L

Exception chemaxon.common.util.GeomCalc.Queue.Underflow

class Underflow extends Exception implements Serializable

serialVersionUID:

-1972826041963082169L

Class chemaxon.common.util.IntMap

class IntMap extends HashMap<K extends Object,Integer> implements Serializable

serialVersionUID:

4318465509620546463L

Record Class chemaxon.common.util.IntPair

class IntPair extends Record implements Serializable

serialVersionUID:

1961353781713733629L

Serialized Fields

left

int left

Deprecated, for removal: This API element is subject to removal in a future version.

right

int right

Deprecated, for removal: This API element is subject to removal in a future version.

Class chemaxon.common.util.IntVector

class IntVector extends Object implements Serializable

serialVersionUID:

-9011852065319440166L

Serialized Fields

data

int[] data

size

int size

Exception chemaxon.common.util.LazyCalculationAlreadyFailedException

class LazyCalculationAlreadyFailedException extends RuntimeException implements Serializable

Class chemaxon.common.util.LongVector

class LongVector extends Object implements Serializable

serialVersionUID:

8437448887389765952L

Serialized Fields

data

long[] data

size

int size

Exception chemaxon.common.util.ResourceCleaner.ResourceClosingException

class ResourceClosingException extends RuntimeException implements Serializable

Exception chemaxon.common.util.ServiceNotFoundException

class ServiceNotFoundException extends RuntimeException implements Serializable

Serialized Fields

serviceType

Class<?> serviceType

Class chemaxon.common.util.ShortVector

class ShortVector extends Object implements Serializable

serialVersionUID:

8407562362886825374L

Serialized Fields

data

short[] data

size

int size

Package chemaxon.core

Exception chemaxon.core.SequenceBuildingException

class SequenceBuildingException extends RuntimeException implements Serializable

Serialized Fields

errorKey

String errorKey

Package chemaxon.core.calculations.valencecheck

Class chemaxon.core.calculations.valencecheck.ValenceCheckOptions

class ValenceCheckOptions extends Object implements Serializable

serialVersionUID:

568843891825099500L

Serialized Fields

localAromatic

boolean localAromatic

traditionalNallowed

boolean traditionalNallowed

Exception chemaxon.core.calculations.valencecheck.ValenceColumnException

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

Exception chemaxon.core.calculations.valencecheck.ValenceException

class ValenceException extends Exception implements Serializable

Exception chemaxon.core.calculations.valencecheck.ValenceTypeException

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

Package chemaxon.core.util

Class chemaxon.core.util.BondTable

class BondTable extends Object implements Serializable

serialVersionUID:

-8372436801118701137L

Serialized Fields

atomCount

int atomCount

The size of the matrix, the number of atoms in the molecule it represents.

Package chemaxon.descriptors

Exception chemaxon.descriptors.MDGeneratorException

class MDGeneratorException extends Exception implements Serializable

Exception chemaxon.descriptors.MDParametersException

class MDParametersException extends RuntimeException implements Serializable

Exception chemaxon.descriptors.MDReaderException

class MDReaderException extends Exception implements Serializable

Exception chemaxon.descriptors.MDWriterException

class MDWriterException extends Exception implements Serializable

Exception chemaxon.descriptors.SimilarityException

class SimilarityException extends Exception implements Serializable

Package chemaxon.formats

Exception chemaxon.formats.MolFormatException

class MolFormatException extends IOException implements Serializable

Serialized Fields

lineNumberInFile

int lineNumberInFile

lineNumberInRecord

int lineNumberInRecord

Package chemaxon.formats.documents.jchemoffice

Exception chemaxon.formats.documents.jchemoffice.BatchProcessingException

class BatchProcessingException extends IOException implements Serializable

serialVersionUID:

1L

Serialized Fields

_exceptions

List<Throwable> _exceptions

Exception chemaxon.formats.documents.jchemoffice.InvalidSizeScaleArgumentException

class InvalidSizeScaleArgumentException extends chemaxon.util.ArgumentException implements Serializable

serialVersionUID:

1L

Package chemaxon.jchem.db

Exception chemaxon.jchem.db.DatabaseSearchException

class DatabaseSearchException extends Exception implements Serializable

Exception chemaxon.jchem.db.MaxSearchFrequencyExceededException

class MaxSearchFrequencyExceededException extends DatabaseSearchException implements Serializable

Exception chemaxon.jchem.db.RecalculationException

class RecalculationException extends Exception implements Serializable

serialVersionUID:

-2767058042924323545L

Exception chemaxon.jchem.db.TransferException

class TransferException extends Exception implements Serializable

serialVersionUID:

-5241498055624956036L

Class chemaxon.jchem.db.UpdateHandler.RowData

class RowData extends Object implements Serializable

serialVersionUID:

-4040824446004135801L

Serialized Fields

chemTermColValues

Map<String,Object> chemTermColValues

descriptorData

byte[][] descriptorData

fingerprint

int[] fingerprint

flags

String flags

formula

String formula

hashCode

int hashCode

markushData

byte[] markushData

molecule

Molecule molecule

molName

String molName

molString

byte[] molString

molWeight

Double molWeight

noRingInfoInFP

boolean noRingInfoInFP

reactionMappingIncomplete

boolean reactionMappingIncomplete

screenDescriptor

byte[] screenDescriptor

smiles

String smiles

sortableFormula

String sortableFormula

tautomer

Molecule tautomer

tautomerFragmentHashCode

int[] tautomerFragmentHashCode

tautomerHashCode

int tautomerHashCode

Exception chemaxon.jchem.db.UpdateHandlerException

class UpdateHandlerException extends Exception implements Serializable

serialVersionUID:

-8755169336283449997L

Class chemaxon.jchem.db.UpdateHandlerMetaData

class UpdateHandlerMetaData extends Object implements Serializable

serialVersionUID:

-6512295793385774884L

Serialized Fields

chemTermColumns

String[] chemTermColumns

chemTermForColumn

Map<String,String> chemTermForColumn

collectionType

chemaxon.jchem.base.storage.StructureCollectionType collectionType

compressedStructureFieldSupported

boolean compressedStructureFieldSupported

descriptorSettings

Map<String,String> descriptorSettings

descriptorTypes

Map<String,String> descriptorTypes

duplicateFilteringOption

boolean duplicateFilteringOption

insertDescriptorNames

List<String> insertDescriptorNames

numberOfCombinedFPColumns

int numberOfCombinedFPColumns

numberOfEdges

int numberOfEdges

numberOfOnes

int numberOfOnes

numberOfStructuralFPColumns

int numberOfStructuralFPColumns

standardizerConfig

String standardizerConfig

structuralKeys

String structuralKeys

tableType

int tableType

tautomerDuplicateFilteringEnabled

boolean tautomerDuplicateFilteringEnabled

tautomerEqualityMode

chemaxon.sss.search.options.TautomerEqualityMode tautomerEqualityMode

updateDescriptorNames

List<String> updateDescriptorNames

Exception chemaxon.jchem.db.UpdateHandlerRowDataException

class UpdateHandlerRowDataException extends UpdateHandlerException implements Serializable

serialVersionUID:

-7274357064259684370L

Serialized Fields

rowData

UpdateHandler.RowData rowData

Class chemaxon.jchem.db.Updater.UpdateInfo

class UpdateInfo extends Object implements Serializable

serialVersionUID:

4160146885445230514L

Serialized Fields

additionalInformation

String[] additionalInformation

Additional information for the entities in same order, if needed.

Since:

JChem 6.0

entityList

String[] entityList

The names of entities (e.g. table names) to be updated, or null.

isOperationRequired

boolean isOperationRequired

Indicates whether the operation is required or not.

Since:

JChem 5.3

isProgressMonitoringSupported

boolean isProgressMonitoringSupported

Indicates whether update process supports progress monitoring.

Since:

JChem 5.1.2

isRegeneration

boolean isRegeneration

Deprecated.

since 5.1.2 use Updater.UpdateInfo.isProgressMonitoringSupported instead.

Indicates if the update process is the regeneration of all tables. Since this can be a lengthy process, progress monitoring may be needed. In this case the table names in Updater.UpdateInfo.entityList can be used directly for UpdateHandler.recalculateTable(chemaxon.util.ConnectionHandler, String, boolean, String, java.util.Map, Boolean, chemaxon.jchem.file.ProgressWriter)

isStructuralChange

boolean isStructuralChange

Indicates whether the operation is required or not.

Since:

JChem 5.8

message

String message

Massage describing what update is necessary and why.

processingMessage

String processingMessage

A message that can be displayed during the update, e.g. "Recalculating tables"

regenerationType

int regenerationType

Indicates the regeneration type.

Since:

JChem 5.2.4

Package chemaxon.jchem.db.cache

Class chemaxon.jchem.db.cache.CachePool

class CachePool extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

cacheHash

Hashtable<String,chemaxon.jchem.db.cache.JChemCache> cacheHash

cacheRemovalMethod

chemaxon.jchem.db.cache.CacheRemovalMethod cacheRemovalMethod

expirationTime

double expirationTime

maxCacheMemory

long maxCacheMemory

maxCacheMemoryCalculated

boolean maxCacheMemoryCalculated

maxCacheSizeMB

int maxCacheSizeMB

minFreeMemMB

int minFreeMemMB

Exception chemaxon.jchem.db.cache.CacheRegistrationException

class CacheRegistrationException extends RuntimeException implements Serializable

serialVersionUID:

1L

Serialized Fields

reason

chemaxon.jchem.db.cache.CacheRegistrationException.Reason reason

Package chemaxon.jep

Class chemaxon.jep.ChemFunction

class ChemFunction extends chemaxon.nfunk.jep.function.PostfixMathCommand implements Serializable

serialVersionUID:

-3446599636099344973L

Serialized Fields

cached

boolean cached

jep

ChemJEP jep

Class chemaxon.jep.ChemJEP

class ChemJEP extends chemaxon.nfunk.jep.JEP implements Serializable

Serialized Fields

context

ChemContext context

The evaluation context object.

Exception chemaxon.jep.ConditionException

class ConditionException extends Exception implements Serializable

Class chemaxon.jep.ContextFunction

class ContextFunction extends chemaxon.nfunk.jep.function.PostfixMathCommand implements Serializable

serialVersionUID:

6471101129584627604L

Serialized Fields

jep

ChemJEP jep

name

String name

Class chemaxon.jep.DissimilarityFunction

class DissimilarityFunction extends chemaxon.jep.ChemFunction implements Serializable

Serialized Fields

className

String className

descriptors

String[] descriptors

Class chemaxon.jep.Evaluator

class Evaluator extends Object implements Serializable

Serialized Fields

builtInConfig

chemaxon.jep.EvaluatorConfiguration builtInConfig

The configuration object containing default function/plugin declarations.

config

chemaxon.jep.EvaluatorConfiguration config

The configuration object.

externalConfig

chemaxon.jep.EvaluatorConfiguration externalConfig

The configuration object containing external function/plugin declarations.

functionalGroupDisplayMolTable

Hashtable<String,String> functionalGroupDisplayMolTable

|functional group name| -> |displayable molecule representation|

licenseEnvironment

String licenseEnvironment

servicesConfigurationPath

String servicesConfigurationPath

services configuration path

Since:

5.10

servicesFunctionTable

Hashtable<String,chemaxon.nfunk.jep.function.PostfixMathCommandI> servicesFunctionTable

Function table for services.

symtab

chemaxon.nfunk.jep.SymbolTable symtab

The base symbol table.

userConfig

chemaxon.jep.EvaluatorConfiguration userConfig

The configuration object containing user defined function/plugin declarations.

verbose

boolean verbose

True if verbose output.

Class chemaxon.jep.EvaluatorFunction

class EvaluatorFunction extends chemaxon.jep.ChemFunction implements Serializable

Serialized Fields

evaluator

Evaluator evaluator

Class chemaxon.jep.MatchFunction

class MatchFunction extends chemaxon.jep.ChemFunction implements Serializable

Serialized Fields

attributes

chemaxon.jep.util.SearchAttributes attributes

className

String className

dir

String dir

licenseEnvironment

String licenseEnvironment

standardizer

chemaxon.jep.Standardizer standardizer

subMatches

Hashtable<Object,chemaxon.jep.MatchFunction> subMatches

type

int type

Package chemaxon.jep.context

Class chemaxon.jep.context.AtomContext

class AtomContext extends MolContext implements Serializable

Serialized Fields

atom

int atom

The input atom index.

Class chemaxon.jep.context.MolContext

class MolContext extends Object implements Serializable

Serialized Fields

fingerprint

int[] fingerprint

Fingerprint of the input molecule.

init

boolean init

reactionContext

ReactionContext reactionContext

reaction wrapped in this context

supplier

Supplier<Molecule> supplier

The molecule supplier.

Class chemaxon.jep.context.ReactionContext

class ReactionContext extends Object implements Serializable

serialVersionUID:

-9162272287141708299L

Serialized Fields

agentAtomMapping

Map<Integer,MolAtom> agentAtomMapping

mapping of AtomMap -> Agent Atom

productAtomMapping

Map<Integer,MolAtom> productAtomMapping

mapping of AtomMap -> Product Atom

reactantAtomMapping

Map<Integer,MolAtom> reactantAtomMapping

mapping of AtomMap -> Reactant Atom

reaction

RxnMolecule reaction

reaction wrapped in this context

Class chemaxon.jep.context.SearchContext

class SearchContext extends MolContext implements Serializable

Serialized Fields

hit

int[] hit

map

int[] map

query

Molecule query

queryFingerprint

int[] queryFingerprint

target

Molecule target

targetFingerprint

int[] targetFingerprint

Package chemaxon.license

Exception chemaxon.license.LicenseException

class LicenseException extends RuntimeException implements Serializable

Serialized Fields

product

String product

Exception chemaxon.license.LicenseProcessingException

class LicenseProcessingException extends Exception implements Serializable

Package chemaxon.marvin

Class chemaxon.marvin.SketchApplication

class SketchApplication extends chemaxon.marvin.AbstractApplication implements Serializable

serialVersionUID:

1L

Serialized Fields

exitAction

Action exitAction

newWindowAction

Action newWindowAction

outSerName

String outSerName

sketchPane

MSketchPane sketchPane

Class chemaxon.marvin.ViewApplication

class ViewApplication extends chemaxon.marvin.AbstractApplication implements Serializable

serialVersionUID:

1L

Serialized Fields

colorKeys

List<String> colorKeys

exitAction

Action exitAction

hasInitalized

boolean hasInitalized

openAction

Action openAction

printAction

Action printAction

viewPane

MViewPane viewPane

Package chemaxon.marvin.alignment

Exception chemaxon.marvin.alignment.AlignmentException

class AlignmentException extends Exception implements Serializable

Exception chemaxon.marvin.alignment.NoConstraintException

class NoConstraintException extends chemaxon.marvin.alignment.AlignmentException implements Serializable

Exception chemaxon.marvin.alignment.OptimizationException

class OptimizationException extends RuntimeException implements Serializable

serialVersionUID:

1L

Class chemaxon.marvin.alignment.ShapeData

class ShapeData extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

atoms

chemaxon.marvin.alignment.ShapeData.Atom[] atoms

bonds

chemaxon.marvin.alignment.ShapeData.Bond[] bonds

coloringScheme

AlignmentProperties.ColoringScheme coloringScheme

maxs

double[] maxs

mins

double[] mins

shapeEnabledAtoms

BitSet shapeEnabledAtoms

Exception chemaxon.marvin.alignment.TooDissimilarException

class TooDissimilarException extends chemaxon.marvin.alignment.AlignmentException implements Serializable

Package chemaxon.marvin.beans

Class chemaxon.marvin.beans.MarvinPane

class MarvinPane extends JRootPane implements Serializable

serialVersionUID:

-9042549845769941129L

Serialized Fields

actionListener

chemaxon.marvin.beans.MarvinPane.MarvinActionListener actionListener

molPanel

chemaxon.marvin.common.swing.MolPanel molPanel

Underlying panel.

params

String params

Parameter string.

Class chemaxon.marvin.beans.MolRenderer

class MolRenderer extends JPanel implements Serializable

serialVersionUID:

7229361698115302929L

Serialized Fields

printer

MolPrinter printer

Class chemaxon.marvin.beans.MSketch

class MSketch extends Object implements Externalizable

serialVersionUID:

0L

Serialization Methods

readExternal

public void readExternal(ObjectInput in)
                  throws IOException,
ClassNotFoundException

Restores the sketcher's state.

Parameters:

in - the stream to read data from in order to restore the object

Throws:

IOException - if I/O errors occur

ClassNotFoundException - If the class for an object being restored cannot be found.

writeExternal

public void writeExternal(ObjectOutput out)
                   throws IOException

Saves the sketcher's state.

Parameters:

out - the stream to write the object to

Throws:

IOException - Includes any I/O exceptions that may occur

Class chemaxon.marvin.beans.MSketchPane

class MSketchPane extends MarvinPane implements Serializable

serialVersionUID:

602496692422927170L

Serialized Fields

commonActions

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

Class chemaxon.marvin.beans.MView

class MView extends Object implements Externalizable

serialVersionUID:

0L

Serialization Methods

readExternal

public void readExternal(ObjectInput in)
                  throws IOException,
ClassNotFoundException

Restores the viewer's state.

Parameters:

in - the stream to read data from in order to restore the object

Throws:

IOException - if I/O errors occur

ClassNotFoundException - If the class for an object being restored cannot be found.

writeExternal

public void writeExternal(ObjectOutput out)
                   throws IOException

Saves the viewer's state.

Parameters:

out - the stream to write the object to

Throws:

IOException - Includes any I/O exceptions that may occur

Class chemaxon.marvin.beans.MViewEditor

class MViewEditor extends AbstractCellEditor implements Serializable

serialVersionUID:

1549621132660875966L

Serialized Fields

editorComponent

MViewPane editorComponent

Class chemaxon.marvin.beans.MViewPane

class MViewPane extends MarvinPane implements Serializable

serialVersionUID:

-4430811090653077262L

Serialized Fields

delayedRepainter

chemaxon.marvin.beans.MViewPane.DelayedRepainter delayedRepainter

preferredSizeSet

boolean preferredSizeSet

tableSupport

TableSupport tableSupport

Class chemaxon.marvin.beans.MViewRenderer

class MViewRenderer extends MViewPane implements Serializable

serialVersionUID:

5566509759455312369L

Package chemaxon.marvin.calculations

Class chemaxon.marvin.calculations.BitPattern

class BitPattern extends BitSet implements Serializable

Package chemaxon.marvin.io

Class chemaxon.marvin.io.Encoding

class Encoding extends Object implements Externalizable

Serialization Methods

readExternal

public void readExternal(ObjectInput arg0)
                  throws IOException

Throws:

IOException

writeExternal

public void writeExternal(ObjectOutput arg0)
                   throws IOException

Throws:

IOException

Exception chemaxon.marvin.io.MolExportException

class MolExportException extends IOException implements Serializable

Serialized Fields

molIndex

int molIndex

Exception chemaxon.marvin.io.MRecordParseException

class MRecordParseException extends Exception implements Serializable

Serialized Fields

position

MRecordReader.Position position

Package chemaxon.marvin.modules.datatransfer

Class chemaxon.marvin.modules.datatransfer.CopyAsDialog

class CopyAsDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable

serialVersionUID:

-4564761584830399025L

Serialized Fields

bundle

ResourceBundle bundle

defaultFormat

String defaultFormat

formats

List<String> formats

prevSelectedIdx

int prevSelectedIdx

selectorList

JList<String> selectorList

Package chemaxon.marvin.plugin

Exception chemaxon.marvin.plugin.PluginException

class PluginException extends Exception implements Serializable

Exception chemaxon.marvin.plugin.PluginInputCheckerException

class PluginInputCheckerException extends PluginException implements Serializable

Package chemaxon.marvin.plugin.concurrent

Exception chemaxon.marvin.plugin.concurrent.PluginExecutionException

class PluginExecutionException extends ExecutionException implements Serializable

Serialized Fields

plugin

CalculatorPlugin plugin

Package chemaxon.marvin.plugin.gui

Class chemaxon.marvin.plugin.gui.CheckList

class CheckList extends JPanel implements Serializable

Serialized Fields

checkboxes

chemaxon.marvin.plugin.gui.CheckList.MCheckBox[] checkboxes

Class chemaxon.marvin.plugin.gui.OptionsPane

class OptionsPane extends JDialog implements Serializable

Serialized Fields

cancel

chemaxon.marvin.swing.ActionButton cancel

key

String key

ok

chemaxon.marvin.swing.ActionButton ok

okActionListener

ActionListener okActionListener

parameterPanel

ParameterPanelHandler parameterPanel

restoreDefaults

chemaxon.marvin.swing.ActionButton restoreDefaults

Class chemaxon.marvin.plugin.gui.ParameterPanel

class ParameterPanel extends JPanel implements Serializable

Serialized Fields

items

chemaxon.marvin.plugin.gui.ParameterItem[] items

Class chemaxon.marvin.plugin.gui.ResultView

class ResultView extends JDialog implements Serializable

serialVersionUID:

-5728800883025815500L

Serialized Fields

bottomComponent

JComponent bottomComponent

bottomTextArea

JTextArea bottomTextArea

chart

com.chemaxon.calculations.gui.MChart chart

chartPanel

JPanel chartPanel

copymi

JMenuItem copymi

detachmi

JMenuItem detachmi

imageFormat

String imageFormat

mpan

chemaxon.marvin.common.swing.MolPanel mpan

popup

JPopupMenu popup

popupcopymi

JMenuItem popupcopymi

resetmi

JMenuItem resetmi

topComponent

JComponent topComponent

topTextArea

JTextArea topTextArea

viewMenu

JMenu viewMenu

viewMol

Molecule viewMol

viewMols

Molecule[] viewMols

viewPanel

chemaxon.marvin.view.swing.ViewPanel viewPanel

viewText

String viewText

viewTexts

String[] viewTexts

Package chemaxon.marvin.services

Exception chemaxon.marvin.services.ServiceException

class ServiceException extends Exception implements Serializable

serialVersionUID:

328496720368460819L

Package chemaxon.marvin.sketch

Class chemaxon.marvin.sketch.History

class History extends Object implements Serializable

Serialized Fields

autoHydrogenizeHist

int[] autoHydrogenizeHist

changeSupport

PropertyChangeSupport changeSupport

cornerHist

Point[] cornerHist

historyOverflow

boolean historyOverflow

molgToZoomHist

MoleculeGraph[][] molgToZoomHist

molHist

MDocument[] molHist

molHistCur

int molHistCur

molHistLen

int molHistLen

molHistMax

int molHistMax

rotateMatrHist

CTransform3D[] rotateMatrHist

scaleHist

double[] scaleHist

scrollBarHist

int[][] scrollBarHist

selectionToZoomHist

boolean[] selectionToZoomHist

Class chemaxon.marvin.sketch.MolEditor

class MolEditor extends Object implements Serializable

serialVersionUID:

2463379690025911142L

Serialization Methods

readObject

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

class EventQueue extends Vector<Object> implements Serializable

Class chemaxon.marvin.space.GraphicScene

class GraphicScene extends JPanel implements Serializable

Serialized Fields

_glListsToDelete

ArrayList<Integer> _glListsToDelete

activeCell

int activeCell

index of the active cell: cells are numbered line-by-line

antialias

boolean antialias

backgroundColor

float[] backgroundColor

we use java.awt.Color in the following cases - when the color does not change too often - when the user can change the given color - when we don't have to give it to OGL2 too often (like color of an atom, etc) These are e.g. : background color, constant component colors

backgroundColorChanged

boolean backgroundColorChanged

canvas

Component canvas

cellCount

int cellCount

number of cells (there might be fewer cells than cells.length())

cells

GraphicCell[] cells

components per cells, line-by-line 0 is the top-left corner

columnCount

int columnCount

layout of the graphic view: number of cells per column

defaultDrawProperties

Map<Object,Object> defaultDrawProperties

eventHandler

chemaxon.marvin.space.MSpaceEventHandler eventHandler

gl

javax.media.opengl.GL2 gl

glAutoDrawable

javax.media.opengl.GLAutoDrawable glAutoDrawable

globalDrawProperties

Properties globalDrawProperties

glu

javax.media.opengl.glu.GLU glu

height

int height

physical height of the entire scene (in pixels)

initialized

boolean initialized

motionmode

int motionmode

standing or moving mode

needsRefresh

int needsRefresh

Indicates with internal index which cell needs redraw. -1 means none, cellCount means all cells.

needsReset

int needsReset

progressBar

chemaxon.marvin.space.gui.JMSpaceProgressBar progressBar

renderTargets

chemaxon.marvin.space.gl.shader.RenderTargets renderTargets

rowCount

int rowCount

layout of the graphic view: number of cells per row

rx

double rx

rotation around x-y-z axises

ry

double ry

rotation around x-y-z axises

rz

double rz

rotation around x-y-z axises

smoothBackground

boolean smoothBackground

synchronousMode

boolean synchronousMode

transparentBackground

int transparentBackground

userSettings

UserSettings userSettings

verboseLevel

int verboseLevel

width

int width

physical width of the entire scene (in pixels)

Package chemaxon.marvin.uif.dialog

Class chemaxon.marvin.uif.dialog.CategoriesDialog

class CategoriesDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable

Serialized Fields

bundle

ResourceBundle bundle

model

chemaxon.marvin.uif.dialog.model.CategoriesModel model

Class chemaxon.marvin.uif.dialog.ConfigurationDialog

class ConfigurationDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable

Serialized Fields

module

chemaxon.marvin.uif.module.GUIModule module

Class chemaxon.marvin.uif.dialog.CustomizeDialog

class CustomizeDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable

Serialized Fields

bundle

ResourceBundle bundle

guiRegistryClone

chemaxon.marvin.uif.model.GUIRegistry guiRegistryClone

model

chemaxon.marvin.uif.dialog.model.CustomizeGUIModel model

moduleConf

chemaxon.marvin.uif.module.ModuleConfiguration moduleConf

Class chemaxon.marvin.uif.dialog.LicenseDialog

class LicenseDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable

Class chemaxon.marvin.uif.dialog.MenuDialog

class MenuDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable

Serialized Fields

bundle

ResourceBundle bundle

model

chemaxon.marvin.uif.dialog.model.MenuManagerModel model

Class chemaxon.marvin.uif.dialog.MenuMoveDialog

class MenuMoveDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable

Serialized Fields

bundle

ResourceBundle bundle

model

chemaxon.marvin.uif.dialog.model.ItemGroupModel model

Class chemaxon.marvin.uif.dialog.PopupDialog

class PopupDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable

Serialized Fields

bundle

ResourceBundle bundle

model

chemaxon.marvin.uif.dialog.model.PopupManagerModel model

Class chemaxon.marvin.uif.dialog.ShortcutEditorDialog

class ShortcutEditorDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable

Serialized Fields

bundle

ResourceBundle bundle

model

chemaxon.marvin.uif.dialog.model.ShortcutModel model

Class chemaxon.marvin.uif.dialog.ToolBarDialog

class ToolBarDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable

Serialized Fields

bundle

ResourceBundle bundle

model

chemaxon.marvin.uif.dialog.model.ToolBarManagerModel model

Package chemaxon.marvin.util

Exception chemaxon.marvin.util.CancelPrintException

class CancelPrintException extends Exception implements Serializable

serialVersionUID:

7380116746554005158L

Class chemaxon.marvin.util.MarvinModule

class MarvinModule extends Object implements Serializable

serialVersionUID:

2763330874643316763L

Class chemaxon.marvin.util.MarvinOLEFrame

class MarvinOLEFrame extends JFrame implements Serializable

serialVersionUID:

7801720334170069726L

Serialized Fields

sp

Semaphore sp

Class chemaxon.marvin.util.MarvinOLEPanel

class MarvinOLEPanel extends JPanel implements Serializable

serialVersionUID:

-6975415959061110410L

Serialized Fields

emfExportOptions

String emfExportOptions

importExceptionCaught

boolean importExceptionCaught

msketch

MSketchPane msketch

retainGUIPropertiesOnPanel

boolean retainGUIPropertiesOnPanel

semaphore

Semaphore semaphore

sketchPanel

chemaxon.marvin.sketch.swing.SketchPanel sketchPanel

structureGUIProperties

MPropertyContainer structureGUIProperties

Class chemaxon.marvin.util.SwingUtil

class SwingUtil extends Object implements Serializable

serialVersionUID:

-1600625160321014724L

Package chemaxon.marvin.util.codeassist

Class chemaxon.marvin.util.codeassist.ChemTermDocument

class ChemTermDocument extends DefaultStyledDocument implements Serializable

serialVersionUID:

-5894946790409031807L

Serialized Fields

comment

MutableAttributeSet comment

constant

MutableAttributeSet constant

constants

Map<String,AttributeSet> constants

currentElementIndex

int currentElementIndex

doc

DefaultStyledDocument doc

fontName

String fontName

fontSize

int fontSize

function

MutableAttributeSet function

functions

Map<String,AttributeSet> functions

HIGHLIGHT_TIMER

Timer HIGHLIGHT_TIMER

keyword

MutableAttributeSet keyword

keywords

Map<String,AttributeSet> keywords

lastPrefixState

boolean lastPrefixState

multiLineComment

boolean multiLineComment

normal

MutableAttributeSet normal

parenLength

int parenLength

parenOffset

int parenOffset

parenthesis

MutableAttributeSet parenthesis

prefix

String prefix

quote

MutableAttributeSet quote

rootElement

Element rootElement

Class chemaxon.marvin.util.codeassist.CompletionItemCellRenderer

class CompletionItemCellRenderer extends DefaultListCellRenderer implements Serializable

serialVersionUID:

6746125418422903808L

Class chemaxon.marvin.util.codeassist.MacroManagerPanel

class MacroManagerPanel extends JPanel implements Serializable

serialVersionUID:

-4703035835623320688L

Serialized Fields

ACCEPT_ACTION

Action ACCEPT_ACTION

acceptButton

JButton acceptButton

acceptEditButton

JButton acceptEditButton

addButton

JButton addButton

CANCEL_ACTION

Action CANCEL_ACTION

cancelButton

JButton cancelButton

cancelEditButton

JButton cancelEditButton

deleteButton

JButton deleteButton

descPane

JTextPane descPane

descScrollPane

JScrollPane descScrollPane

editButton

JButton editButton

editedItem

int editedItem

editPanel

JPanel editPanel

helper

chemaxon.marvin.util.codeassist.CodeAssistMacrosHelper helper

layout

CardLayout layout

listPanel

JPanel listPanel

macroList

JList macroList

macroListScroll

JScrollPane macroListScroll

macroPane

JTextPane macroPane

macroScrollPane

JScrollPane macroScrollPane

nameField

JTextField nameField

Package chemaxon.marvin.view

Exception chemaxon.marvin.view.MDocStorage.CancellationException

class CancellationException extends Exception implements Serializable

Exception chemaxon.marvin.view.MDocStorage.RecordUnavailableException

class RecordUnavailableException extends Exception implements Serializable

Serialized Fields

recordIndex

int recordIndex

Package chemaxon.marvin.view.swing

Class chemaxon.marvin.view.swing.TwoLists

class TwoLists extends JPanel implements Serializable

Serialized Fields

addAllButton

JButton addAllButton

addButton

JButton addButton

allSelected

boolean allSelected

list1

JList list1

list2

JList list2

listData1

String[] listData1

listData2

String[] listData2

removeAllButton

JButton removeAllButton

removeButton

JButton removeButton

Class chemaxon.marvin.view.swing.ViewCanvas

class ViewCanvas extends chemaxon.marvin.common.swing.MolCanvas implements Serializable

serialVersionUID:

3979819797881974530L

Serialization Methods

writeObject

private void writeObject(ObjectOutputStream arg0)
                  throws IOException

Throws:

IOException

Serialized Fields

cellIndex

int cellIndex

document

MDocument document

error

boolean error

highlightedAtom

int highlightedAtom

inZoomWindow

boolean inZoomWindow

markedAtom

int markedAtom

moleculeBackground

Color moleculeBackground

moleculeCenter

DPoint3 moleculeCenter

nextV

Vector<Object[]> nextV

painter

chemaxon.marvin.paint.internal.MolPainter painter

preferredSize1

Dimension preferredSize1

rescaleNeeded

boolean rescaleNeeded

rsize

Dimension rsize

viewFrame

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

viewPanel

chemaxon.marvin.view.swing.ViewPanel viewPanel

windowAction

chemaxon.marvin.swing.MAction windowAction

winScale

double winScale

Class chemaxon.marvin.view.swing.ViewHandler

class ViewHandler extends Object implements Serializable

Serialized Fields

cellFiller

chemaxon.marvin.view.swing.CellFiller cellFiller

debug

boolean debug

visibleDocs

chemaxon.marvin.view.swing.VisibleDocuments visibleDocs

Class chemaxon.marvin.view.swing.ViewPanel

class ViewPanel extends chemaxon.marvin.common.swing.MolPanel implements Serializable

serialVersionUID:

802342314015862847L

Serialization Methods

readObject

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

class WholeNumberField extends JTextField implements Serializable

Serialized Fields

integerFormatter

NumberFormat integerFormatter

options

int options

toolkit

Toolkit toolkit

Class chemaxon.marvin.view.swing.WholeNumberField.WholeNumberDocument

class WholeNumberDocument extends PlainDocument implements Serializable

Package chemaxon.naming

Exception chemaxon.naming.NameFormatException

class NameFormatException extends MolFormatException implements Serializable

Serialized Fields

prefix

String prefix

Exception chemaxon.naming.NameFormatException.FilteredCase

class FilteredCase extends NameFormatException implements Serializable

Exception chemaxon.naming.NamePrefixException

class NamePrefixException extends NameFormatException implements Serializable

Serialized Fields

token

String token

Package chemaxon.naming.document

Exception chemaxon.naming.document.D2SOptionsParser.UnknownOptionException

class UnknownOptionException extends Exception implements Serializable

Class chemaxon.naming.document.D2SPdfParser

class D2SPdfParser extends org.apache.tika.parser.pdf.ExtendablePdfParser implements Serializable

Class chemaxon.naming.document.D2STextParser

class D2STextParser extends Object implements Serializable

Exception chemaxon.naming.document.EncryptedDocumentException

class EncryptedDocumentException extends IOException implements Serializable

Class chemaxon.naming.document.OsrParser

class OsrParser extends org.apache.tika.parser.AbstractParser implements Serializable

Class chemaxon.naming.document.SafeOfficeParser

class SafeOfficeParser extends org.apache.tika.parser.microsoft.OfficeParser implements Serializable

Exception chemaxon.naming.document.TimeoutException

class TimeoutException extends IOException implements Serializable

Serialized Fields

timeoutMS

long timeoutMS

Class chemaxon.naming.document.TrivialXmlParser

class TrivialXmlParser extends org.apache.tika.parser.AbstractParser implements Serializable

Package chemaxon.naming.document.annotate

Exception chemaxon.naming.document.annotate.AnnotationException

class AnnotationException extends IOException implements Serializable

Package chemaxon.reaction

Class chemaxon.reaction.PatternProperty

class PatternProperty extends Object implements Serializable

serialVersionUID:

-3617253669859174882L

Serialized Fields

representation

String representation

Exception chemaxon.reaction.ReactionException

class ReactionException extends Exception implements Serializable

serialVersionUID:

1L

Package chemaxon.sss.search

Class chemaxon.sss.search.JChemSearchOptions

class JChemSearchOptions extends SearchOptions implements Serializable

serialVersionUID:

-6025435983286725061L

Serialized Fields

absoluteStereo

int absoluteStereo

cacheRegistrationNeeded

boolean cacheRegistrationNeeded

Can be set to false in case of readonly databases and jcsearch. Only for internal use!

descriptorConfig

String descriptorConfig

configuration for descriptor dissim. calculations

descriptorName

String descriptorName

the identifier of stored descriptor used for dissim. calculations, null means pure fingerprint similarity is performed

dissimilarityMetric

String dissimilarityMetric

Dissimilarity metric name, or null for default.

dissimilarityMetricParameters

String dissimilarityMetricParameters

Dissimilarity metric parameters.

dissimilarityThreshold

float dissimilarityThreshold

dissimilarityThresholdExcluded

boolean dissimilarityThresholdExcluded

filterQuery

String filterQuery

formulaSearchQuery

String formulaSearchQuery

Query of the formula search.

formulaSearchType

int formulaSearchType

Type of the formula search. See: chemaxon.sss.formula.FormulaSearch

haltOnError

HaltOnErrorOption haltOnError

Error handling of the search.

See Also:

• HaltOnErrorOption

markushScreeningOptions

Set<chemaxon.sss.search.options.MarkushScreeningType> markushScreeningOptions

Set containing all enabled Markush screen methods

matchCountOptions

MatchCountOptions matchCountOptions

maxResultCount

int maxResultCount

optimizeQueries

boolean optimizeQueries

Shows whether the query should be enumerated to improve search

returnsNonHits

boolean returnsNonHits

totalSearchTimeoutLimitMilliseconds

int totalSearchTimeoutLimitMilliseconds

The search on a database timeouts reaching this number of milliseconds.

Class chemaxon.sss.search.MarkushFeature

class MarkushFeature extends Object implements Serializable

serialVersionUID:

8770437891053649928L

Serialized Fields

data

int[] data

Reference data to expanded object. Different for each type:

• MarkushFeature.RGROUP: {R-atom union index, R-group definition index}
• MarkushFeature.LINKNODE: {link atom union index}
• MarkushFeature.REPUNIT: {RepeatingUnitSgroup sgroup index in markush}
• MarkushFeature.ATOMLIST: {list atom union index}
• MarkushFeature.BONDLIST: {list bond union bond index}
• MarkushFeature.MULTIBOND: {union bond index, MulticenterSgroup sgroup index in markush}

R-group definition index: the index returned by RgMolecule.findRgroupIndex(int).

hashCode

int hashCode

type

int type

Expansion type.

Class chemaxon.sss.search.MatchCountOptions

class MatchCountOptions extends Object implements Serializable

serialVersionUID:

6422092438307828424L

Serialized Fields

matchCountHighLimit

int matchCountHighLimit

matchCountHighLimitInclusive

boolean matchCountHighLimitInclusive

matchCounthitLimit

int matchCounthitLimit

matchCountIncludesZero

boolean matchCountIncludesZero

matchCountLowLimit

int matchCountLowLimit

matchCountLowLimitInclusive

boolean matchCountLowLimitInclusive

matchCountRelation

String matchCountRelation

mode

int mode

Class chemaxon.sss.search.MolSearchOptions

class MolSearchOptions extends SearchOptions implements Serializable

serialVersionUID:

-6364233804214700841L

Serialized Fields

hitIncludesRNodes

boolean hitIncludesRNodes

If true, the result hit will contain R-nodes with dummy indexes

hitIndexType

int hitIndexType

In case of Markush search specifies the representation of the Markush structure on which the hit indexes are retrieved. (default MARKUSH_HIT_ORIGINAL)

ignoreChiralityForAtoms

chemaxon.common.util.IntVector ignoreChiralityForAtoms

Contains query atom numbers which should be ignored at the chirality check in case of exact stereo searching. It has a package visibility.

markushEnabled

boolean markushEnabled

Decides whether targets with Markush features should be treated as Markush libraries (true) or just "strange" molecules (false) (default value: false).

queryAbsoluteStereo

boolean queryAbsoluteStereo

If true, chiral centers in the query molecules are regarded as absolute stereo, ignoring the chiral flag. If the molecule contains any enhanced stereo labels, this flag has no effect.

recursiveSMARTSMode

boolean recursiveSMARTSMode

true: at findAll searches only hits are retrieved where the first atom differs as well.

switchOffAllProtectsForTDF

boolean switchOffAllProtectsForTDF

If true, all protect features are switched of during generic tautomer creation

targetAbsoluteStereo

boolean targetAbsoluteStereo

If true, chiral centers in the target molecules are regarded as absolute stereo, ignoring the chiral flag. If the molecule contains any enhanced stereo labels, this flag has no effect.

tautomerEqualityMode

chemaxon.sss.search.options.TautomerEqualityMode tautomerEqualityMode

The way tautomer duplication is checked. Used only at duplicate, full and full fragment searches. Internal use only.

Exception chemaxon.sss.search.SearchException

class SearchException extends Exception implements Serializable

serialVersionUID:

1698586463587833734L

Class chemaxon.sss.search.SearchOptions

class SearchOptions extends Object implements Serializable

serialVersionUID:

-6845044337680993338L

Serialized Fields

attachedDataMatch

int attachedDataMatch

Specifies attached data match type Default is SearchConstants.ATTACHED_DATA_MATCH_IGNORE

attachedDataPrefixes

String attachedDataPrefixes

Data sgroup name prefixes that will be used for comparison When null, all data sgroups will be used.

bridgingRAllowed

boolean bridgingRAllowed

True: different undefined R-atoms can match the same group of atoms. Default value: false.

changedUserComparator

boolean changedUserComparator

true if user-defined comparators has changed

chargeMatching

int chargeMatching

Specifies the charge searching behaviour. Default is CHARGE_MATCHING_DEFAULT (charged query matches only charged target, noncharged query matches all)

checkSpHyb

boolean checkSpHyb

If we need to check the sp-hybridization state of the atoms. If used together with vagueBond-4 (SearchConstants.VAGUE_BOND_LEVEL4) option then the bond types are ignored, but the sp hybridization state is still calculated considering the bond types. Benzene matches cyclohexene with double bonds outside (O=C1C(=O)C(=O)C(=O)C(=O)C(=O)1), both planar but different bonds.

Since:

5.1

chemTermsFilterOption

chemaxon.sss.search.options.ChemTermsFilterOption chemTermsFilterOption

completeHG

boolean completeHG

Specifies if only complete structures should match on target homology groups.

copolymerMatching

boolean copolymerMatching

True: Polymers in copolymers can only be matched by copolymers. (default: false)

dirty

boolean dirty

This flag is set to true whenever any of the options change. It can be used by Search objects to check whether options changed since the previous initialization. (They set the dirty flag to false during their own initialization.)

doubleBondStereoMatchingMode

int doubleBondStereoMatchingMode

Defines the double bond stereo matching mode. Default is DBS_MARKED.

Since:

JChem 2.2

See Also:

• SearchOptions.setDoubleBondStereoMatchingMode(int)

endGroupMatching

boolean endGroupMatching

True: polymer endgroups must match (default: false)

exactBondMatching

boolean exactBondMatching

true, if query bonds match only the same query bonds

exactQueryAtomMatching

boolean exactQueryAtomMatching

If true, query information (eg atom list, any atom, number of hydrogens, aromaticity, etc) in atoms will not be evaluated, but rather exact matching of these information is required. It is useful for searching in query databases. Default is false.

Since:

JChem 2.2

exactSpecialAtomMatching

String exactSpecialAtomMatching

exhaustiveModeLimit

int exhaustiveModeLimit

Upon reaching this number of steps, the search switches to exhaustive mode from fast mode.

hCountMatching

int hCountMatching

Defines the interpretation of H count in the query. Default is HCOUNT_MATCHING_AUTO.

hitOrdering

int hitOrdering

Specifies hit ordering, currently used in ordering undefined R-atom group matchings Default is SearchConstants.HIT_ORDERING_NONE.

homologyBroadTranslation

HomologyTranslationOption homologyBroadTranslation

If pseudo atoms with homology names are present in the target, they should be handled as homology group not as pseudo atoms. false - handle as pseudo atoms.

homologyNarrowTranslation

HomologyTranslationOption homologyNarrowTranslation

If pseudo atoms with homology names are present in the query, they should be handled as homology group not as pseudo atoms. false - handle as pseudo atoms.

ignoreAxialStereo

boolean ignoreAxialStereo

See Also:

• SearchOptions.setIgnoreAxialStereo(boolean)

ignoreCumuleneCisTransStereo

boolean ignoreCumuleneCisTransStereo

See Also:

• SearchOptions.setIgnoreCumuleneOrRingCisTransStereo(boolean)

ignoreDoubleBondStereo

boolean ignoreDoubleBondStereo

See Also:

• SearchOptions.setIgnoreDoubleBondStereo(boolean)

ignoreSynAntiStereo

boolean ignoreSynAntiStereo

See Also:

• SearchOptions.setIgnoreSynAntiStereo(boolean)

ignoreTetrahedralStereo

boolean ignoreTetrahedralStereo

See Also:

• SearchOptions.setIgnoreTetrahedralStereo(boolean)

implicitHMatching

int implicitHMatching

Specifies match between explicit and implicit hydrogens. Default is IMPLICIT_H_MATCHING_DEFAULT (matching depends on the circumstances of search)

isotopeMatching

int isotopeMatching

Specifies the isotope searching behaviour. Default is ISOTOPE_MATCHING_DEFAULT (isotope query matches only isotope target, nonisotope query matches all)

keepQueryOrder

boolean keepQueryOrder

True: instructs search to rearrange query atoms for better search performance.

markushAromHandling

MarkushAromaticityHandlingOption markushAromHandling

Specifies handling Markush aromatization information (ambiguous aromatic rings) during Markush search. Currently, the default is MarkushAromaticityHandlingOption.ALL_MATCH_AMBIG: consider Markush aromatization during Markush search, but do not check the hit afterwards.

mixSgroupMatching

boolean mixSgroupMatching

True: consider COM, MIX and FOR sgroups during search (default value: true).

orderSensitiveSearch

boolean orderSensitiveSearch

Specifies whether the same set of target atoms found in a different order should be considered as a different hit.

phaseShift

boolean phaseShift

True: the phase-shifted polymers are matching on each other. (default: true)

polymerMatching

boolean polymerMatching

True: consider polymer sgroups during search (default value: true).

radicalMatching

int radicalMatching

Specifies the radical searching behaviour. Default is RADICAL_MATCHING_DEFAULT (radical query matches only radical target, nonradical query matches all)

reactionUnpairedMapMatching

boolean reactionUnpairedMapMatching

True: in reaction search unpaired (orphan and widow) atom maps can match any atom map (default value: true).

rLigandEqualityCheck

boolean rLigandEqualityCheck

True: undefined R-atoms with the same R-group ID should match the same structure. Default value: true.

searchType

int searchType

Search type: global mode of search.

ssrOption

SetOfSmallestRingsOption ssrOption

Which set of smallest rings to use for property calculations.

stereoModel

int stereoModel

Specifies the used stereo model.

stereoSearchType

int stereoSearchType

The way stereo information is considered in searching. Default is SearchConstants.STEREO_SPECIFIC.

See Also:

• SearchOptions.setStereoSearchType(int)

targetHomologyMatchingMode

TargetHomologyMatchingMode targetHomologyMatchingMode

tautomerSearch

boolean tautomerSearch

True: tautomer searching is enabled (default value: false).

tautomerSearchOption

int tautomerSearchOption

Specifies the tautomer searching behavior. Default: non-tautomer search, except: duplicate search in tautomer duplicate table

tautomerSearchOptionLeftDefault

boolean tautomerSearchOptionLeftDefault

Shows that tautomerSearch value has not been set.

throwExceptionOnTimeout

boolean throwExceptionOnTimeout

If the search should throw exception upon timeout.

timeoutLimitMilliseconds

int timeoutLimitMilliseconds

The search on a single target timeouts reaching this number of milliseconds.

transformMonomer

boolean transformMonomer

True: monomers are transformed to structural repeating units. (default: true)

undefinedRAtom

int undefinedRAtom

Specifies match of undefined r-atom in query Default is SearchConstants.UNDEF_R_MATCHING_GROUP.

undefinedRAtomUserDefined

boolean undefinedRAtomUserDefined

True if undefinedRAtom option is user defined, false if automatically set by RGroupDecomposition depending on whether the original query has undefined R-atoms. Used in RGroupDecomposition only.

userComparators

ArrayList<MolComparator> userComparators

User defined MolComparators

vagueBondLevel

int vagueBondLevel

Option for less strict evaluation of query bonds (e.g. ambiguious aromaticity). Default value is SearchConstants.VAGUE_BOND_LEVEL_HALF

valenceMatching

boolean valenceMatching

True: valence is checked during search (default value: true).

verbose

boolean verbose

For debugging purposes. Public, because it does not count for the dirty flag.

Exception chemaxon.sss.search.SearchTimeoutException

class SearchTimeoutException extends SearchException implements Serializable

serialVersionUID:

-78126823565453833L

Exception chemaxon.sss.search.UnsupportedQueryException

class UnsupportedQueryException extends IllegalArgumentException implements Serializable

serialVersionUID:

6255906179820229430L

Package chemaxon.sss.search.options

Class chemaxon.sss.search.options.ChemTermsFilterOption

class ChemTermsFilterOption extends Object implements Serializable

serialVersionUID:

8226348996476285704L

Serialized Fields

chemTermsFilter

String chemTermsFilter

chemTermsFilterConfig

String chemTermsFilterConfig

ignoreCTExceptions

boolean ignoreCTExceptions

Package chemaxon.standardizer.advancedactions

Class chemaxon.standardizer.advancedactions.GroupList

class GroupList extends ArrayList<GroupDefinition> implements Serializable

Package chemaxon.struc

Class chemaxon.struc.CTransform3D

class CTransform3D extends Object implements Externalizable

serialVersionUID:

0L

Serialization Methods

readExternal

public void readExternal(ObjectInput in)
                  throws IOException

Deserializes a transformation matrix.

Parameters:

in - the object input stream

Throws:

IOException

Since:

3.5, 11/02/2004

writeExternal

public void writeExternal(ObjectOutput out)
                   throws IOException

Serializes a transformation matrix.

Parameters:

out - the object output stream

Throws:

IOException

Since:

3.5, 11/02/2004

Class chemaxon.struc.DefaultDictionary

class DefaultDictionary extends HashMap<String,SuperatomSgroup> implements Serializable

serialVersionUID:

8013155936541949713L

Class chemaxon.struc.DPoint3

class DPoint3 extends Object implements Externalizable

serialVersionUID:

0L

Serialization Methods

readExternal

public void readExternal(ObjectInput in)
                  throws IOException,
ClassNotFoundException

Deserializes a 3D point.

Parameters:

in - the object input stream

Throws:

IOException

ClassNotFoundException

writeExternal

public void writeExternal(ObjectOutput out)
                   throws IOException

Serializes a 3D point.

Parameters:

out - the object output stream

Throws:

IOException

Class chemaxon.struc.ExtraAtomProperties

class ExtraAtomProperties extends Object implements Serializable

serialVersionUID:

-1980229820290558380L

Serialized Fields

aliasstr

String aliasstr

attachParentSgroup

Sgroup attachParentSgroup

countFlags

int countFlags

electronProp

int electronProp

extrargbs

long extrargbs

extrastr

String extrastr

flags

int flags

linkNodeOuterBonds

int linkNodeOuterBonds

list

int[] list

order

int order

qprops

Map<String,Object> qprops

querystr

String querystr

repetitionBits

int repetitionBits

rgroupId

short rgroupId

temporaryObjects

Map<String,Object> temporaryObjects

valence1

short valence1

Exception chemaxon.struc.MacroMolecule.BadMoleculeException

class BadMoleculeException extends Exception implements Serializable

serialVersionUID:

9037472982065239933L

Class chemaxon.struc.MDocument

class MDocument extends Object implements Serializable

serialVersionUID:

553557622036381832L

Serialization Methods

readObject

private void readObject(ObjectInputStream ois)
                 throws ClassNotFoundException,
IOException

Deserializes a document. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

ois - the object input stream

Throws:

ClassNotFoundException

IOException

writeObject

private void writeObject(ObjectOutputStream oos)
                  throws IOException

Serializes a document. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

oos - the object output stream

Throws:

IOException

Class chemaxon.struc.MDocument.Prop

class Prop extends MProp implements Serializable

Class chemaxon.struc.MDocumentUtil

class MDocumentUtil extends Object implements Serializable

serialVersionUID:

12600100100892L

Serialized Fields

doc

MDocument doc

Class chemaxon.struc.MObject

class MObject extends Object implements Serializable

serialVersionUID:

2435517510938087080L

Serialization Methods

readObject

private void readObject(ObjectInputStream ois)
                 throws IOException

Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

ois - the object input stream

Throws:

IOException

writeObject

private void writeObject(ObjectOutputStream oos)
                  throws IOException

Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

oos - the object output stream

Throws:

IOException

Class chemaxon.struc.MolAtom

class MolAtom extends Object implements Serializable

serialVersionUID:

-3974070468228529467L

Serialization Methods

readObject

private void readObject(ObjectInputStream ois)
                 throws ClassNotFoundException,
IOException

Deserializes an atom. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

ois - the object input stream

Throws:

ClassNotFoundException

IOException

writeObject

private void writeObject(ObjectOutputStream oos)
                  throws IOException

Serializes an atom. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

oos - the object output stream

Throws:

IOException

Serialized Fields

angle

double angle

isValenceCheckNeeded

boolean isValenceCheckNeeded

Class chemaxon.struc.MolBond

class MolBond extends Object implements Serializable

serialVersionUID:

3656012871856958335L

Serialization Methods

readObject

private void readObject(ObjectInputStream ois)
                 throws ClassNotFoundException,
IOException

Deserializes a bond. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

ois - the object input stream

Throws:

ClassNotFoundException

IOException

writeObject

private void writeObject(ObjectOutputStream oos)
                  throws IOException

Serializes a bond. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

oos - the object output stream

Throws:

IOException

Class chemaxon.struc.Molecule

class Molecule extends MoleculeGraph implements Serializable

serialVersionUID:

7275486436840296305L

Serialization Methods

readObject

private void readObject(ObjectInputStream ois)
                 throws ClassNotFoundException,
IOException

Deserializes a molecule. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

ois - the object input stream

Throws:

ClassNotFoundException

IOException

writeObject

private void writeObject(ObjectOutputStream oos)
                  throws IOException

Serializes a molecule. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

oos - the object output stream

Throws:

IOException

Serialized Fields

id

String id

Class chemaxon.struc.MoleculeGraph

class MoleculeGraph extends Object implements Serializable

serialVersionUID:

-2053719583816270190L

Serialization Methods

readObject

private void readObject(ObjectInputStream ois)
                 throws ClassNotFoundException,
IOException

Deserializes a molecule graph. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

ois - the object input stream

Throws:

ClassNotFoundException

IOException

writeObject

private void writeObject(ObjectOutputStream oos)
                  throws IOException

Serializes a molecule graph. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

oos - the object output stream

Throws:

IOException

Serialized Fields

fragmentTracker

chemaxon.struc.MoleculeGraph.FragmentTracker fragmentTracker

hasBicycloStereo

boolean hasBicycloStereo

Molecule has bicyclo stereo information. Can be set by MolAtom.setBicycloStereo(BicycloStereoDescriptor[]).

valenceCheckOptions

ValenceCheckOptions valenceCheckOptions

Valence check options for the molecule.

Class chemaxon.struc.MPoint

class MPoint extends MObject implements Serializable

serialVersionUID:

-3067277054033050963L

Serialization Methods

readObject

private void readObject(ObjectInputStream ois)
                 throws ClassNotFoundException,
IOException

Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

ois - the object input stream

Throws:

ClassNotFoundException

IOException

writeObject

private void writeObject(ObjectOutputStream oos)
                  throws IOException

Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

oos - the object output stream

Throws:

IOException

Class chemaxon.struc.MProp

class MProp extends Object implements Serializable

serialVersionUID:

-5699803671884637223L

Serialized Fields

coordDependent

boolean coordDependent

grinvCC

long grinvCC

Class chemaxon.struc.MPropertyContainer

class MPropertyContainer extends Object implements Externalizable

serialVersionUID:

-2575268570438177098L

Serialization Methods

readExternal

public void readExternal(ObjectInput in)
                  throws IOException,
ClassNotFoundException

Restores the property container's state.

Parameters:

in - the stream to read data from in order to restore the object

Throws:

IOException - if I/O errors occur

ClassNotFoundException - If the class for an object being restored cannot be found.

writeExternal

public void writeExternal(ObjectOutput out)
                   throws IOException

Saves the property container's state.

Parameters:

out - the stream to write the object to

Throws:

IOException - Includes any I/O exceptions that may occur

Class chemaxon.struc.MSelectionDocument

class MSelectionDocument extends MDocument implements Serializable

serialVersionUID:

2379294894434293119L

Class chemaxon.struc.PageSettings

class PageSettings extends Object implements Externalizable

serialVersionUID:

-7674028514396457694L

Serialization Methods

readExternal

public void readExternal(ObjectInput arg0)
                  throws IOException,
ClassNotFoundException

Throws:

IOException

ClassNotFoundException

writeExternal

public void writeExternal(ObjectOutput arg0)
                   throws IOException

Throws:

IOException

Class chemaxon.struc.QueryBond

class QueryBond extends MolBond implements Serializable

serialVersionUID:

-5025485107616067648L

Serialization Methods

readObject

private void readObject(ObjectInputStream ois)
                 throws ClassNotFoundException,
IOException

Deserializes a bond. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

ois - the object input stream

Throws:

ClassNotFoundException

IOException

writeObject

private void writeObject(ObjectOutputStream oos)
                  throws IOException

Serializes a bond. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

oos - the object output stream

Throws:

IOException

Class chemaxon.struc.RgMolecule

class RgMolecule extends Molecule implements Serializable

serialVersionUID:

-939153732283455787L

Serialization Methods

readObject

private void readObject(ObjectInputStream ois)
                 throws ClassNotFoundException,
IOException

Deserializes an RgMolecule. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

ois - the object input stream

Throws:

ClassNotFoundException

IOException

writeObject

private void writeObject(ObjectOutputStream oos)
                  throws IOException

Serializes an RgMolecule. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

oos - the object output stream

Throws:

IOException

Class chemaxon.struc.RxnMolecule

class RxnMolecule extends Molecule implements Serializable

serialVersionUID:

-2863036104564183121L

Serialization Methods

readObject

private void readObject(ObjectInputStream ois)
                 throws ClassNotFoundException,
IOException

Deserializes a reaction. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

ois - the object input stream

Throws:

ClassNotFoundException

IOException

writeObject

private void writeObject(ObjectOutputStream oos)
                  throws IOException

Serializes a reaction. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

oos - the object output stream

Throws:

IOException

Class chemaxon.struc.SelectionMolecule

class SelectionMolecule extends MoleculeGraph implements Serializable

serialVersionUID:

234062772192819675L

Class chemaxon.struc.SelectionRgMolecule

class SelectionRgMolecule extends SelectionMolecule implements Serializable

Class chemaxon.struc.Sgroup

class Sgroup extends Object implements Serializable

serialVersionUID:

-6209766549185582411L

Serialization Methods

readObject

private void readObject(ObjectInputStream ois)
                 throws ClassNotFoundException,
IOException

Deserializes an Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

ois - the object input stream

Throws:

ClassNotFoundException

IOException

writeObject

private void writeObject(ObjectOutputStream oos)
                  throws IOException

Serializes an Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

oos - the object output stream

Throws:

IOException

Serialized Fields

atomSet

Set<MolAtom> atomSet

Set for storing the atoms of the s-group's graph.

id

String id

Class chemaxon.struc.StaticMolecule

class StaticMolecule extends Object implements Serializable

serialVersionUID:

-6974806277329432018L

Serialized Fields

arrayFlags

int arrayFlags

atomCount

int atomCount

atomLists

byte[][] atomLists

atomMap

short[] atomMap

atomStereo

byte[] atomStereo

atomType

short[] atomType

bondAtom1

short[] bondAtom1

bondAtom2

short[] bondAtom2

bondCount

int bondCount

bondFlags

int[] bondFlags

charge

byte[] charge

connectionTable

short[] connectionTable

explicitHcount

byte[] explicitHcount

extendedAtomType

int[] extendedAtomType

hybridization

byte[] hybridization

implicitHcount

byte[] implicitHcount

massno

byte[] massno

name

String name

neighborCount

byte[] neighborCount

nodeEdgeList

short[][] nodeEdgeList

queryProperty

byte[][] queryProperty

radical

byte[] radical

rgroupId

short[] rgroupId

ringPerception

boolean ringPerception

sgroupId

String[] sgroupId

valence

byte[] valence

Package chemaxon.struc.graphics

Class chemaxon.struc.graphics.MAnalysisBox

class MAnalysisBox extends MTextBox implements Serializable

serialVersionUID:

-7630363128405095856L

Serialized Fields

mol

Molecule mol

terms

List<chemaxon.struc.graphics.analysis.MAnalysisBoxTerm> terms

Class chemaxon.struc.graphics.MAssigner

class MAssigner extends MPolyline implements Serializable

Serialized Fields

order

int order

Class chemaxon.struc.graphics.MAtomSetPoint

class MAtomSetPoint extends MPoint implements Serializable

serialVersionUID:

5932389976054063500L

Serialization Methods

readObject

private void readObject(ObjectInputStream ois)
                 throws ClassNotFoundException,
IOException

Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

ois - the object input stream

Throws:

ClassNotFoundException

IOException

writeObject

private void writeObject(ObjectOutputStream oos)
                  throws IOException

Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

oos - the object output stream

Throws:

IOException

Class chemaxon.struc.graphics.MBracket

class MBracket extends MRectangle implements Serializable

serialVersionUID:

-5775562691065011181L

Serialization Methods

readObject

private void readObject(ObjectInputStream ois)
                 throws IOException

Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

ois - the object input stream

Throws:

IOException

writeObject

private void writeObject(ObjectOutputStream oos)
                  throws IOException

Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

oos - the object output stream

Throws:

IOException

Serialized Fields

bracketOrientation

int bracketOrientation

Bracket orientation, bracket can have two sides (T_DOUBLE) or just one (T_SINGLE). Possible values: T_SINGLE, T_DOUBLE

bracketType

int bracketType

Class chemaxon.struc.graphics.MChemicalStruct

class MChemicalStruct extends MObject implements Serializable

serialVersionUID:

7098670860634457343L

Serialization Methods

readObject

private void readObject(ObjectInputStream ois)
                 throws ClassNotFoundException,
IOException

Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

ois - the object input stream

Throws:

ClassNotFoundException

IOException

writeObject

private void writeObject(ObjectOutputStream oos)
                  throws IOException

Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

oos - the object output stream

Throws:

IOException

Class chemaxon.struc.graphics.MEFlow

class MEFlow extends MPolyline implements Serializable

serialVersionUID:

891769518407563834L

Serialization Methods

readObject

private void readObject(ObjectInputStream ois)
                 throws IOException

Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

ois - the object input stream

Throws:

IOException

writeObject

private void writeObject(ObjectOutputStream oos)
                  throws IOException

Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

oos - the object output stream

Throws:

IOException

Serialized Fields

baseElectronContainerIndex

int baseElectronContainerIndex

baseElectronIndexInContainer

int baseElectronIndexInContainer

Class chemaxon.struc.graphics.MEFlowBasePoint

class MEFlowBasePoint extends MPoint implements Serializable

serialVersionUID:

1053944912020926984L

Serialization Methods

readObject

private void readObject(ObjectInputStream ois)
                 throws ClassNotFoundException,
IOException

Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

ois - the object input stream

Throws:

ClassNotFoundException

IOException

writeObject

private void writeObject(ObjectOutputStream oos)
                  throws IOException

Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

oos - the object output stream

Throws:

IOException

Serialized Fields

electronIndex

int electronIndex

electronLabel

String electronLabel

Class chemaxon.struc.graphics.MElectron

class MElectron extends MAtomSetPoint implements Serializable

Serialization Methods

readObject

private void readObject(ObjectInputStream 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

class 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

class MEllipse extends MRectangle implements Serializable

Serialization Methods

readObject

private void readObject(ObjectInputStream ois)
                 throws ClassNotFoundException,
IOException

Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

ois - the object input stream

Throws:

ClassNotFoundException

IOException

writeObject

private void writeObject(ObjectOutputStream oos)
                  throws IOException

Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

oos - the object output stream

Throws:

IOException

Class chemaxon.struc.graphics.MFont

class MFont extends Object implements Serializable

serialVersionUID:

-7769715209509613515L

Serialization Methods

readObject

private void readObject(ObjectInputStream ois)
                 throws ClassNotFoundException,
IOException

Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

ois - the object input stream

Throws:

ClassNotFoundException

IOException

writeObject

private void writeObject(ObjectOutputStream oos)
                  throws IOException

Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

oos - the object output stream

Throws:

IOException

Class chemaxon.struc.graphics.MMidPoint

class MMidPoint extends MPoint implements Serializable

serialVersionUID:

5307361876930807239L

Serialization Methods

readObject

private void readObject(ObjectInputStream ois)
                 throws ClassNotFoundException,
IOException

Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

ois - the object input stream

Throws:

ClassNotFoundException

IOException

writeObject

private void writeObject(ObjectOutputStream oos)
                  throws IOException

Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

oos - the object output stream

Throws:

IOException

Class chemaxon.struc.graphics.MMidPoint.Sticky

class Sticky extends MMidPoint implements Serializable

serialVersionUID:

3223068581543532992L

Class chemaxon.struc.graphics.MMoleculeMovie

class MMoleculeMovie extends MObject implements Serializable

serialVersionUID:

6476041884742537582L

Serialization Methods

readObject

private void readObject(ObjectInputStream arg0)
                 throws ClassNotFoundException,
IOException

Throws:

ClassNotFoundException

IOException

writeObject

private void writeObject(ObjectOutputStream arg0)
                  throws IOException

Throws:

IOException

Class chemaxon.struc.graphics.MNameTextBox

class 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

class MPolyline extends MObject implements Serializable

serialVersionUID:

4958026600768388648L

Serialization Methods

readObject

private void readObject(ObjectInputStream ois)
                 throws ClassNotFoundException,
IOException

Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

ois - the object input stream

Throws:

ClassNotFoundException

IOException

writeObject

private void writeObject(ObjectOutputStream oos)
                  throws IOException

Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

oos - the object output stream

Throws:

IOException

Serialized Fields

internalPointAddCount

int internalPointAddCount

internalPointPos

int internalPointPos

Class chemaxon.struc.graphics.MRArrow

class MRArrow extends MPolyline implements Serializable

serialVersionUID:

8638690394107448092L

Serialization Methods

readObject

private void readObject(ObjectInputStream arg0)
                 throws ClassNotFoundException,
IOException

Throws:

ClassNotFoundException

IOException

writeObject

private void writeObject(ObjectOutputStream arg0)
                  throws IOException

Throws:

IOException

Class chemaxon.struc.graphics.MReactionSign

class MReactionSign extends MTextBox implements Serializable

serialVersionUID:

-7025949002857142442L

Class chemaxon.struc.graphics.MRectangle

class MRectangle extends MPolyline implements Serializable

serialVersionUID:

2948229815278089239L

Serialization Methods

readObject

private void readObject(ObjectInputStream ois)
                 throws ClassNotFoundException,
IOException

Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

ois - the object input stream

Throws:

ClassNotFoundException

IOException

writeObject

private void writeObject(ObjectOutputStream oos)
                  throws IOException

Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

oos - the object output stream

Throws:

IOException

Class chemaxon.struc.graphics.MRectanglePoint

class MRectanglePoint extends MPoint implements Serializable

serialVersionUID:

-3067277054033050963L

Serialization Methods

readObject

private void readObject(ObjectInputStream ois)
                 throws ClassNotFoundException,
IOException

Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

ois - the object input stream

Throws:

ClassNotFoundException

IOException

writeObject

private void writeObject(ObjectOutputStream oos)
                  throws IOException

Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

oos - the object output stream

Throws:

IOException

Class chemaxon.struc.graphics.MRectanglePoint.Sticky

class Sticky extends MRectanglePoint implements Serializable

serialVersionUID:

3364078480306200948L

Class chemaxon.struc.graphics.MRoundedRectangle

class MRoundedRectangle extends MRectangle implements Serializable

Serialization Methods

readObject

private void readObject(ObjectInputStream ois)
                 throws ClassNotFoundException,
IOException

Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

ois - the object input stream

Throws:

ClassNotFoundException

IOException

writeObject

private void writeObject(ObjectOutputStream oos)
                  throws IOException

Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

oos - the object output stream

Throws:

IOException

Serialized Fields

arcHeight

double arcHeight

arcWidth

double arcWidth

Class chemaxon.struc.graphics.MTextAttributes

class MTextAttributes extends Object implements Externalizable

serialVersionUID:

6561552003080652755L

Serialization Methods

readExternal

public void readExternal(ObjectInput in)
                  throws IOException,
ClassNotFoundException

Throws:

IOException

ClassNotFoundException

writeExternal

public void writeExternal(ObjectOutput out)
                   throws IOException

Throws:

IOException

Class chemaxon.struc.graphics.MTextBox

class MTextBox extends MRectangle implements Serializable

serialVersionUID:

-7272723232157967384L

Serialization Methods

readObject

private void readObject(ObjectInputStream ois)
                 throws ClassNotFoundException,
IOException

Deserializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

ois - the object input stream

Throws:

ClassNotFoundException

IOException

writeObject

private void writeObject(ObjectOutputStream oos)
                  throws IOException

Serializes the object. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

oos - the object output stream

Throws:

IOException

Serialized Fields

actionMap

ActionMap actionMap

Class chemaxon.struc.graphics.MTextDocument

class MTextDocument extends Object implements Externalizable

serialVersionUID:

6305880304790247656L

Serialization Methods

readExternal

public void readExternal(ObjectInput in)
                  throws IOException,
ClassNotFoundException

Restores the document.

Parameters:

in - the stream to read data from in order to restore the object

Throws:

IOException - if I/O errors occur

ClassNotFoundException - If the class for an object being restored cannot be found.

writeExternal

public void writeExternal(ObjectOutput out)
                   throws IOException

Saves the document.

Parameters:

out - the stream to write the object to

Throws:

IOException - Includes any I/O exceptions that may occur

Package chemaxon.struc.prop

Class chemaxon.struc.prop.MBooleanProp

class MBooleanProp extends MProp implements Serializable

serialVersionUID:

-5366978422380739811L

Serialization Methods

readObject

private void readObject(ObjectInputStream in)
                 throws IOException,
ClassNotFoundException

Restores the property's state.

Parameters:

in - the stream to read data from in order to restore the object

Throws:

IOException - if I/O errors occur

ClassNotFoundException - If the class for an object being restored cannot be found.

writeObject

private void writeObject(ObjectOutputStream out)
                  throws IOException

Saves the property's state.

Parameters:

out - the stream to write the object to

Throws:

IOException - Includes any I/O exceptions that may occur

Class chemaxon.struc.prop.MByteArrayProp

class MByteArrayProp extends MProp implements Serializable

serialVersionUID:

-4046371792715339701L

Serialization Methods

readObject

private void readObject(ObjectInputStream arg0)
                 throws IOException,
ClassNotFoundException

Throws:

IOException

ClassNotFoundException

writeObject

private void writeObject(ObjectOutputStream arg0)
                  throws IOException

Throws:

IOException

Class chemaxon.struc.prop.MCollectionProp

class MCollectionProp extends MProp implements Serializable

serialVersionUID:

-7479938988131387052L

Class chemaxon.struc.prop.MDoubleArrayProp

class MDoubleArrayProp extends MProp implements Serializable

serialVersionUID:

-5670039985685584647L

Serialization Methods

readObject

private void readObject(ObjectInputStream in)
                 throws IOException,
ClassNotFoundException

Restores the property's state.

Parameters:

in - the stream to read data from in order to restore the object

Throws:

IOException - if I/O errors occur

ClassNotFoundException - If the class for an object being restored cannot be found.

writeObject

private void writeObject(ObjectOutputStream out)
                  throws IOException

Saves the property's state.

Parameters:

out - the stream to write the object to

Throws:

IOException - Includes any I/O exceptions that may occur

Class chemaxon.struc.prop.MDoubleProp

class MDoubleProp extends MProp implements Serializable

serialVersionUID:

-1221776439131689653L

Serialization Methods

readObject

private void readObject(ObjectInputStream in)
                 throws IOException,
ClassNotFoundException

Restores the property's state.

Parameters:

in - the stream to read data from in order to restore the object

Throws:

IOException - if I/O errors occur

ClassNotFoundException - If the class for an object being restored cannot be found.

writeObject

private void writeObject(ObjectOutputStream out)
                  throws IOException

Saves the property's state.

Parameters:

out - the stream to write the object to

Throws:

IOException - Includes any I/O exceptions that may occur

Class chemaxon.struc.prop.MFontProp

class MFontProp extends MProp implements Serializable

serialVersionUID:

2369581307328116455L

Serialization Methods

readObject

private void readObject(ObjectInputStream arg0)
                 throws IOException,
ClassNotFoundException

Throws:

IOException

ClassNotFoundException

writeObject

private void writeObject(ObjectOutputStream arg0)
                  throws IOException

Throws:

IOException

Class chemaxon.struc.prop.MHashProp

class MHashProp extends MCollectionProp implements Serializable

serialVersionUID:

5457649877894058447L

Serialization Methods

readObject

private void readObject(ObjectInputStream in)
                 throws IOException,
ClassNotFoundException

Restores the property's state.

Parameters:

in - the stream to read data from in order to restore the object

Throws:

IOException - if I/O errors occur

ClassNotFoundException - If the class for an object being restored cannot be found.

writeObject

private void writeObject(ObjectOutputStream out)
                  throws IOException

Saves the property's state.

Parameters:

out - the stream to write the object to

Throws:

IOException - Includes any I/O exceptions that may occur

Class chemaxon.struc.prop.MHCoords3DProp

class MHCoords3DProp extends MProp implements Serializable

serialVersionUID:

6646271128663088908L

Serialization Methods

readObject

private void readObject(ObjectInputStream in)
                 throws IOException,
ClassNotFoundException

Restores the property's state.

Parameters:

in - the stream to read data from in order to restore the object

Throws:

IOException - if I/O errors occur

ClassNotFoundException - If the class for an object being restored cannot be found.

writeObject

private void writeObject(ObjectOutputStream out)
                  throws IOException

Saves the property's state.

Parameters:

out - the stream to write the object to

Throws:

IOException - Includes any I/O exceptions that may occur

Class chemaxon.struc.prop.MIntegerArrayProp

class MIntegerArrayProp extends MProp implements Serializable

serialVersionUID:

6651869314046996057L

Serialization Methods

readObject

private void readObject(ObjectInputStream in)
                 throws IOException,
ClassNotFoundException

Restores the property's state.

Parameters:

in - the stream to read data from in order to restore the object

Throws:

IOException - if I/O errors occur

ClassNotFoundException - If the class for an object being restored cannot be found.

writeObject

private void writeObject(ObjectOutputStream out)
                  throws IOException

Saves the property's state.

Parameters:

out - the stream to write the object to

Throws:

IOException - Includes any I/O exceptions that may occur

Class chemaxon.struc.prop.MIntegerProp

class MIntegerProp extends MProp implements Serializable

serialVersionUID:

-7179550727198941747L

Serialization Methods

readObject

private void readObject(ObjectInputStream in)
                 throws IOException,
ClassNotFoundException

Restores the property's state.

Parameters:

in - the stream to read data from in order to restore the object

Throws:

IOException - if I/O errors occur

ClassNotFoundException - If the class for an object being restored cannot be found.

writeObject

private void writeObject(ObjectOutputStream out)
                  throws IOException

Saves the property's state.

Parameters:

out - the stream to write the object to

Throws:

IOException - Includes any I/O exceptions that may occur

Class chemaxon.struc.prop.MListProp

class MListProp extends MCollectionProp implements Serializable

serialVersionUID:

5360371881677476960L

Serialization Methods

readObject

private void readObject(ObjectInputStream in)
                 throws IOException,
ClassNotFoundException

Restores the property's state.

Parameters:

in - the stream to read data from in order to restore the object

Throws:

IOException - if I/O errors occur

ClassNotFoundException - If the class for an object being restored cannot be found.

writeObject

private void writeObject(ObjectOutputStream out)
                  throws IOException

Saves the property's state.

Parameters:

out - the stream to write the object to

Throws:

IOException - Includes any I/O exceptions that may occur

Class chemaxon.struc.prop.MMoleculeProp

class MMoleculeProp extends MProp implements Serializable

serialVersionUID:

-7687559780023024273L

Serialization Methods

readObject

private void readObject(ObjectInputStream in)
                 throws IOException,
ClassNotFoundException

Restores the property's state.

Parameters:

in - the stream to read data from in order to restore the object

Throws:

IOException - if I/O errors occur

ClassNotFoundException - If the class for an object being restored cannot be found.

writeObject

private void writeObject(ObjectOutputStream out)
                  throws IOException

Saves the property's state.

Parameters:

out - the stream to write the object to

Throws:

IOException - Includes any I/O exceptions that may occur

Class chemaxon.struc.prop.MMoleculeStringProp

class MMoleculeStringProp extends MStringProp implements Serializable

serialVersionUID:

-1005074014113755196L

Serialization Methods

readObject

private void readObject(ObjectInputStream 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

class MObjectProp extends MProp implements Serializable

serialVersionUID:

4005646748655675692L

Serialization Methods

readObject

private void readObject(ObjectInputStream in)
                 throws IOException,
ClassNotFoundException

Restores the property's state.

Parameters:

in - the stream to read data from in order to restore the object

Throws:

IOException - if I/O errors occur

ClassNotFoundException - If the class for an object being restored cannot be found.

writeObject

private void writeObject(ObjectOutputStream out)
                  throws IOException

Saves the property's state.

Parameters:

out - the stream to write the object to

Throws:

IOException - Includes any I/O exceptions that may occur

Class chemaxon.struc.prop.MStringProp

class MStringProp extends MProp implements Serializable

serialVersionUID:

1373831606368751112L

Serialization Methods

readObject

private void readObject(ObjectInputStream in)
                 throws IOException,
ClassNotFoundException

Restores the property's state.

Parameters:

in - the stream to read data from in order to restore the object

Throws:

IOException - if I/O errors occur

ClassNotFoundException - If the class for an object being restored cannot be found.

writeObject

private void writeObject(ObjectOutputStream out)
                  throws IOException

Saves the property's state.

Parameters:

out - the stream to write the object to

Throws:

IOException - Includes any I/O exceptions that may occur

Package chemaxon.struc.sgroup

Class chemaxon.struc.sgroup.AminoAcidSgroup

class AminoAcidSgroup extends SuperatomSgroup implements Serializable

serialVersionUID:

-4078870750580716173L

Serialization Methods

readObject

private void readObject(ObjectInputStream arg0)
                 throws ClassNotFoundException,
IOException

Throws:

ClassNotFoundException

IOException

writeObject

private void writeObject(ObjectOutputStream arg0)
                  throws IOException

Throws:

IOException

Serialized Fields

modified

boolean modified

oneLetterName

String oneLetterName

threeLetterName

String threeLetterName

Class chemaxon.struc.sgroup.AttachmentPoint

class AttachmentPoint extends Object implements Serializable

serialVersionUID:

-7484860308765339862L

Serialized Fields

atom

MolAtom atom

bond

MolBond bond

order

int order

Class chemaxon.struc.sgroup.DataSgroup

class DataSgroup extends Sgroup implements Serializable

serialVersionUID:

-3132191586564122343L

Serialization Methods

readObject

private void readObject(ObjectInputStream ois)
                 throws ClassNotFoundException,
IOException

Deserializes a data Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

ois - the object input stream

Throws:

ClassNotFoundException

IOException

writeObject

private void writeObject(ObjectOutputStream oos)
                  throws IOException

Serializes a data Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

oos - the object output stream

Throws:

IOException

Serialized Fields

labelPosition

chemaxon.struc.sgroup.DataSgroup.AbstractPosition labelPosition

sb

StringBuffer sb

temporary variable for getLineOnScreen

Class chemaxon.struc.sgroup.MulticenterSgroup

class MulticenterSgroup extends Sgroup implements Serializable

serialVersionUID:

-7213879722783498112L

Serialization Methods

readObject

private void readObject(ObjectInputStream ois)
                 throws ClassNotFoundException,
IOException

Deserializes a Multicenter Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

ois - the object input stream

Throws:

ClassNotFoundException

IOException

writeObject

private void writeObject(ObjectOutputStream oos)
                  throws IOException

Serializes a Multicenter Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

oos - the object output stream

Throws:

IOException

Class chemaxon.struc.sgroup.MultipleSgroup

class MultipleSgroup extends Sgroup implements Serializable

serialVersionUID:

-1146464131016252826L

Serialization Methods

readObject

private void readObject(ObjectInputStream ois)
                 throws ClassNotFoundException,
IOException

Deserializes a multiple Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

ois - the object input stream

Throws:

ClassNotFoundException

IOException

writeObject

private void writeObject(ObjectOutputStream oos)
                  throws IOException

Serializes a multiple Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

oos - the object output stream

Throws:

IOException

Exception chemaxon.struc.sgroup.NoFreeAttachmentPointException

class NoFreeAttachmentPointException extends RuntimeException implements Serializable

serialVersionUID:

2226630752133341633L

Serialized Fields

sga

SgroupAtom sga

Class chemaxon.struc.sgroup.RepeatingUnitSgroup

class RepeatingUnitSgroup extends Sgroup implements Serializable

serialVersionUID:

-3209611525734625009L

Serialization Methods

readObject

private void readObject(ObjectInputStream ois)
                 throws ClassNotFoundException,
IOException

Deserializes an SRU Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

ois - the object input stream

Throws:

ClassNotFoundException

IOException

writeObject

private void writeObject(ObjectOutputStream oos)
                  throws IOException

Serializes an SRU Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

oos - the object output stream

Throws:

IOException

Class chemaxon.struc.sgroup.SgroupAtom

class SgroupAtom extends MolAtom implements Serializable

serialVersionUID:

-3185634359981637075L

Serialization Methods

readObject

private void readObject(ObjectInputStream ois)
                 throws ClassNotFoundException,
IOException

Deserializes an Sgroup superatom. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

ois - the object input stream

Throws:

ClassNotFoundException

IOException

writeObject

private void writeObject(ObjectOutputStream oos)
                  throws IOException

Serializes an Sgroup superatom. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

oos - the object output stream

Throws:

IOException

Serialized Fields

labelCenter

int labelCenter

Class chemaxon.struc.sgroup.SuperatomSgroup

class SuperatomSgroup extends Sgroup implements Serializable

serialVersionUID:

2968529752634209305L

Serialization Methods

readObject

private void readObject(ObjectInputStream ois)
                 throws ClassNotFoundException,
IOException

Deserializes a superatom Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

ois - the object input stream

Throws:

ClassNotFoundException

IOException

writeObject

private void writeObject(ObjectOutputStream oos)
                  throws IOException

Serializes a superatom Sgroup. Be extremely cautious when editing this method! Backward compatibility must be maintained.

Parameters:

oos - the object output stream

Throws:

IOException

Serialized Fields

apContainer

chemaxon.struc.sgroup.AttachmentPointContainer apContainer

Attachment Point container object

Package chemaxon.util

Exception chemaxon.util.ArgumentException

class ArgumentException extends Exception implements Serializable

serialVersionUID:

-8949782741678573705L

Exception chemaxon.util.Heap.HeapException

class HeapException extends RuntimeException implements Serializable

Class chemaxon.util.SearchAttributes

class SearchAttributes extends chemaxon.jep.util.SearchAttributes implements Serializable

Exception chemaxon.util.SupplierException

class SupplierException extends RuntimeException implements Serializable

Package com.chemaxon.calculations.gui

Class com.chemaxon.calculations.gui.MChart

class MChart extends chemaxon.marvin.util.MarvinModule implements Serializable

Serialized Fields

chart

com.objectplanet.chart.LineChart chart

colors

Color[] colors

legendMols

Molecule[] legendMols

legendTexts

String[] legendTexts

precision

int precision

Package com.chemaxon.calculations.io

Exception com.chemaxon.calculations.io.OrderedInputProcessingException

class OrderedInputProcessingException extends IllegalArgumentException implements Serializable

Serialized Fields

inputIndex

int inputIndex

Deprecated, for removal: This API element is subject to removal in a future version.

Package com.chemaxon.clustering.framework

Class com.chemaxon.clustering.framework.RemoveSidechainsMolwalk

class RemoveSidechainsMolwalk extends Object implements Serializable

Class com.chemaxon.clustering.framework.RemoveSidechainsSc

class RemoveSidechainsSc extends Object implements Serializable

Serialized Fields

keepUnsaturatedConnections

boolean keepUnsaturatedConnections

Class com.chemaxon.clustering.framework.SimpleFrameworkAssociation

class SimpleFrameworkAssociation extends Object implements Serializable

Serialized Fields

indexToFramework

List<T extends Object> indexToFramework

Package com.chemaxon.descriptors.alignment

Class com.chemaxon.descriptors.alignment.AbstractShapeComparator

class AbstractShapeComparator extends Object implements Serializable

Serialized Fields

generator

DescriptorGenerator<T extends ShapeDescriptor> generator

Class com.chemaxon.descriptors.alignment.AbstractShapeGenerator

class AbstractShapeGenerator extends Object implements Serializable

Serialized Fields

parameters

P extends AbstractShapeGeneratorParameter parameters

Class com.chemaxon.descriptors.alignment.AbstractShapeGeneratorParameter

class AbstractShapeGeneratorParameter extends Object implements Serializable

Serialized Fields

atomTyping

AtomTyping atomTyping

The setting for available shape coloring methods.

Class com.chemaxon.descriptors.alignment.BaseShapeComparatorParameter

class BaseShapeComparatorParameter extends Object implements Serializable

Serialized Fields

flexibilityMode

AlignmentProperties.FlexibilityMode flexibilityMode

shapeFunction

ShapeFunction shapeFunction

tryCount

com.google.common.base.Optional<Integer> tryCount

Exception com.chemaxon.descriptors.alignment.ShapeComparatorException

class ShapeComparatorException extends RuntimeException implements Serializable

serialVersionUID:

1L

Exception com.chemaxon.descriptors.alignment.ShapeGeneratorException

class ShapeGeneratorException extends RuntimeException implements Serializable

serialVersionUID:

1L

Package com.chemaxon.descriptors.common

Package com.chemaxon.descriptors.fingerprints.cfp

Class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters

class CfpParameters extends Object implements Serializable

serialVersionUID:

0L

Serialized Fields

bitsPerPattern

int bitsPerPattern

Bits set for each pattern.

bondCount

int bondCount

Max pattern length considered (bond count).

length

int length

Fingerprint length (bit count).

rings

boolean rings

Consider rings in fingerprint generation.

Package com.chemaxon.descriptors.fingerprints.ecfp

Class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters

class EcfpParameters extends Object implements Serializable

serialVersionUID:

0L

Serialized Fields

atomTypizer

EcfpAtomTypizers atomTypizer

Atom typizer to use.

diameter

int diameter

Diameter parameter.

identifierConfigurationXml

com.google.common.base.Optional<String> identifierConfigurationXml

Identifier configuration for custom XML mode.

length

int length

Fingerprint length (bit count).

Class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpParameters

class ThreadLocalizedEcfpParameters extends Object implements Serializable

serialVersionUID:

0L

Serialized Fields

params

EcfpParameters params

Package com.chemaxon.descriptors.fingerprints.maccs

Class com.chemaxon.descriptors.fingerprints.maccs.MaccsParameters

class MaccsParameters extends Object implements Serializable

Package com.chemaxon.descriptors.fingerprints.pf2d

Class com.chemaxon.descriptors.fingerprints.pf2d.PfComparatorImpl

class PfComparatorImpl extends Object implements Serializable

Class com.chemaxon.descriptors.fingerprints.pf2d.PfParameters

class PfParameters extends Object implements Serializable

serialVersionUID:

0L

Serialized Fields

xmlConfig

com.google.common.base.Optional<String> xmlConfig

XML configuration string.

Class com.chemaxon.descriptors.fingerprints.pf2d.PharmacophoreFPImpl

class PharmacophoreFPImpl extends com.chemaxon.descriptors.common.realvector.FloatVectorDescriptorImpl implements Serializable

Serialized Fields

fingerprint

PharmacophoreFingerprint fingerprint

Class com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfParameters

class ThreadLocalizedPfParameters extends Object implements Serializable

serialVersionUID:

0L

Serialized Fields

xmlConfig

com.google.common.base.Optional<String> xmlConfig

Package com.chemaxon.descriptors.metrics

Class com.chemaxon.descriptors.metrics.TverskyParameters

class TverskyParameters extends Object implements Serializable

serialVersionUID:

0L

Serialized Fields

coeffQuery

double coeffQuery

Coefficient for query only part.

coeffTarget

double coeffTarget

Coefficient for target only part.

Package com.chemaxon.descriptors.vectors.binary

Class com.chemaxon.descriptors.vectors.binary.BvGeneratorImpl

class BvGeneratorImpl extends Object implements Serializable

serialVersionUID:

0L

Serialized Fields

parameters

BvParameters parameters

Class com.chemaxon.descriptors.vectors.binary.BvParameters

class BvParameters extends Object implements Serializable

serialVersionUID:

0L

Serialized Fields

endianness

BinaryVectors.Endianness endianness

Endianness of long-int-byte-binary packing operations.

length

int length

Fingerprint length (bit count).

stringFormat

BvParameters.StringFormat stringFormat

String format to use.

Package com.chemaxon.descriptors.vectors.floats

Class com.chemaxon.descriptors.vectors.floats.FvGeneratorImpl

class FvGeneratorImpl extends Object implements Serializable

serialVersionUID:

0L

Serialized Fields

parameters

FvParameters parameters

Class com.chemaxon.descriptors.vectors.floats.FvParameters

class FvParameters extends Object implements Serializable

serialVersionUID:

0L

Serialized Fields

length

int length

Fingerprint length (bit count).

numericRepresentation

FvParameters.NumericRepresentation numericRepresentation

Numeric representation.

scaledMax

double scaledMax

Maximum value for scaling.

scaledMin

double scaledMin

Minimum value for scaling.

sparseCompression

FvParameters.SparseCompression sparseCompression

Optimization for sparse vectors.

Package com.chemaxon.overlap.io

Class com.chemaxon.overlap.io.AllAbsentMasterMoleculeStorage

class AllAbsentMasterMoleculeStorage extends Object implements Serializable

Serialized Fields

size

long size

Deprecated, for removal: This API element is subject to removal in a future version.

Class com.chemaxon.overlap.io.ArraysBackedStorageTools.Builder

class Builder extends Object implements Serializable

Serialized Fields

builtPages

List<C extends Serializable> builtPages

currentPage

List<E extends Serializable> currentPage

elementType

Class<E extends Serializable> elementType

getFromPage

com.chemaxon.descriptors.common.reflect.SerializableBiFunction<C extends Serializable,Integer,E extends Serializable> getFromPage

initialSkips

long initialSkips

listToPage

com.chemaxon.descriptors.common.reflect.SerializableFunction<List<E extends Serializable>,C extends Serializable> listToPage

pageSize

int pageSize

totalAbsents

long totalAbsents

totalSize

long totalSize

Class com.chemaxon.overlap.io.ArraysBackedStorageTools.Storage

class Storage extends Object implements Serializable

Serialized Fields

elementType

Class<E extends Object> elementType

getFromPage

com.chemaxon.descriptors.common.reflect.SerializableBiFunction<C extends Object,Integer,E extends Object> getFromPage

initialSkips

long initialSkips

pages

List<C extends Object> pages

pageSize

int pageSize

totalAbsents

long totalAbsents

totalSize

long totalSize

Class com.chemaxon.overlap.io.CompactStringStorage

class CompactStringStorage extends Object implements Serializable

serialVersionUID:

0L

Serialized Fields

absentCount

long absentCount

Deprecated, for removal: This API element is subject to removal in a future version.

pagesize

int pagesize

Deprecated, for removal: This API element is subject to removal in a future version.

size

long size

Deprecated, for removal: This API element is subject to removal in a future version.

skips

long skips

Deprecated, for removal: This API element is subject to removal in a future version.

starts

int[][] starts

Deprecated, for removal: This API element is subject to removal in a future version.

storage

byte[][] storage

Deprecated, for removal: This API element is subject to removal in a future version.

storedByteCount

long storedByteCount

Deprecated, for removal: This API element is subject to removal in a future version.

Class com.chemaxon.overlap.io.CompactStringStorage.Metadata

class Metadata extends Object implements Serializable

Serialized Fields

absentCount

long absentCount

bytes

long bytes

lastPageSize

int lastPageSize

pageCount

int pageCount

pageSize

int pageSize

size

long size

skips

long skips

storeSizes

int[] storeSizes

storeStart

long storeStart

Class com.chemaxon.overlap.io.MasterMoleculeStorageImpl

class MasterMoleculeStorageImpl extends Object implements Serializable

serialVersionUID:

0L

Serialized Fields

importOptsOrNull

String importOptsOrNull

Deprecated, for removal: This API element is subject to removal in a future version.

sources

com.chemaxon.overlap.io.CompactStringStorage sources

Deprecated, for removal: This API element is subject to removal in a future version.

Package com.chemaxon.search.transformation

Exception com.chemaxon.search.transformation.TransformationException

class TransformationException extends Exception implements Serializable