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Serialized Form

Package chemaxon.alchemist

Class chemaxon.alchemist.Alchemist extends javax.swing.JFrame implements Serializable

serialVersionUID: -8534640475268404709L

Serialized Fields

controller

AlchemistController controller
The main controller of Alchemist

jContentPane

javax.swing.JPanel jContentPane
the main contentpane of Alchemist

pnlHolder

javax.swing.JPanel pnlHolder
JPanel for holding AlchemistPanels

buttBack

javax.swing.JButton buttBack
the Back button object

buttCancel

javax.swing.JButton buttCancel
the Cancel button object

buttNext

javax.swing.JButton buttNext
the Next button object

buttFinish

javax.swing.JButton buttFinish
the Finish button object

pnlNavigation

javax.swing.JPanel pnlNavigation
JPanel for holding navigation buttons

pnlMain

javax.swing.JPanel pnlMain
the main panel, references to the current page in view

innerRootPane

javax.swing.JRootPane innerRootPane
main panel's root pane

sidebar

javax.swing.JPanel sidebar
the sidebar

helpLabel

AlchemistLabel helpLabel
the online help label

licenseLabel

AlchemistLabel licenseLabel
the show license handler label

toggleSidebarLabel

AlchemistLabel toggleSidebarLabel
the show/hide sidebar label

navCollapsed

boolean navCollapsed
flag indicating sidebar is collapsed

sidebarBgr1

java.awt.Color sidebarBgr1
top gradient background color of alchemist sidebar

sidebarBgr2

java.awt.Color sidebarBgr2
bottom gradient background color of alchemist sidebar

lastPageMode

boolean lastPageMode
last page mode for cancel/close label

Class chemaxon.alchemist.AlchemistApplication.AboutAction extends javax.swing.AbstractAction implements Serializable

serialVersionUID: -2737789389723967011L

Class chemaxon.alchemist.AlchemistApplication.ExitApplicationAction extends javax.swing.AbstractAction implements Serializable

serialVersionUID: -8963958737852702895L

Class chemaxon.alchemist.AlchemistApplication.HelpAction extends javax.swing.AbstractAction implements Serializable

serialVersionUID: 7756132244804825111L

Class chemaxon.alchemist.AlchemistApplication.LicenseManagerAction extends javax.swing.AbstractAction implements Serializable

serialVersionUID: 3222854582920316186L

Class chemaxon.alchemist.AlchemistApplication.NewDocumentAction extends javax.swing.AbstractAction implements Serializable

serialVersionUID: -3839082790538196785L

Class chemaxon.alchemist.AlchemistApplication.OpenDocumentAction extends javax.swing.AbstractAction implements Serializable

serialVersionUID: -3077101533489465876L

Class chemaxon.alchemist.AlchemistApplication.SaveDocumentAction extends javax.swing.AbstractAction implements Serializable

serialVersionUID: 8876874402609783013L

Class chemaxon.alchemist.AlchemistApplication.SaveDocumentAsAction extends javax.swing.AbstractAction implements Serializable

serialVersionUID: -907903154360820879L

Class chemaxon.alchemist.AlchemistBanner extends javax.swing.JPanel implements Serializable

serialVersionUID: 6880633873706063894L

Serialized Fields

leftImage

java.awt.Image leftImage
left part of the banner image

expandableImage

java.awt.Image expandableImage
center part of the banner image, should be a repeatable image

rightImage

java.awt.Image rightImage
right part of the banner image

leftPanel

javax.swing.JPanel leftPanel
panel displaying leftImage

expandablePanel

javax.swing.JPanel expandablePanel
panel displaying expandableImage

rightPanel

javax.swing.JPanel rightPanel
panel displaying rightImage

Class chemaxon.alchemist.AlchemistGlassPage extends AlchemistPage implements Serializable

serialVersionUID: 1836082717872977708L

Serialized Fields

backgroundImage

java.awt.Image backgroundImage

fadeDelay

int fadeDelay

fadeStep

float fadeStep

fadeDirection

int fadeDirection

fadeValue

float fadeValue

fadeComposite

java.awt.Composite fadeComposite

isFading

boolean isFading

lastFadePropertyValue

int lastFadePropertyValue

fadeTimer

javax.swing.Timer fadeTimer

Class chemaxon.alchemist.AlchemistPage extends javax.swing.JPanel implements Serializable

serialVersionUID: -3963996127180616976L

Serialized Fields

notifier

javax.swing.event.SwingPropertyChangeSupport notifier
SwingPropertyChangeSupport to notify changes

pageEnabled

boolean pageEnabled
state of page

pnlTop

javax.swing.JPanel pnlTop
Panel for displaying the message at the top of the panel BorderLayout have to be used, text will be shown in NORTH section

topIsVisible

boolean topIsVisible
for determining actions of top messagebar visibility

bottomIsVisible

boolean bottomIsVisible
for determining actions of bottom messagebar visibility

pnlBottom

javax.swing.JPanel pnlBottom
Panel for displaying the message at the bottom of the panel BorderLayout have to be used, text will be shown in SOUTH section

lblBottom

javax.swing.JLabel lblBottom
JLabel for displaying simple message at the bottom of the panel BorderLayout have to be used, text will be shown in SOUTH section

progressBar

javax.swing.JProgressBar progressBar
ProgressBar displaying status for long calculations

progressLabel

javax.swing.JLabel progressLabel
Label displaying informations for progressbar

progressPanel

javax.swing.JPanel progressPanel
Panel containing progress bar and label for long calculations

cancelButton

javax.swing.JButton cancelButton

Class chemaxon.alchemist.AlchemistProgressLabel extends javax.swing.JLabel implements Serializable

serialVersionUID: -2026203285204334201L

Serialized Fields

jumpAction

javax.swing.Action jumpAction
action for handling jumps between progress steps

state

java.lang.String state
item state

text

java.lang.String text
item text

iconMap

java.util.Map<K,V> iconMap
map of icons

id

int id
progress label id

Package chemaxon.alchemist.commonpages

Class chemaxon.alchemist.commonpages.FileListHandlerPanel extends AlchemistPage implements Serializable

serialVersionUID: -1923661099622302455L

Serialized Fields

contentPanel

javax.swing.JPanel contentPanel
content panel

addButton

javax.swing.JButton addButton
add files button

removeButton

javax.swing.JButton removeButton
remove selected files button

scrollPane

javax.swing.JScrollPane scrollPane
scroll for file list

previewSplit

javax.swing.JSplitPane previewSplit
molecule preview splitpane

fileList

javax.swing.JList fileList
list for files

openDialog

AlchemistFileChooser openDialog
filechooser for file open

upButton

javax.swing.JButton upButton
button for move selected items upwards in the list

downButton

javax.swing.JButton downButton
button for move selected items downwards in the list

preview

boolean preview
flag indictatind preview panel is attached

view

AlchemistMoleculeView view
molecule preview

ADD_FILE_ACTION

javax.swing.Action ADD_FILE_ACTION

REMOVE_FILE_ACTION

javax.swing.Action REMOVE_FILE_ACTION

MOVE_UP_ACTION

javax.swing.Action MOVE_UP_ACTION

MOVE_DOWN_ACTION

javax.swing.Action MOVE_DOWN_ACTION

Class chemaxon.alchemist.commonpages.ProgressPanel extends AlchemistPage implements Serializable

serialVersionUID: -5032783126037811156L

Serialized Fields

currentState

int currentState
current stat

doneAction

javax.swing.Action doneAction
action handling progress done

task

AlchemistTask task
super task

currentTask

AlchemistTask currentTask
current task working background

timer

javax.swing.Timer timer
timer for refreshing view

processingPanel

javax.swing.JPanel processingPanel
the main processing panel

progressBar

javax.swing.JProgressBar progressBar
progressbar object showing progress staus

statusLabel

javax.swing.JLabel statusLabel
label showing progress staus

cancelButton

javax.swing.JButton cancelButton
button for canceling progress

summaryPanel

javax.swing.JPanel summaryPanel
panel showing summary

summaryCaption

javax.swing.JLabel summaryCaption
caption of summary panel

summaryScrollPane

javax.swing.JScrollPane summaryScrollPane
scroll for summary

summaryDetails

javax.swing.JTextArea summaryDetails
summary details

resultPanel

javax.swing.JPanel resultPanel
panel showing results

resultCaption

javax.swing.JLabel resultCaption
caption of result panel

resultScrollPanel

javax.swing.JScrollPane resultScrollPanel
scroll for result

resultDetails

javax.swing.JTextArea resultDetails
result details

dummyPanel

javax.swing.JPanel dummyPanel
dummy panel

resultView

AlchemistMoleculeView resultView
result molecule view

resultButton

javax.swing.JButton resultButton
button for showing results

outputFilePath

java.lang.String outputFilePath
path of output file

contentPanel

javax.swing.JPanel contentPanel
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

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

ConfigElementPresentationChooser presentationChooser
presentation chooser for elements

profile

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

ADD_ACTION

javax.swing.AbstractAction ADD_ACTION

REMOVE_ACTION

javax.swing.AbstractAction REMOVE_ACTION

MOVE_UP_ACTION

javax.swing.AbstractAction MOVE_UP_ACTION

MOVE_DOWN_ACTION

javax.swing.AbstractAction MOVE_DOWN_ACTION

OPEN_FILE_ACTION

javax.swing.Action OPEN_FILE_ACTION
open file handler action

SAVE_FILE_ACTION

javax.swing.Action SAVE_FILE_ACTION
save file handler action

listSelectionListener

javax.swing.event.ListSelectionListener listSelectionListener
Listener for leftList and rightList selection changes. Handles control panel update, and order-modification actions

elementPropertyChangeListener

java.beans.PropertyChangeListener elementPropertyChangeListener

editorPropertyChangeListener

java.beans.PropertyChangeListener editorPropertyChangeListener

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.utils

Class chemaxon.alchemist.utils.AbstractAlchemistMoleculeEditor extends AlchemistMoleculeView implements Serializable

serialVersionUID: 3614400467166560723L

Serialized Fields

editedMolecules

java.util.HashMap<K,V> editedMolecules

currentMoleculeIndexes

java.util.List<E> currentMoleculeIndexes

localMolecules

java.util.List<E> localMolecules

indexArray

AbstractAlchemistMoleculeEditor.MoleculeIndexArray indexArray

isLoading

boolean isLoading

sketch

MSketchPane sketch

notifier

javax.swing.event.SwingPropertyChangeSupport notifier

editedMoleculeIndex

int editedMoleculeIndex

listSelectionListener

javax.swing.event.ListSelectionListener listSelectionListener

ADD_MOLECULE_ACTION

javax.swing.AbstractAction ADD_MOLECULE_ACTION
Action for perform add molecule to the editor. Hides viewer panel, and shows editor panel.

EDIT_MOLECULE_ACTION

javax.swing.AbstractAction EDIT_MOLECULE_ACTION
Action for perform edit selected molecule. Sets selected molecule into editor. Hides viewer panel, and shows editor pane

APPLY_MOLECULE_EDIT_ACTION

javax.swing.AbstractAction APPLY_MOLECULE_EDIT_ACTION
This method applies performed molecule modification action

CANCEL_MOLECULE_EDIT_ACTION

javax.swing.AbstractAction CANCEL_MOLECULE_EDIT_ACTION
This method cancels performed molecule modification action

REMOVE_MOLECULE_ACTION

javax.swing.AbstractAction REMOVE_MOLECULE_ACTION
This method removes the selected molecule from the table.

Class chemaxon.alchemist.utils.AbstractAlchemistMoleculeView extends javax.swing.JPanel implements Serializable

serialVersionUID: 149611228245166836L

Serialized Fields

rowNum

int rowNum

colNum

int colNum

view

javax.swing.JTable view

dataModel

javax.swing.table.TableModel dataModel

holderPanel

javax.swing.JPanel holderPanel

waitPanel

AlchemistWaitPanel waitPanel

layout

java.awt.CardLayout layout

isMoleculeLabelVisible

boolean isMoleculeLabelVisible

waitMode

boolean waitMode

minimumSize

java.awt.Dimension minimumSize

renderer

MoleculeTableCellRenderer renderer

Class chemaxon.alchemist.utils.AlchemistApplicationInnerDialog extends AlchemistGlassPage implements Serializable

serialVersionUID: -5459818957972696228L

Serialized Fields

acceptAction

javax.swing.Action acceptAction

cancelAction

javax.swing.Action cancelAction

closeAction

javax.swing.Action closeAction

acceptButton

javax.swing.JButton acceptButton

cancelButton

javax.swing.JButton cancelButton

closeButton

javax.swing.JButton closeButton

application

AlchemistApplication application

mainPanel

javax.swing.JPanel mainPanel

messageLabel

AlchemistLabel messageLabel

hideAction

javax.swing.AbstractAction hideAction
Action responsible for hiding the dialog when accept, cancel or close pressed

Class chemaxon.alchemist.utils.AlchemistApplicationLicenseHandlerInnerDialog extends AlchemistApplicationInnerDialog implements Serializable

serialVersionUID: -861857238241346070L

Serialized Fields

content

javax.swing.JPanel content
the main content

licenseMan

chemaxon.license.LicenseManagerGUI licenseMan
license manager

Class chemaxon.alchemist.utils.AlchemistDashedBorder extends javax.swing.border.LineBorder implements Serializable

serialVersionUID: 4638234623453024011L

Class chemaxon.alchemist.utils.AlchemistFileChooser extends javax.swing.JFileChooser implements Serializable

serialVersionUID: -6086509067396340514L

Serialized Fields

accessory

AlchemistMViewAccessory accessory
marvin view accessory

Class chemaxon.alchemist.utils.AlchemistFileTextBox extends javax.swing.JPanel implements Serializable

serialVersionUID: 8770285887133439479L

Serialized Fields

pathText

javax.swing.JTextField pathText
file path

clearButton

javax.swing.JButton clearButton
path clear button

browseButton

javax.swing.JButton browseButton
file browse button

infoLabel

javax.swing.JLabel infoLabel
caption

fileChooser

AlchemistFileChooser fileChooser
filechooser

notifier

javax.swing.event.SwingPropertyChangeSupport notifier
property change support

editEnabled

boolean editEnabled
flag indicating path editing is enabled

label

java.lang.String label
text of label

PROPERTY_KEY_FILE_PATH

java.lang.String PROPERTY_KEY_FILE_PATH
property key file path

mode

int mode
file chooser mode

Class chemaxon.alchemist.utils.AlchemistLabel extends javax.swing.JLabel implements Serializable

serialVersionUID: -3985998359923330546L

Serialized Fields

style

int style

decorated

boolean decorated

customPath

java.lang.String customPath

Class chemaxon.alchemist.utils.AlchemistLauncher extends javax.swing.JFrame implements Serializable

serialVersionUID: 3343421093394560591L

Serialized Fields

jPanel

javax.swing.JPanel jPanel

jScrollPane

javax.swing.JScrollPane jScrollPane

lstLaunchables

javax.swing.JList lstLaunchables

pnlMenu

javax.swing.JPanel pnlMenu

buttLaunch

javax.swing.JButton buttLaunch

buttCancel

javax.swing.JButton buttCancel

Class chemaxon.alchemist.utils.AlchemistLinearMoleculeView extends javax.swing.JPanel implements Serializable

serialVersionUID: -341731579595741305L

Serialized Fields

orientation

int orientation
orientation of component

moleculeList

java.util.List<E> moleculeList
list of molecules

scroll

javax.swing.JScrollPane scroll
scroll for molecules

itemHolder

javax.swing.JPanel itemHolder
panel holding molecules

showArrows

boolean showArrows
displaying arrows

disabledImage

java.awt.image.BufferedImage disabledImage
the disabled image

reactionNamesArray

java.lang.String[] reactionNamesArray
array of names rendered above reaction arrows

reactionNames

java.util.Map<K,V> reactionNames
array of names rendered above reaction arrows, and used as tool tip on reaction arrows

isWaiting

boolean isWaiting
is waiting flag

isAdjusting

boolean isAdjusting

waitPanel

javax.swing.JPanel waitPanel
wait panel

disabledPanel

javax.swing.JPanel disabledPanel
disabled panel

waitLabel

javax.swing.JLabel waitLabel
wait label

selectable

boolean selectable
selectable flag

selectionIndexes

int[] selectionIndexes

listSelectionListeners

java.util.Set<E> listSelectionListeners
listeners set

Class chemaxon.alchemist.utils.AlchemistMoleculeEditor extends AbstractAlchemistMoleculeEditor implements Serializable

serialVersionUID: 3614400467166560723L

Serialized Fields

sketchPanel

javax.swing.JPanel sketchPanel

buttonHolderPanel

javax.swing.JPanel buttonHolderPanel

applyEditButton

javax.swing.JButton applyEditButton

cancelEditButton

javax.swing.JButton cancelEditButton

addMoleculeButton

javax.swing.JButton addMoleculeButton

editMoleculeButton

javax.swing.JButton editMoleculeButton

removeMoleculeButton

javax.swing.JButton removeMoleculeButton

northPanel

javax.swing.JPanel northPanel
Panel holds toolbar

toolBar

javax.swing.JToolBar toolBar
Toolbar with add/edit/remove buttons

Class chemaxon.alchemist.utils.AlchemistMoleculeView extends AbstractAlchemistMoleculeView implements Serializable

serialVersionUID: -7071325616152351849L

Serialized Fields

currentRowNum

int currentRowNum

maxMolecules

int maxMolecules

scrollBar

javax.swing.JScrollBar scrollBar

topPanel

javax.swing.JPanel topPanel

rowLabel

javax.swing.JLabel rowLabel

rowComboBox

javax.swing.JComboBox rowComboBox

columnLabel

javax.swing.JLabel columnLabel

columnComboBox

javax.swing.JComboBox columnComboBox

maxRowNum

int maxRowNum

maxColNum

int maxColNum

isToolbarVisible

boolean isToolbarVisible

percent

int percent

importer

MolImporter importer

inputStream

java.io.InputStream inputStream

loading

boolean loading

isChangingGrid

boolean isChangingGrid

cancelBackgroundLoaderThread

boolean cancelBackgroundLoaderThread

adjustPosition

javax.swing.JTextArea adjustPosition

tooltip

javax.swing.Popup tooltip

mousePosition

java.awt.Point mousePosition

backgroundLoader

java.lang.Runnable backgroundLoader

Class chemaxon.alchemist.utils.AlchemistMViewAccessory extends javax.swing.JPanel implements Serializable

serialVersionUID: -5123713451624419144L

Serialized Fields

chkPreview

javax.swing.JCheckBox chkPreview
the preview checkbox, to switch preview on or off

mainPanel

javax.swing.JPanel mainPanel
the main panel

view

SimpleAlchemistMoleculeView view
the view object

thread

java.lang.Thread thread
molecule counter thread

molImporter

MolImporter molImporter
the molimporter used for preview

forceStop

boolean forceStop

containerPanel

AlchemistWaitPanel containerPanel

controlPanel

javax.swing.JPanel controlPanel

prevLabel

javax.swing.JLabel prevLabel

nextLabel

javax.swing.JLabel nextLabel

firstLabel

javax.swing.JLabel firstLabel

lastLabel

javax.swing.JLabel lastLabel

countLabel

javax.swing.JLabel countLabel

molPos

int molPos
the showed molecule in selected file

maxMolecules

int maxMolecules
molecule count in current file

status

int status

autoChangeMode

int autoChangeMode

notClick

boolean notClick

delayCount

int delayCount

MOLECULE_AUTO_CHANGE_DELAY_MOD

int MOLECULE_AUTO_CHANGE_DELAY_MOD

cantShowLeft

int cantShowLeft

errorRect

java.awt.Rectangle errorRect

lastProcessedFile

java.io.File lastProcessedFile

selectedFile

java.io.File selectedFile

autoChangeTimer

javax.swing.Timer autoChangeTimer

Class chemaxon.alchemist.utils.AlchemistSpinBox extends javax.swing.JPanel implements Serializable

serialVersionUID: 6551641768720523287L

Serialized Fields

value

int value

minimum

int minimum

maximum

int maximum

direction

int direction

repeatDelay

int repeatDelay

textField

javax.swing.JTextField textField

incButton

javax.swing.JPanel incButton

decButton

javax.swing.JPanel decButton

repeatTimer

javax.swing.Timer repeatTimer

INC_ACTION

javax.swing.AbstractAction INC_ACTION

DEC_ACTION

javax.swing.AbstractAction DEC_ACTION

Class chemaxon.alchemist.utils.AlchemistTableSizeConfigurerComponent extends javax.swing.JPanel implements Serializable

serialVersionUID: 9173737079514680200L

Serialized Fields

maxRows

int maxRows
maximum number of rows

maxCols

int maxCols
maximum number of columns

currentRows

int currentRows
current row number

currentCols

int currentCols
current col number

viewPanel

javax.swing.JPanel viewPanel
panel for visual representation

rowSlider

javax.swing.JSlider rowSlider
slider for row selection

colSlider

javax.swing.JSlider colSlider
slider for col selection

sizeLabel

javax.swing.JLabel sizeLabel
label showing current size

applyLabel

javax.swing.JLabel applyLabel
clickable label for apply

listener

java.awt.event.ActionListener listener
accept action listener

Class chemaxon.alchemist.utils.AlchemistWaitPanel extends javax.swing.JPanel implements Serializable

serialVersionUID: -7381714533289285787L

Serialized Fields

wheelColors

int[] wheelColors

barGauge3DEffectColors

int[] barGauge3DEffectColors

barGaugeBeamEffectColors

int[] barGaugeBeamEffectColors

barPulseColors

int[] barPulseColors

barBackgroundColor

int barBackgroundColor

barGaugeColors

int[] barGaugeColors

maxWheelSize

int maxWheelSize

minWheelSize

int minWheelSize

barHeight

int barHeight

wheelSize

int wheelSize

candybarStripeCount

int candybarStripeCount

candyOffset

int candyOffset

pulseOffset

int pulseOffset

skipWheel

boolean skipWheel

barGaugeShadePaint

java.awt.GradientPaint barGaugeShadePaint

barGaugeBeam1Paint

java.awt.GradientPaint barGaugeBeam1Paint

barGaugeBeam2Paint

java.awt.GradientPaint barGaugeBeam2Paint

barGaugePaint

java.awt.GradientPaint barGaugePaint

barPulse1Paint

java.awt.GradientPaint barPulse1Paint

barPulse2Paint

java.awt.GradientPaint barPulse2Paint

barRect

java.awt.Rectangle barRect

wheelTopLeft

java.awt.Point wheelTopLeft

backgroundImage

java.awt.Image backgroundImage

wheelVisible

boolean wheelVisible

barVisible

boolean barVisible

barPulsing

boolean barPulsing

barStyle

int barStyle

progress

float progress

timerStatusBeforeHide

boolean timerStatusBeforeHide

animationTimer

javax.swing.Timer animationTimer

Class chemaxon.alchemist.utils.CheckBoxList extends javax.swing.JList implements Serializable

serialVersionUID: 1846281488928756436L

Class chemaxon.alchemist.utils.InnerMarvinSketch extends AlchemistApplicationInnerDialog implements Serializable

serialVersionUID: 2046946054931656588L

Serialized Fields

sketch

MSketchPane sketch

Class chemaxon.alchemist.utils.MoleculeListCellRenderer extends javax.swing.JPanel implements Serializable

serialVersionUID: -1798448947968101596L

Serialized Fields

selected

boolean selected

hasFocus

boolean hasFocus

molecule

Molecule molecule

assignedList

javax.swing.JList assignedList

markWidth

int markWidth

Class chemaxon.alchemist.utils.MoleculeTableCellEditor extends javax.swing.AbstractCellEditor implements Serializable

serialVersionUID: 1L

Serialized Fields

pane

MSketchPane pane

clickCountToStart

int clickCountToStart

Class chemaxon.alchemist.utils.MoleculeTableCellRenderer extends javax.swing.JComponent implements Serializable

serialVersionUID: -6909830842650161321L

Serialized Fields

molecule

Molecule molecule

panel

javax.swing.JPanel panel

label

javax.swing.JLabel label

useCustomLabel

java.lang.Boolean useCustomLabel

isLabelVisible

java.lang.Boolean isLabelVisible

customLabels

java.util.Map<K,V> customLabels

dispOpts

int dispOpts

Class chemaxon.alchemist.utils.ScrollableCellEditor extends javax.swing.DefaultCellEditor implements Serializable

serialVersionUID: -6001312178682303639L

Serialized Fields

textArea

javax.swing.JTextArea textArea

scrollPane

javax.swing.JScrollPane scrollPane

Class chemaxon.alchemist.utils.SimpleAlchemistMoleculeView extends AbstractAlchemistMoleculeView implements Serializable

serialVersionUID: 6429374294058734448L

Serialized Fields

useCustomLabel

boolean useCustomLabel

customLabels

java.util.Map<K,V> customLabels
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

Class chemaxon.clustering.LibraryMCS2 extends java.lang.Object 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.CachePool extends java.lang.Object implements Serializable

Serialized Fields

cacheHash

java.util.Hashtable<K,V> cacheHash

maxCacheMemory

long maxCacheMemory

expirationTime

double expirationTime

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

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.StructureCache sCache

positiveScreenCount

int positiveScreenCount

hits

int hits

currentId

int currentId

message

java.lang.String message

maxResultCountReached

boolean maxResultCountReached

maxTimeReached

boolean maxTimeReached

stopped

boolean stopped

killed

boolean killed

resultVector

chemaxon.util.IntVector resultVector

finalResultVector

chemaxon.util.IntVector finalResultVector

dissimVector

chemaxon.util.FloatVector dissimVector

screenedVector

chemaxon.util.IntVector screenedVector

progressiveReturnArray

chemaxon.util.BlockingIntArrayQueue progressiveReturnArray

startTime

long startTime

searchUsingOriginalTarget

boolean searchUsingOriginalTarget

printScreenedIntoLog

boolean printScreenedIntoLog

infoToErrBuf

java.lang.StringBuffer infoToErrBuf

querySmarts

java.lang.String querySmarts

screeningTime

long screeningTime

screenedCount

int screenedCount

searchTime

long searchTime

cachingTime

long cachingTime

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

chemTermReaderPreparedStatement

java.sql.PreparedStatement chemTermReaderPreparedStatement

chemTermReaderSQL

java.lang.String chemTermReaderSQL

filter

chemaxon.util.IntVector filter

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.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.util.IntVector allDissimID

allDissimDissim

chemaxon.util.FloatVector allDissimDissim

threads

int threads

thread

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

cxsmis

chemaxon.marvin.io.formats.smiles.CxsmilesImport[] cxsmis

dbMols

Molecule[] dbMols

molSearch

MolSearch[] molSearch

evaluator

Evaluator[] evaluator

jep

ChemJEP[] jep

context

MolContext[] context

standardizer

Standardizer[] standardizer

queryStandOrder

int[] queryStandOrder

currentIndex

int currentIndex

threadPriority

int threadPriority

pstmtForSmilesRead

java.sql.PreparedStatement pstmtForSmilesRead

usePreparedStatements

boolean usePreparedStatements

pstmtForScreening

java.sql.PreparedStatement pstmtForScreening

pstmtSQLForScreening

java.lang.String pstmtSQLForScreening

queryIsStructuralKey

boolean queryIsStructuralKey

enumeratedSearch

boolean enumeratedSearch

regCode

long regCode

enumeratedFeatures

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

See Also:
EnumeratorFactory.isEnumerable(chemaxon.struc.Molecule, int)

everyTargetIsHit

boolean everyTargetIsHit

returnAllStructures

boolean returnAllStructures

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

propertySupport

java.beans.PropertyChangeSupport propertySupport

vetoableChangeSupport

java.beans.VetoableChangeSupport vetoableChangeSupport
Utility field used by constrained properties.

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

tautomerDuplicateSearchTable

boolean tautomerDuplicateSearchTable

genericTautomerProtectsChirality

boolean genericTautomerProtectsChirality

markushTable

boolean markushTable

filterIDList

int[] filterIDList
Holds value of property filterIDList.

origFilterIdList

int[] origFilterIdList

filterIDNotList

int[] filterIDNotList

filterIDListSorted

boolean filterIDListSorted

filterIDNotListSorted

boolean filterIDNotListSorted

filtering

boolean filtering

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.

structureCaching

boolean structureCaching
Holds value of property structureCaching.

infoToStdError

boolean infoToStdError
Holds value of property infoToStdError.

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

tautomerizationPlugin

TautomerizationPlugin tautomerizationPlugin

preCalculatedSmiles

java.lang.String preCalculatedSmiles

preCalculatedSmilesSet

boolean preCalculatedSmilesSet

smiles

java.lang.String 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.TransferException extends java.lang.Exception implements Serializable

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

Serialized Fields

mode

int mode

additionalColumnsString

java.lang.String additionalColumnsString

numberOfBits

int numberOfBits

numberOfStrucFPCols

int numberOfStrucFPCols

structuralKeys

java.lang.String structuralKeys

numberOfCFpCols

int numberOfCFpCols

numberOfOnes

int numberOfOnes

numberOfEdges

int numberOfEdges

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

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

jcsearch

JChemSearch jcsearch

duplicateFiltering

boolean duplicateFiltering

setChiralFlag

boolean setChiralFlag

doNotImport

boolean doNotImport

standardize

boolean standardize

ignoreCTErrors

boolean ignoreCTErrors

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

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. "Regenerating 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
Package chemaxon.jchem.webservice

Class chemaxon.jchem.webservice.ConnectionHandlerIDNotFoundException extends java.lang.Exception implements Serializable

Class chemaxon.jchem.webservice.IDGenerationException extends java.lang.Exception implements Serializable

Class chemaxon.jchem.webservice.InvalidInputException extends java.lang.Exception implements Serializable

Class chemaxon.jchem.webservice.SearchIDNotFoundException extends java.lang.Exception implements Serializable

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.

symtab

chemaxon.nfunk.jep.SymbolTable symtab
The base symbol table.

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

tagName

java.lang.String tagName

colorKeys

java.util.List<E> colorKeys

viewPane

MViewPane viewPane

spaceDimensions

int spaceDimensions

realTimeMovieThread

java.lang.Thread realTimeMovieThread

openAction

javax.swing.Action openAction

printAction

javax.swing.Action printAction

exitAction

javax.swing.Action exitAction
Package chemaxon.marvin.alignment

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

Class chemaxon.marvin.alignment.AssignedConstraintList$1 extends java.lang.Object implements Serializable

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

Serialized Fields

colorOfAtom

int[] colorOfAtom

mins

float[] mins

maxs

float[] maxs

coloredAtomCount

int coloredAtomCount

index

int[][] index

anchoredAtom

int anchoredAtom

range

chemaxon.marvin.alignment.DistanceRange range

Class chemaxon.marvin.alignment.DistanceRangeSetPH extends chemaxon.marvin.alignment.DistanceRangeSet implements Serializable

Serialized Fields

donor

java.util.BitSet donor

acceptor

java.util.BitSet acceptor

aromatic

java.util.BitSet aromatic

hydr

java.util.BitSet hydr

pos

java.util.BitSet pos

neg

java.util.BitSet neg

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

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

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

Serialized Fields

stacktrace

java.lang.String stacktrace

status

int status

alignedCrd

double[][] alignedCrd

molID

int molID

dihedralCount

int dihedralCount

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

Serialized Fields

stacktrace

java.lang.String stacktrace

status

int status

stepCount

int stepCount

time

int time

score

double score

energy

double energy

stmols

java.util.Vector<E> stmols

constraintCount

int constraintCount

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.

changeListeners

java.beans.PropertyChangeSupport changeListeners

userSettings

UserSettings userSettings
The user settings object.

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.common

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

serialVersionUID: 845433654876173303L

Serialized Fields

WITHOUT_CHECK_OVERWRITEABLE_PROPS

java.lang.String[] WITHOUT_CHECK_OVERWRITEABLE_PROPS
Variables at marvin.properties, which have to be overwritten with every save event.

Since:
Marvin 5.0.1

userprops

java.util.Properties userprops

changeListeners

java.beans.PropertyChangeSupport changeListeners

owners

java.util.Vector<E> owners

sketchColorScheme

java.lang.String sketchColorScheme

viewColorScheme

java.lang.String viewColorScheme

sketchMolbg2d

java.awt.Color sketchMolbg2d

sketchMolbg3d

java.awt.Color sketchMolbg3d

viewMolbg2d

java.awt.Color viewMolbg2d

viewMolbg3d

java.awt.Color viewMolbg3d

sketchBondDraggedAlong

boolean sketchBondDraggedAlong

sketchValenceErrorVisible

boolean sketchValenceErrorVisible

sketchReactionErrorVisible

boolean sketchReactionErrorVisible

lonePairAutoCalc

boolean lonePairAutoCalc

sketchImplicitH

java.lang.String sketchImplicitH

viewValenceErrorVisible

boolean viewValenceErrorVisible

viewImplicitH

java.lang.String viewImplicitH

viewExplicitH

boolean viewExplicitH
Deprecated. since 5.3

viewLayout

int viewLayout

viewAnyBond

java.lang.String viewAnyBond

sketchAnyBond

java.lang.String sketchAnyBond

viewCarbonVisibility

java.lang.String viewCarbonVisibility

sketchCarbonVisibility

java.lang.String sketchCarbonVisibility

downWedge

java.lang.String downWedge

sketchRendering2d

java.lang.String sketchRendering2d

sketchRendering3d

java.lang.String sketchRendering3d

viewRendering2d

java.lang.String viewRendering2d

viewRendering3d

java.lang.String viewRendering3d

viewNavmode2d

java.lang.String viewNavmode2d

viewNavmode3d

java.lang.String viewNavmode3d

clean2dOpts

java.lang.String clean2dOpts

cleanHOption

boolean cleanHOption

clean3dOpts

java.lang.String clean3dOpts

copyAsFormat

java.lang.String copyAsFormat

defaultSaveFormat

java.lang.String defaultSaveFormat

transformationEnabled

boolean transformationEnabled

aromatizeLevel

int aromatizeLevel

atomMappingLevel

int atomMappingLevel

atomFont

java.awt.Font atomFont

atomSize

double atomSize

bondSpacing

double bondSpacing

wireThickness

double wireThickness

stickThickness

double stickThickness

ballRadius

double ballRadius

ezVisible

boolean ezVisible

chiralitySupport

java.lang.String chiralitySupport

absLabelVis

java.lang.String absLabelVis

sketchArrowHeadLength

double sketchArrowHeadLength

sketchArrowHeadWidth

double sketchArrowHeadWidth

sketchArrowTailLength

double sketchArrowTailLength

sketchArrowTailWidth

double sketchArrowTailWidth

viewRecentFileList

java.util.List<E> viewRecentFileList

viewRecentFileListSize

int viewRecentFileListSize

sketchRecentFileList

java.util.List<E> sketchRecentFileList

sketchRecentFileListSize

int sketchRecentFileListSize

viewLoadWorkingDir

java.lang.String viewLoadWorkingDir

viewSaveWorkingDir

java.lang.String viewSaveWorkingDir

sketchLoadWorkingDir

java.lang.String sketchLoadWorkingDir

sketchSaveWorkingDir

java.lang.String sketchSaveWorkingDir

loadSaveLocation

java.lang.String loadSaveLocation

loadWorkingDir

java.lang.String loadWorkingDir

saveLoadZoomFactorToMRV

boolean saveLoadZoomFactorToMRV

autoCheckStructure

boolean autoCheckStructure

lastModified

long lastModified
Package chemaxon.marvin.io

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

Serialization Methods

readExternal

public void readExternal(java.io.ObjectInput 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.util.BondClassifier ringFinder

reactantRingCount

int reactantRingCount

productRingCount

int productRingCount

keepAllRings

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

finishedAt

long finishedAt

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

Serialized Fields

template_local

java.lang.String[] template_local

timeStart

long timeStart

timeStart_structure

long timeStart_structure

timeLimit

long timeLimit

timeLimit_structure

long timeLimit_structure

MoleculeInvariants

chemaxon.util.IntVector[] MoleculeInvariants

CageMolInv

chemaxon.util.IntVector[] CageMolInv

Debug

int Debug

molCount

int molCount

opt

chemaxon.marvin.modules.Clean2D.PartialOptimization opt

removeCTEither

boolean removeCTEither

partialCleanForMolecules

boolean partialCleanForMolecules

partialClean

boolean partialClean

fixedAtoms

int[] fixedAtoms

use_2D_Alignment

boolean use_2D_Alignment

addHydrogensToChiralAtoms

boolean addHydrogensToChiralAtoms

addExplicitHToCageSystem

boolean addExplicitHToCageSystem

setParities

boolean setParities

useStereoFromFlags

boolean useStereoFromFlags

wedgeClean

boolean wedgeClean

onlyWedgeClean

boolean onlyWedgeClean

forceTemplates

boolean forceTemplates

ORIG

MoleculeGraph ORIG

levelAheadLimit

int levelAheadLimit

stepLimit

int stepLimit

cssr

int[][] cssr

ctab

int[][] ctab

btab

int[][] btab

fragID

int[] fragID

intang

double[][] intang

ringBitset

java.util.BitSet[] ringBitset

isRingBond

boolean[] isRingBond

atomInRing

int[][] atomInRing

commRingAtomNu

int[][] commRingAtomNu

coll_dist_sq

double coll_dist_sq

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

Serialized Fields

MERGETOBUILDMOL

boolean MERGETOBUILDMOL

restrictConformerCount

boolean restrictConformerCount

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

Serialized Fields

modeFlag

int modeFlag

stereo

int[] stereo

calculatedChirality

int[] calculatedChirality

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

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

Serialized Fields

mol

MoleculeGraph mol

origmol

MoleculeGraph origmol

bondIndexToExpanded

int[] bondIndexToExpanded

atomIndexToExpanded

int[] atomIndexToExpanded

lastGrinvCC

long lastGrinvCC

lastGrinvCCEZ

long lastGrinvCCEZ

step

int step

ctab

int[][] ctab

btab

int[][] btab

asymmetric

boolean[] asymmetric

chiralcenter

boolean[] chiralcenter

canhaveparity

boolean[] canhaveparity

isRingBond

boolean[] isRingBond

eqGrinv

boolean[] eqGrinv

stereoGrinv

int[] stereoGrinv

parity0D

int[] parity0D

hasWedge

boolean[] hasWedge

xyz

double[] xyz

isHydrogen

boolean[] isHydrogen

isLP

boolean[] isLP

parity3D

int[] parity3D

arommol

MoleculeGraph arommol

chiralityCalculated

boolean chiralityCalculated

chirality

int[] chirality

ezCalculated

boolean ezCalculated

ez

int[] ez

ringCount

int[] ringCount

atomInSmallestRing

int[] atomInSmallestRing

hasContractedGroup

boolean hasContractedGroup

useOnlyFirstAtom

boolean useOnlyFirstAtom

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.sketch

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

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

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.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

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

Serialized Fields

groupType

int groupType

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

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

rotMethod

int rotMethod

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

flyingBondMol

MoleculeGraph flyingBondMol

curfragMoved

boolean curfragMoved

canRotCurfrag

boolean canRotCurfrag

canMovCurfrag

boolean canMovCurfrag

curfragR

double curfragR

rotO

DPoint3 rotO

rotateZPhi

double rotateZPhi

rotate3dPhiX

double rotate3dPhiX

rotate3dPhiY

double rotate3dPhiY

rotate3dPhi

double rotate3dPhi

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

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

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.SelectSM extends chemaxon.marvin.sketch.SketchMode implements Serializable

serialVersionUID: 1430844896216918052L

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

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.SgroupSM extends chemaxon.marvin.sketch.SketchMode implements Serializable

serialVersionUID: 5435507500908348259L

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

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

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

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

serialVersionUID: 2763330874643316763L

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

serialVersionUID: 7801720334170069726L

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

serialVersionUID: -6975415959061110410L

Serialized Fields

msketch

MSketchPane msketch

sketchPanel

chemaxon.marvin.sketch.swing.SketchPanel sketchPanel

log

java.util.logging.Logger log

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

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

serialVersionUID: -5798208351774983109L

Serialized Fields

width

int width
Width.

height

int height
Height.

scale

double scale
Scaling factor.

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

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

serialVersionUID: -1600625160321014724L

Package chemaxon.marvin.util.codeassist

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

serialVersionUID: -5894946790409031807L

Serialized Fields

doc

javax.swing.text.DefaultStyledDocument doc

rootElement

javax.swing.text.Element rootElement

multiLineComment

boolean multiLineComment

normal

javax.swing.text.MutableAttributeSet normal

comment

javax.swing.text.MutableAttributeSet comment

quote

javax.swing.text.MutableAttributeSet quote

keyword

javax.swing.text.MutableAttributeSet keyword

function

javax.swing.text.MutableAttributeSet function

parenthesis

javax.swing.text.MutableAttributeSet parenthesis

constant

javax.swing.text.MutableAttributeSet constant

keywords

java.util.Map<K,V> keywords

functions

java.util.Map<K,V> functions

constants

java.util.Map<K,V> constants

fontSize

int fontSize

fontName

java.lang.String fontName

parenOffset

int parenOffset

parenLength

int parenLength

currentElementIndex

int currentElementIndex

prefix

java.lang.String prefix

lastPrefixState

boolean lastPrefixState

HIGHLIGHT_TIMER

javax.swing.Timer HIGHLIGHT_TIMER

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

serialVersionUID: 6746125418422903808L

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

serialVersionUID: -4703035835623320688L

Serialized Fields

macroListScroll

javax.swing.JScrollPane macroListScroll

macroList

javax.swing.JList macroList

addButton

javax.swing.JButton addButton

editButton

javax.swing.JButton editButton

deleteButton

javax.swing.JButton deleteButton

listPanel

javax.swing.JPanel listPanel

editPanel

javax.swing.JPanel editPanel

layout

java.awt.CardLayout layout

acceptButton

javax.swing.JButton acceptButton

cancelButton

javax.swing.JButton cancelButton

nameField

javax.swing.JTextField nameField

descScrollPane

javax.swing.JScrollPane descScrollPane

macroScrollPane

javax.swing.JScrollPane macroScrollPane

macroPane

javax.swing.JTextPane macroPane

descPane

javax.swing.JTextPane descPane

acceptEditButton

javax.swing.JButton acceptEditButton

cancelEditButton

javax.swing.JButton cancelEditButton

editedItem

int editedItem

helper

chemaxon.marvin.util.codeassist.CodeAssistMacrosHelper helper

ACCEPT_ACTION

javax.swing.Action ACCEPT_ACTION

CANCEL_ACTION

javax.swing.Action CANCEL_ACTION
Package chemaxon.marvin.view

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

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

Serialized Fields

recordIndex

int recordIndex
Package chemaxon.marvin.view.swing

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

Serialized Fields

listData1

java.lang.String[] listData1

listData2

java.lang.String[] listData2

list1

javax.swing.JList list1

list2

javax.swing.JList list2

addButton

javax.swing.JButton addButton

addAllButton

javax.swing.JButton addAllButton

removeButton

javax.swing.JButton removeButton

removeAllButton

javax.swing.JButton removeAllButton

allSelected

boolean allSelected

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

serialVersionUID: 3979819797881974530L

Serialization Methods

writeObject

private void writeObject(java.io.ObjectOutputStream arg0)
                  throws java.lang.ClassNotFoundException,
                         java.io.IOException
Throws:
java.lang.ClassNotFoundException
java.io.IOException
Serialized Fields

windowAction

chemaxon.marvin.swing.MAction windowAction

document

MDocument document

inZoomWindow

boolean inZoomWindow

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

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

Class chemaxon.naming.NamePrefixException extends NameFormatException implements Serializable

Package chemaxon.reaction

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.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

reactIterator

chemaxon.reaction.ReactIterator reactIterator

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.

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

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.

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.

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.util.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

maxTime

long maxTime

maxResultCount

int maxResultCount

returnsNonHits

boolean returnsNonHits

dissimilarityMetric

java.lang.String dissimilarityMetric
Dissimilarity metric name, or null for deafult.

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

matchCountOptions

MatchCountOptions matchCountOptions

optimizeQueries

boolean optimizeQueries
Shows whether the query should be enumerated to improve search

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.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.

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).

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)

qhomologyHandling

boolean qhomologyHandling
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.

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)

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.

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.

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.

timeoutLimit

int timeoutLimit
The search timeouts reaching this number of steps.

tautomerDuplicateFiltering

boolean tautomerDuplicateFiltering
If true, generic tautomer used as query and target

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

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

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.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.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 java.lang.Exception 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

driver

java.lang.String driver

loginName

java.lang.String loginName

password

java.lang.String password

propertyTableName

java.lang.String propertyTableName

rememberPassword

boolean rememberPassword

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

Serialized Fields

elementData

double[] elementData

expectedElementCount

int expectedElementCount

elementCount

int elementCount

capacityIncrement

int capacityIncrement

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

Serialized Fields

exception

java.lang.Throwable exception

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

Serialized Fields

elementData

float[] elementData
The array buffer into which the components of the FloatVector are stored. The capacity of the FloatVector is the length of this array buffer.

elementCount

int elementCount
The number of valid components in the FloatVector.

capacityIncrement

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

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.IntVector extends java.lang.Object implements Serializable

Serialized Fields

elementData

int[] elementData

expectedElementCount

int expectedElementCount

elementCount

int elementCount

capacityIncrement

int capacityIncrement

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

Serialized Fields

elementData

long[] elementData

expectedElementCount

int expectedElementCount

elementCount

int elementCount

capacityIncrement

int capacityIncrement

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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