Serialized Form

Package de.modlab.smilib.exceptions

Class de.modlab.smilib.exceptions.ReactionSchemeException extends SmiLibException implements Serializable

Class de.modlab.smilib.exceptions.SmiLibConformityException extends SmiLibException implements Serializable

Class de.modlab.smilib.exceptions.SmiLibException extends java.lang.Exception implements Serializable

Class de.modlab.smilib.exceptions.SmiLibIOException extends SmiLibException implements Serializable

Class de.modlab.smilib.exceptions.SmiLibSdfException extends SmiLibException implements Serializable

Package de.modlab.smilib.gui

Class de.modlab.smilib.gui.BusyWindow extends javax.swing.JFrame implements Serializable

Serialized Fields

parentFrame

SmiLibFrame parentFrame

progress

int progress

jButton1

javax.swing.JButton jButton1

jLabel1

javax.swing.JLabel jLabel1

jLabel2

javax.swing.JLabel jLabel2

jLabel3

javax.swing.JLabel jLabel3

jLabel4

javax.swing.JLabel jLabel4

jLabel5

javax.swing.JLabel jLabel5

jLabel6

javax.swing.JLabel jLabel6

jPanel2

javax.swing.JPanel jPanel2

jPanel3

javax.swing.JPanel jPanel3

jPanel4

javax.swing.JPanel jPanel4

jProgressBar1

javax.swing.JProgressBar jProgressBar1

Class de.modlab.smilib.gui.ControlPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

parentFrame

SmiLibFrame parentFrame

saveAsFile

boolean saveAsFile

saveAsSmiles

boolean saveAsSmiles

saveAsSD

boolean saveAsSD

addHydrogens

boolean addHydrogens

showLibrary

boolean showLibrary

buttonGroup1

javax.swing.ButtonGroup buttonGroup1

jButton1

javax.swing.JButton jButton1

jButton2

javax.swing.JButton jButton2

jButton3

javax.swing.JButton jButton3

jCheckBox1

javax.swing.JCheckBox jCheckBox1

jCheckBox2

javax.swing.JCheckBox jCheckBox2

jCheckBox3

javax.swing.JCheckBox jCheckBox3

jLabel5

javax.swing.JLabel jLabel5

jLabel6

javax.swing.JLabel jLabel6

jPanel1

javax.swing.JPanel jPanel1

jPanel7

javax.swing.JPanel jPanel7

jRadioButton1

javax.swing.JRadioButton jRadioButton1

jRadioButton2

javax.swing.JRadioButton jRadioButton2

jTextField1

javax.swing.JTextField jTextField1

Class de.modlab.smilib.gui.HelpAboutFrame extends javax.swing.JFrame implements Serializable

Serialized Fields

launcher

edu.stanford.ejalbert.BrowserLauncher launcher

Launcher for lauching a web browser

helpFrame

HelpFrame helpFrame

Reference to the HelpFrame for License displaying

buildLabel

javax.swing.JLabel buildLabel

copyrightTextArea

javax.swing.JTextArea copyrightTextArea

jButton1

javax.swing.JButton jButton1

jEditorPane1

javax.swing.JEditorPane jEditorPane1

jLabel1

javax.swing.JLabel jLabel1

jLabel2

javax.swing.JLabel jLabel2

jLabel3

javax.swing.JLabel jLabel3

jLabel4

javax.swing.JLabel jLabel4

jPanel1

javax.swing.JPanel jPanel1

jScrollPane1

javax.swing.JScrollPane jScrollPane1

jScrollPane2

javax.swing.JScrollPane jScrollPane2

jScrollPane3

javax.swing.JScrollPane jScrollPane3

jScrollPane4

javax.swing.JScrollPane jScrollPane4

jTextArea3

javax.swing.JTextArea jTextArea3

licenseButton

javax.swing.JButton licenseButton

referenceTextArea

javax.swing.JTextArea referenceTextArea

titleLabel

javax.swing.JLabel titleLabel

Class de.modlab.smilib.gui.HelpFrame extends javax.swing.JFrame implements Serializable

Serialized Fields

helpContent

java.lang.String[] helpContent

header

java.lang.String[] header

jButton1

javax.swing.JButton jButton1

jLabel1

javax.swing.JLabel jLabel1

jMenu1

javax.swing.JMenu jMenu1

jMenu2

javax.swing.JMenu jMenu2

jMenuBar1

javax.swing.JMenuBar jMenuBar1

jMenuItem1

javax.swing.JMenuItem jMenuItem1

jMenuItem2

javax.swing.JMenuItem jMenuItem2

jMenuItem3

javax.swing.JMenuItem jMenuItem3

jMenuItem4

javax.swing.JMenuItem jMenuItem4

jMenuItem5

javax.swing.JMenuItem jMenuItem5

jMenuItem6

javax.swing.JMenuItem jMenuItem6

jMenuItem7

javax.swing.JMenuItem jMenuItem7

jPanel1

javax.swing.JPanel jPanel1

jScrollPane1

javax.swing.JScrollPane jScrollPane1

jSeparator1

javax.swing.JSeparator jSeparator1

jSeparator2

javax.swing.JSeparator jSeparator2

jSeparator3

javax.swing.JSeparator jSeparator3

jTextArea1

javax.swing.JTextArea jTextArea1

Class de.modlab.smilib.gui.JButtonMenu extends javax.swing.JMenu implements Serializable

Class de.modlab.smilib.gui.LibraryPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

progress

int progress

jLabel1

javax.swing.JLabel jLabel1

jLabel10

javax.swing.JLabel jLabel10

jLabel2

javax.swing.JLabel jLabel2

jLabel3

javax.swing.JLabel jLabel3

jLabel4

javax.swing.JLabel jLabel4

jLabel5

javax.swing.JLabel jLabel5

jLabel6

javax.swing.JLabel jLabel6

jLabel7

javax.swing.JLabel jLabel7

jLabel8

javax.swing.JLabel jLabel8

jLabel9

javax.swing.JLabel jLabel9

jPanel1

javax.swing.JPanel jPanel1

jPanel2

javax.swing.JPanel jPanel2

jScrollPane1

javax.swing.JScrollPane jScrollPane1

jSeparator1

javax.swing.JSeparator jSeparator1

jSeparator2

javax.swing.JSeparator jSeparator2

jSeparator3

javax.swing.JSeparator jSeparator3

jSeparator4

javax.swing.JSeparator jSeparator4

jTextArea1

javax.swing.JTextArea jTextArea1

Class de.modlab.smilib.gui.SmiLibFrame extends javax.swing.JFrame implements Serializable

Serialized Fields

messageBox

javax.swing.JOptionPane messageBox

JOptionPane which dislays messages

logoMenu

javax.swing.JMenu logoMenu

Menu that holds the SmiLib logo

source

SourcePanel source

panel with source SMILES for molecules (scaff, linker and bb)

control

ControlPanel control

panel containing the control elements

library

LibraryPanel library

panel where the combinatorial library will be shown

sRunner

SmiLibRunner sRunner

thread that contains methods to enumerate the library

viewState

boolean viewState

boolean necessary to switch between library/source panel true: source false: library

cwd

java.lang.String cwd

current working directory - starts from folder that contains program

busy

BusyWindow busy

status window shown while library is created

help

HelpFrame help

frame for SmiLib help

about

HelpAboutFrame about

frame for the about box

iterator

SmiLibIterator iterator

SmiLib iterator over virtual reactions

enumerationStopped

boolean enumerationStopped

boolean that indicates whether the enumeration was stopped by the user or not

checkSmiles

boolean checkSmiles

check SMILES for SmiLib rule conformity true/false

errorOccured

boolean errorOccured

enumeration cancelled because of an error true/false

firstEnumeration

boolean firstEnumeration

enumeration was first enumeration true/false

javaHeapSizeOverflowLimit

int javaHeapSizeOverflowLimit

limit of molecules - if you show more in the GUI you may provoke a Java Heap Size Overflow

jCheckBoxMenuItem1

javax.swing.JCheckBoxMenuItem jCheckBoxMenuItem1

jLabel1

javax.swing.JLabel jLabel1

jMenu1

javax.swing.JMenu jMenu1

jMenu2

javax.swing.JMenu jMenu2

jMenu3

javax.swing.JMenu jMenu3

jMenu4

javax.swing.JMenu jMenu4

jMenuBar1

javax.swing.JMenuBar jMenuBar1

jMenuItem1

javax.swing.JMenuItem jMenuItem1

jMenuItem10

javax.swing.JMenuItem jMenuItem10

jMenuItem11

javax.swing.JMenuItem jMenuItem11

jMenuItem12

javax.swing.JMenuItem jMenuItem12

jMenuItem2

javax.swing.JMenuItem jMenuItem2

jMenuItem3

javax.swing.JMenuItem jMenuItem3

jMenuItem4

javax.swing.JMenuItem jMenuItem4

jMenuItem5

javax.swing.JMenuItem jMenuItem5

jMenuItem6

javax.swing.JMenuItem jMenuItem6

jMenuItem7

javax.swing.JMenuItem jMenuItem7

jMenuItem8

javax.swing.JMenuItem jMenuItem8

jMenuItem9

javax.swing.JMenuItem jMenuItem9

jSeparator1

javax.swing.JSeparator jSeparator1

jSeparator2

javax.swing.JSeparator jSeparator2

jSeparator3

javax.swing.JSeparator jSeparator3

Class de.modlab.smilib.gui.SourcePanel extends javax.swing.JPanel implements Serializable

Serialized Fields

parentFrame

SmiLibFrame parentFrame

scaffoldsAvailable

boolean scaffoldsAvailable

linkersAvailable

boolean linkersAvailable

buildingBlocksAvailable

boolean buildingBlocksAvailable

reactionSchemeAvailable

boolean reactionSchemeAvailable

reactionSchemeRequired

boolean reactionSchemeRequired

includeEmptyLinker

boolean includeEmptyLinker

allSourcesAvailable

boolean allSourcesAvailable

emptyLinkers

java.lang.String[] emptyLinkers

buttonGroup1

javax.swing.ButtonGroup buttonGroup1

jButton1

javax.swing.JButton jButton1

jButton2

javax.swing.JButton jButton2

jButton3

javax.swing.JButton jButton3

jButton4

javax.swing.JButton jButton4

jCheckBox1

javax.swing.JCheckBox jCheckBox1

jLabel1

javax.swing.JLabel jLabel1

jLabel2

javax.swing.JLabel jLabel2

jLabel3

javax.swing.JLabel jLabel3

jLabel4

javax.swing.JLabel jLabel4

jLabel5

javax.swing.JLabel jLabel5

jLabel6

javax.swing.JLabel jLabel6

jLabel7

javax.swing.JLabel jLabel7

jPanel1

javax.swing.JPanel jPanel1

jPanel2

javax.swing.JPanel jPanel2

jPanel3

javax.swing.JPanel jPanel3

jPanel4

javax.swing.JPanel jPanel4

jPanel5

javax.swing.JPanel jPanel5

jPanel6

javax.swing.JPanel jPanel6

jPanel7

javax.swing.JPanel jPanel7

jPanel8

javax.swing.JPanel jPanel8

jRadioButton1

javax.swing.JRadioButton jRadioButton1

jRadioButton2

javax.swing.JRadioButton jRadioButton2

jScrollPane4

javax.swing.JScrollPane jScrollPane4

jScrollPane5

javax.swing.JScrollPane jScrollPane5

jScrollPane6

javax.swing.JScrollPane jScrollPane6

jScrollPane7

javax.swing.JScrollPane jScrollPane7

jTextArea4

javax.swing.JTextArea jTextArea4

jTextArea5

javax.swing.JTextArea jTextArea5

jTextArea6

javax.swing.JTextArea jTextArea6

jTextArea7

javax.swing.JTextArea jTextArea7