Serialized Form

Package chemaxon.enumeration

Class chemaxon.enumeration.ExpansionCounter.ArithmeticOverflowException extends java.lang.ArithmeticException implements Serializable

Class chemaxon.enumeration.ExpansionException extends java.lang.Exception implements Serializable

Serialized Fields

e

java.lang.Throwable e

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

Serialized Fields

e

java.lang.Throwable e

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.

symtab

chemaxon.nfunk.jep.SymbolTable symtab

The base symbol table.

verbose

boolean verbose

True if verbose output.

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

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

environment

java.lang.String environment

licensePath

java.lang.String licensePath

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

tagName

java.lang.String tagName

colorKeys

java.util.ArrayList<E> colorKeys

viewPane

MViewPane viewPane

The MarvinView bean.

viewTableUtil

chemaxon.marvin.view.swing.ViewTableUtil viewTableUtil

spaceDimensions

int spaceDimensions

Dimension of structures

tableOptions

chemaxon.marvin.view.swing.TableOptions tableOptions

realTimeMovieThread

java.lang.Thread realTimeMovieThread

openAction

javax.swing.Action openAction

printAction

javax.swing.Action printAction

exitAction

javax.swing.Action exitAction

tableOptionsAction

javax.swing.Action tableOptionsAction

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.

changeListeners

java.beans.PropertyChangeSupport changeListeners

userSettings

UserSettings userSettings

The user settings object.

actionListener

chemaxon.marvin.beans.MarvinPane.MarvinActionListener actionListener

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

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.DefaultCellEditor implements Serializable

Serialized Fields

currentMol

Molecule currentMol

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

serialVersionUID: -4430811090653077262L

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

Package chemaxon.marvin.common

Class chemaxon.marvin.common.UserSettings extends java.lang.Object implements Serializable

serialVersionUID: 845433654876173303L

Serialized Fields

WITHOUT_CHECK_OVERWRITEABLE_PROPS

java.lang.String[] WITHOUT_CHECK_OVERWRITEABLE_PROPS

Variables at marvin.properties, which have to be overwritten with every save event.

Since:

Marvin 5.0.1

userprops

java.util.Properties userprops

changeListeners

java.beans.PropertyChangeSupport changeListeners

owners

java.util.Vector<E> owners

sketchColorScheme

java.lang.String sketchColorScheme

viewColorScheme

java.lang.String viewColorScheme

sketchMolbg2d

java.awt.Color sketchMolbg2d

sketchMolbg3d

java.awt.Color sketchMolbg3d

viewMolbg2d

java.awt.Color viewMolbg2d

viewMolbg3d

java.awt.Color viewMolbg3d

sketchBondDraggedAlong

boolean sketchBondDraggedAlong

sketchValenceErrorVisible

boolean sketchValenceErrorVisible

sketchReactionErrorVisible

boolean sketchReactionErrorVisible

lonePairAutoCalc

boolean lonePairAutoCalc

sketchImplicitH

java.lang.String sketchImplicitH

viewValenceErrorVisible

boolean viewValenceErrorVisible

viewImplicitH

java.lang.String viewImplicitH

viewExplicitH

boolean viewExplicitH

viewAnyBond

java.lang.String viewAnyBond

sketchAnyBond

java.lang.String sketchAnyBond

viewCarbonVisibility

java.lang.String viewCarbonVisibility

sketchCarbonVisibility

java.lang.String sketchCarbonVisibility

downWedge

java.lang.String downWedge

sketchRendering2d

java.lang.String sketchRendering2d

sketchRendering3d

java.lang.String sketchRendering3d

viewRendering2d

java.lang.String viewRendering2d

viewRendering3d

java.lang.String viewRendering3d

viewNavmode2d

java.lang.String viewNavmode2d

viewNavmode3d

java.lang.String viewNavmode3d

clean2dOpts

java.lang.String clean2dOpts

clean3dOpts

java.lang.String clean3dOpts

copyAsFormat

java.lang.String copyAsFormat

copyOpts

java.lang.String copyOpts

defaultSaveFormat

java.lang.String defaultSaveFormat

aromatizeLevel

int aromatizeLevel

atomMappingLevel

int atomMappingLevel

atomFont

java.awt.Font atomFont

atomSize

double atomSize

bondSpacing

double bondSpacing

wireThickness

double wireThickness

stickThickness

double stickThickness

ballRadius

double ballRadius

sketchArrowHeadLength

double sketchArrowHeadLength

sketchArrowHeadWidth

double sketchArrowHeadWidth

sketchArrowTailLength

double sketchArrowTailLength

sketchArrowTailWidth

double sketchArrowTailWidth

viewRecentFileList

java.util.List<E> viewRecentFileList

viewRecentFileListSize

int viewRecentFileListSize

sketchRecentFileList

java.util.List<E> sketchRecentFileList

sketchRecentFileListSize

int sketchRecentFileListSize

viewLoadWorkingDir

java.lang.String viewLoadWorkingDir

viewSaveWorkingDir

java.lang.String viewSaveWorkingDir

sketchLoadWorkingDir

java.lang.String sketchLoadWorkingDir

sketchSaveWorkingDir

java.lang.String sketchSaveWorkingDir

loadSaveLocation

java.lang.String loadSaveLocation

loadWorkingDir

java.lang.String loadWorkingDir

saveLoadZoomFactorToMRV

boolean saveLoadZoomFactorToMRV

lastModified

long lastModified

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

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

Serialized Fields

position

MRecordReader.Position position

Package chemaxon.marvin.io.formats.name.nameexport

Class chemaxon.marvin.io.formats.name.nameexport.IUPACNamer.Error extends MolExportException implements Serializable

Class chemaxon.marvin.io.formats.name.nameexport.IUPACNamer.TimeoutError extends IUPACNamer.Error implements Serializable

Serialized Fields

timeout

int timeout

Class chemaxon.marvin.io.formats.name.nameexport.IUPACNamer.UnsupportedError extends java.lang.RuntimeException implements Serializable

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)

css

chemaxon.marvin.modules.MCS css

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

ringFinder

chemaxon.util.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

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

Serialized Fields

e

java.lang.Throwable e

Class chemaxon.marvin.modules.Clean2D extends chemaxon.marvin.util.MarvinModule implements Serializable

Serialized Fields

template_local

java.lang.String[] template_local

timeStart

long timeStart

timeStart_structure

long timeStart_structure

timeLimit

long timeLimit

timeLimit_structure

long timeLimit_structure

MoleculeInvariants

chemaxon.util.IntVector[] MoleculeInvariants

CageMolInv

chemaxon.util.IntVector[] CageMolInv

Debug

int Debug

molCount

int molCount

opt

chemaxon.marvin.modules.Clean2D.PartialOptimization opt

removeCTEither

boolean removeCTEither

partialCleanForMolecules

boolean partialCleanForMolecules

partialClean

boolean partialClean

fixedAtoms

int[] fixedAtoms

use_2D_Alignment

boolean use_2D_Alignment

addExplicitHToCageSystem

boolean addExplicitHToCageSystem

setParities

boolean setParities

useStereoFromFlags

boolean useStereoFromFlags

forceTemplates

boolean forceTemplates

ORIG

MoleculeGraph ORIG

levelAheadLimit

int levelAheadLimit

stepLimit

int stepLimit

cssr

int[][] cssr

ctab

int[][] ctab

btab

int[][] btab

fragID

int[] fragID

intang

double[][] intang

ringBitset

java.util.BitSet[] ringBitset

isRingBond

boolean[] isRingBond

atomInRing

int[][] atomInRing

commRingAtomNu

int[][] commRingAtomNu

atomFlags

int[] atomFlags

coll_dist_sq

double coll_dist_sq

Class chemaxon.marvin.modules.Clean3D extends chemaxon.marvin.util.MarvinModule implements Serializable

Serialized Fields

MERGETOBUILDMOL

boolean MERGETOBUILDMOL

Merge build sequence to build.mol

restrictConformerCount

boolean restrictConformerCount

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

Serialized Fields

modeFlag

int modeFlag

Flag to set calculation mode

stereo

int[] stereo

Contains whether the atoms of the molecule have stereo features. The elements can be the constants below.

calculatedChirality

int[] calculatedChirality

Previously calculated chirality values, (passed to getLocalChirality).

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

Class chemaxon.marvin.modules.MacroMolecule.BadMoleculeException extends java.lang.Exception implements Serializable

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.Parity extends chemaxon.marvin.util.MarvinModule implements Serializable

Serialized Fields

mol

MoleculeGraph mol

Original or the cloned molecule if it is expanded

origmol

MoleculeGraph origmol

Original molecule

bondIndexToExpanded

int[] bondIndexToExpanded

Bond index conversion array from original to expanded molecule

atomIndexToExpanded

int[] atomIndexToExpanded

Atom index conversion array from original to expanded molecule

lastGrinvCC

long lastGrinvCC

state of the grinv check sum

step

int step

step count in recursion

arommol

MoleculeGraph arommol

For chirality calculation the aromatized molecule

chiralityCalculated

boolean chiralityCalculated

If the chirality is calculated already

ctab

int[][] ctab

connection table

btab

int[][] btab

bond table

canbechiral

boolean[] canbechiral

Atom can be chiral

canhaveparity

boolean[] canhaveparity

Atom can be have parity

isRingBond

boolean[] isRingBond

Bond is in ring

parity0D

int[] parity0D

Parity of 0D molecule

hasWedge

boolean[] hasWedge

Atom has wedge

xyz

double[] xyz

Atoms x y z coordinate one after the other

isHydrogen

boolean[] isHydrogen

Atom is hydrogen

isLP

boolean[] isLP

Atom is LP

parity3D

int[] parity3D

Parity of 2D 3D molecule

chirality

int[] chirality

Chirality

ringCount

int[] ringCount

The ring count the atom is located

atomInSmallestRing

int[] atomInSmallestRing

What is the smallest ring size in which the atom can be found 0 if it is not in ring

hasContractedGroup

boolean hasContractedGroup

the molecule has contracted SGroup

useOnlyFirstAtom

boolean useOnlyFirstAtom

Use only the first node of the bond for parity/chirality calculation.

Class chemaxon.marvin.modules.ReactionExtractor extends java.lang.Object implements Serializable

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.MolPainterCommon 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.plugin

Class chemaxon.marvin.plugin.CommandPlugger extends java.lang.Object implements Serializable

serialVersionUID: 2693596825215818164L

Serialization Methods

readObject

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

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

Throws:

java.io.IOException

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

Serialized Fields

e

java.lang.Exception e

The wrapped exception.

level

int level

Error level.

Package chemaxon.marvin.plugin.concurrent

Class chemaxon.marvin.plugin.concurrent.PluginExecutionException extends edu.emory.mathcs.backport.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

javax.swing.JCheckBox[] 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

Serialized Fields

mpan

chemaxon.marvin.common.swing.MolPanel mpan

spane

javax.swing.JComponent spane

tpane

javax.swing.JComponent tpane

bottomTextArea

javax.swing.JTextArea bottomTextArea

bottomPanel

javax.swing.JPanel bottomPanel

topTextArea

javax.swing.JTextArea topTextArea

topPanel

javax.swing.JPanel topPanel

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

imageCopyPaste

chemaxon.marvin.util.MarvinModule imageCopyPaste

imageFormat

java.lang.String imageFormat

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.GeomCalc.GeomCalcException extends java.lang.RuntimeException implements Serializable

Class chemaxon.marvin.util.GeomCalc.Queue.Overflow extends java.lang.Exception implements Serializable

Class chemaxon.marvin.util.GeomCalc.Queue.Underflow 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

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

Width.

height

int height

Height.

scale

double scale

Scaling factor.

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

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

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.struc

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

serialVersionUID: 5220503088168062320L

Serialization Methods

readObject

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

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

Throws:

java.io.IOException

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

serialVersionUID: 6209968193612740707L

Serialization Methods

readObject

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

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

Throws:

java.io.IOException

Serialized Fields

grinvOptions

int grinvOptions

Options used to last calculate CGraph.grinv.

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

serialVersionUID: -7646006430497877205L

Serialization Methods

readObject

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

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

Throws:

java.io.IOException

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

qprops

java.util.HashMap<K,V> qprops

Query properties

querystr

java.lang.String querystr

String containing query atom properties.

aliasstr

java.lang.String aliasstr

Atom alias string.

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.XPARITY_OFF, ExtraAtomProperties.XPARITY_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

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 CNode implements Serializable

serialVersionUID: 293134874065432398L

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 CEdge implements Serializable

serialVersionUID: 6532576325442840116L

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 CGraph implements Serializable

serialVersionUID: -4663655945908176002L

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.Objec