float[] weights
chemaxon.clustering.ChemicalSpace.InvertedFile inv
int dimensions
int fpsize
java.util.BitSet emptyset
java.util.BitSet checked
boolean willett
byte[] data
int size
double[] data
int size
float[] data
int size
int left
int right
int[] data
int size
long[] data
int size
short[] data
int size
boolean localAromatic
boolean traditionalNallowed
int atomCount
int lineNumberInRecord
int lineNumberInFile
java.util.List<E> _exceptions
byte[] molString
int[] fingerprint
int hashCode
java.lang.Double molWeight
java.lang.String formula
java.lang.String sortableFormula
java.lang.String smiles
boolean noRingInfoInFP
boolean reactionMappingIncomplete
byte[] markushData
Molecule molecule
java.util.Map<K,V> chemTermColValues
Molecule tautomer
java.lang.String flags
java.lang.String molName
int tautomerHashCode
int[] tautomerFragmentHashCode
byte[] screenDescriptor
byte[][] descriptorData
int tableType
chemaxon.jchem.base.storage.StructureCollectionType collectionType
boolean tautomerDuplicateFilteringEnabled
chemaxon.sss.search.options.TautomerTransformationMode tautomerEqualityMode
boolean duplicateFilteringOption
java.lang.String standardizerConfig
int numberOfStructuralFPColumns
int numberOfCombinedFPColumns
java.lang.String structuralKeys
int numberOfEdges
int numberOfOnes
java.lang.String[] chemTermColumns
java.util.Map<K,V> chemTermForColumn
boolean compressedStructureFieldSupported
java.util.List<E> insertDescriptorNames
java.util.List<E> updateDescriptorNames
java.util.Map<K,V> descriptorTypes
java.util.Map<K,V> descriptorSettings
UpdateHandler.RowData rowData
java.lang.String message
java.lang.String[] entityList
null
.java.lang.String processingMessage
boolean isRegeneration
Updater.UpdateInfo.isProgressMonitoringSupported
instead.Updater.UpdateInfo.entityList
can be used
directly for
UpdateHandler.recalculateTable(chemaxon.util.ConnectionHandler,
String, boolean, String, java.util.Map, Boolean, chemaxon.jchem.file.ProgressWriter)
boolean isProgressMonitoringSupported
int regenerationType
boolean isOperationRequired
boolean isStructuralChange
java.lang.String[] additionalInformation
java.util.Hashtable<K,V> cacheHash
int maxCacheSizeMB
int minFreeMemMB
long maxCacheMemory
boolean maxCacheMemoryCalculated
double expirationTime
chemaxon.jchem.db.cache.CacheRemovalMethod cacheRemovalMethod
chemaxon.jchem.db.cache.CacheRegistrationException.Reason reason
ChemJEP jep
boolean cached
java.lang.Class<T> contextClass
ChemContext context
java.lang.String name
ChemJEP jep
java.lang.String className
java.lang.String[] descriptors
chemaxon.jep.EvaluatorConfiguration builtInConfig
chemaxon.jep.EvaluatorConfiguration externalConfig
chemaxon.jep.EvaluatorConfiguration userConfig
chemaxon.jep.EvaluatorConfiguration config
java.util.Hashtable<K,V> servicesFunctionTable
chemaxon.nfunk.jep.SymbolTable symtab
java.util.Hashtable<K,V> functionalGroupDisplayMolTable
boolean verbose
java.lang.String licenseEnvironment
java.lang.String servicesConfigurationPath
Evaluator evaluator
java.lang.String className
java.util.Hashtable<K,V> subMatches
int type
chemaxon.util.SearchAttributes attributes
java.lang.String dir
chemaxon.jep.Standardizer standardizer
java.lang.String licenseEnvironment
int atom
com.google.common.base.Supplier<T> supplier
int[] fingerprint
ReactionContext reactionContext
boolean init
RxnMolecule reaction
java.util.Map<K,V> reactantAtomMapping
java.util.Map<K,V> productAtomMapping
java.util.Map<K,V> agentAtomMapping
MSketchPane sketchPane
java.lang.String outSerName
javax.swing.Action newWindowAction
javax.swing.Action exitAction
java.util.List<E> colorKeys
MViewPane viewPane
javax.swing.Action openAction
javax.swing.Action printAction
javax.swing.Action exitAction
boolean hasInitalized
java.util.BitSet shapeEnabledAtoms
chemaxon.marvin.alignment.ShapeData.Atom[] atoms
chemaxon.marvin.alignment.ShapeData.Bond[] bonds
AlignmentProperties.ColoringScheme coloringScheme
double[] mins
double[] maxs
chemaxon.marvin.common.swing.MolPanel molPanel
java.lang.String params
chemaxon.marvin.beans.MarvinPane.MarvinActionListener actionListener
MolPrinter printer
public void readExternal(java.io.ObjectInput in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
- if I/O errors occurjava.lang.ClassNotFoundException
- If the class for an object being restored cannot be found.public void writeExternal(java.io.ObjectOutput out) throws java.io.IOException
java.io.IOException
- Includes any I/O exceptions that may occurchemaxon.marvin.common.swing.action.CommonActions commonActions
public void readExternal(java.io.ObjectInput in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
- if I/O errors occurjava.lang.ClassNotFoundException
- If the class for an object being restored cannot be found.public void writeExternal(java.io.ObjectOutput out) throws java.io.IOException
java.io.IOException
- Includes any I/O exceptions that may occurMViewPane editorComponent
TableSupport tableSupport
boolean preferredSizeSet
chemaxon.marvin.beans.MViewPane.DelayedRepainter delayedRepainter
public void readExternal(java.io.ObjectInput arg0) throws java.io.IOException
java.io.IOException
public void writeExternal(java.io.ObjectOutput arg0) throws java.io.IOException
java.io.IOException
int molIndex
MRecordReader.Position position
java.util.ResourceBundle bundle
java.util.List<E> formats
java.lang.String defaultFormat
javax.swing.JList<E> selectorList
int prevSelectedIdx
int level
CalculatorPlugin plugin
chemaxon.marvin.plugin.gui.CheckList.MCheckBox[] checkboxes
ParameterPanelHandler parameterPanel
java.awt.event.ActionListener okActionListener
java.lang.String key
java.lang.String title
chemaxon.marvin.swing.ActionButton ok
chemaxon.marvin.swing.ActionButton cancel
chemaxon.marvin.swing.ActionButton restoreDefaults
chemaxon.marvin.plugin.gui.ParameterItem[] items
chemaxon.marvin.common.swing.MolPanel mpan
javax.swing.JTextArea bottomTextArea
javax.swing.JComponent bottomComponent
javax.swing.JTextArea topTextArea
javax.swing.JComponent topComponent
javax.swing.JPanel chartPanel
chemaxon.marvin.util.MarvinModule chart
javax.swing.JMenu viewMenu
javax.swing.JMenuItem copymi
javax.swing.JMenuItem popupcopymi
javax.swing.JMenuItem resetmi
javax.swing.JPopupMenu popup
javax.swing.JMenuItem detachmi
Molecule[] viewMols
java.lang.String[] viewTexts
chemaxon.marvin.view.swing.ViewPanel viewPanel
Molecule viewMol
java.lang.String viewText
java.lang.String imageFormat
MDocument[] molHist
java.awt.Point[] cornerHist
double[] scaleHist
int[] autoHydrogenizeHist
int[][] scrollBarHist
boolean[] selectionToZoomHist
MoleculeGraph[][] molgToZoomHist
CTransform3D[] rotateMatrHist
int molHistLen
int molHistCur
int molHistMax
boolean historyOverflow
java.beans.PropertyChangeSupport changeSupport
private void readObject(java.io.ObjectInputStream arg0) throws java.lang.ClassNotFoundException, java.io.IOException
java.lang.ClassNotFoundException
java.io.IOException
chemaxon.marvin.sketch.tool.EditorTool currentTool
int moveMode
boolean persistentMoveMode
MDocument document
MSelectionDocument selectionDoc
java.util.List<E> elements
java.util.Set<E> queryAtoms
java.util.Set<E> extraBonds
java.util.Set<E> atomStrings
java.util.Set<E> disabledAliases
boolean lpEnabled
boolean starEnabled
boolean reactionSupported
double stickdst
double mergedst
chemaxon.marvin.sketch.History history
chemaxon.marvin.paint.internal.MolPainter painter
MDocument curfrag
MDocument prevCurfrag
MoleculeGraph flyingBondMol
boolean curfragMoved
boolean canRotCurfrag
boolean canMovCurfrag
int atomSelectionMode
double curfragR
DPoint3 rotO
DPoint3 rotAxisPoint
boolean isAxisSet
double rotateZPhi
double rotate3dPhiX
double rotate3dPhiY
double rotate3dPhi
double rotate3dx
double rotate3dy
int rotate3direction
Molecule atomBranchPiece
Molecule piece
Molecule pieceOriginalObject
Molecule showMolecule
boolean bondDrawMode
int lastBondFlags
java.lang.String lastQueryBondString
MolAtom jointAtom
com.chemaxon.marvin.editor.molecule.fusion.MolJoin curfragJoin
boolean bondDraggedAlong
boolean historizeEnabled
boolean documentEdited
boolean isDataSgroupLabelPointed
DataSgroup dataSgroupObject
boolean hadSelection
int[] scrollBarVals
MDocument lastSelectionDoc
java.awt.Point lastSelectionCorner
double lastSelectionScale
boolean selectionHistorized
boolean historizeUnSelection
boolean deleteRemovesTerminalAtoms
int rotation3DMode
boolean newKeyboardMotion
DPoint3[] selectionHPoints
chemaxon.marvin.space.MSpaceEventHandler eventHandler
chemaxon.marvin.space.gui.JMSpaceProgressBar progressBar
int rowCount
int columnCount
int activeCell
GraphicCell[] cells
int cellCount
int needsRefresh
int needsReset
boolean initialized
boolean antialias
boolean synchronousMode
int verboseLevel
int motionmode
int width
int height
float[] backgroundColor
boolean backgroundColorChanged
int transparentBackground
boolean smoothBackground
double rx
double ry
double rz
javax.media.opengl.GL2 gl
javax.media.opengl.glu.GLU glu
javax.media.opengl.GLAutoDrawable glAutoDrawable
java.awt.Component canvas
chemaxon.marvin.space.util.GLText gltext
java.util.ArrayList<E> _glListsToDelete
java.util.Properties globalDrawProperties
java.util.Map<K,V> defaultDrawProperties
UserSettings userSettings
chemaxon.marvin.space.gl.shader.RenderTargets renderTargets
chemaxon.marvin.uif.dialog.model.CategoriesModel model
java.util.ResourceBundle bundle
chemaxon.marvin.uif.module.GUIModule module
java.util.ResourceBundle bundle
chemaxon.marvin.uif.dialog.model.CustomizeGUIModel model
chemaxon.marvin.uif.model.GUIRegistry guiRegistryClone
chemaxon.marvin.uif.module.ModuleConfiguration moduleConf
chemaxon.marvin.uif.dialog.model.MenuManagerModel model
java.util.ResourceBundle bundle
java.util.ResourceBundle bundle
chemaxon.marvin.uif.dialog.model.ItemGroupModel model
chemaxon.marvin.uif.dialog.model.PopupManagerModel model
java.util.ResourceBundle bundle
chemaxon.marvin.uif.dialog.model.ShortcutModel model
java.util.ResourceBundle bundle
java.util.ResourceBundle bundle
chemaxon.marvin.uif.dialog.model.ToolBarManagerModel model
java.util.concurrent.Semaphore sp
java.lang.String emfExportOptions
MSketchPane msketch
chemaxon.marvin.sketch.swing.SketchPanel sketchPanel
java.util.concurrent.Semaphore semaphore
boolean importExceptionCaught
boolean retainGUIPropertiesOnPanel
MPropertyContainer structureGUIProperties
javax.swing.text.DefaultStyledDocument doc
javax.swing.text.Element rootElement
boolean multiLineComment
javax.swing.text.MutableAttributeSet normal
javax.swing.text.MutableAttributeSet comment
javax.swing.text.MutableAttributeSet quote
javax.swing.text.MutableAttributeSet keyword
javax.swing.text.MutableAttributeSet function
javax.swing.text.MutableAttributeSet parenthesis
javax.swing.text.MutableAttributeSet constant
java.util.Map<K,V> keywords
java.util.Map<K,V> functions
java.util.Map<K,V> constants
int fontSize
java.lang.String fontName
int parenOffset
int parenLength
int currentElementIndex
java.lang.String prefix
boolean lastPrefixState
javax.swing.Timer HIGHLIGHT_TIMER
javax.swing.JScrollPane macroListScroll
javax.swing.JList<E> macroList
javax.swing.JButton addButton
javax.swing.JButton editButton
javax.swing.JButton deleteButton
javax.swing.JPanel listPanel
javax.swing.JPanel editPanel
java.awt.CardLayout layout
javax.swing.JButton acceptButton
javax.swing.JButton cancelButton
javax.swing.JTextField nameField
javax.swing.JScrollPane descScrollPane
javax.swing.JScrollPane macroScrollPane
javax.swing.JTextPane macroPane
javax.swing.JTextPane descPane
javax.swing.JButton acceptEditButton
javax.swing.JButton cancelEditButton
int editedItem
chemaxon.marvin.util.codeassist.CodeAssistMacrosHelper helper
javax.swing.Action ACCEPT_ACTION
javax.swing.Action CANCEL_ACTION
int recordIndex
java.lang.String[] listData1
java.lang.String[] listData2
javax.swing.JList<E> list1
javax.swing.JList<E> list2
javax.swing.JButton addButton
javax.swing.JButton addAllButton
javax.swing.JButton removeButton
javax.swing.JButton removeAllButton
boolean allSelected
private void writeObject(java.io.ObjectOutputStream arg0) throws java.io.IOException
java.io.IOException
chemaxon.marvin.swing.MAction windowAction
MDocument document
boolean inZoomWindow
int markedAtom
int highlightedAtom
chemaxon.marvin.view.swing.ViewPanel viewPanel
chemaxon.marvin.view.swing.modules.MViewFrame viewFrame
int cellIndex
double winScale
DPoint3 moleculeCenter
java.awt.Dimension preferredSize1
java.awt.Dimension rsize
boolean error
chemaxon.marvin.paint.internal.MolPainter painter
java.awt.Color moleculeBackground
java.util.Vector<E> nextV
boolean rescaleNeeded
boolean debug
chemaxon.marvin.view.swing.VisibleDocuments visibleDocs
chemaxon.marvin.view.swing.CellFiller cellFiller
private void readObject(java.io.ObjectInputStream arg0) throws java.lang.ClassNotFoundException, java.io.IOException
java.lang.ClassNotFoundException
java.io.IOException
java.awt.Window molFrame0
chemaxon.marvin.view.swing.ViewActions viewActions
chemaxon.marvin.swing.MAction[] navigationActions
java.lang.String[] molStrings
java.lang.String molString
java.lang.String[] rasmolScripts
chemaxon.marvin.common.AtomSelectionHandler[] moleculeSelections
chemaxon.marvin.view.swing.ViewHandler viewHandler
java.awt.Font defaultFieldFont
java.util.Map<K,V> fieldFontMap
javax.swing.Action findAction
javax.swing.Action findAgainAction
javax.swing.Action clearStateOnOpenAction
double winScale
int borderWidth
java.awt.Color borderColor
double tabScale
boolean autoTabScale
boolean tabScaleCalcNeeded
boolean animSynchronized
boolean startLoad
int rows
int cols
chemaxon.marvin.view.swing.modules.MViewAnimator animator
boolean selectable
int editable
boolean importEnabled
chemaxon.marvin.view.modules.sketchbridge.MViewSketch skbridge
chemaxon.marvin.view.swing.modules.FindText findTextModule
int selected
boolean detachable
int tabScaleCalcInProgress
boolean draggable
java.util.Map<K,V> molbgMap
TableSupport tableSupport
chemaxon.marvin.common.swing.action.CommonActions commonActions
boolean molEdited
int oldMarkedCell
int oldMarkedAtom
boolean atomMarkAndHighlightEnabled
int options
java.awt.Toolkit toolkit
java.text.NumberFormat integerFormatter
java.lang.String casNumber
java.lang.String casNumber
chemaxon.naming.n2s.lex.data.Token[] tokens
java.lang.String prefix
java.lang.String token
Molecule mol
int hashcode
long grinvCC
java.lang.String representation
int data
java.lang.String id
RxnMolecule rxn
java.lang.String reactantMatchingRule
java.lang.String reactivityRule
java.lang.String selectivityRule
double[] tolerances
int[] map2nopar
int[] map2map
int[] smaps
int[] emaps
int[] rbondtypes
int[] pbondtypes
int bcount
int[] map2stereo
java.util.List<E>[] rmaps
java.util.List<E>[] pmaps
int[] map2raindex
int[] map2paindex
int[] map2rindex
int[] map2pindex
int[] rindex2map
int[] pindex2map
java.util.ArrayList<E> rparities
java.util.ArrayList<E> pparities
java.util.ArrayList<E> rcistrans
java.util.ArrayList<E> pcistrans
Molecule[] reactants
Molecule[] products
chemaxon.reaction.Reaction reaction
chemaxon.reaction.ReactionSearcher searcher
ReactionContext context
int[] origmaps
java.util.ArrayList<E> rligandsets
java.util.ArrayList<E> rcistranssets
Molecule[] reactants
Molecule[] currentReactants
java.util.ArrayList<E> productsets
chemaxon.reaction.ProductSet transformedProductSet
boolean absStereo
chemaxon.reaction.ReactorOptions options
java.lang.String baseProductID
int globalProductIndex
java.util.Properties reactantProperties
java.util.ArrayList<E> stgrpMap
java.util.Map<K,V> reactionMap
chemaxon.reaction.ReactorLogger reactorLogger
java.lang.String licenseEnvironment
chemaxon.reaction.ReactionResultEnumerator rre
chemaxon.reaction.Reaction reaction
chemaxon.reaction.ReactionPerformer performer
Standardizer explicitStandardizer
Standardizer reactionDefinedStandardizer
boolean ignoreReactionDefinedStandardizer
Reactor.reactionDefinedStandardizer
.int outputReactionMappingStyle
int fakeResultType
Reactor.FUSED_REACTION_OUTPUT
Molecule[] originalInputReactants
Molecule[] reactants
boolean first
int pieces
int currentPieces
chemaxon.reaction.ReactorOptions options
int resultType
int duplicateFilteringMethod
int ignoreRules
int[] ratio
int[] pinds
boolean reverse
boolean excludeOverlappingHits
boolean mapResult
boolean single
boolean rmduprefs
boolean cached
java.lang.String searchOptionsString
java.lang.String reactionIDProp
java.lang.String[] reactantIDProps
java.lang.String[] productIDProps
boolean copyAllReactantProperties
java.lang.String[][] sourceProperties
java.lang.String[][] targetProperties
java.util.Map<K,V> patternBasedProperties
boolean showUnsuccessfulReactions
boolean generateMinorProducts
boolean markReactionCenter
java.util.ArrayList<E> hitDataList
boolean complete
int absoluteStereo
java.lang.String filterQuery
float dissimilarityThreshold
boolean dissimilarityThresholdExcluded
int maxResultCount
boolean returnsNonHits
java.lang.String dissimilarityMetric
null
for default.java.lang.String dissimilarityMetricParameters
java.lang.String descriptorConfig
java.lang.String descriptorName
null
means pure fingerprint similarity is performedint formulaSearchType
java.lang.String formulaSearchQuery
MatchCountOptions matchCountOptions
boolean optimizeQueries
boolean cacheRegistrationNeeded
int totalSearchTimeoutLimitMilliseconds
java.util.Set<E> markushScreeningOptions
HaltOnErrorOption haltOnError
HaltOnErrorOption
int type
int[] data
MarkushFeature.RGROUP
: {R-atom union index, R-group definition index}MarkushFeature.LINKNODE
: {link atom union index}MarkushFeature.REPUNIT
: {RepeatingUnitSgroup sgroup index in markush}MarkushFeature.ATOMLIST
: {list atom union index}MarkushFeature.BONDLIST
: {list bond union bond index}MarkushFeature.MULTIBOND
: {union bond index, MulticenterSgroup sgroup index in markush}RgMolecule.findRgroupIndex(int)
.int hashCode
boolean matchCountIncludesZero
int mode
int matchCountLowLimit
int matchCountHighLimit
boolean matchCountLowLimitInclusive
boolean matchCountHighLimitInclusive
int matchCounthitLimit
java.lang.String matchCountRelation
chemaxon.common.util.IntVector ignoreChiralityForAtoms
boolean hitIncludesRNodes
boolean queryAbsoluteStereo
boolean targetAbsoluteStereo
int hitIndexType
boolean markushEnabled
boolean recursiveSMARTSMode
boolean switchOffAllProtectsForTDF
chemaxon.sss.search.options.TautomerTransformationMode tautomerEqualityMode
boolean dirty
boolean exactQueryAtomMatching
int doubleBondStereoMatchingMode
SearchOptions.setDoubleBondStereoMatchingMode(int)
int hCountMatching
boolean verbose
int searchType
int vagueBondLevel
SearchConstants.VAGUE_BOND_LEVEL_HALF
boolean completeHG
boolean exactBondMatching
boolean orderSensitiveSearch
boolean keepQueryOrder
boolean tautomerSearch
int tautomerSearchOption
boolean tautomerSearchOptionLeftDefault
int isotopeMatching
int chargeMatching
boolean valenceMatching
int radicalMatching
boolean mixSgroupMatching
boolean polymerMatching
boolean endGroupMatching
boolean transformMonomer
boolean phaseShift
boolean copolymerMatching
HomologyTranslationOption homologyNarrowTranslation
HomologyTranslationOption homologyBroadTranslation
SetOfSmallestRingsOption ssrOption
int stereoModel
int stereoSearchType
SearchConstants.STEREO_SPECIFIC
.SearchOptions.setStereoSearchType(int)
boolean ignoreTetrahedralStereo
boolean ignoreDoubleBondStereo
boolean ignoreAxialStereo
boolean ignoreCumuleneCisTransStereo
boolean ignoreSynAntiStereo
boolean checkSpHyb
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.int implicitHMatching
boolean reactionUnpairedMapMatching
int undefinedRAtom
SearchConstants.UNDEF_R_MATCHING_GROUP
.boolean undefinedRAtomUserDefined
boolean bridgingRAllowed
boolean rLigandEqualityCheck
int hitOrdering
SearchConstants.HIT_ORDERING_NONE
.int attachedDataMatch
SearchConstants.ATTACHED_DATA_MATCH_IGNORE
java.lang.String attachedDataPrefixes
java.lang.String exactSpecialAtomMatching
chemaxon.sss.search.options.ChemTermsFilterOption chemTermsFilterOption
boolean changedUserComparator
java.util.ArrayList<E> userComparators
int exhaustiveModeLimit
int timeoutLimitMilliseconds
boolean throwExceptionOnTimeout
MarkushAromaticityHandlingOption markushAromHandling
MarkushAromaticityHandlingOption.ALL_MATCH_AMBIG
: consider Markush
aromatization during Markush search, but do not check the hit afterwards.TargetHomologyMatchingMode targetHomologyMatchingMode
java.lang.String chemTermsFilter
java.lang.String chemTermsFilterConfig
boolean ignoreCTExceptions
public void readExternal(java.io.ObjectInput in) throws java.io.IOException
java.io.IOException
public void writeExternal(java.io.ObjectOutput out) throws java.io.IOException
java.io.IOException
public void readExternal(java.io.ObjectInput in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
public void writeExternal(java.io.ObjectOutput out) throws java.io.IOException
java.io.IOException
Sgroup attachParentSgroup
short valence1
int order
java.util.Map<K,V> qprops
java.lang.String querystr
java.lang.String aliasstr
java.lang.String extrastr
long extrargbs
int[] list
int flags
short rgroupId
int countFlags
int repetitionBits
int linkNodeOuterBonds
int electronProp
java.util.Map<K,V> temporaryObjects
private void readObject(java.io.ObjectInputStream ois) throws java.lang.ClassNotFoundException, java.io.IOException
java.lang.ClassNotFoundException
java.io.IOException
private void writeObject(java.io.ObjectOutputStream oos) throws java.io.IOException
java.io.IOException
MDocument doc
private void readObject(java.io.ObjectInputStream ois) throws java.io.IOException
java.io.IOException
private void writeObject(java.io.ObjectOutputStream oos) throws java.io.IOException
java.io.IOException
private void readObject(java.io.ObjectInputStream ois) throws java.lang.ClassNotFoundException, java.io.IOException
java.lang.ClassNotFoundException
java.io.IOException
private void writeObject(java.io.ObjectOutputStream oos) throws java.io.IOException
java.io.IOException
boolean isValenceCheckNeeded
double angle
private void readObject(java.io.ObjectInputStream ois) throws java.lang.ClassNotFoundException, java.io.IOException
java.lang.ClassNotFoundException
java.io.IOException
private void writeObject(java.io.ObjectOutputStream oos) throws java.io.IOException
java.io.IOException
private void readObject(java.io.ObjectInputStream ois) throws java.lang.ClassNotFoundException, java.io.IOException
java.lang.ClassNotFoundException
java.io.IOException
private void writeObject(java.io.ObjectOutputStream oos) throws java.io.IOException
java.io.IOException
java.lang.String id
private void readObject(java.io.ObjectInputStream ois) throws java.lang.ClassNotFoundException, java.io.IOException
java.lang.ClassNotFoundException
java.io.IOException
private void writeObject(java.io.ObjectOutputStream oos) throws java.io.IOException
java.io.IOException
boolean hasBicycloStereo
MolAtom.setBicycloStereo(BicycloStereoDescriptor[])
.ValenceCheckOptions valenceCheckOptions
chemaxon.struc.MoleculeGraph.FragmentTracker fragmentTracker
private void readObject(java.io.ObjectInputStream ois) throws java.lang.ClassNotFoundException, java.io.IOException
java.lang.ClassNotFoundException
java.io.IOException
private void writeObject(java.io.ObjectOutputStream oos) throws java.io.IOException
java.io.IOException
long grinvCC
boolean coordDependent
public void readExternal(java.io.ObjectInput in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
- if I/O errors occurjava.lang.ClassNotFoundException
- If the class for an object being
restored cannot be found.public void writeExternal(java.io.ObjectOutput out) throws java.io.IOException
java.io.IOException
- Includes any I/O exceptions that may occurpublic void readExternal(java.io.ObjectInput arg0) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
public void writeExternal(java.io.ObjectOutput arg0) throws java.io.IOException
java.io.IOException
private void readObject(java.io.ObjectInputStream ois) throws java.lang.ClassNotFoundException, java.io.IOException
java.lang.ClassNotFoundException
java.io.IOException
private void writeObject(java.io.ObjectOutputStream oos) throws java.io.IOException
java.io.IOException
private void readObject(java.io.ObjectInputStream ois) throws java.lang.ClassNotFoundException, java.io.IOException
java.lang.ClassNotFoundException
java.io.IOException
private void writeObject(java.io.ObjectOutputStream oos) throws java.io.IOException
java.io.IOException
private void readObject(java.io.ObjectInputStream ois) throws java.lang.ClassNotFoundException, java.io.IOException
java.lang.ClassNotFoundException
java.io.IOException
private void writeObject(java.io.ObjectOutputStream oos) throws java.io.IOException
java.io.IOException
private void readObject(java.io.ObjectInputStream ois) throws java.lang.ClassNotFoundException, java.io.IOException
java.lang.ClassNotFoundException
java.io.IOException
private void writeObject(java.io.ObjectOutputStream oos) throws java.io.IOException
java.io.IOException
java.lang.String id
java.util.Set<E> atomSet
boolean ringPerception
java.lang.String name
int arrayFlags
int atomCount
short[] connectionTable
byte[] neighborCount
short[][] nodeEdgeList
int bondCount
short[] atomType
short[] bondAtom1
short[] bondAtom2
int[] bondFlags
int[] extendedAtomType
byte[][] atomLists
byte[] hybridization
byte[] atomStereo
byte[] implicitHcount
byte[] explicitHcount
byte[] valence
byte[][] queryProperty
byte[] radical
byte[] charge
byte[] massno
short[] atomMap
short[] rgroupId
java.lang.String[] sgroupId
Molecule mol
java.util.List<E> terms
int order
private void readObject(java.io.ObjectInputStream ois) throws java.lang.ClassNotFoundException, java.io.IOException
java.lang.ClassNotFoundException
java.io.IOException
private void writeObject(java.io.ObjectOutputStream oos) throws java.io.IOException
java.io.IOException
private void readObject(java.io.ObjectInputStream ois) throws java.io.IOException
java.io.IOException
private void writeObject(java.io.ObjectOutputStream oos) throws java.io.IOException
java.io.IOException
int bracketType
int bracketOrientation
private void readObject(java.io.ObjectInputStream ois) throws java.lang.ClassNotFoundException, java.io.IOException
java.lang.ClassNotFoundException
java.io.IOException
private void writeObject(java.io.ObjectOutputStream oos) throws java.io.IOException
java.io.IOException
private void readObject(java.io.ObjectInputStream ois) throws java.io.IOException
java.io.IOException
private void writeObject(java.io.ObjectOutputStream oos) throws java.io.IOException
java.io.IOException
int baseElectronContainerIndex
int baseElectronIndexInContainer
private void readObject(java.io.ObjectInputStream ois) throws java.lang.ClassNotFoundException, java.io.IOException
java.lang.ClassNotFoundException
java.io.IOException
private void writeObject(java.io.ObjectOutputStream oos) throws java.io.IOException
java.io.IOException
int electronIndex
java.lang.String electronLabel
private void readObject(java.io.ObjectInputStream arg0) throws java.io.IOException
java.io.IOException
private void writeObject(java.io.ObjectOutputStream arg0) throws java.io.IOException
java.io.IOException
DPoint3 difLoc
boolean isPointed
private void readObject(java.io.ObjectInputStream arg0) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
private void writeObject(java.io.ObjectOutputStream arg0) throws java.io.IOException
java.io.IOException
chemaxon.struc.graphics.MElectron[] electrons
boolean[] electronOccupation
boolean radical
private void readObject(java.io.ObjectInputStream ois) throws java.lang.ClassNotFoundException, java.io.IOException
java.lang.ClassNotFoundException
java.io.IOException
private void writeObject(java.io.ObjectOutputStream oos) throws java.io.IOException
java.io.IOException
private void readObject(java.io.ObjectInputStream ois) throws java.lang.ClassNotFoundException, java.io.IOException
java.lang.ClassNotFoundException
java.io.IOException
private void writeObject(java.io.ObjectOutputStream oos) throws java.io.IOException
java.io.IOException
private void readObject(java.io.ObjectInputStream ois) throws java.lang.ClassNotFoundException, java.io.IOException
java.lang.ClassNotFoundException
java.io.IOException
private void writeObject(java.io.ObjectOutputStream oos) throws java.io.IOException
java.io.IOException
private void readObject(java.io.ObjectInputStream arg0) throws java.lang.ClassNotFoundException, java.io.IOException
java.lang.ClassNotFoundException
java.io.IOException
private void writeObject(java.io.ObjectOutputStream arg0) throws java.io.IOException
java.io.IOException
private void readObject(java.io.ObjectInputStream arg0) throws java.lang.ClassNotFoundException, java.io.IOException
java.lang.ClassNotFoundException
java.io.IOException
private void writeObject(java.io.ObjectOutputStream arg0) throws java.io.IOException
java.io.IOException
private void readObject(java.io.ObjectInputStream ois) throws java.lang.ClassNotFoundException, java.io.IOException
java.lang.ClassNotFoundException
java.io.IOException
private void writeObject(java.io.ObjectOutputStream oos) throws java.io.IOException
java.io.IOException
int internalPointPos
int internalPointAddCount
private void readObject(java.io.ObjectInputStream arg0) throws java.lang.ClassNotFoundException, java.io.IOException
java.lang.ClassNotFoundException
java.io.IOException
private void writeObject(java.io.ObjectOutputStream arg0) throws java.io.IOException
java.io.IOException
private void readObject(java.io.ObjectInputStream ois) throws java.lang.ClassNotFoundException, java.io.IOException
java.lang.ClassNotFoundException
java.io.IOException
private void writeObject(java.io.ObjectOutputStream oos) throws java.io.IOException
java.io.IOException
private void readObject(java.io.ObjectInputStream ois) throws java.lang.ClassNotFoundException, java.io.IOException
java.lang.ClassNotFoundException
java.io.IOException
private void writeObject(java.io.ObjectOutputStream oos) throws java.io.IOException
java.io.IOException
private void readObject(java.io.ObjectInputStream ois) throws java.lang.ClassNotFoundException, java.io.IOException
java.lang.ClassNotFoundException
java.io.IOException
private void writeObject(java.io.ObjectOutputStream oos) throws java.io.IOException
java.io.IOException
double arcWidth
double arcHeight
public void readExternal(java.io.ObjectInput in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
public void writeExternal(java.io.ObjectOutput out) throws java.io.IOException
java.io.IOException
private void readObject(java.io.ObjectInputStream ois) throws java.lang.ClassNotFoundException, java.io.IOException
java.lang.ClassNotFoundException
java.io.IOException
private void writeObject(java.io.ObjectOutputStream oos) throws java.io.IOException
java.io.IOException
javax.swing.ActionMap actionMap
public void readExternal(java.io.ObjectInput in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
- if I/O errors occurjava.lang.ClassNotFoundException
- If the class for an object being
restored cannot be found.public void writeExternal(java.io.ObjectOutput out) throws java.io.IOException
java.io.IOException
- Includes any I/O exceptions that may occurprivate void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
- if I/O errors occurjava.lang.ClassNotFoundException
- If the class for an object being
restored cannot be found.private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
- Includes any I/O exceptions that may occurprivate void readObject(java.io.ObjectInputStream arg0) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
private void writeObject(java.io.ObjectOutputStream arg0) throws java.io.IOException
java.io.IOException
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
- if I/O errors occurjava.lang.ClassNotFoundException
- If the class for an object being
restored cannot be found.private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
- Includes any I/O exceptions that may occurprivate void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
- if I/O errors occurjava.lang.ClassNotFoundException
- If the class for an object being
restored cannot be found.private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
- Includes any I/O exceptions that may occurprivate void readObject(java.io.ObjectInputStream arg0) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
private void writeObject(java.io.ObjectOutputStream arg0) throws java.io.IOException
java.io.IOException
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
- if I/O errors occurjava.lang.ClassNotFoundException
- If the class for an object being
restored cannot be found.private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
- Includes any I/O exceptions that may occurprivate void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
- if I/O errors occurjava.lang.ClassNotFoundException
- If the class for an object being
restored cannot be found.private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
- Includes any I/O exceptions that may occurprivate void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
- if I/O errors occurjava.lang.ClassNotFoundException
- If the class for an object being
restored cannot be found.private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
- Includes any I/O exceptions that may occurprivate void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
- if I/O errors occurjava.lang.ClassNotFoundException
- If the class for an object being
restored cannot be found.private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
- Includes any I/O exceptions that may occurprivate void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
- if I/O errors occurjava.lang.ClassNotFoundException
- If the class for an object being
restored cannot be found.private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
- Includes any I/O exceptions that may occurprivate void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
- if I/O errors occurjava.lang.ClassNotFoundException
- If the class for an object being
restored cannot be found.private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
- Includes any I/O exceptions that may occurprivate void readObject(java.io.ObjectInputStream arg0) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
private void writeObject(java.io.ObjectOutputStream arg0) throws java.io.IOException
java.io.IOException
java.lang.String format
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
- if I/O errors occurjava.lang.ClassNotFoundException
- If the class for an object being
restored cannot be found.private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
- Includes any I/O exceptions that may occurprivate void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
- if I/O errors occurjava.lang.ClassNotFoundException
- If the class for an object being
restored cannot be found.private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
- Includes any I/O exceptions that may occurprivate void readObject(java.io.ObjectInputStream arg0) throws java.lang.ClassNotFoundException, java.io.IOException
java.lang.ClassNotFoundException
java.io.IOException
private void writeObject(java.io.ObjectOutputStream arg0) throws java.io.IOException
java.io.IOException
java.lang.String oneLetterName
java.lang.String threeLetterName
boolean modified
private void readObject(java.io.ObjectInputStream ois) throws java.lang.ClassNotFoundException, java.io.IOException
java.lang.ClassNotFoundException
java.io.IOException
private void writeObject(java.io.ObjectOutputStream oos) throws java.io.IOException
java.io.IOException
java.lang.StringBuffer sb
chemaxon.struc.sgroup.DataSgroup.AbstractPosition labelPosition
private void readObject(java.io.ObjectInputStream arg0) throws java.lang.ClassNotFoundException, java.io.IOException
java.lang.ClassNotFoundException
java.io.IOException
private void writeObject(java.io.ObjectOutputStream arg0) throws java.io.IOException
java.io.IOException
java.lang.String alternativeName
private void readObject(java.io.ObjectInputStream ois) throws java.lang.ClassNotFoundException, java.io.IOException
java.lang.ClassNotFoundException
java.io.IOException
private void writeObject(java.io.ObjectOutputStream oos) throws java.io.IOException
java.io.IOException
private void readObject(java.io.ObjectInputStream ois) throws java.lang.ClassNotFoundException, java.io.IOException
java.lang.ClassNotFoundException
java.io.IOException
private void writeObject(java.io.ObjectOutputStream oos) throws java.io.IOException
java.io.IOException
SgroupAtom sga
private void readObject(java.io.ObjectInputStream ois) throws java.lang.ClassNotFoundException, java.io.IOException
java.lang.ClassNotFoundException
java.io.IOException
private void writeObject(java.io.ObjectOutputStream oos) throws java.io.IOException
java.io.IOException
private void readObject(java.io.ObjectInputStream ois) throws java.lang.ClassNotFoundException, java.io.IOException
java.lang.ClassNotFoundException
java.io.IOException
private void writeObject(java.io.ObjectOutputStream oos) throws java.io.IOException
java.io.IOException
int labelCenter
private void readObject(java.io.ObjectInputStream ois) throws java.lang.ClassNotFoundException, java.io.IOException
java.lang.ClassNotFoundException
java.io.IOException
private void writeObject(java.io.ObjectOutputStream oos) throws java.io.IOException
java.io.IOException
chemaxon.struc.sgroup.AttachmentPointContainer apContainer
boolean stereoSearch
int doubleBondStereoMatchingMode
boolean subgraphSearch
boolean exactAtomMatching
boolean exactStereoMatching
boolean orderSensitiveSearch
int inputIndex
boolean keepUnsaturatedConnections
java.util.List<E> indexToFramework
DescriptorGenerator<B extends Descriptor> generator
AbstractShapeGeneratorParameter parameters
AtomTyping atomTyping
AlignmentProperties.FlexibilityMode flexibilityMode
ShapeFunction shapeFunction
com.google.common.base.Optional<T> tryCount
int bitsPerPattern
int length
int bondCount
boolean rings
int diameter
int length
EcfpAtomTypizers atomTypizer
com.google.common.base.Optional<T> identifierConfigurationXml
EcfpParameters params
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit1
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit2
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit8
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com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit162
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit163
com.chemaxon.descriptors.fingerprints.maccs.GsSearch bit165
Molecule mol
java.util.BitSet ringAtoms
Molecule mol
java.util.BitSet ringBonds
com.google.common.base.Optional<T> xmlConfig
PharmacophoreFingerprint fingerprint
com.google.common.base.Optional<T> xmlConfig
double coeffTarget
double coeffQuery
BvParameters parameters
int length
BvParameters.StringFormat stringFormat
BinaryVectors.Endianness endianness
FvParameters parameters
int length
FvParameters.NumericRepresentation numericRepresentation
double scaledMin
double scaledMax
FvParameters.SparseCompression sparseCompression
long size
com.chemaxon.descriptors.common.reflect.SerializableFunction<F,T> listToPage
com.chemaxon.descriptors.common.reflect.SerializableBiFunction<T,U,R> getFromPage
long initialSkips
int pageSize
java.util.List<E> builtPages
java.util.List<E> currentPage
java.lang.Class<T> elementType
long totalSize
long totalAbsents
java.util.List<E> pages
java.lang.Class<T> elementType
com.chemaxon.descriptors.common.reflect.SerializableBiFunction<T,U,R> getFromPage
long initialSkips
int pageSize
long totalSize
long totalAbsents
int pagesize
long absentCount
long size
long storedByteCount
long skips
int[][] starts
byte[][] storage
long size
long bytes
long skips
long absentCount
int pageSize
int pageCount
int lastPageSize
long storeStart
int[] storeSizes
java.lang.String importOptsOrNull
com.chemaxon.overlap.io.CompactStringStorage sources