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.ExitApplicationAction extends chemaxon.alchemist.utils.menu.AlchemistAction implements Serializable

serialVersionUID: -8963958737852702895L

Class chemaxon.alchemist.AlchemistApplication.LicenseManagerAction extends chemaxon.alchemist.utils.menu.AlchemistAction implements Serializable

serialVersionUID: 3222854582920316186L

Class chemaxon.alchemist.AlchemistApplication.NewDocumentAction extends chemaxon.alchemist.utils.menu.AlchemistAction implements Serializable

serialVersionUID: -3839082790538196785L

Class chemaxon.alchemist.AlchemistApplication.OpenDocumentAction extends chemaxon.alchemist.utils.menu.AlchemistAction implements Serializable

serialVersionUID: -3077101533489465876L

Class chemaxon.alchemist.AlchemistApplication.SaveDocumentAction extends chemaxon.alchemist.utils.menu.AlchemistAction implements Serializable

serialVersionUID: 8876874402609783013L

Class chemaxon.alchemist.AlchemistApplication.SaveDocumentAsAction extends chemaxon.alchemist.utils.menu.AlchemistAction 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

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

serialVersionUID: -3011618698897966506L

Serialized Fields

jumpaction

javax.swing.Action jumpaction

Deprecated.

action for handling jumps between progress steps

colorNormal

java.awt.Color colorNormal

Deprecated.

configurable colors for states

colorActive

java.awt.Color colorActive

Deprecated.

colorDone

java.awt.Color colorDone

Deprecated.

colorDisabled

java.awt.Color colorDisabled

Deprecated.

normalIcon

javax.swing.Icon normalIcon

Deprecated.

configurable icons for states

activeIcon

javax.swing.Icon activeIcon

Deprecated.

doneIcon

javax.swing.Icon doneIcon

Deprecated.

disabledIcon

javax.swing.Icon disabledIcon

Deprecated.

label

java.lang.String label

Deprecated.

the text of progress object

state

int state

Deprecated.

the actual state of progress object

txtMessage

javax.swing.JTextPane txtMessage

Deprecated.

the JTextPane for displaying message

lblIcon

javax.swing.JLabel lblIcon

Deprecated.

a JLabel object for displaying state icon

id

int id

Deprecated.

Identification number in the progress chain

collapsed

boolean collapsed

Deprecated.

Flag indicating progress object is collapsed or not

Package chemaxon.alchemist.commonpages

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

serialVersionUID: -1923661099622302455L

Serialized Fields

pnlEast

javax.swing.JPanel pnlEast

panel holding buttons

buttAdd

javax.swing.JButton buttAdd

add files button

buttRemove

javax.swing.JButton buttRemove

remove selected files button

scrlPane

javax.swing.JScrollPane scrlPane

scroll for file list

lstFile

javax.swing.JList lstFile

list for files

openDialog

AlchemistFileChooser openDialog

filechooser for file open

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.ConfigBuilderItemPanelHolder extends javax.swing.JPanel implements Serializable

serialVersionUID: 1777890792661630429L

Serialized Fields

listToValidate

javax.swing.JList listToValidate

Deprecated.

selected items list to validate

myBuilder

ConfigBuilder myBuilder

Deprecated.

config builder of this instance

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

serialVersionUID: -5629285442401894577L

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

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

Serialized Fields

relatedItem

ConfigItem relatedItem

Deprecated.

the related configitem

readOnly

boolean readOnly

Deprecated.

propertyChangeSupport

javax.swing.event.SwingPropertyChangeSupport propertyChangeSupport

Deprecated.

property change support

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

serialVersionUID: -3388658786205768765L

Serialized Fields

source

javax.swing.JList source

Deprecated.

the source list

target

javax.swing.JList target

Deprecated.

the target list

configBuilder

ConfigBuilder configBuilder

Deprecated.

the config builder

Class chemaxon.alchemist.configbuilder.EmptyPanel extends ConfigItemPanel implements Serializable

serialVersionUID: -2143324406554850952L

Serialized Fields

jLabel

javax.swing.JLabel jLabel

Deprecated.

Package chemaxon.alchemist.utils

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

serialVersionUID: 3614400467166560723L

Serialized Fields

editedMolecules

java.util.HashMap<K,V> editedMolecules

currentMoleculeIndeces

java.util.List<E> currentMoleculeIndeces

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

isMoleculeLabelVisible

boolean isMoleculeLabelVisible

minimumSize

java.awt.Dimension minimumSize

renderer

MoleculeTableCellRenderer renderer

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

serialVersionUID: -5459818957972696228L

Serialized Fields

defaultSize

java.awt.Dimension defaultSize

compactSize

java.awt.Dimension compactSize

extendedSize

java.awt.Dimension extendedSize

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

viewMode

int viewMode

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.HashMap<K,V> reactionNames

array of names rendered above reaction arrows, and used as tool tip on reaction arrows

isWaiting

boolean isWaiting

is waiting flag

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

selectionIndex

int selectionIndex

selection index

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

source

MolImporter source

inputStream

java.io.InputStream inputStream

isChangingGrid

boolean isChangingGrid

adjustPosition

javax.swing.JTextArea adjustPosition

tooltip

javax.swing.Popup tooltip

mousePosition

java.awt.Point mousePosition

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

lastFileName

java.lang.String lastFileName

last opened file name

containerPanel

javax.swing.JPanel containerPanel

statusLabel

javax.swing.JLabel statusLabel

lastEvent

java.beans.PropertyChangeEvent lastEvent

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

moleculeFilePath

java.lang.String moleculeFilePath

current file path

autoChangeMode

int autoChangeMode

notClick

boolean notClick

delayCount

int delayCount

MOLECULE_AUTO_CHANGE_DELAY_MOD

int MOLECULE_AUTO_CHANGE_DELAY_MOD

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.JFormattedTextField 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.AlchemistSplitPane extends javax.swing.JSplitPane implements Serializable

serialVersionUID: -4852599367397705734L

Serialized Fields

invertedSizeKeeping

boolean invertedSizeKeeping

Deprecated.

width

int width

Deprecated.

oldWidth

int oldWidth

Deprecated.

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.CheckBoxList extends javax.swing.JList implements Serializable

serialVersionUID: 1846281488928756436L

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.HashMap<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.HashMap<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

Package chemaxon.enumeration

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

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

Serialized Fields

e

java.lang.Throwable e

Package chemaxon.formats

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

Serialized Fields

lineNumberInRecord

int lineNumberInRecord

lineNumberInFile

int lineNumberInFile

Package chemaxon.jchem

Class chemaxon.jchem.JChemManager extends javax.swing.JApplet implements Serializable

Serialized Fields

mainWindow

chemaxon.jchem.gui.JChemFrame mainWindow

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

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

hashCodeScreeningForExact

boolean hashCodeScreeningForExact

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

progressiveStopped

boolean progressiveStopped

progressiveError

edu.emory.mathcs.backport.java.util.concurrent.atomic.AtomicReference progressiveError

resultVector

chemaxon.util.IntVector resultVector

progressiveReturnArray

IntArray progressiveReturnArray

finalResultVector

chemaxon.util.IntVector finalResultVector

dissimVector

chemaxon.util.FloatVector dissimVector

screenedVector

chemaxon.util.IntVector screenedVector

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:

MolEnumerator.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

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.

descriptorConfig

java.lang.String descriptorConfig

configuration for descriptor dissim. calculations

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

progressiveReturnIdx

int progressiveReturnIdx

Index into JChemSearch.resultVector pointing to the next hit not yet returned to the client.

nextNotifProgrArraySize

int nextNotifProgrArraySize

Notify the thread waiting on JChemSearch.progressiveReturnArray the next time when JChemSearch.progressiveReturnArray size reaches this value.

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

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

elemanal

ElementalAnalyser elemanal

cartridgeMode

boolean cartridgeMode

indexedTable

java.lang.String indexedTable

indexedColumn

java.lang.String indexedColumn

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

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 #isProgressMonitoringNeeded 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.regenerateTable(chemaxon.util.ConnectionHandler, String, chemaxon.jchem.file.ProgressWriter)

isProgressMonitoringSupported

boolean isProgressMonitoringSupported

Indicates whether update process supports progress monitoring.

Since:

JChem 5.1.2

Package chemaxon.jep

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

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

Serialized Fields

jep

ChemJEP jep

The JEP object.

cached

boolean cached

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

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

Serialized Fields

contextClass

java.lang.Class<T> contextClass

The evaluation context class.

context

ChemContext context

The evaluation context object.

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

Serialized Fields

e

java.lang.Throwable e

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

Serialized Fields

name

java.lang.String name

The context element callback function name.

jep

ChemJEP jep

The JEP object.

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

Serialized Fields

className

java.lang.String className

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

descriptors

java.lang.String[] descriptors

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

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

Serialized Fields

builtInConfig

chemaxon.jep.EvaluatorConfiguration builtInConfig

The configuration object containing default function/plugin declarations.

externalConfig

chemaxon.jep.EvaluatorConfiguration externalConfig

The configuration object containing external function/plugin declarations.

userConfig

chemaxon.jep.EvaluatorConfiguration userConfig

The configuration object containing user defined function/plugin declarations.

config

chemaxon.jep.EvaluatorConfiguration config

The configuration object.

symtab

chemaxon.nfunk.jep.SymbolTable symtab

The base symbol table.

verbose

boolean verbose

True if verbose output.

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

Serialized Fields

evaluator

Evaluator evaluator

The evaluator object.

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

Serialized Fields

className

java.lang.String className

subMatches

java.util.Hashtable<K,V> subMatches

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

type

int type

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

attributes

chemaxon.util.SearchAttributes attributes

The search attribute storing object.

dir

java.lang.String dir

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

standardizer

Standardizer standardizer

Package chemaxon.jep.context