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Serialized Form

Package chemaxon.alchemist.configbuilder

Class chemaxon.alchemist.configbuilder.ConfigBuilderPanel extends javax.swing.JPanel implements Serializable

serialVersionUID: 1831281487952208191L

Serialized Fields

mainLayout

java.awt.CardLayout mainLayout

the base cardlayout

controlLayout

java.awt.CardLayout controlLayout

the cardlayout of bottom section

normalViewSplit

javax.swing.JSplitPane normalViewSplit

main panel split

controlPanel

javax.swing.JPanel controlPanel

bottom panel for item configuration panels

mainPanel

javax.swing.JPanel mainPanel

the main panel holding lists and list controls

helpPanel

javax.swing.JPanel helpPanel

the panel for displaying help text

helpPanelLabel

javax.swing.JLabel helpPanelLabel

the label for displaying help title

helpTextArea

javax.swing.JTextArea helpTextArea

the textarea for displaying help text

leftListFilter

javax.swing.JComboBox leftListFilter

left list filter and view switch

sourcePanel

javax.swing.JPanel sourcePanel

panel for source controls

leftListScroll

javax.swing.JScrollPane leftListScroll

scrollpane for left list

rightListScroll

javax.swing.JScrollPane rightListScroll

scrollpane for right list

addButton

javax.swing.JButton addButton

button for add items from left to right

removeButton

javax.swing.JButton removeButton

button for clear items from the right list

moveUpButton

javax.swing.JButton moveUpButton

button for moving selected item up in the right list (ordering)

moveDownButton

javax.swing.JButton moveDownButton

button for moving selected item down in the right list (ordering)

leftList

javax.swing.JList leftList

left list with available items

rightList

javax.swing.JList rightList

right list with available items

presentationChooser

chemaxon.alchemist.configbuilder.ConfigElementPresentationChooser presentationChooser

presentation chooser for elements

profile

chemaxon.alchemist.AlchemistProfile profile

alchemist profile used

openFileButton

javax.swing.JButton openFileButton

save button for file support

saveFileButton

javax.swing.JButton saveFileButton

open button for file support

firstResized

boolean firstResized

initial resize flag

ignoreMissingLicense

boolean ignoreMissingLicense

flag for showing/hiding the custom display when license is missing

elementPropertyChangeSupport

javax.swing.event.SwingPropertyChangeSupport elementPropertyChangeSupport

element property change support

validConfiguration

boolean validConfiguration

configuration valid flag

readingConfiguration

boolean readingConfiguration

flag indicates currently reading a configuration

fileSupportEnabled

boolean fileSupportEnabled

flag indicates file support

defaultHelpText

java.lang.String defaultHelpText

default help text

licenseSupport

chemaxon.alchemist.configbuilder.LicenseSupport licenseSupport

ADD_ACTION

javax.swing.AbstractAction ADD_ACTION

An Action implementation which performs config element add

REMOVE_ACTION

javax.swing.AbstractAction REMOVE_ACTION

An Action implementation which performs config element remove

MOVE_UP_ACTION

javax.swing.AbstractAction MOVE_UP_ACTION

An Action implementation which performs config element move up

MOVE_DOWN_ACTION

javax.swing.AbstractAction MOVE_DOWN_ACTION

An Action implementation which performs config element move down

openFileAction

javax.swing.Action openFileAction

open file handler action

saveFileAction

javax.swing.Action saveFileAction

save file handler action

Class chemaxon.alchemist.configbuilder.ConfigBuilderPanel.LeftListModel extends chemaxon.alchemist.utils.SynchronizedAbstractFilterListModel implements Serializable

serialVersionUID: 2968756310518353393L

Class chemaxon.alchemist.configbuilder.ConfigElementListCellRenderer extends javax.swing.DefaultListCellRenderer implements Serializable

serialVersionUID: 4235697770529912189L

Serialized Fields

ignoreStatus

boolean ignoreStatus

flag for hiding status icon

ignoreLicense

boolean ignoreLicense

flag for hiding missing license icon

Class chemaxon.alchemist.configbuilder.ConfigElementTransferHandler extends javax.swing.TransferHandler implements Serializable

serialVersionUID: 9146587976990656436L

Serialized Fields

source

javax.swing.JList source

the source JList

destination

javax.swing.JList destination

the destination JList

configBuilderPanel

ConfigBuilderPanel configBuilderPanel

the config builder panel instance of this transfer handler

Package chemaxon.alchemist.markushview

Class chemaxon.alchemist.markushview.CollapseTreeAction extends javax.swing.AbstractAction implements Serializable

serialVersionUID: -3113135295396732422L

Class chemaxon.alchemist.markushview.CompactMarkushViewer extends javax.swing.JPanel implements Serializable

Serialized Fields

markushViewer

chemaxon.alchemist.markushview.MarkushViewerComponent markushViewer

The MarkushViewerComponent.

autoSizeFragmentsButton

javax.swing.JToggleButton autoSizeFragmentsButton

A JButton on the toolbar.

alwaysShowScaffoldButton

javax.swing.JToggleButton alwaysShowScaffoldButton

A JButton on the toolbar.

nestingViewButton

javax.swing.JToggleButton nestingViewButton

A JButton on the toolbar.

molsInTreeButton

javax.swing.JToggleButton molsInTreeButton

A JButton on the toolbar.

separatorLinesButton

javax.swing.JToggleButton separatorLinesButton

A JButton on the toolbar.

nodeLinesButton

javax.swing.JToggleButton nodeLinesButton

A JButton on the toolbar.

collapseTreeButton

javax.swing.JButton collapseTreeButton

expandTreeButton

javax.swing.JButton expandTreeButton

A JButton on the toolbar.

helpButton

javax.swing.JButton helpButton

tools

javax.swing.JPanel tools

The toolbar

Class chemaxon.alchemist.markushview.ExpandTreeAction extends javax.swing.AbstractAction implements Serializable

serialVersionUID: -2838423581212165652L

Class chemaxon.alchemist.markushview.MarkushListCellRenderer extends javax.swing.JLabel implements Serializable

Class chemaxon.alchemist.markushview.MarkushMoleculeFullViewPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

molecules

javax.swing.JComboBox molecules

A JComboBox to select a molecule from the opened ones to display.

view

chemaxon.marvin.swing.moleculeview.MoleculeViewComponent view

A MoleculeViewComponent to display molecules

selectedRGroups

java.util.List<E> selectedRGroups

the list of the selected R-Groups. One item of this List contains a Set of the selected R-Groups of the opened molecules with the same index of this item. *

selectedIndex

int selectedIndex

The index of the selected molecule in the JComboBox.

renderer

chemaxon.alchemist.markushview.MarkushListCellRenderer renderer

The renderer of the JComboBox

common

chemaxon.marvin.paint.internal.MolPainterCommon common

the MolPainterCommon that contains the display settings of the MoleculeViewComponent.

Class chemaxon.alchemist.markushview.MarkushNestingViewPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

linears

java.util.List<E> linears

The list of the nesting views.

nodes

java.util.List<E> nodes

The list of the nesting views.

linearPanel

javax.swing.JPanel linearPanel

A panel for the actual nesting view.

buttonPanel

javax.swing.JPanel buttonPanel

A panel for the buttons.

previousButton

javax.swing.JButton previousButton

A button to switch the displayed nesting view to the previous selected one's. From the first view it switches to the last one. If there is only one selected molecule, this button is disabled.

nextButton

javax.swing.JButton nextButton

A button to switch the displayed nesting view to the next selected one's. From the last view it switches to the first one. If there is only one selected molecule, this button is disabled.

currentLinearIndex

int currentLinearIndex

The index of the displayed view.

Class chemaxon.alchemist.markushview.MarkushViewComboBoxModel extends javax.swing.AbstractListModel implements Serializable

serialVersionUID: 1878311321410981978L

Serialized Fields

molecules

Molecule[] molecules

The selectable molecules.

selection

Molecule selection

the selected molecule

Class chemaxon.alchemist.markushview.MarkushViewerComponent extends javax.swing.JPanel implements Serializable

serialVersionUID: 2561953223042733755L

Serialized Fields

detailsPane

javax.swing.JTabbedPane detailsPane

A tabbed pane for the Fragment View and the Markush View.

fragmentsPane

chemaxon.alchemist.markushview.RGroupViewPane fragmentsPane

A scrollable component for displaying the selected R-group fragments.

fullViewPanel

javax.swing.JPanel fullViewPanel

A component for displaying user messages or for viewing the loaded molecules

common

chemaxon.marvin.paint.internal.MolPainterCommon common

The display settings for the fragment view and the markush view.

fullView

chemaxon.alchemist.markushview.MarkushMoleculeFullViewPanel fullView

A component for viewing the loaded molecules.

nestingViewPanel

chemaxon.alchemist.markushview.MarkushNestingViewPanel nestingViewPanel

A component for displaying the nesting view of the selected R-Groups.

treeScrollPane

javax.swing.JScrollPane treeScrollPane

The scrollpane that contains the molecule tree.

splitPane

javax.swing.JSplitPane splitPane

A split pane for separating the molecule tree from the detail components.

mainSplit

javax.swing.JSplitPane mainSplit

A split pane for separating the nesting view and the other components.

moleculeTree

chemaxon.alchemist.utils.moleculetree.AlchemistMoleculeTree moleculeTree

The molecule tree to show the R-Group topology.

showPath

boolean showPath

A boolean that indicates if the nesting view display is on.

alwaysShowScaffold

boolean alwaysShowScaffold

A boolean that indicates if scaffolds should be shown always in Fragments view.

autosizeFragments

boolean autosizeFragments

rootMolecules

java.util.List<E> rootMolecules

The List of the RgMolecules we want to overlook. These RgMolecules are identical to the loaded ones, if they are R-Group molecules. If not, the original molecule is wrapped into an R-Group molecule as a scaffold.

hitIndexes

java.util.Map<K,V> hitIndexes

A Map for storing Query hit Rgroup numbers.

Map contains: key - molecule ID, value - color data of the molecules
color data Map contains: key - the color of the atom set, value: the Set of the atom indexes

cancelled

boolean cancelled

loadingThread

java.lang.Thread loadingThread

Class chemaxon.alchemist.markushview.MarkushViewerPrintPane extends javax.swing.JPanel implements Serializable

Serialized Fields

printTabbedPane

javax.swing.JTabbedPane printTabbedPane

printMarkushTreePanel

javax.swing.JPanel printMarkushTreePanel

printFragmentsViewPanel

javax.swing.JPanel printFragmentsViewPanel

printNestingViewPanel

javax.swing.JPanel printNestingViewPanel

buttonPanel

javax.swing.JPanel buttonPanel

Class chemaxon.alchemist.markushview.RGroupViewPane extends javax.swing.JScrollPane implements Serializable

Serialized Fields

mainPanel

javax.swing.JPanel mainPanel

The viewportview of the RGroupViewPane.

rViews

java.util.List<E> rViews

The list of panels.

autoScaffoldIndexes

java.util.List<E> autoScaffoldIndexes

The list of the indexes of the auto scaffold panels.

common

chemaxon.marvin.paint.internal.MolPainterCommon common

The display settings of the molecules.

resizedView

java.awt.Component resizedView

The component which is being resized.

previousPoint

java.awt.Point previousPoint

the previous dragging Point relative to this component.

currentPoint

java.awt.Point currentPoint

the current dragging Point relative to this component.

defaultBackGroundColor

java.awt.Color defaultBackGroundColor

resizeMouseListener

java.awt.event.MouseListener resizeMouseListener

A MouseListener for handling events to resize panels

resizeMouseMotionListener

java.awt.event.MouseMotionListener resizeMouseMotionListener

A MouseMotionListener for resizing definition panels on mousedrag

Class chemaxon.alchemist.markushview.TogglePathAction extends chemaxon.alchemist.utils.menu.AlchemistToggleAction implements Serializable

serialVersionUID: -3200824810790351535L

Package chemaxon.calculations

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

serialVersionUID: 1L

Package chemaxon.clustering

Class chemaxon.clustering.ChemicalSpace extends java.util.Vector implements Serializable

Serialized Fields

weights

float[] weights

inv

chemaxon.clustering.ChemicalSpace.InvertedFile inv

dimensions

int dimensions

fpsize

int fpsize

emptyset

java.util.BitSet emptyset

checked

java.util.BitSet checked

willett

boolean willett

Class chemaxon.clustering.ClusteringException extends java.lang.Exception implements Serializable

Class chemaxon.clustering.InvalidLicenseKeyException extends java.lang.Exception implements Serializable

Package chemaxon.descriptors

Class chemaxon.descriptors.MDGeneratorException extends java.lang.Exception implements Serializable

Class chemaxon.descriptors.MDParametersException extends java.lang.RuntimeException implements Serializable

Class chemaxon.descriptors.MDReaderException extends java.lang.Exception implements Serializable

Class chemaxon.descriptors.MDWriterException extends java.lang.Exception implements Serializable

Class chemaxon.descriptors.SimilarityException extends java.lang.Exception implements Serializable

Package chemaxon.formats

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

Serialized Fields

lineNumberInRecord

int lineNumberInRecord

lineNumberInFile

int lineNumberInFile

Package chemaxon.jchem.db

Class chemaxon.jchem.db.ChemicalTermsUpdateHandlerException extends UpdateHandlerException implements Serializable

Class chemaxon.jchem.db.DatabaseSearchException extends chemaxon.util.ChemaxonException implements Serializable

Class chemaxon.jchem.db.JChemSearch extends ErrorHandler implements Serializable

Serialized Fields

incidents

chemaxon.jchem.db.status.incidentsets.JCSIncidents incidents

New status mechanism.

jchemObserverImpl

chemaxon.jchem.db.JChemObserverImpl jchemObserverImpl

New status mechanism.

fingerprint

byte[] fingerprint

fingerprintInInts

int[] fingerprintInInts

fingerprintNoRings

int[] fingerprintNoRings

querySetAsFingerprint

boolean querySetAsFingerprint

cofp

chemaxon.sss.screen.CombinedFingerprint cofp

order

int order

numberOfBits

int numberOfBits

numberOfOnes

int numberOfOnes

numberOfEdges

int numberOfEdges

fpCount

int fpCount

cfpCount

int cfpCount

structuralFPCount

int structuralFPCount

batchSize

int batchSize

emptyQuery

boolean emptyQuery

isMarkushQuery

boolean isMarkushQuery

hashCodeScreeningForFull

boolean hashCodeScreeningForFull

prevEmptyQuery

java.lang.Boolean prevEmptyQuery

reactionTable

boolean reactionTable

reactionFingerprint

ReactionFingerprint reactionFingerprint

existsBitwiseAND

boolean existsBitwiseAND

existsBitwiseANDOperator

boolean existsBitwiseANDOperator

nameOfBitwiseANDFunction

java.lang.String nameOfBitwiseANDFunction

columnCountsAtScreenening

int[] columnCountsAtScreenening

isScreening

boolean isScreening

isBitwiseScreening

boolean isBitwiseScreening

isBitwiseScreeningLocally

boolean isBitwiseScreeningLocally

isBitwiseScreeningLocallyUsingCache

boolean isBitwiseScreeningLocallyUsingCache

isSimilarityCheckingFromCache

boolean isSimilarityCheckingFromCache

isHashScreening

boolean isHashScreening

sCache

chemaxon.jchem.db.JChemCache sCache

isScreenedContainsIndices

boolean isScreenedContainsIndices

Shows whether the screened list contains
- index of the cd_id
- OR the cd_id itself

screenedHandler

chemaxon.jchem.db.ScreenedHandler screenedHandler

hits

int hits

currentId

int currentId

message

java.lang.String message

maxResultCountReached

boolean maxResultCountReached

maxTimeReached

boolean maxTimeReached

stopped

boolean stopped

stopRequested

boolean stopRequested

resultVector

chemaxon.common.util.IntVector resultVector

finalResultVector

chemaxon.common.util.IntVector finalResultVector

dissimVector

chemaxon.common.util.FloatVector dissimVector

screenedVector

chemaxon.common.util.IntVector screenedVector

beforeEnumScreenedVector

chemaxon.common.util.IntVector beforeEnumScreenedVector

In case of enumerated search this vector stores candidates filtered by a before enum screening step

progressiveReturnArray

chemaxon.util.BlockingIntArrayQueue progressiveReturnArray

startTime

long startTime

searchUsingOriginalTarget

boolean searchUsingOriginalTarget

infoToErrBuf

java.lang.StringBuilder infoToErrBuf

queryCxsmarts

java.lang.String queryCxsmarts

screenAndAbasStartTime

long screenAndAbasStartTime

screenMonitor

chemaxon.jchem.db.Monitor screenMonitor

screenedCount

int screenedCount

searchTime

long searchTime

cachingTime

long cachingTime

firstHitTime

long firstHitTime

filterQueryTime

long filterQueryTime

cacheLoaded

boolean cacheLoaded

cacheUpdated

boolean cacheUpdated

con

java.sql.Connection con

searchThread

chemaxon.jchem.db.JChemSearch.SearchThread searchThread

tableInitialized

boolean tableInitialized

tableNameInitialized

boolean tableNameInitialized

connectionInitialized

boolean connectionInitialized

queryInitialized

boolean queryInitialized

filterInitialized

boolean filterInitialized

chemTermFilterInitialized

boolean chemTermFilterInitialized

chemTermColumnsInitialized

boolean chemTermColumnsInitialized

rowReaderPreparedStatement

java.sql.PreparedStatement rowReaderPreparedStatement

rowReaderSQL

java.lang.String rowReaderSQL

formulaSearch

FormulaSearch formulaSearch

filterVector

chemaxon.common.util.IntVector filterVector

Vector containing all IDs returned by executing filterQuery

orderByFilter

boolean orderByFilter

dbProp

DatabaseProperties dbProp

queryMode

int queryMode

queryModeBoolean

boolean queryModeBoolean

searchOptions

JChemSearchOptions searchOptions

Object to store all search parameters. This is used during the search and stores the settings of the previous search.

publicSearchOptions

JChemSearchOptions publicSearchOptions

The publicly visible SearchOptions object. Settings from this are copied to JChemSearch.searchOptions during initialization.

whereClause

java.lang.String whereClause

rdbms

int rdbms

modifiedfFilterExpression

java.lang.String modifiedfFilterExpression

substitutedCTColumns

java.lang.String[] substitutedCTColumns

filterConfigFile

java.lang.String filterConfigFile

cartridgeMode

boolean cartridgeMode

cartridgeIndexedTable

java.lang.String cartridgeIndexedTable

cartridgeIndexedColumn

java.lang.String cartridgeIndexedColumn

nonHits

chemaxon.common.util.IntVector nonHits

hash

int hash

hc

HashCode hc

cacheError

java.lang.String cacheError

maxCacheSize

int maxCacheSize

minNonCachedMemory

int minNonCachedMemory

cacheExpirationTime

double cacheExpirationTime

prevTimeStamp

java.lang.String prevTimeStamp

prevTableName

java.lang.String prevTableName

timeStamp

java.lang.String timeStamp

timeout

int timeout

timout value in seconds. o means no timeout

lastCheck

long lastCheck

stores the time of the last check (for timeout)

allDissimID

chemaxon.common.util.IntVector allDissimID

allDissimDissim

chemaxon.common.util.FloatVector allDissimDissim

threadsCount

int threadsCount

simThread

chemaxon.jchem.db.JChemSearch.SimilarityThread[] simThread

thread

chemaxon.jchem.db.JChemSearch.ABASThread[] thread

molSearch

MolSearch[] molSearch

evaluator

Evaluator[] evaluator

jep

ChemJEP[] jep

context

MolContext[] context

standardizer

Standardizer[] standardizer

simScreened

chemaxon.common.util.IntVector[] simScreened

simDissimVector

chemaxon.common.util.FloatVector[] simDissimVector

threadPriority

int threadPriority

pstmtForSmilesRead

java.sql.PreparedStatement pstmtForSmilesRead

usePreparedStatements

boolean usePreparedStatements

pstmtForScreening

java.sql.PreparedStatement pstmtForScreening

pstmtSQLForScreening

java.lang.String pstmtSQLForScreening

queryIsStructuralKey

boolean queryIsStructuralKey

isEnumeratedSearch

boolean isEnumeratedSearch

regCode

long regCode

enumeratedFeatures

int enumeratedFeatures

What query features should be enumerated. Depends on other settings, set during initialization.

enumCount

int enumCount

everyTargetIsHit

boolean everyTargetIsHit

noScreenReturnAll

boolean noScreenReturnAll

We do not care about the structure (empty), just other constraints

chemicalTermsSubstitution

boolean chemicalTermsSubstitution

absStereoMode

boolean absStereoMode

results

int[] results

dissimilarityResults

float[] dissimilarityResults

queryStructure

java.lang.String queryStructure

The query molecule set as a String

queryMolecule

Molecule queryMolecule

The query molecule set as a Molecule

queryMol

Molecule queryMol

the actual query mol (standardized, etc)

originalQuery

Molecule originalQuery

holds the original query during enumeration

structureTable

java.lang.String structureTable

Holds value of property structureTable.

tableType

int tableType

Determines how query and markush structures shoudl be treated

tautomerDuplicateSearch

boolean tautomerDuplicateSearch

tautomerDupSearchUsesOrigQuery

boolean tautomerDupSearchUsesOrigQuery

tautomerDuplicateSearchTable

boolean tautomerDuplicateSearchTable

genericTautomerProtectsChirality

boolean genericTautomerProtectsChirality

switchOffAllProtectionsForTDF

boolean switchOffAllProtectionsForTDF

markushTable

boolean markushTable

filterIDList

int[] filterIDList

Holds value of property filterIDList.

origFilterIdList

int[] origFilterIdList

filterIDNotList

int[] filterIDNotList

filterIDListSorted

boolean filterIDListSorted

filterIDNotListSorted

boolean filterIDNotListSorted

filterTable

java.lang.String filterTable

Holds value of property filterTable.

deleteFilterTableWhenReady

boolean deleteFilterTableWhenReady

Holds value of property deleteFilterTableWhenReady.

resultTable

java.lang.String resultTable

Holds value of property resultTable.

resultTableMode

int resultTableMode

Holds value of property resultTableMode.

infoToStdError

boolean infoToStdError

Holds value of property infoToStdError.

firstEnumeratedStructure

boolean firstEnumeratedStructure

Bookkeeping of first enumerated structure

connectionHandler

ConnectionHandler connectionHandler

Holds value of property connectionHandler.

standardizationDisabled

boolean standardizationDisabled

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

preCalculatedHashCode

java.lang.Integer preCalculatedHashCode

preCalculatedGenericTautomer

Molecule preCalculatedGenericTautomer

preCalculatedSmiles

byte[] preCalculatedSmiles

preCalculatedSmilesSet

boolean preCalculatedSmilesSet

smiles

byte[] smiles

runMode

int runMode

licenseEnvironment

java.lang.String licenseEnvironment

stopRecorded

boolean stopRecorded

Class chemaxon.jchem.db.MaxSearchFrequencyExceededException extends DatabaseSearchException implements Serializable

Class chemaxon.jchem.db.PropertyNotSetException extends java.lang.Exception implements Serializable

Class chemaxon.jchem.db.RecalculationException extends chemaxon.util.ChemaxonException implements Serializable

Class chemaxon.jchem.db.TransferException extends java.lang.Exception implements Serializable

Class chemaxon.jchem.db.UpdateHandler extends ErrorHandler implements Serializable

Serialized Fields

numberOfFPCols

int numberOfFPCols

mode

int mode

additionalColumnsString

java.lang.String additionalColumnsString

cfp

chemaxon.sss.screen.CombinedFingerprint cfp

dbOptions

chemaxon.jchem.db.DatabaseOptions dbOptions

conh

ConnectionHandler conh

con

java.sql.Connection con

tableName

java.lang.String tableName

mol

Molecule mol

structure

byte[] structure

smiles

java.lang.String smiles

formula

java.lang.String formula

sortableFormula

java.lang.String sortableFormula

molWeight

java.lang.Double molWeight

fingerprint

int[] fingerprint

hash

int hash

flags

java.lang.String flags

molName

java.lang.String molName

genericTautomer

Molecule genericTautomer

isMarkush

boolean isMarkush

noRingInfoInFP

boolean noRingInfoInFP

reactionMappingIncomplete

boolean reactionMappingIncomplete

markushData

byte[] markushData

superGraph

chemaxon.enumeration.supergraph.Supergraph superGraph

hc

HashCode hc

additionalColumns

java.util.ArrayList<E> additionalColumns

Stores AdditionalColumn objects

pstmt

java.sql.PreparedStatement pstmt

counter

int counter

max

int max

alwaysCreateNew

boolean alwaysCreateNew

totalMemoryAt1000

long totalMemoryAt1000

spoiledMax

boolean spoiledMax

lastId

int lastId

timeStamp

java.lang.String timeStamp

regenerateMode

boolean regenerateMode

inputFormat

java.lang.String inputFormat

rowData

UpdateHandler.RowData rowData

bigLOBs

java.util.ArrayList<E> bigLOBs

activeFieldList

chemaxon.jchem.db.UpdateHandler.ActiveFieldList activeFieldList

lastActiveFieldList

chemaxon.jchem.db.UpdateHandler.ActiveFieldList lastActiveFieldList

tableType

int tableType

tautomerDuplicateSearch

boolean tautomerDuplicateSearch

switchOffAllProtectionsForTDF

boolean switchOffAllProtectionsForTDF

genericTautomerProtectsChirality

boolean genericTautomerProtectsChirality

elemanal

ElementalAnalyser elemanal

cartridgeMode

boolean cartridgeMode

indexedTable

java.lang.String indexedTable

indexedColumn

java.lang.String indexedColumn

firstExecuteCall

boolean firstExecuteCall

inputMoleculeSet

boolean inputMoleculeSet

structureSourceSet

boolean structureSourceSet

tempTableToWrite

java.lang.String tempTableToWrite

fields

chemaxon.jchem.db.UpdateHandler.Field[] fields

dbms

int dbms

emptyStructuresAllowed

boolean emptyStructuresAllowed

descriptorNames

java.lang.String[] descriptorNames

cd_id

int cd_id

rowID

java.lang.String rowID

smilesLength

int smilesLength

standardizer

Standardizer standardizer

lastIdPrepStmt

java.sql.PreparedStatement lastIdPrepStmt

storeUpdateLogPrepStmt

java.sql.PreparedStatement storeUpdateLogPrepStmt

jcsearch

JChemSearch jcsearch

duplicateFiltering

boolean duplicateFiltering

isDuplicateFilteringTO

boolean isDuplicateFilteringTO

if true duplicate filtering upon insert should be specified based on the table option.

setChiralFlag

boolean setChiralFlag

doNotImport

boolean doNotImport

standardize

boolean standardize

ignoreCTErrors

boolean ignoreCTErrors

loggingEnabled

boolean loggingEnabled

inputMol

Molecule inputMol

chemTermColCfg

java.util.Map<K,V> chemTermColCfg

chemTermColValues

java.util.Map<K,V> chemTermColValues

molContext

MolContext molContext

chemTermCalcNeeded

boolean chemTermCalcNeeded

molNameField

java.lang.String molNameField

singleInsertLog

boolean singleInsertLog

storedUpdateLogDbProp

DatabaseProperties storedUpdateLogDbProp

registeredCaches

java.util.ArrayList<E> registeredCaches

cacheTimestamp

java.lang.String cacheTimestamp

updateLogCache

chemaxon.jchem.db.UpdateLogCache updateLogCache

bufferedLogString

java.lang.StringBuffer bufferedLogString

bufferedIdsNo

int bufferedIdsNo

defaultMarkushHandler

chemaxon.jchem.db.cdmarkush.CDMarkushHandler defaultMarkushHandler

Default handler used for CD_MARKUSH field

lastPstmtMode

int lastPstmtMode

Class chemaxon.jchem.db.UpdateHandlerException extends chemaxon.util.ChemaxonException implements Serializable

Class chemaxon.jchem.db.Updater.UpdateInfo extends java.lang.Object implements Serializable

Serialized Fields

message

java.lang.String message

Massage describing what update is necessary and why.

entityList

java.lang.String[] entityList

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

processingMessage

java.lang.String processingMessage

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

isRegeneration

boolean isRegeneration

Deprecated. since 5.1.2 use Updater.UpdateInfo.isProgressMonitoringSupported instead.

Indicates if the update process is the regeneration of all tables. Since this can be a lengthy process, progress monitoring may be needed. In this case the table names in Updater.UpdateInfo.entityList can be used directly for

UpdateHandler.recalculateTable(chemaxon.util.ConnectionHandler, 
  String, boolean, String, java.util.Map, Boolean, chemaxon.jchem.file.ProgressWriter)

isProgressMonitoringSupported

boolean isProgressMonitoringSupported

Indicates whether update process supports progress monitoring.

Since:: JChem 5.1.2

regenerationType

int regenerationType

Indicates the regeneration type.

Since:: JChem 5.2.4

isOperationRequired

boolean isOperationRequired

Indicates whether the operation is required or not.

Since:: JChem 5.3

isStructuralChange

boolean isStructuralChange

Indicates whether the operation is required or not.

Since:: JChem 5.8

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

cached

boolean cached

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

jep

ChemJEP jep

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

Serialized Fields

className

java.lang.String className

descriptors

java.lang.String[] descriptors

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

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

Serialized Fields

className

java.lang.String className

subMatches

java.util.Hashtable<K,V> subMatches

type

int type

attributes

chemaxon.util.SearchAttributes attributes

dir

java.lang.String dir

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

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 arg0)
                  throws java.io.IOException

Throws:: java.io.IOException

writeExternal

public void writeExternal(java.io.ObjectOutput arg0)
                   throws java.io.IOException

Throws:: java.io.IOException

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

chart

com.objectplanet.chart.LineChart chart

precision

int precision

legendMols

Molecule[] legendMols

legendTexts

java.lang.String[] legendTexts

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

zobjclean

java.lang.Object[] zobjclean

zranks

long[] zranks

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

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 arg0)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException

Throws:: java.lang.ClassNotFoundException; java.io.IOException

writeObject

private void writeObject(java.io.ObjectOutputStream arg0)
                  throws java.io.IOException

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 arg0)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException

Throws:: java.lang.ClassNotFoundException; java.io.IOException

writeObject

private void writeObject(java.io.ObjectOutputStream arg0)
                  throws java.io.IOException

Throws:: java.io.IOException

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

Serialized Fields

incType

boolean incType

changeUp

boolean changeUp

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

serialVersionUID: 6282033706405196916L

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream arg0)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException

Throws:: java.lang.ClassNotFoundException; java.io.IOException

writeObject

private void writeObject(java.io.ObjectOutputStream arg0)
                  throws java.io.IOException

Throws:: java.io.IOException

Serialized Fields

incType

boolean incType

wasDoubleBeforeClick

boolean wasDoubleBeforeClick

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

cornerHist

java.awt.Point[] cornerHist

scaleHist

double[] scaleHist

autoHydrogenizeHist

int[] autoHydrogenizeHist

scrollBarHist

int[][] scrollBarHist

selectionToZoomHist

boolean[] selectionToZoomHist

molgToZoomHist

MoleculeGraph[][] molgToZoomHist

rotateMatrHist

CTransform3D[] rotateMatrHist

molHistLen

int molHistLen

molHistCur

int molHistCur

molHistMax

int molHistMax

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 arg0)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException

Throws:: java.lang.ClassNotFoundException; java.io.IOException

writeObject

private void writeObject(java.io.ObjectOutputStream arg0)
                  throws java.io.IOException

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 arg0)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException

Throws:: java.lang.ClassNotFoundException; java.io.IOException

writeObject

private void writeObject(java.io.ObjectOutputStream arg0)
                  throws java.io.IOException

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 arg0)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException

Throws:: java.lang.ClassNotFoundException; java.io.IOException

Serialized Fields

moveMode

int moveMode

persistentMoveMode

boolean persistentMoveMode

document

MDocument document

selectionDoc

MSelectionDocument selectionDoc

elements

java.util.List<E> elements

queryAtoms

java.util.List<E> queryAtoms

extraBonds

java.util.List<E> extraBonds

atomStrings

java.util.List<E> atomStrings

reactionSupported

boolean reactionSupported

chiralitySupport

int chiralitySupport

atomSize

double atomSize

bondSpacing

double bondSpacing

stickdst

double stickdst

mergedst

double mergedst

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

prevCurfrag

MDocument prevCurfrag

flyingBondMol

MoleculeGraph flyingBondMol

curfragMoved

boolean curfragMoved

canRotCurfrag

boolean canRotCurfrag

canMovCurfrag

boolean canMovCurfrag

atomSelectionMode

int atomSelectionMode

curfragR

double curfragR

rotO

DPoint3 rotO

rotAxisPoint

DPoint3 rotAxisPoint

isAxisSet

boolean isAxisSet

rotateZPhi

double rotateZPhi

rotatePhi

double rotatePhi

rotate3dPhiX

double rotate3dPhiX

rotate3dPhiY

double rotate3dPhiY

rotate3dPhi

double rotate3dPhi

rotate3dx

double rotate3dx

rotate3dy

double rotate3dy

rotate3direction

int rotate3direction

indexToRot

int indexToRot

pointIndexToRot

int pointIndexToRot

atomBranchPiece

Molecule atomBranchPiece

piece

Molecule piece

pieceOriginalObject

Molecule pieceOriginalObject

showMolecule

Molecule showMolecule

paintOnlyShowMolecule

boolean paintOnlyShowMolecule

sketchMode

chemaxon.marvin.sketch.SketchMode sketchMode

bondrawMode

boolean bondrawMode

thisBondlen

double thisBondlen

lastBondFlags

int lastBondFlags

lastQueryBondString

java.lang.String lastQueryBondString

newSelection

boolean newSelection

jointAtom

MolAtom jointAtom

curfragJoin

chemaxon.marvin.sketch.MolJoin curfragJoin

bondDraggedAlong

boolean bondDraggedAlong

historizeEnabled

boolean historizeEnabled

documentEdited

boolean documentEdited

isDataSgroupLabelPointed

boolean isDataSgroupLabelPointed

dataSgroupLabelMoving

boolean dataSgroupLabelMoving

dataSgroupObject

DataSgroup dataSgroupObject

hadSelection

boolean hadSelection

scrollBarVals

int[] scrollBarVals

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

other

MoleculeGraph other

tother

MoleculeGraph tother

atoms

java.util.List<E> atoms

bonds

java.util.List<E> bonds

pri

MolAtom[] pri

sec

MolAtom[] sec

corrupt

MolBond[] corrupt

mergedst

double mergedst

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 arg0)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException

Throws:: java.lang.ClassNotFoundException; java.io.IOException

writeObject

private void writeObject(java.io.ObjectOutputStream arg0)
                  throws java.io.IOException

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 arg0)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException

Throws:: java.lang.ClassNotFoundException; java.io.IOException

writeObject

private void writeObject(java.io.ObjectOutputStream arg0)
                  throws java.io.IOException

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 arg0)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException

Throws:: java.lang.ClassNotFoundException; java.io.IOException

writeObject

private void writeObject(java.io.ObjectOutputStream arg0)
                  throws java.io.IOException

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

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 arg0)
                  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

highlightedAtom

int highlightedAtom

viewPanel

chemaxon.marvin.view.swing.ViewPanel viewPanel

viewFrame

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

cellIndex

int cellIndex

winScale

double winScale

moleculeCenter

DPoint3 moleculeCenter

preferredSize1

java.awt.Dimension preferredSize1

rsize

java.awt.Dimension rsize

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 arg0)
                 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

borderWidth

int borderWidth

borderColor

java.awt.Color borderColor

tabScale

double tabScale

autoTabScale

boolean autoTabScale

tabScaleCalcNeeded

boolean tabScaleCalcNeeded

animSynchronized

boolean animSynchronized

startLoad

boolean startLoad

rows

int rows

cols

int cols

animator

chemaxon.marvin.util.MarvinModule animator

selectable

boolean selectable

editable

int editable

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.metabolizer

Class chemaxon.metabolizer.MetabolizerException extends java.lang.Exception implements Serializable

serialVersionUID: -8484316066857620143L

Class chemaxon.metabolizer.MetabolizerExecutor_Stub extends java.rmi.server.RemoteStub implements Serializable

serialVersionUID: 2L

Class chemaxon.metabolizer.MetabolizerIOException extends java.lang.Exception implements Serializable

serialVersionUID: -2023591357549300197L

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.reaction

Class chemaxon.reaction.EqualableMolecule extends Molecule implements Serializable

Serialized Fields

mol

Molecule mol

hashcode

int hashcode

Class chemaxon.reaction.GroupDefinition extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

abbreviation

java.lang.String abbreviation

The abbreviation (name) of the group.

group

Molecule group

The group definition as a molecule.

Class chemaxon.reaction.GroupList extends java.lang.Object implements Serializable

serialVersionUID: 7511499720792606114L

Serialized Fields

abbreviations

java.util.List<E> abbreviations

The contents of each user defined group definitions gets into the abbreviation list, and a part of (or the whole) default abbreviation group is contained by this.

aminoAcids

java.util.List<E> aminoAcids

Only the contents, or a part of contents of default amino-acid groups are contained by this

Class chemaxon.reaction.MoleculeData extends java.lang.Object implements Serializable

Serialized Fields

grinvCC

long grinvCC

The graph invariant change count corresponding to the molecule at the time when the search was performed.

Class chemaxon.reaction.PatternProperty extends java.lang.Object implements Serializable

serialVersionUID: -3617253669859174882L

Serialized Fields

representation

java.lang.String representation

The string representation of the pattern

Class chemaxon.reaction.Reaction extends java.lang.Object implements Serializable

Serialized Fields

data

int data

Deprecated.

The required data to be stored.

id

java.lang.String id

Deprecated.

The reaction ID.

rxn

RxnMolecule rxn

Deprecated.

The reaction molecule.

rjep

ChemJEP rjep

Deprecated.

The JEP object that evaluates the reactivity (acceptance) rule.

sjep

ChemJEP sjep

Deprecated.

The JEP object that evaluates the selectivity (measure) rule.

tolerances

double[] tolerances

Deprecated.

The tolerance value corresponding to the selectivity rule.

map2nopar

int[] map2nopar

Deprecated.

Auxiliary array to store no-parity info.

map2map

int[] map2map

Deprecated.

Identical maps.

smaps

int[] smaps

Deprecated.

Start map numbers: bond atom1.

emaps

int[] emaps

Deprecated.

End map numbers: bond atom2.

rbondtypes

int[] rbondtypes

Deprecated.

Reactant bond types.

pbondtypes

int[] pbondtypes

Deprecated.

Product bond types.

bcount

int bcount

Deprecated.

Number of changed bonds.

map2stereo

int[] map2stereo

Deprecated.

Map -> reaction stereo info array.

rmaps

java.util.ArrayList<E>[] rmaps

Deprecated.

Reactant map data: the i-th element is a list of (map, atom index) pairs corresponding to the i-th reactant.

pmaps

java.util.ArrayList<E>[] pmaps

Deprecated.

Product map data: the i-th element is a list of (map, atom index) pairs corresponding to the i-th product.

map2raindex

int[] map2raindex

Deprecated.

Map -> reaction reactant atom index array.

map2paindex

int[] map2paindex

Deprecated.

Map -> reaction product atom index array.

map2rindex

int[] map2rindex

Deprecated.

Map number -> reactant index array. Shows which reactant a given atom map belongs to. The product index is set to -1 if the mapped atom exists only on the product side.

map2pindex

int[] map2pindex

Deprecated.

Map number -> product index array. Shows which product a given atom map belongs to. The product index is set to -1 if the mapped atom exists only on the reactant side.

rindex2map

int[] rindex2map

Deprecated.

Reactant index -> map number array. Shows a representative map number from the reactant.

pindex2map

int[] pindex2map

Deprecated.

Product index -> map number array. Shows a representative map number from the product.

rparities

java.util.ArrayList<E> rparities

Deprecated.

Stores parity info (reactant-side). Stores reactant-side parity-info in int[7] arrays. 0: central atom map 1-4: ligand atom maps 5: parity sign 6: parity

pparities

java.util.ArrayList<E> pparities

Deprecated.

Stores parity info (product-side). Stores product-side parity-info in int[7] arrays. 0: central atom map 1-4: ligand atom maps 5: parity sign 6: parity

rcistrans

java.util.ArrayList<E> rcistrans

Deprecated.

Stores double bond stereo info (reactant-side). Stores reactant-side reaction stereo2 (cis/trans) info in int[5] arrays. 0-3: the A1-A2=A3-A4 atom maps 4: the cis/trans constant

See Also:: StereoConstants.CIS, StereoConstants.TRANS, StereoConstants.CTUNSPEC

pcistrans

java.util.ArrayList<E> pcistrans

Deprecated.

Stores double bond stereo info (product-side). Stores product-side reaction stereo2 (cis/trans) info in int[5] arrays. 0-3: the A1-A2=A3-A4 atom maps 4: the cis/trans constant

See Also:: StereoConstants.CIS, StereoConstants.TRANS, StereoConstants.CTUNSPEC

reactants

Molecule[] reactants

Deprecated.

Reaction reactants (in visual order).

products

Molecule[] products

Deprecated.

Reaction products (in visual order).

Class chemaxon.reaction.ReactionException extends chemaxon.util.ChemaxonException implements Serializable

Class chemaxon.reaction.Reactor extends java.lang.Object implements Serializable

Serialized Fields

licenseEnvironment

java.lang.String licenseEnvironment

rre

chemaxon.reaction.ReactionResultEnumerator rre

reaction

Reaction reaction

The reaction scheme with rules

performer

chemaxon.reaction.ReactionPerformer performer

The reaction performer.

standardizer

Standardizer standardizer

The reactant standardizer object.

reactionDefinedStandardizer

Standardizer reactionDefinedStandardizer

The reactant standardizer object created using ReactorConfiguration.STANDARDIZATION_TAG as standardizer config.

ignoreReactionDefinedStandardizer

boolean ignoreReactionDefinedStandardizer

Ignore standardizer defined in ReactorConfiguration.STANDARDIZATION_TAG.

productStandardizer

Standardizer productStandardizer

The product standardizer object.

outputReactionMappingStyle

int outputReactionMappingStyle

Output reaction mapping style.

fakeResultType

int fakeResultType

Fake result type. Can be Reactor.FUSED_REACTION_OUTPUT

skipReactionMappingCheck

boolean skipReactionMappingCheck

True if reaction mapping check should be skipped.

originalInputReactants

Molecule[] originalInputReactants

The original input reactants.

reactants

Molecule[] reactants

The reactant array.

first

boolean first

True if first hit is to be returned.

pieces

int pieces

The number of result items to be returned for one reactant set

currentPieces

int currentPieces

options

chemaxon.reaction.ReactorOptions options

Class chemaxon.reaction.ReactorConfiguration extends java.lang.Object implements Serializable

Serialized Fields

dir

java.lang.String dir

The config file directory.

root

org.dom4j.Element root

The XML representation.

evaluator

Evaluator evaluator

The expression evaluator object.

standardizer

Standardizer standardizer

The standardizer object

productStandardizer

Standardizer productStandardizer

The product standardizer object.

unique

boolean unique

True if unique product lists required.

cached

boolean cached

True if calculation/search results should be cached.

stset

boolean stset

True if standardizer has been set.

pstset

boolean pstset

True if product standardizer has been set.

addRules

boolean addRules

True if rules to be added.

rootElementName

java.lang.String rootElementName

The reactions root element name. The reactions root is the parent element of the Reaction elements.

Class chemaxon.reaction.ReactorOptions extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

resultType

int resultType

The result (or output) type.

duplicateFilteringMethod

int duplicateFilteringMethod

Duplicate product list filtering method.

norules

int norules

Ignore rules type.

ratio

int[] ratio

The ratio array

pinds

int[] pinds

The product indexes to be returned (null if all products).

reverse

boolean reverse

The "reverse" property: true if the reaction is to be processed in reversed direction, that is, the product and reactant sides are swapped. Default: false.

transform

boolean transform

True if transform mode: transforms original reactant (standardizer).

excludeOverlappingHits

boolean excludeOverlappingHits

True if overlapping hits should be excluded.

mapResult

boolean mapResult

true if reactants / products should be mapped according to reaction.

single

boolean single

True if single mode: returns only single product lists.

rmduprefs

boolean rmduprefs

True if duplicate product references have to be removed from the generated product sets.

cached

boolean cached

True if search results are to be stored and reused.

attributes

chemaxon.util.SearchAttributes attributes

The search attributes.

searchOptionsString

java.lang.String searchOptionsString

The search options string.

reactionIDProp

java.lang.String reactionIDProp

Reaction ID property name.

reactantIDProps

java.lang.String[] reactantIDProps

Reactant ID property names.

productIDProps

java.lang.String[] productIDProps

Product ID property names.

copyAllReactantProperties

boolean copyAllReactantProperties

Copy all reactant properties to output products/reactions

sourceProperties

java.lang.String[][] sourceProperties

Reactant properties which should be copied to products.

targetProperties

java.lang.String[][] targetProperties

Target property names (for property copy).

patternBasedProperties

java.util.Map<K,V> patternBasedProperties

Properties, that are calculated based on a pattern. Contains pairs, where the pattern is the string representation of PatternProperty

showUnsuccessfulReactions

boolean showUnsuccessfulReactions

Sets if unsuccessful reactions (reactions which do not result products) should be shown in output.

Class chemaxon.reaction.RxnException extends chemaxon.sss.search.SearchException implements Serializable

Class chemaxon.reaction.SearchData extends chemaxon.reaction.MoleculeData implements Serializable

Serialized Fields

hitDataList

java.util.ArrayList<E> hitDataList

Stores the HitData list corresponding to the stored search hits.

complete

boolean complete

True if all search hits have been stored.

Class chemaxon.reaction.Standardizer extends java.lang.Object implements Serializable

Serialized Fields

licenseEnvironment

java.lang.String licenseEnvironment

stdata

chemaxon.reaction.StandardizerData[] stdata

The standardizer data built from the data in the config xml.

finalStereoFix

boolean finalStereoFix

appliedTask

boolean[] appliedTask

appliedTask[i] is true if task i has modified the molecule.

cldata

chemaxon.reaction.StandardizerData cldata

Final clean task.

cleanTemplates

Molecule[] cleanTemplates

Default template based clean templates.

partialClean

boolean partialClean

true if partial cleaning of changed atom is required at the end.

activeGroups

java.lang.String[] activeGroups

The active task groups array. If set, then only tasks belonging to at least one of these groups and those belonging to no groups will be executed, otherwise all tasks will be executed.

inactiveTasks

java.util.HashSet<E> inactiveTasks

Inactive tasks list.

atomIndexQuery

boolean atomIndexQuery

True if atom index query is enabled: see Standardizer.getOldToNew() and Standardizer.getNewToOld(). Default: false.

old2new

int[] old2new

The old -> new atom index map.

new2old

int[] new2old

The new -> old atom index map.

isReaction

boolean isReaction

True if input molecule is RxnMolecule

Class chemaxon.reaction.StandardizerConfiguration extends chemaxon.reaction.ReactorConfiguration implements Serializable

Serialized Fields

data

java.util.ArrayList<E> data

Stores the StandardizerData records.

Class chemaxon.reaction.StandardizerException extends chemaxon.reaction.RxnException implements Serializable

Package chemaxon.sss.screen

Class chemaxon.sss.screen.ReducedGraph extends chemaxon.enumeration.supergraph.Supergraph implements Serializable

Serialized Fields

mixedHetero

boolean mixedHetero

indicates if hetero trees can contain carbon atoms. THis means that during reduction these are merged. In rings they are always merged, otherwise heteroRings would be difficult to express in terms of reduced atoms.

reducedType

int reducedType

If this molecule is on the query side.

original

Molecule original

maxID

int maxID

maximal rgroup id in the original molecule

reduced

RgMolecule reduced

the continuously reduced molecule until the supergraph merging

union

MoleculeGraph union

in case of ReducedGraph.preMerge() this is the union of the whole markush molecule in case of ReducedGraph.mergeOnMarkush() this is the selection of the given rgroup member.

bClass

chemaxon.core.calculations.RingClassifier bClass

bond classifier for merging on the markush structure

sgMerge

boolean sgMerge

if we are merging on supergraph or it's still the RGMolecule

Package chemaxon.sss.search

Class chemaxon.sss.search.JChemSearchOptions extends SearchOptions implements Serializable

Serialized Fields

absoluteStereo

int absoluteStereo

filterQuery

java.lang.String filterQuery

dissimilarityThreshold

float dissimilarityThreshold

dissimilarityThresholdExcluded

boolean dissimilarityThresholdExcluded

maxTime

long maxTime

maxResultCount

int maxResultCount

returnsNonHits

boolean returnsNonHits

dissimilarityMetric

java.lang.String dissimilarityMetric

Dissimilarity metric name, or null for default.

dissimilarityMetricParameters

java.lang.String dissimilarityMetricParameters

Dissimilarity metric parameters.

descriptorConfig

java.lang.String descriptorConfig

configuration for descriptor dissim. calculations

descriptorName

java.lang.String descriptorName

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

formulaSearchType

int formulaSearchType

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

formulaSearchQuery

java.lang.String formulaSearchQuery

Query of the formula search.

matchCountOptions

MatchCountOptions matchCountOptions

optimizeQueries

boolean optimizeQueries

Shows whether the query should be enumerated to improve search

cacheRegistrationNeeded

boolean cacheRegistrationNeeded

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

markushScreeningOptions

java.util.Set<E> markushScreeningOptions

Set containing all enabled Markush screen methods

haltOnError

chemaxon.sss.search.options.HaltOnErrorOption haltOnError

Error handling of the search.

See Also:: HaltOnErrorOption

Class chemaxon.sss.search.MarkushFeature extends java.lang.Object implements Serializable

serialVersionUID: 8770437891053649928L

Serialized Fields

type

int type

Expansion type.

data

int[] data

Reference data to expanded object. Different for each type:

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

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

hashCode

int hashCode

Class chemaxon.sss.search.MatchCountOptions extends java.lang.Object implements Serializable

Serialized Fields

matchCountIncludesZero

boolean matchCountIncludesZero

mode

int mode

matchCountLowLimit

int matchCountLowLimit

matchCountHighLimit

int matchCountHighLimit

matchCountLowLimitInclusive

boolean matchCountLowLimitInclusive

matchCountHighLimitInclusive

boolean matchCountHighLimitInclusive

matchCounthitLimit

int matchCounthitLimit

matchCountRelation

java.lang.String matchCountRelation

Class chemaxon.sss.search.MolSearchOptions extends SearchOptions implements Serializable

Serialized Fields

ignoreChiralityForAtoms

chemaxon.common.util.IntVector ignoreChiralityForAtoms

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

hitIncludesRNodes

boolean hitIncludesRNodes

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

queryAbsoluteStereo

boolean queryAbsoluteStereo

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

targetAbsoluteStereo

boolean targetAbsoluteStereo

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

hitIndexType

int hitIndexType

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

markushEnabled

boolean markushEnabled

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

recursiveSMARTSMode

boolean recursiveSMARTSMode

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

switchOffAllProtectsForTDF

boolean switchOffAllProtectsForTDF

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

markushArom

int markushArom

Specifies handling Markush aromatization information (ambiguous aromatic rings) during Markush search. Default is MARKUSH_AROM_FINAL_CHECK (consider Markush aromatization during Markush search and check the hit afterwards).

Class chemaxon.sss.search.SearchException extends chemaxon.util.ChemaxonException implements Serializable

Class chemaxon.sss.search.SearchOptions extends java.lang.Object implements Serializable

Serialized Fields

dirty

boolean dirty

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

exactQueryAtomMatching

boolean exactQueryAtomMatching

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

Since:: JChem 2.2

doubleBondStereoMatchingMode

int doubleBondStereoMatchingMode

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

Since:: JChem 2.2
See Also:: SearchOptions.setDoubleBondStereoMatchingMode(int)

HCountMatching

int HCountMatching

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

verbose

boolean verbose

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

superstructureSearch

boolean superstructureSearch

True if the current search type is superstructure search. Cannot be set on its own, only indirectly through setSearchType.

options

int[] options

Field to store various options of the search.

searchType

int searchType

Search type: global mode of search.

See Also:: SearchOptions.setSearchType(int)

vagueBondLevel

int vagueBondLevel

Option for less strict evaluation of query bonds (e.g. ambiguious aromaticity). Default value is VAGUE_BOND_LEVEL1

completeHG

boolean completeHG

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

exactTopologyMatching

boolean exactTopologyMatching

true for e.g. full structure matching, false for substructure matching

exactBondMatching

boolean exactBondMatching

true, if query bonds match only the same query bonds

orderSensitiveSearch

boolean orderSensitiveSearch

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

keepQueryOrder

boolean keepQueryOrder

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

exactFragment

boolean exactFragment

True: the query should only match to full fragments of the target. (No heavy atoms outside the match and each query fragment corresponds to a target fragment.)

tautomerSearch

boolean tautomerSearch

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

tautomerSearchOption

int tautomerSearchOption

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

tautomerSearchOptionLeftDefault

boolean tautomerSearchOptionLeftDefault

Shows that tautomerSearch value has not been set.

isotopeMatching

int isotopeMatching

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

chargeMatching

int chargeMatching

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

valenceMatching

boolean valenceMatching

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

radicalMatching

int radicalMatching

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

mixSgroupMatching

boolean mixSgroupMatching

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

polymerMatching

boolean polymerMatching

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

endGroupMatching

boolean endGroupMatching

True: polymer endgroups must match (default: false)

transformMonomer

boolean transformMonomer

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

phaseShift

boolean phaseShift

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

copolymerMatching

boolean copolymerMatching

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

homologyNarrowTranslation

HomologyTranslationOption homologyNarrowTranslation

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

homologyBroadTranslation

HomologyTranslationOption homologyBroadTranslation

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

ssrOption

SetOfSmallestRingsOption ssrOption

Which set of smallest rings to use for property calculations.

stereoModel

int stereoModel

Specifies the used stereo model. Default is STEREO_MODEL_LOCAL (it may change in the future!)

stereoSearchType

int stereoSearchType

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

See Also:: SearchOptions.setStereoSearchType(int)

ignoreTetrahedralStereo

boolean ignoreTetrahedralStereo

See Also:: SearchOptions.setIgnoreTetrahedralStereo(boolean)

ignoreDoubleBondStereo

boolean ignoreDoubleBondStereo

See Also:: SearchOptions.setIgnoreDoubleBondStereo(boolean)

ignoreAxialStereo

boolean ignoreAxialStereo

See Also:: SearchOptions.setIgnoreAxialStereo(boolean)

ignoreAlleneStereo

boolean ignoreAlleneStereo

See Also:: SearchOptions.setIgnoreAlleneStereo(boolean)

ignoreSynAntiStereo

boolean ignoreSynAntiStereo

See Also:: SearchOptions.setIgnoreSynAntiStereo(boolean)

checkSpHyb

boolean checkSpHyb

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

Since:: 5.1

implicitHMatching

int implicitHMatching

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

reactionUnpairedMapMatching

boolean reactionUnpairedMapMatching

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

chemTermsFilter

java.lang.String chemTermsFilter

chemTermsFilterConfig

java.lang.String chemTermsFilterConfig

undefinedRAtom

int undefinedRAtom

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

undefinedRAtomUserDefined

boolean undefinedRAtomUserDefined

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

bridgingRAllowed

boolean bridgingRAllowed

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

RLigandEqualityCheck

boolean RLigandEqualityCheck

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

hitOrdering

int hitOrdering

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

attachedDataMatch

int attachedDataMatch

Specifies attached data match type Default is SearchConstants.ATTACHED_DATA_MATCH_IGNORE

attachedDataPrefixes

java.lang.String attachedDataPrefixes

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

exactSpecialAtomMatching

java.lang.String exactSpecialAtomMatching

ignoreCTExceptions

boolean ignoreCTExceptions

changedUserComparator

boolean changedUserComparator

true if user-defined comparators has changed

userComparators

java.util.ArrayList<E> userComparators

User defined MolComparators

exhaustiveModeLimit

int exhaustiveModeLimit

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

timeoutLimitSteps

int timeoutLimitSteps

The search timeouts reaching this number of steps.

timeoutLimitMilliseconds

int timeoutLimitMilliseconds

The search timeouts reaching this number of milliseconds.

throwExceptionOnTimeout

boolean throwExceptionOnTimeout

If the search should throw exception upon timeout.

tautomerDuplicateFiltering

boolean tautomerDuplicateFiltering

Deprecated. since 5.5

If true, generic tautomer used as query and target

See Also:: SearchOptions.tautomerSearchOption

Class chemaxon.sss.search.SearchTimeoutException extends chemaxon.sss.search.SearchException implements Serializable

Class chemaxon.sss.search.StructureSearch.ParityCannotBeEvaluatedYetException extends java.lang.Exception implements Serializable

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

qprops

java.util.Map<K,V> qprops

querystr

java.lang.String querystr

aliasstr

java.lang.String aliasstr

extrastr

java.lang.String extrastr

extrargbs

long extrargbs

list

int[] list

flags

int flags

rgroupId

short rgroupId

countFlags

int countFlags

repetitionBits

int repetitionBits

linkNodeOuterBonds

int linkNodeOuterBonds

electronProp

int electronProp

temporaryObjects

java.util.Map<K,V> temporaryObjects

bicycloStereoDescriptors

chemaxon.struc.BicycloStereoDescriptor[] bicycloStereoDescriptors

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 arg0)
                  throws java.io.IOException,
                         java.lang.ClassNotFoundException

Throws:: java.io.IOException; java.lang.ClassNotFoundException

writeExternal

public void writeExternal(java.io.ObjectOutput arg0)
                   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

connectionTable

short[] connectionTable

neighborCount

byte[] neighborCount

nodeEdgeList

short[][] nodeEdgeList

bondCount

int bondCount

atomType

short[] atomType

bondAtom1

short[] bondAtom1

bondAtom2

short[] bondAtom2

bondFlags

int[] bondFlags

extendedAtomType

int[] extendedAtomType

atomLists

byte[][] atomLists

hybridization

byte[] hybridization

atomStereo

byte[] atomStereo

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

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 arg0)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException

Throws:: java.lang.ClassNotFoundException; java.io.IOException

writeObject

private void writeObject(java.io.ObjectOutputStream arg0)
                  throws java.io.IOException

Throws:: java.io.IOException

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

serialVersionUID: 6302424343157644471L

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream arg0)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException

Throws:: java.lang.ClassNotFoundException; java.io.IOException

writeObject

private void writeObject(java.io.ObjectOutputStream arg0)
                  throws java.io.IOException

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 arg0)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException

Throws:: java.lang.ClassNotFoundException; java.io.IOException

writeObject

private void writeObject(java.io.ObjectOutputStream arg0)
                  throws java.io.IOException

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 arg0)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

Throws:: java.io.IOException; java.lang.ClassNotFoundException

writeObject

private void writeObject(java.io.ObjectOutputStream arg0)
                  throws java.io.IOException

Throws:: java.io.IOException

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

serialVersionUID: -7479938988131387052L

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

serialVersionUID: -5670039985685584647L

Serialization Methods

readObject

private void readObject(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 arg0)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

Throws:: java.io.IOException; java.lang.ClassNotFoundException

writeObject

private void writeObject(java.io.ObjectOutputStream arg0)
                  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 arg0)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

Throws:: java.io.IOException; java.lang.ClassNotFoundException

writeObject

private void writeObject(java.io.ObjectOutputStream arg0)
                  throws java.io.IOException

Throws:: java.io.IOException

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 arg0)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException

Throws:: java.lang.ClassNotFoundException; java.io.IOException

writeObject

private void writeObject(java.io.ObjectOutputStream arg0)
                  throws java.io.IOException

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.BadExpressionException extends java.lang.Exception implements Serializable

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

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

Serialized Fields

elementData

boolean[] elementData

The array buffer into which the components of the BooleanVector are stored. The capacity of the BooleanVector is the length of this array buffer.

elementCount

int elementCount

The number of valid components in the BooleanVector.

capacityIncrement

int capacityIncrement

The amount by which the capacity of the BooleanVector is automatically incremented when its size becomes greater than its capacity. If the capacity increment is 0, the capacity of the BooleanVector is doubled each time it needs to grow.

Class chemaxon.util.ChemaxonException extends chemaxon.util.search.SearchException implements Serializable

Class chemaxon.util.CmdLine.CmdLineException extends java.lang.RuntimeException implements Serializable

Class chemaxon.util.ConnectionHandler extends ErrorHandler implements Serializable

Serialized Fields

propertySupport

java.beans.PropertyChangeSupport propertySupport

con

java.sql.Connection con

url

java.lang.String url

driverName

java.lang.String driverName

driver

java.lang.String driver

loginName

java.lang.String loginName

password

java.lang.String password

commitable

boolean commitable

true, if the connection can be committed at the discretion of JChem. Please note, that no commit or multiple commits may occur in this case.

Since:: JChem 5.9

propertyTableName

java.lang.String propertyTableName

rememberPassword

boolean rememberPassword

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

Serialized Fields

exception

java.lang.Throwable exception

Class chemaxon.util.Heap.HeapException extends java.lang.RuntimeException implements Serializable

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

Serialized Fields

elementData

int[][] elementData

The array buffer into which the components of the IntArray are stored. The capacity of the IntArray is the length of this array buffer.

blockCount

int blockCount

currentCapacity

int currentCapacity

firstElements

int[] firstElements

elementCount

int elementCount

The number of valid components in the IntArray.

blockSize

int blockSize

The amount by which the capacity of the IntArray is automatically incremented when its size becomes greater than its capacity.

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.MolHandler extends ErrorHandler implements Serializable

Serialized Fields

mol

Molecule mol

molAligner

MolAligner molAligner

molAlignerSet

boolean molAlignerSet

queryMode

boolean queryMode

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

Serialized Fields

stereoSearch

boolean stereoSearch

doubleBondStereoMatchingMode

int doubleBondStereoMatchingMode

subgraphSearch

boolean subgraphSearch

exactAtomMatching

boolean exactAtomMatching

exactStereoMatching

boolean exactStereoMatching

orderSensitiveSearch

boolean orderSensitiveSearch

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

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