Serialized Form

Package chemaxon.calculations

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

serialVersionUID: 1L

Package chemaxon.formats

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

Serialized Fields

lineNumberInRecord

int lineNumberInRecord

lineNumberInFile

int lineNumberInFile

Package chemaxon.jep

Class chemaxon.jep.ChemContext extends java.lang.Object implements Serializable

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

Serialized Fields

jep

ChemJEP jep

The JEP object.

cached

boolean cached

True if cache mode (evalutaion results are stored in molecule property objects).

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

Serialized Fields

contextClass

java.lang.Class<T> contextClass

The evaluation context class.

context

ChemContext context

The evaluation context object.

Class chemaxon.jep.ConditionException extends java.lang.Exception implements Serializable

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

Serialized Fields

name

java.lang.String name

The context element callback function name.

jep

ChemJEP jep

The JEP object.

Class chemaxon.jep.DissimilarityFunction extends chemaxon.jep.ChemFunction implements Serializable

Serialized Fields

className

java.lang.String className

Name of the class which is used for dissimilarity calculation. Must be a subclass of this class.

descriptors

java.lang.String[] descriptors

The list of descriptors (predefined type names or class names)

Class chemaxon.jep.Evaluator extends java.lang.Object implements Serializable

Serialized Fields

builtInConfig

chemaxon.jep.EvaluatorConfiguration builtInConfig

The configuration object containing default function/plugin declarations.

externalConfig

chemaxon.jep.EvaluatorConfiguration externalConfig

The configuration object containing external function/plugin declarations.

userConfig

chemaxon.jep.EvaluatorConfiguration userConfig

The configuration object containing user defined function/plugin declarations.

config

chemaxon.jep.EvaluatorConfiguration config

The configuration object.

servicesFunctionTable

java.util.Hashtable<K,V> servicesFunctionTable

Function table for services.

symtab

chemaxon.nfunk.jep.SymbolTable symtab

The base symbol table.

functionalGroupDisplayMolTable

java.util.Hashtable<K,V> functionalGroupDisplayMolTable

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

verbose

boolean verbose

True if verbose output.

licenseEnvironment

java.lang.String licenseEnvironment

Class chemaxon.jep.EvaluatorFunction extends chemaxon.jep.ChemFunction implements Serializable

Serialized Fields

evaluator

Evaluator evaluator

The evaluator object.

Class chemaxon.jep.MatchFunction extends chemaxon.jep.ChemFunction implements Serializable

Serialized Fields

className

java.lang.String className

subMatches

java.util.Hashtable<K,V> subMatches

Query string -> MatchFunction object table used for processing query collections.

type

int type

The result type: MatchFunction.CHECK, MatchFunction.COUNT or MatchFunction.DISJOINT_COUNT.

attributes

chemaxon.util.SearchAttributes attributes

The search attribute storing object.

dir

java.lang.String dir

The config file directory (root dir for query rel. path).

standardizer

Standardizer standardizer

licenseEnvironment

java.lang.String licenseEnvironment

Package chemaxon.jep.context

Class chemaxon.jep.context.AtomContext extends MolContext implements Serializable

Serialized Fields

atom

int atom

The input atom index.

Class chemaxon.jep.context.MolContext extends ChemContext implements Serializable

Serialized Fields

mol

Molecule mol

The input molecule.

fingerprint

int[] fingerprint

Fingerprint of the input molecule.

Class chemaxon.jep.context.ReactionContext extends ChemContext implements Serializable

Serialized Fields

reactants

Molecule[] reactants

The reactants.

products

Molecule[] products

The products.

map2ratom

MolAtom[] map2ratom

The map -> reactant atom array.

map2patom

MolAtom[] map2patom

The map -> product atom array.

copy

boolean copy

True if map arrays should be copied.

Class chemaxon.jep.context.SearchContext extends MolContext implements Serializable

Serialized Fields

query

Molecule query

The query molecule.

queryFingerprint

int[] queryFingerprint

Fingerprint of the query molecule.

map

int[] map

The map -> query atom index array.

hit

int[] hit

The hit: query atom index -> target atom index array, with negative target atom indices denoting matches on implicit H-s.

Package chemaxon.license

Class chemaxon.license.LicenseException extends java.lang.RuntimeException implements Serializable

Serialized Fields

product

java.lang.String product

Class chemaxon.license.LicenseProcessingException extends java.lang.Exception implements Serializable

Package chemaxon.marvin

Class chemaxon.marvin.Sketch extends javax.swing.JFrame implements Serializable

Serialized Fields

sketchPane

MSketchPane sketchPane

outSerName

java.lang.String outSerName

newWindowAction

javax.swing.Action newWindowAction

exitAction

javax.swing.Action exitAction

Class chemaxon.marvin.View extends javax.swing.JFrame implements Serializable

Serialized Fields

colorKeys

java.util.List<E> colorKeys

viewPane

MViewPane viewPane

The MarvinView bean.

realTimeMovieThread

java.lang.Thread realTimeMovieThread

openAction

javax.swing.Action openAction

printAction

javax.swing.Action printAction

exitAction

javax.swing.Action exitAction

hasInitalized

boolean hasInitalized

Package chemaxon.marvin.alignment

Class chemaxon.marvin.alignment.AlignmentException extends java.lang.Exception implements Serializable

Class chemaxon.marvin.alignment.AlignmentMolecule extends java.lang.Object implements Serializable

Serialized Fields

nodes

chemaxon.marvin.alignment.NodeList<T extends chemaxon.marvin.alignment.Node> nodes

mins

double[] mins

maxs

double[] maxs

bonds

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

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

Class chemaxon.marvin.alignment.NodeColor extends java.lang.Object implements Serializable

Serialized Fields

user

java.util.List<E> user

notSpec

AlignmentProperties.ColorNotSpecifiedCase notSpec

scheme

AlignmentProperties.ColoringScheme scheme

Class chemaxon.marvin.alignment.NodeColor.AtomTypeColoring extends chemaxon.marvin.alignment.NodeColor implements Serializable

Class chemaxon.marvin.alignment.NodeColor.ExtendedAtomColoring extends chemaxon.marvin.alignment.NodeColor implements Serializable

Class chemaxon.marvin.alignment.NodeColor.PharmacophoreColoring extends chemaxon.marvin.alignment.NodeColor implements Serializable

Class chemaxon.marvin.alignment.NodeColor.SameColoring extends chemaxon.marvin.alignment.NodeColor implements Serializable

Class chemaxon.marvin.alignment.NoMCSException extends chemaxon.marvin.alignment.AlignmentException implements Serializable

Class chemaxon.marvin.alignment.Status extends java.lang.Object implements Serializable

Serialized Fields

volumeScore

double volumeScore

constraintScore

double constraintScore

stepCount

int stepCount

time

long time

converged

boolean converged

timeLimeitReached

boolean timeLimeitReached

stepLimeitReached

boolean stepLimeitReached

mols

java.util.ArrayList<E> mols

Class chemaxon.marvin.alignment.StatusMol extends java.lang.Object implements Serializable

Serialized Fields

status

int status

alignedCrd

double[][] alignedCrd

molID

int molID

dihedralCount

int dihedralCount

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

Package chemaxon.marvin.beans

Class chemaxon.marvin.beans.MarvinPane extends javax.swing.JRootPane implements Serializable

serialVersionUID: -9042549845769941129L

Serialized Fields

molPanel

chemaxon.marvin.common.swing.MolPanel molPanel

Underlying panel.

params

java.lang.String params

Parameter string.

actionListener

chemaxon.marvin.beans.MarvinPane.MarvinActionListener actionListener

Class chemaxon.marvin.beans.MolRenderer extends javax.swing.JPanel implements Serializable

Serialized Fields

printer

MolPrinter printer

Class chemaxon.marvin.beans.MSketch extends java.lang.Object implements Serializable

serialVersionUID: 0L

Serialization Methods

readExternal

public void readExternal(java.io.ObjectInput in)
                  throws java.io.IOException,
                         java.lang.ClassNotFoundException

Restores the sketcher's state.

Throws:

java.io.IOException - if I/O errors occur

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

writeExternal

public void writeExternal(java.io.ObjectOutput out)
                   throws java.io.IOException

Saves the sketcher's state.

Throws:

java.io.IOException - Includes any I/O exceptions that may occur

Class chemaxon.marvin.beans.MSketchPane extends MarvinPane implements Serializable

serialVersionUID: 602496692422927170L

Serialized Fields

commonActions

chemaxon.marvin.common.swing.CommonActions commonActions

Class chemaxon.marvin.beans.MView extends java.lang.Object implements Serializable

serialVersionUID: 0L

Serialization Methods

readExternal

public void readExternal(java.io.ObjectInput in)
                  throws java.io.IOException,
                         java.lang.ClassNotFoundException

Restores the viewer's state.

Throws:

java.io.IOException - if I/O errors occur

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

writeExternal

public void writeExternal(java.io.ObjectOutput out)
                   throws java.io.IOException

Saves the viewer's state.

Throws:

java.io.IOException - Includes any I/O exceptions that may occur

Class chemaxon.marvin.beans.MViewEditor extends javax.swing.AbstractCellEditor implements Serializable

Serialized Fields

editorComponent

MViewPane editorComponent

Class chemaxon.marvin.beans.MViewPane extends MarvinPane implements Serializable

serialVersionUID: -4430811090653077262L

Serialized Fields

tableSupport

TableSupport tableSupport

preferredSizeSet

boolean preferredSizeSet

myActionListener

java.awt.event.ActionListener myActionListener

Handles menu item actions.

Class chemaxon.marvin.beans.MViewRenderer extends MViewPane implements Serializable

Package chemaxon.marvin.io

Class chemaxon.marvin.io.Encoding extends java.lang.Object implements Serializable

Serialization Methods

readExternal

public void readExternal(java.io.ObjectInput in)
                  throws java.io.IOException

Restores object state. For internal use only!

Throws:

java.io.IOException - if I/O errors occur

writeExternal

public void writeExternal(java.io.ObjectOutput out)
                   throws java.io.IOException

Saves object state.

Throws:

java.io.IOException - Includes any I/O exceptions that may occur

Class chemaxon.marvin.io.MolExportException extends MolExportException implements Serializable

Serialized Fields

molIndex

int molIndex

Class chemaxon.marvin.io.MRecordParseException extends java.lang.Exception implements Serializable

Serialized Fields

position

MRecordReader.Position position

Package chemaxon.marvin.modules

Class chemaxon.marvin.modules.AutoMapper extends chemaxon.marvin.util.MarvinModule implements Serializable

Serialized Fields

reaction

RxnMolecule reaction

current reaction to be auto-mapped

mappingStyle

int mappingStyle

current mapping style (see related constants above)

mappingStrategy

int mappingStrategy

Current mapping strategy. Mapping strategies determine the trafe-off between speed and accuracy.

ignoreH

boolean ignoreH

by default all explicit hydrogens are mapped

iterator

chemaxon.marvin.modules.AutoMapper.RxnMoleculeAtomIterator iterator

iterator to enumerate reactant/product atoms

embeddedIterator

chemaxon.marvin.modules.AutoMapper.RxnMoleculeAtomIterator embeddedIterator

another iterator object used in methods wich are called from inside an iterator loop

productAtomCount

int productAtomCount

total number of atoms on product side

reactantAtomCount

int reactantAtomCount

total number of atoms on reactant side

preMappedAtoms

int[][] preMappedAtoms

atoms that are already mapped in the input reaction

preMappedAtomCount

int preMappedAtomCount

number of direct mapped atoms (mapped in the initial rxn molecule)

preMappedReactantAtomCount

int preMappedReactantAtomCount

number of direct mapped atoms on the reactant side of the reaction

mcsMappedAtoms

int[][] mcsMappedAtoms

atoms that are mapped in an maximum common substructure search

mcsMappedAtomCount

int mcsMappedAtomCount

number of atoms matched by the MCS procedure

initialMapIndex

boolean[] initialMapIndex

Set of initial map indices. Map ids are not neccessarily consecutive, input reaction can contain arbitrary yet valid ids.

fixedMapIndex

boolean[] fixedMapIndex

initial map indices plus those set by mcs based mapping

currentSize

int currentSize

temporarily used during initialisation, size of state[] already used

size

int size

backtrack problem size

maxMapIndex

int maxMapIndex

maximal map index found in either side of the original reaction

currentMapIndex

int currentMapIndex

used in nextMapIndex()

complexityThreshold

double complexityThreshold

lastStopCause

int lastStopCause

stepCountLimit

long stepCountLimit

maximumum allowed number of search steps

stepCountLimitReached

boolean stepCountLimitReached

stepCount

long stepCount

steps taken in current search

timeLimit

long timeLimit

time limit in miliseconds, applied to a single mcs search

startTime

long startTime

state

int[] state

current state in the search space: a number written in a mixed number system; element 0 is the highest order digit; this is the heart of the backtracking procedure

baseNumber

int[] baseNumber

base number of the mixed number system in each position

carry

boolean carry

carry flag of the mixed number state, indicates end of search

pos

int pos

the leftmost position (highest significant digit) where the state represented by the mixed number state does not satisfy solution or partial solution conditions

isWidow

boolean[] isWidow

indicates if a reactant atom is a widow, that is, missing from product side

positionToReactantAtom

int[] positionToReactantAtom

associates digit to reactant side atom index

valueToProductAtom

int[][] valueToProductAtom

associates mixed number digit values to product atoms

productAtomMap

int[][] productAtomMap

current mappings of product atoms

reactantAtomMap

int[][] reactantAtomMap

current mappings of reactant atoms

productAtoms

int[] productAtoms

temporarily used during initialisation: product atom indices to be inserted, see addAtomToBacktracking( int compositeId, int atomNumber, int atomMassno )

reactantMapMatrix

int[] reactantMapMatrix

productMapMatrix

int[] productMapMatrix

maps

int[][] maps

solutions maps stored in order of rank (score), smallest (best) first

scores

float[] scores

scored associated to maps, sorted in ascending order, best first

storedMapsCount

int storedMapsCount

number of stored maps (actual size of maps[][] and scores)

steps

long[] steps

css

chemaxon.marvin.modules.MCS css

common structure search to spped up mapping (decrease search space)

ringFinder

chemaxon.core.calculations.BondClassifier ringFinder

reactantRingCount

int reactantRingCount

productRingCount

int productRingCount

keepAllRings

boolean keepAllRings

if ractant and product side have the same number of rings regardless the number of product, reactants then all rings must be kept intact, there is probably no ring opening or closure

finishedAt

long finishedAt

WIDOWSCORE

int WIDOWSCORE

sortedReactants

Molecule[] sortedReactants

Performs maximum common edge subgraph search on the reaction to find those subgraph of the reactant and the product structures that are identical (isomorph), thus can be mapped directly. This speed up atomapping significantly by reducing the combinatorial degree of freedom (by reducing the number of atoms to be mapped in a trial-and-error like mapping process.

Class chemaxon.marvin.modules.AutoMapperException extends java.lang.Exception implements Serializable

Class chemaxon.marvin.modules.LonePairPainter extends chemaxon.marvin.util.MarvinModule implements Serializable

Serialized Fields

lonePairCoords

java.util.List<E> lonePairCoords

radicalCoords

java.util.List<E> radicalCoords

Class chemaxon.marvin.modules.MChart extends chemaxon.marvin.util.MarvinModule implements Serializable

Serialized Fields

colors

java.awt.Color[] colors

Sample colors.

chart

com.objectplanet.chart.LineChart chart

The wrapped line-chart object.

precision

int precision

Double precision: number of fractional digits.

legendMols

Molecule[] legendMols

Legend molecules (also shown in viewer).

legendTexts

java.lang.String[] legendTexts

Legend texts (hidden, shown in separate viewer).

Class chemaxon.marvin.modules.Spacefill extends chemaxon.marvin.util.MarvinModule implements Serializable

Serialized Fields

bgcolor

java.awt.Color bgcolor

fgcolor

java.awt.Color fgcolor

painter

chemaxon.marvin.paint.internal.MolPainter painter

mag

double mag

colorScheme

int colorScheme

setColoringEnabled

boolean setColoringEnabled

Class chemaxon.marvin.modules.SubstructureSearch.SearchException extends java.lang.RuntimeException implements Serializable

Class chemaxon.marvin.modules.Threedim extends chemaxon.marvin.util.MarvinModule implements Serializable

Serialized Fields

zobjtmp

java.lang.Object[] zobjtmp

Temporarily contains the objects to Z sort.

zobjclean

java.lang.Object[] zobjclean

Contains nulls which to initialize zobjtmp.

zranks

long[] zranks

Contains the Z values of sorting the atoms and bonds.

Package chemaxon.marvin.modules.datatransfer

Class chemaxon.marvin.modules.datatransfer.CopyAsDialog extends chemaxon.marvin.uif.util.swing.AbstractDialog implements Serializable

serialVersionUID: -4564761584830399025L

Serialized Fields

bundle

java.util.ResourceBundle bundle

formats

java.util.List<E> formats

defaultFormat

java.lang.String defaultFormat

selectorList

javax.swing.JList selectorList

prevSelectedIdx

int prevSelectedIdx

Package chemaxon.marvin.plugin

Class chemaxon.marvin.plugin.PluginException extends java.lang.Exception implements Serializable

Serialized Fields

level

int level

Error level.

Package chemaxon.marvin.plugin.concurrent

Class chemaxon.marvin.plugin.concurrent.PluginExecutionException extends java.util.concurrent.ExecutionException implements Serializable

Serialized Fields

plugin

CalculatorPlugin plugin

Package chemaxon.marvin.plugin.gui

Class chemaxon.marvin.plugin.gui.CheckList extends javax.swing.JPanel implements Serializable

Serialized Fields

checkboxes

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

The checkbox array.

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

Serialized Fields

parameterPanel

ParameterPanelHandler parameterPanel

okActionListener

java.awt.event.ActionListener okActionListener

key

java.lang.String key

title

java.lang.String title

ok

chemaxon.marvin.swing.ActionButton ok

cancel

chemaxon.marvin.swing.ActionButton cancel

restoreDefaults

chemaxon.marvin.swing.ActionButton restoreDefaults

Class chemaxon.marvin.plugin.gui.ParameterPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

items

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

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

serialVersionUID: -5728800883025815500L

Serialized Fields

mpan

chemaxon.marvin.common.swing.MolPanel mpan

bottomTextArea

javax.swing.JTextArea bottomTextArea

bottomComponent

javax.swing.JComponent bottomComponent

topTextArea

javax.swing.JTextArea topTextArea

topComponent

javax.swing.JComponent topComponent

chartPanel

javax.swing.JPanel chartPanel

chart

chemaxon.marvin.util.MarvinModule chart

viewMenu

javax.swing.JMenu viewMenu

copymi

javax.swing.JMenuItem copymi

popupcopymi

javax.swing.JMenuItem popupcopymi

resetmi

javax.swing.JMenuItem resetmi

popup

javax.swing.JPopupMenu popup

detachmi

javax.swing.JMenuItem detachmi

viewMols

Molecule[] viewMols

viewTexts

java.lang.String[] viewTexts

viewPanel

chemaxon.marvin.view.swing.ViewPanel viewPanel

viewMol

Molecule viewMol

viewText

java.lang.String viewText

imageFormat

java.lang.String imageFormat

Package chemaxon.marvin.services

Class chemaxon.marvin.services.ServiceException extends java.lang.Exception implements Serializable

serialVersionUID: 328496720368460819L

Package chemaxon.marvin.sketch

Class chemaxon.marvin.sketch.AbstractSelectSM extends chemaxon.marvin.sketch.SketchMode implements Serializable

serialVersionUID: -3234421161340066358L

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Serialized Fields

selectUtil

chemaxon.marvin.sketch.SelectUtil selectUtil

selectingText

boolean selectingText

draggedObject

MObject draggedObject

Class chemaxon.marvin.sketch.AtomSM extends chemaxon.marvin.sketch.SketchMode implements Serializable

serialVersionUID: -5009627643303957609L

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Class chemaxon.marvin.sketch.BoldModeSM extends chemaxon.marvin.sketch.SketchMode implements Serializable

Serialized Fields

incType

boolean incType

Changes boldness for mouse click.

changeUp

boolean changeUp

Changes direction of Up-Aromatic bond at clikcking continously.

Class chemaxon.marvin.sketch.BondSM extends chemaxon.marvin.sketch.SketchMode implements Serializable

serialVersionUID: 6282033706405196916L

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Serialized Fields

incType

boolean incType

Increase bond type by one for mouse click.

wasDoubleBeforeClick

boolean wasDoubleBeforeClick

Bond order was double before the user clicked on it first.

Class chemaxon.marvin.sketch.ChainSM extends chemaxon.marvin.sketch.BondSM implements Serializable

serialVersionUID: 6282033706405196916L

Serialized Fields

curvedchainTool

boolean curvedchainTool

Class chemaxon.marvin.sketch.GroupSelectSM extends chemaxon.marvin.sketch.AbstractSelectSM implements Serializable

Serialized Fields

groupType

int groupType

Class chemaxon.marvin.sketch.HashedModeSM extends chemaxon.marvin.sketch.SketchMode implements Serializable

serialVersionUID: 2600395801827365930L

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

Serialized Fields

molHist

MDocument[] molHist

Molecule history.

cornerHist

java.awt.Point[] cornerHist

Left bottom corner history.

scaleHist

double[] scaleHist

Scaling factor history.

autoHydrogenizeHist

int[] autoHydrogenizeHist

Automatic hydrogenization state history.

scrollBarHist

int[][] scrollBarHist

selectionToZoomHist

boolean[] selectionToZoomHist

molgToZoomHist

MoleculeGraph[][] molgToZoomHist

rotateMatrHist

CTransform3D[] rotateMatrHist

View rotation matrix history.

molHistLen

int molHistLen

Molecule history length.

molHistCur

int molHistCur

Current index in history; undo/redo decrements/increments it.

molHistMax

int molHistMax

Maximum index in history. molecule-changing operations increment it.

historyOverflow

boolean historyOverflow

changeSupport

java.beans.PropertyChangeSupport changeSupport

Class chemaxon.marvin.sketch.LassoSelectSM extends chemaxon.marvin.sketch.AbstractSelectSM implements Serializable

Class chemaxon.marvin.sketch.MObjectSM extends chemaxon.marvin.sketch.SketchMode implements Serializable

serialVersionUID: 8408081115999010988L

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Class chemaxon.marvin.sketch.MoleculeSM extends chemaxon.marvin.sketch.SketchMode implements Serializable

serialVersionUID: 879978814934682047L

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Serialized Fields

parentSketchMode

chemaxon.marvin.sketch.SketchMode parentSketchMode

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

serialVersionUID: 2463379690025911142L

Serialization Methods

readObject

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

Serialized Fields

moveMode

int moveMode

Fragment movement mode.

persistentMoveMode

boolean persistentMoveMode

Indicates the persistency of the current fragment movement mode.

document

MDocument document

The molecule on the board.

selectionDoc

MSelectionDocument selectionDoc

The selection.

elements

java.util.List<E> elements

Allowed elements

queryAtoms

java.util.List<E> queryAtoms

Allowed query atoms

extraBonds

java.util.List<E> extraBonds

Allowed extra bonds

atomStrings

java.util.List<E> atomStrings

Allowed atom strings

reactionSupported

boolean reactionSupported

Are reactions supported?

chiralitySupport

int chiralitySupport

When can the atom stereo flags be edited. Never (0), if ABSC flag set in molecule (1) or always (2).

atomSize

double atomSize

The atoms size in C-C bond length units.

bondSpacing

double bondSpacing

The bond width in C-C bond length units.

stickdst

double stickdst

The stick distance of atoms in bond length units.

mergedst

double mergedst

The merge distance of atoms in bond length units.

mouseInside

boolean mouseInside

dragged

boolean dragged

modifiers

int modifiers

ptrX

double ptrX

ptrY

double ptrY

ptrZ

double ptrZ

prevPtrX

double prevPtrX

prevPtrY

double prevPtrY

prevPtrZ

double prevPtrZ

history

chemaxon.marvin.sketch.History history

painter

chemaxon.marvin.paint.internal.MolPainter painter

sketchCanvas

chemaxon.marvin.util.CallbackIface sketchCanvas

curfrag

MDocument curfrag

Current fragment.

prevCurfrag

MDocument prevCurfrag

Previous fragment to save during selecting the axis point in case of 3D rotation at Arbitrary Axis.

flyingBondMol

MoleculeGraph flyingBondMol

Unit length bond in bond drawing mode. Created if the user draws a unit length bond in the air.

curfragMoved

boolean curfragMoved

The current fragment was moved to another place. This variable is needed at mouseUp; mouseDrag may change its value.

canRotCurfrag

boolean canRotCurfrag

Can we rotate the current fragment?

canMovCurfrag

boolean canMovCurfrag

Can move the current fragment?

atomSelectionMode

int atomSelectionMode

In 3D rotaion mode in case of arbitrary axis was choosen, axis has to be defined by selecting the proper quantity of atoms. (1 or 2).

curfragR

double curfragR

Current fragment's average radius.

rotO

DPoint3 rotO

Current fragment's rotation center.

rotAxisPoint

DPoint3 rotAxisPoint

Current fragment's 3D rotation's arbitrary axis's second point, first is rotO.

isAxisSet

boolean isAxisSet

rotateZPhi

double rotateZPhi

Current fragment's angle of rotation.

rotatePhi

double rotatePhi

Current fragment's angle of rotation divided by 15 degree.

rotate3dPhiX

double rotate3dPhiX

Current fragment's normal vector of rotation to draw "blue picture".

rotate3dPhiY

double rotate3dPhiY

Current fragment's normal vector of rotation to draw "blue picture".

rotate3dPhi

double rotate3dPhi

Current fragment's angle of rotation to draw "blue picture".

rotate3dx

double rotate3dx

Actual difference of x coordinates of mouse's movements, to be able follow "big" mouse movements.

rotate3dy

double rotate3dy

Actual difference of y coordinates of mouse's movements, to be able follow "big" mouse movements.

rotate3direction

int rotate3direction

Direction of 3D rotation. Value can be 0, -1, 1. 0: no direction, 1: rotate around x axis, -1: rotate around y axis.

indexToRot

int indexToRot

Index of the closest atom of the curfrag to the screenpointer. Needed to 15 degrees rotation.

pointIndexToRot

int pointIndexToRot

atomBranchPiece

Molecule atomBranchPiece

Current atom, bond, charge or molecule template.

piece

Molecule piece

Current atom, bond, charge or molecule template.

pieceOriginalObject

Molecule pieceOriginalObject

The original piece object.

showMolecule

Molecule showMolecule

To show and after click draw the simmetric template/abbrev group for spiro/sprout

paintOnlyShowMolecule

boolean paintOnlyShowMolecule

sketchMode

chemaxon.marvin.sketch.SketchMode sketchMode

bondrawMode

boolean bondrawMode

Bond drawing mode.

thisBondlen

double thisBondlen

lastBondFlags

int lastBondFlags

lastQueryBondString

java.lang.String lastQueryBondString

newSelection

boolean newSelection

jointAtom

MolAtom jointAtom

The rotation center for the molecule. The a newly created MolJoin will contain it as the first primary join point in both molecules - even if the molecules actually do not have this atom. Useful if you want to rotate a fragment of a molecule about an atom.

curfragJoin

chemaxon.marvin.sketch.MolJoin curfragJoin

bondDraggedAlong

boolean bondDraggedAlong

Structure/bond in hand not shown if nonzero.

historizeEnabled

boolean historizeEnabled

documentEdited

boolean documentEdited

isDataSgroupLabelPointed

boolean isDataSgroupLabelPointed

dataSgroupLabelMoving

boolean dataSgroupLabelMoving

dataSgroupObject

DataSgroup dataSgroupObject

Actual data sgroup: the one being dragged, edited, etc.

hadSelection

boolean hadSelection

scrollBarVals

int[] scrollBarVals

Used for history counting between SkacthPanel and MolPainter scrollBarVals are needed until a new scrollBar implementation

lastSelectionDoc

MDocument lastSelectionDoc

lastSelectionCorner

java.awt.Point lastSelectionCorner

lastSelectionScale

double lastSelectionScale

selectionHistorized

boolean selectionHistorized

historizeUnSelection

boolean historizeUnSelection

deleteRemovesTerminalAtoms

boolean deleteRemovesTerminalAtoms

rotation3DMode

int rotation3DMode

newKeyboardMotion

boolean newKeyboardMotion

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

serialVersionUID: 1880834186820654343L

Serialized Fields

that

Molecule that

The molecule.

other

MoleculeGraph other

The molecule which will be joined to that.

tother

MoleculeGraph tother

A transformed clone of the other molecule.

atoms

java.util.List<E> atoms

Atoms which are not part of the other molecule.

bonds

java.util.List<E> bonds

Bonds which are not part of the other molecule.

pri

MolAtom[] pri

Primary joins.

sec

MolAtom[] sec

Secondary joins.

corrupt

MolBond[] corrupt

Corrupted bonds which will be removed at merge().

mergedst

double mergedst

Merge distance for the secondary joins.

theFindOptions

int theFindOptions

Class chemaxon.marvin.sketch.RectangleSelectSM extends chemaxon.marvin.sketch.AbstractSelectSM implements Serializable

Class chemaxon.marvin.sketch.RubberSM extends chemaxon.marvin.sketch.SketchMode implements Serializable

serialVersionUID: -7010050364100540729L

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Serialized Fields

selectUtil

chemaxon.marvin.sketch.SelectUtil selectUtil

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

serialVersionUID: 4143211204478415057L

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Serialized Fields

groupType

int groupType

groupCreationDialogHandler

chemaxon.marvin.util.CallbackIface groupCreationDialogHandler

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

serialVersionUID: 511717688630484043L

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Class chemaxon.marvin.sketch.StructureSelectSM extends chemaxon.marvin.sketch.AbstractSelectSM implements Serializable

Package chemaxon.marvin.space

Class chemaxon.marvin.space.EventQueue extends java.util.Vector implements Serializable

Class chemaxon.marvin.space.GraphicScene extends javax.swing.JPanel implements Serializable

Serialized Fields

eventHandler

chemaxon.marvin.space.MSpaceEventHandler eventHandler

progressBar

chemaxon.marvin.space.gui.JMSpaceProgressBar progressBar

rowCount

int rowCount

layout of the graphic view: number of cells per row

columnCount

int columnCount

layout of the graphic view: number of cells per column

activeCell

int activeCell

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

cells

GraphicCell[] cells

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

cellCount

int cellCount

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

needsRefresh

int needsRefresh

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

needsReset

int needsReset

initialized

boolean initialized

antialias

boolean antialias

synchronousMode

boolean synchronousMode

verboseLevel

int verboseLevel

motionmode

int motionmode

standing or moving mode

width

int width

physical width of the entire scene (in pixels)

height

int height

physical height of the entire scene (in pixels)

backgroundColor

java.awt.Color 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 OGL too often (like color of an atom, etc) These are e.g. : background color, constant component colors

backgroundColorChanged

boolean backgroundColorChanged

transparentBackground

int transparentBackground

smoothBackground

boolean smoothBackground

rx

double rx

rotation around x-y-z axises

ry

double ry

rotation around x-y-z axises

rz

double rz

rotation around x-y-z axises

gl

javax.media.opengl.GL gl

glu

javax.media.opengl.glu.GLU glu

glAutoDrawable

javax.media.opengl.GLAutoDrawable glAutoDrawable

canvas

javax.media.opengl.GLCanvas canvas

capabilities

javax.media.opengl.GLCapabilities capabilities

gltext

chemaxon.marvin.space.util.GLText gltext

this is used to display warning about unregistered product

globalDrawProperties

java.util.Properties globalDrawProperties

Package chemaxon.marvin.util

Class chemaxon.marvin.util.CancelPrintException extends java.lang.Exception implements Serializable

Class chemaxon.marvin.util.MarvinModule extends java.lang.Object implements Serializable

serialVersionUID: 2763330874643316763L

Class chemaxon.marvin.util.MarvinOLEFrame extends javax.swing.JFrame implements Serializable

serialVersionUID: 7801720334170069726L

Class chemaxon.marvin.util.MarvinOLEPanel extends javax.swing.JPanel implements Serializable

serialVersionUID: -6975415959061110410L

Serialized Fields

msketch

MSketchPane msketch

sketchPanel

chemaxon.marvin.sketch.swing.SketchPanel sketchPanel

log

java.util.logging.Logger log

importExceptionCaught

boolean importExceptionCaught

Class chemaxon.marvin.util.MolExportException extends java.io.IOException implements Serializable

Class chemaxon.marvin.util.MolImageSize extends java.lang.Object implements Serializable

serialVersionUID: -5798208351774983109L

Serialized Fields

width

int width

Deprecated.

Width.

height

int height

Deprecated.

Height.

scale

double scale

Deprecated.

Scaling factor.

Class chemaxon.marvin.util.MolNameFormatException extends java.lang.RuntimeException implements Serializable

Class chemaxon.marvin.util.SwingUtil extends java.lang.Object implements Serializable

serialVersionUID: -1600625160321014724L

Package chemaxon.marvin.util.codeassist

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

serialVersionUID: -5894946790409031807L

Serialized Fields

doc

javax.swing.text.DefaultStyledDocument doc

rootElement

javax.swing.text.Element rootElement

multiLineComment

boolean multiLineComment

normal

javax.swing.text.MutableAttributeSet normal

comment

javax.swing.text.MutableAttributeSet comment

quote

javax.swing.text.MutableAttributeSet quote

keyword

javax.swing.text.MutableAttributeSet keyword

function

javax.swing.text.MutableAttributeSet function

parenthesis

javax.swing.text.MutableAttributeSet parenthesis

constant

javax.swing.text.MutableAttributeSet constant

keywords

java.util.Map<K,V> keywords

functions

java.util.Map<K,V> functions

constants

java.util.Map<K,V> constants

fontSize

int fontSize

fontName

java.lang.String fontName

parenOffset

int parenOffset

parenLength

int parenLength

currentElementIndex

int currentElementIndex

prefix

java.lang.String prefix

lastPrefixState

boolean lastPrefixState

HIGHLIGHT_TIMER

javax.swing.Timer HIGHLIGHT_TIMER

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

serialVersionUID: 6746125418422903808L

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

serialVersionUID: -4703035835623320688L

Serialized Fields

macroListScroll

javax.swing.JScrollPane macroListScroll

macroList

javax.swing.JList macroList

addButton

javax.swing.JButton addButton

editButton

javax.swing.JButton editButton

deleteButton

javax.swing.JButton deleteButton

listPanel

javax.swing.JPanel listPanel

editPanel

javax.swing.JPanel editPanel

layout

java.awt.CardLayout layout

acceptButton

javax.swing.JButton acceptButton

cancelButton

javax.swing.JButton cancelButton

nameField

javax.swing.JTextField nameField

descScrollPane

javax.swing.JScrollPane descScrollPane

macroScrollPane

javax.swing.JScrollPane macroScrollPane

macroPane

javax.swing.JTextPane macroPane

descPane

javax.swing.JTextPane descPane

acceptEditButton

javax.swing.JButton acceptEditButton

cancelEditButton

javax.swing.JButton cancelEditButton

editedItem

int editedItem

helper

chemaxon.marvin.util.codeassist.CodeAssistMacrosHelper helper

ACCEPT_ACTION

javax.swing.Action ACCEPT_ACTION

CANCEL_ACTION

javax.swing.Action CANCEL_ACTION

Package chemaxon.marvin.view

Class chemaxon.marvin.view.MDocStorage.CancellationException extends java.lang.Exception implements Serializable

Class chemaxon.marvin.view.MDocStorage.RecordUnavailableException extends java.lang.Exception implements Serializable

Serialized Fields

recordIndex

int recordIndex

Package chemaxon.marvin.view.swing

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

Serialized Fields

listData1

java.lang.String[] listData1

listData2

java.lang.String[] listData2

list1

javax.swing.JList list1

list2

javax.swing.JList list2

addButton

javax.swing.JButton addButton

addAllButton

javax.swing.JButton addAllButton

removeButton

javax.swing.JButton removeButton

removeAllButton

javax.swing.JButton removeAllButton

allSelected

boolean allSelected

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

serialVersionUID: 3979819797881974530L

Serialization Methods

writeObject

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

Throws:

java.io.IOException

Serialized Fields

windowAction

chemaxon.marvin.swing.MAction windowAction

document

MDocument document

inZoomWindow

boolean inZoomWindow

markedAtom

int markedAtom

The atomnumber of the marked atom. -1 if no atom is marked.

highlightedAtom

int highlightedAtom

the atomnumber of the highlighted atom. -1 if no atom is highlighted.

viewPanel

chemaxon.marvin.view.swing.ViewPanel viewPanel

viewFrame

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

cellIndex

int cellIndex

winScale

double winScale

Preferred magnification.

moleculeCenter

DPoint3 moleculeCenter

preferredSize1

java.awt.Dimension preferredSize1

Preferred size of window corresponding to winScale

rsize

java.awt.Dimension rsize

Requested size.

error

boolean error

painter

chemaxon.marvin.paint.internal.MolPainter painter

moleculeBackground

java.awt.Color moleculeBackground

nextV

java.util.Vector<E> nextV

isLowQuality

boolean isLowQuality

Class chemaxon.marvin.view.swing.ViewHandler extends java.lang.Object implements Serializable

Serialized Fields

debug

boolean debug

visibleDocs

chemaxon.marvin.view.swing.VisibleDocuments visibleDocs

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

serialVersionUID: 802342314015862847L

Serialization Methods

readObject

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

Serialized Fields

molFrame0

java.awt.Window molFrame0

viewActions

chemaxon.marvin.view.swing.ViewActions viewActions

navigationActions

chemaxon.marvin.swing.MAction[] navigationActions

molStrings

java.lang.String[] molStrings

molString

java.lang.String molString

rasmolScripts

java.util.Vector<E>[] rasmolScripts

moleculeSelections

chemaxon.marvin.common.AtomSelectionHandler[] moleculeSelections

rasmolScripters

chemaxon.marvin.util.MarvinModule[] rasmolScripters

viewHandler

chemaxon.marvin.view.swing.ViewHandler viewHandler

defaultFieldFont

java.awt.Font defaultFieldFont

fieldFontMap

java.util.Map<K,V> fieldFontMap

findAction

javax.swing.Action findAction

findAgainAction

javax.swing.Action findAgainAction

winScale

double winScale

Magnification in the zoom window.

Since:

Marvin 2.9.1

borderWidth

int borderWidth

Border between cells.

borderColor

java.awt.Color borderColor

tabScale

double tabScale

Magnification in the table or -1.

Since:

Marvin 2.9.1

autoTabScale

boolean autoTabScale

TabScale is changed automatically.

Since:

Marvin 2.9.2

tabScaleCalcNeeded

boolean tabScaleCalcNeeded

Recalculation of tabScale needed.

animSynchronized

boolean animSynchronized

startLoad

boolean startLoad

rows

int rows

Number of rows of big cells

cols

int cols

Number of columns of big cells

animator

chemaxon.marvin.util.MarvinModule animator

selectable

boolean selectable

Cells are selectable or not.

editable

int editable

View only (0) or editable (1 or 2). If 2, then double click launches MarvinSketch.

importEnabled

boolean importEnabled

skbridge

chemaxon.marvin.util.CallbackIface skbridge

findTextModule

chemaxon.marvin.util.CallbackIface findTextModule

selected

int selected

detachable

boolean detachable

tabScaleCalcInProgress

int tabScaleCalcInProgress

draggable

boolean draggable

molbgMap

java.util.Map<K,V> molbgMap

sketchMoleculeProvider

chemaxon.marvin.common.swing.MoleculeProvider sketchMoleculeProvider

tableSupport

TableSupport tableSupport

commonActions

chemaxon.marvin.common.swing.CommonActions commonActions

oldMarkedCell

int oldMarkedCell

oldMarkedAtom

int oldMarkedAtom

atomMarkAndHighlightEnabled

boolean atomMarkAndHighlightEnabled

Class chemaxon.marvin.view.swing.WholeNumberField extends javax.swing.JTextField implements Serializable

Serialized Fields

options

int options

toolkit

java.awt.Toolkit toolkit

integerFormatter

java.text.NumberFormat integerFormatter

Class chemaxon.marvin.view.swing.WholeNumberField.WholeNumberDocument extends javax.swing.text.PlainDocument implements Serializable

Package chemaxon.naming

Class chemaxon.naming.NameFormatException extends MolFormatException implements Serializable

Serialized Fields

tokens

chemaxon.naming.n2s.lex.data.Token[] tokens

Class chemaxon.naming.NameFormatException.FilteredCase extends NameFormatException implements Serializable

Class chemaxon.naming.NamePrefixException extends NameFormatException implements Serializable

Serialized Fields

prefix

java.lang.String prefix

token

java.lang.String token

Package chemaxon.struc

Class chemaxon.struc.CTransform3D extends java.lang.Object implements Serializable

serialVersionUID: 0L

Serialization Methods

readExternal

public void readExternal(java.io.ObjectInput in)
                  throws java.io.IOException

Deserializes a transformation matrix.

Throws:

java.io.IOException

Since:

3.5, 11/02/2004

writeExternal

public void writeExternal(java.io.ObjectOutput out)
                   throws java.io.IOException

Serializes a transformation matrix.

Throws:

java.io.IOException

Since:

3.5, 11/02/2004

Class chemaxon.struc.DPoint3 extends java.lang.Object implements Serializable

serialVersionUID: 0L

Serialization Methods

readExternal

public void readExternal(java.io.ObjectInput in)
                  throws java.io.IOException,
                         java.lang.ClassNotFoundException

Deserializes a 3D point.

Throws:

java.io.IOException

java.lang.ClassNotFoundException

writeExternal

public void writeExternal(java.io.ObjectOutput out)
                   throws java.io.IOException

Serializes a 3D point.

Throws:

java.io.IOException

Class chemaxon.struc.ExtraAtomProperties extends java.lang.Object implements Serializable

serialVersionUID: -1980229820290558380L

Serialized Fields

attachParentSgroup

Sgroup attachParentSgroup

valence1

short valence1

order

int order

Order of multiple R-group attachment point for atom type MolAtom.RGROUP_ATTACHMENT

qprops

java.util.Map<K,V> qprops

Query properties

querystr

java.lang.String querystr

String containing query atom properties.

aliasstr

java.lang.String aliasstr

Atom alias/pseudo string. The value is different according to atom type: - Alias string value for all atom types except MolAtom.PSEUDO - Pseudo string for atom type MolAtom.PSEUDO

extrastr

java.lang.String extrastr

Extra label "label" or "label1|label2"

extrargbs

long extrargbs

Extra label color(s): lower 32 bits and upper 32 bits as (alpha<<24 + red<<16 + green<<8 + blue).

list

int[] list

Atom list

flags

int flags

Query, stereochemical and isotope flags. attachment point (2 bits), reaction stereo (2 bit), parity (6 bits) and stereochemical group type (2 bits), special isotope symbol (1 bit).

See Also:

ExtraAtomProperties.ATTACH_OFF, ExtraAtomProperties.ATTACH_MASK, ExtraAtomProperties.RXNSTEREO_OFF, ExtraAtomProperties.RXNSTEREO_MASK, ExtraAtomProperties.STGRP_TYPE_OFF, ExtraAtomProperties.STGRP_TYPE_MASK, ExtraAtomProperties.ISOTOPE_SPEC_SYM_FLAG

rgroupId

short rgroupId

R-group ID.

See Also:

ExtraAtomProperties.getRgroup()

countFlags

int countFlags

Extra count flags. Charge (8 bits), implicit H (8 bits), stereochemical group number (16 bits).

repetitionBits

int repetitionBits

Link node repetition counts.

linkNodeOuterBonds

int linkNodeOuterBonds

Indexes of link node outer bonds. (Bond to neighbours which do not repeat.)

electronProp

int electronProp

The lone pairs or radical setting state.

Since:

Marvin 5.1.1 08/03/2008

See Also:

ExtraAtomProperties.LP_NOT_SET, ExtraAtomProperties.RD_NOT_SET, ExtraAtomProperties.UNDEFINED

temporaryObjects

java.util.Map<K,V> temporaryObjects

Query properties

bicycloStereoDescriptors

chemaxon.struc.BicycloStereoDescriptor[] bicycloStereoDescriptors

Descriptors of bicyclo stereo information.

Class chemaxon.struc.MacroMolecule.BadMoleculeException extends java.lang.Exception implements Serializable

Class chemaxon.struc.MDocument extends java.lang.Object implements Serializable

serialVersionUID: 553557622036381832L

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Class chemaxon.struc.MDocument.Prop extends MProp implements Serializable

Class chemaxon.struc.MObject extends java.lang.Object implements Serializable

serialVersionUID: 2435517510938087080L

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Class chemaxon.struc.MolAtom extends java.lang.Object implements Serializable

serialVersionUID: -3974070468228529467L

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Class chemaxon.struc.MolBond extends java.lang.Object implements Serializable

serialVersionUID: 3656012871856958335L

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Class chemaxon.struc.Molecule extends MoleculeGraph implements Serializable

serialVersionUID: 7275486436840296305L

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Class chemaxon.struc.MoleculeGraph extends java.lang.Object implements Serializable

serialVersionUID: -2053719583816270190L

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Class chemaxon.struc.MPoint extends MObject implements Serializable

serialVersionUID: -3067277054033050963L

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Class chemaxon.struc.MProp extends java.lang.Object implements Serializable

serialVersionUID: -5699803671884637223L

Serialized Fields

grinvCC

long grinvCC

coordDependent

boolean coordDependent

Class chemaxon.struc.MPropertyContainer extends java.lang.Object implements Serializable

serialVersionUID: -2575268570438177098L

Serialization Methods

readExternal

public void readExternal(java.io.ObjectInput in)
                  throws java.io.IOException,
                         java.lang.ClassNotFoundException

Restores the property container's state.

Throws:

java.io.IOException - if I/O errors occur

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

writeExternal

public void writeExternal(java.io.ObjectOutput out)
                   throws java.io.IOException

Saves the property container's state.

Throws:

java.io.IOException - Includes any I/O exceptions that may occur

Class chemaxon.struc.MSelectionDocument extends MDocument implements Serializable

serialVersionUID: 2379294894434293119L

Class chemaxon.struc.PageSettings extends java.lang.Object implements Serializable

serialVersionUID: -7674028514396457694L

Serialization Methods

readExternal

public void readExternal(java.io.ObjectInput in)
                  throws java.io.IOException,
                         java.lang.ClassNotFoundException

Throws:

java.io.IOException

java.lang.ClassNotFoundException

writeExternal

public void writeExternal(java.io.ObjectOutput out)
                   throws java.io.IOException

Throws:

java.io.IOException

Class chemaxon.struc.QueryBond extends MolBond implements Serializable

serialVersionUID: -5025485107616067648L

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Class chemaxon.struc.RgMolecule extends Molecule implements Serializable

serialVersionUID: -939153732283455787L

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Class chemaxon.struc.RxnMolecule extends Molecule implements Serializable

serialVersionUID: -2863036104564183121L

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Class chemaxon.struc.SelectionMolecule extends MoleculeGraph implements Serializable

Class chemaxon.struc.SelectionRgMolecule extends SelectionMolecule implements Serializable

Class chemaxon.struc.Sgroup extends java.lang.Object implements Serializable

serialVersionUID: -6209766549185582411L

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Class chemaxon.struc.StaticMolecule extends java.lang.Object implements Serializable

Serialized Fields

ringPerception

boolean ringPerception

name

java.lang.String name

arrayFlags

int arrayFlags

atomCount

int atomCount

Current number of atoms.

connectionTable

short[] connectionTable

lower triangle representation of the adjacency matrix, non-zero value represents bond type, see BOND_* contants

neighborCount

byte[] neighborCount

[i][j] is the index of the j-th neighbour of node i

nodeEdgeList

short[][] nodeEdgeList

bondCount

int bondCount

atomType

short[] atomType

element number

bondAtom1

short[] bondAtom1

bondAtom2

short[] bondAtom2

bondFlags

int[] bondFlags

extendedAtomType

int[] extendedAtomType

atomLists

byte[][] atomLists

hybridization

byte[] hybridization

hybridization state, see HYBR_* constants

atomStereo

byte[] atomStereo

Parity and chirality.

implicitHcount

byte[] implicitHcount

explicitHcount

byte[] explicitHcount

valence

byte[] valence

queryProperty

byte[][] queryProperty

radical

byte[] radical

charge

byte[] charge

massno

byte[] massno

atomMap

short[] atomMap

rgroupId

short[] rgroupId

sgroupId

java.lang.String[] sgroupId

gearch

chemaxon.struc.gearch.SmoleculeGearch gearch

bond index enumerator

Package chemaxon.struc.graphics

Class chemaxon.struc.graphics.MAssigner extends MPolyline implements Serializable

Serialized Fields

order

int order

Class chemaxon.struc.graphics.MAtomSetPoint extends MPoint implements Serializable

serialVersionUID: 5932389976054063500L

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Class chemaxon.struc.graphics.MBracket extends MRectangle implements Serializable

serialVersionUID: -5775562691065011181L

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Serialized Fields

bracketType

int bracketType

bracketOrientation

int bracketOrientation

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

Class chemaxon.struc.graphics.MChemicalStruct extends MObject implements Serializable

serialVersionUID: 7098670860634457343L

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Class chemaxon.struc.graphics.MEFlow extends MPolyline implements Serializable

serialVersionUID: 891769518407563834L

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Class chemaxon.struc.graphics.MEFlowBasePoint extends MPoint implements Serializable

serialVersionUID: 1053944912020926984L

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Class chemaxon.struc.graphics.MEllipse extends MRectangle implements Serializable

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Class chemaxon.struc.graphics.MFont extends java.lang.Object implements Serializable

serialVersionUID: -7769715209509613515L

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Class chemaxon.struc.graphics.MMidPoint extends MPoint implements Serializable

serialVersionUID: 5307361876930807239L

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Class chemaxon.struc.graphics.MMidPoint.Sticky extends MMidPoint implements Serializable

serialVersionUID: 3223068581543532992L

Class chemaxon.struc.graphics.MMoleculeMovie extends MObject implements Serializable

serialVersionUID: 6476041884742537582L

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Class chemaxon.struc.graphics.MNameTextBox extends MTextBox implements Serializable

serialVersionUID: 6302424343157644471L

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Class chemaxon.struc.graphics.MPolyline extends MObject implements Serializable

serialVersionUID: 4958026600768388648L

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Class chemaxon.struc.graphics.MRArrow extends MPolyline implements Serializable

serialVersionUID: 8638690394107448092L

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Class chemaxon.struc.graphics.MRectangle extends MPolyline implements Serializable

serialVersionUID: 2948229815278089239L

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Class chemaxon.struc.graphics.MRectanglePoint extends MPoint implements Serializable

serialVersionUID: -3067277054033050963L

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Class chemaxon.struc.graphics.MRectanglePoint.Sticky extends MRectanglePoint implements Serializable

serialVersionUID: 3364078480306200948L

Class chemaxon.struc.graphics.MRoundedRectangle extends MRectangle implements Serializable

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Serialized Fields

arcWidth

double arcWidth

arcHeight

double arcHeight

Class chemaxon.struc.graphics.MTextAttributes extends java.lang.Object implements Serializable

serialVersionUID: 6561552003080652755L

Serialization Methods

readExternal

public void readExternal(java.io.ObjectInput in)
                  throws java.io.IOException,
                         java.lang.ClassNotFoundException

Throws:

java.io.IOException

java.lang.ClassNotFoundException

writeExternal

public void writeExternal(java.io.ObjectOutput out)
                   throws java.io.IOException

Throws:

java.io.IOException

Class chemaxon.struc.graphics.MTextBox extends MRectangle implements Serializable

serialVersionUID: -7272723232157967384L

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Serialized Fields

actionMap

javax.swing.ActionMap actionMap

Class chemaxon.struc.graphics.MTextDocument extends java.lang.Object implements Serializable

serialVersionUID: 6305880304790247656L

Serialization Methods

readExternal

public void readExternal(java.io.ObjectInput in)
                  throws java.io.IOException,
                         java.lang.ClassNotFoundException

Restores the document.

Throws:

java.io.IOException - if I/O errors occur

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

writeExternal

public void writeExternal(java.io.ObjectOutput out)
                   throws java.io.IOException

Saves the document.

Throws:

java.io.IOException - Includes any I/O exceptions that may occur

Package chemaxon.struc.prop

Class chemaxon.struc.prop.MBooleanProp extends MProp implements Serializable

serialVersionUID: -5366978422380739811L

Serialization Methods

readObject

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

Restores the property's state.

Throws:

java.io.IOException - if I/O errors occur

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

writeObject

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

Saves the property's state.

Throws:

java.io.IOException - Includes any I/O exceptions that may occur

Class chemaxon.struc.prop.MByteArrayProp extends MProp implements Serializable

serialVersionUID: -4046371792715339701L

Serialization Methods

readObject

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

Restores the property's state.

Throws:

java.io.IOException - if I/O errors occur

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

writeObject

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

Saves the property's state.

Throws:

java.io.IOException - Includes any I/O exceptions that may occur

Class chemaxon.struc.prop.MCollectionProp extends MProp implements Serializable

serialVersionUID: -7479938988131387052L

Class chemaxon.struc.prop.MDoubleArrayProp extends MProp implements Serializable

serialVersionUID: -5670039985685584647L

Serialization Methods

readObject

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

Restores the property's state.

Throws:

java.io.IOException - if I/O errors occur

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

writeObject

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

Saves the property's state.

Throws:

java.io.IOException - Includes any I/O exceptions that may occur

Class chemaxon.struc.prop.MDoubleProp extends MProp implements Serializable

serialVersionUID: -1221776439131689653L

Serialization Methods

readObject

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

Restores the property's state.

Throws:

java.io.IOException - if I/O errors occur

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

writeObject

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

Saves the property's state.

Throws:

java.io.IOException - Includes any I/O exceptions that may occur

Class chemaxon.struc.prop.MFontProp extends MProp implements Serializable

serialVersionUID: 2369581307328116455L

Serialization Methods

readObject

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

Throws:

java.io.IOException

java.lang.ClassNotFoundException

writeObject

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

Throws:

java.io.IOException

Class chemaxon.struc.prop.MHashProp extends MCollectionProp implements Serializable

serialVersionUID: 5457649877894058447L

Serialization Methods

readObject

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

Restores the property's state.

Throws:

java.io.IOException - if I/O errors occur

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

writeObject

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

Saves the property's state.

Throws:

java.io.IOException - Includes any I/O exceptions that may occur

Class chemaxon.struc.prop.MHCoords3DProp extends MProp implements Serializable

serialVersionUID: 6646271128663088908L

Serialization Methods

readObject

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

Restores the property's state.

Throws:

java.io.IOException - if I/O errors occur

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

writeObject

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

Saves the property's state.

Throws:

java.io.IOException - Includes any I/O exceptions that may occur

Class chemaxon.struc.prop.MIntegerArrayProp extends MProp implements Serializable

serialVersionUID: 6651869314046996057L

Serialization Methods

readObject

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

Restores the property's state.

Throws:

java.io.IOException - if I/O errors occur

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

writeObject

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

Saves the property's state.

Throws:

java.io.IOException - Includes any I/O exceptions that may occur

Class chemaxon.struc.prop.MIntegerProp extends MProp implements Serializable

serialVersionUID: -7179550727198941747L

Serialization Methods

readObject

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

Restores the property's state.

Throws:

java.io.IOException - if I/O errors occur

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

writeObject

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

Saves the property's state.

Throws:

java.io.IOException - Includes any I/O exceptions that may occur

Class chemaxon.struc.prop.MListProp extends MCollectionProp implements Serializable

serialVersionUID: 5360371881677476960L

Serialization Methods

readObject

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

Restores the property's state.

Throws:

java.io.IOException - if I/O errors occur

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

writeObject

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

Saves the property's state.

Throws:

java.io.IOException - Includes any I/O exceptions that may occur

Class chemaxon.struc.prop.MMoleculeProp extends MProp implements Serializable

serialVersionUID: -7687559780023024273L

Serialization Methods

readObject

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

Restores the property's state.

Throws:

java.io.IOException - if I/O errors occur

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

writeObject

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

Saves the property's state.

Throws:

java.io.IOException - Includes any I/O exceptions that may occur

Class chemaxon.struc.prop.MMoleculeStringProp extends MStringProp implements Serializable

serialVersionUID: -1005074014113755196L

Serialization Methods

readObject

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

Restores the property's state.

Throws:

java.io.IOException - if I/O errors occur

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

writeObject

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

Saves the property's state.

Throws:

java.io.IOException - Includes any I/O exceptions that may occur

Serialized Fields

format

java.lang.String format

Class chemaxon.struc.prop.MObjectProp extends MProp implements Serializable

serialVersionUID: 4005646748655675692L

Serialization Methods

readObject

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

Restores the property's state.

Throws:

java.io.IOException - if I/O errors occur

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

writeObject

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

Saves the property's state.

Throws:

java.io.IOException - Includes any I/O exceptions that may occur

Class chemaxon.struc.prop.MStringProp extends MProp implements Serializable

serialVersionUID: 1373831606368751112L

Serialization Methods

readObject

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

Restores the property's state.

Throws:

java.io.IOException - if I/O errors occur

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

writeObject

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

Saves the property's state.

Throws:

java.io.IOException - Includes any I/O exceptions that may occur

Package chemaxon.struc.sgroup

Class chemaxon.struc.sgroup.DataSgroup extends Sgroup implements Serializable

serialVersionUID: -3132191586564122343L

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Serialized Fields

sb

java.lang.StringBuffer sb

temporary variable for getLineOnScreen

Class chemaxon.struc.sgroup.MulticenterSgroup extends Sgroup implements Serializable

serialVersionUID: -7213879722783498112L

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Class chemaxon.struc.sgroup.MultipleSgroup extends Sgroup implements Serializable

serialVersionUID: -1146464131016252826L

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Class chemaxon.struc.sgroup.RepeatingUnitSgroup extends Sgroup implements Serializable

serialVersionUID: -3209611525734625009L

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Class chemaxon.struc.sgroup.SgroupAtom extends MolAtom implements Serializable

serialVersionUID: -3185634359981637075L

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Serialized Fields

labelCenter

int labelCenter

Class chemaxon.struc.sgroup.SuperatomSgroup extends Sgroup implements Serializable

serialVersionUID: 2968529752634209305L

Serialization Methods

readObject

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

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

Throws:

java.lang.ClassNotFoundException

java.io.IOException

writeObject

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

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

Throws:

java.io.IOException

Package chemaxon.util

Class chemaxon.util.ArgumentException extends java.lang.Exception implements Serializable

Class chemaxon.util.BitPattern extends java.util.BitSet implements Serializable

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

serialVersionUID: 4318465509620546463L

Class chemaxon.util.ModuleNotAvailableException extends java.lang.RuntimeException implements Serializable

serialVersionUID: -6604248360050432512L

Class chemaxon.util.SearchAttributes extends java.lang.Object implements Serializable

Serialized Fields

stereoSearch

boolean stereoSearch

Deprecated.

Tells if stereo information should be considered

doubleBondStereoMatchingMode

int doubleBondStereoMatchingMode

Deprecated.

Tells if double bond stereo information should be considered only if stereo search box was checked when the molecule was drawn

subgraphSearch

boolean subgraphSearch

Deprecated.

false for full structure matching, true for subgraph structure matching

exactAtomMatching

boolean exactAtomMatching

Deprecated.

false for matching elements and evaluating atom queries, true for matching all atom types even query atoms

exactStereoMatching

boolean exactStereoMatching

Deprecated.

false for stereospecific matching, true for absolute stereo matching

orderSensitiveSearch

boolean orderSensitiveSearch

Deprecated.

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

Package chemaxon.util.concurrent.processors

Class chemaxon.util.concurrent.processors.InputProducerException extends java.lang.Exception implements Serializable

Class chemaxon.util.concurrent.processors.WorkUnitException extends java.lang.Exception implements Serializable