A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

A

A - Variable in class cct.modelling.NonbondedPair
 
a - Variable in class cct.oogl.Color
 
a - Variable in class cct.oogl.Face
 
a - Variable in class cct.tools.Crystal
 
a - Variable in class cct.tools.Face
 
a1 - Variable in class cct.modelling.Bond
 
a2 - Variable in class cct.modelling.Bond
 
a2fEdgeDirection - Static variable in class cct.math.polyg.Polygonizer
 
a2fVertexOffset - Static variable in class cct.math.polyg.Polygonizer
 
a2iEdgeConnection - Static variable in class cct.math.polyg.Polygonizer
 
a2iTetrahedronEdgeConnection - Static variable in class cct.math.polyg.Polygonizer
 
a2iTetrahedronsInACube - Static variable in class cct.math.polyg.Polygonizer
 
a2iTetrahedronTriangles - Variable in class cct.math.polyg.Polygonizer
 
a2iTriangleConnectionTable - Static variable in class cct.math.polyg.Polygonizer
 
aAppear - Variable in class cct.j3d.AtomNode
 
ABS_PATH_EXECUTABLE - Static variable in class cct.grid.JobDescription
 
ACC - Variable in class cct.math.Minimizer
 
accept(File) - Method in class cct.tools.FileFilterImpl
 
accept(String, boolean) - Method in class cct.tools.FileFilterImpl
 
Account_Name - Variable in class cct.grid.PBSJobStatus
 
actionPerformed(ActionEvent) - Method in class cct.amber.AmberSubmitMenuHandler
 
actionPerformed(ActionEvent) - Method in class cct.amber.ReadPrmtopDialog_browsePrmtopButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.amber.ReadPrmtopDialog_cancelButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.amber.ReadPrmtopDialog_coordButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.amber.ReadPrmtopDialog_helpButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.amber.ReadPrmtopDialog_loadButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.amber.Sander8Frame_AboutBox
Close the dialog on a button event.
actionPerformed(ActionEvent) - Method in class cct.amber.Sander8Frame_DRMS_TextField_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.amber.Sander8Frame_DX0_TextField_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.amber.Sander8Frame_Edit_MenuItem_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.amber.Sander8Frame_jButton1_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.amber.Sander8Frame_jButton2_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.amber.Sander8Frame_jButton3_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.amber.Sander8Frame_jMenuFileExit_ActionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.amber.Sander8Frame_jMenuHelpAbout_ActionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.amber.Sander8Frame_jMenuItem1_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.amber.Sander8Frame_jMenuItem2_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.amber.Sander8Frame_MAXCYC_TextField_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.amber.Sander8Frame_NCYC_TextField_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.amber.Sander8Frame_NSTLIM_TextField_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.amber.Sander8Frame_saveFile_Button_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.amber.Sander9Frame_AboutBox
Close the dialog on a button event.
actionPerformed(ActionEvent) - Method in class cct.amber.Sander9Frame_DRMS_TextField_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.amber.Sander9Frame_DX0_TextField_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.amber.Sander9Frame_Edit_MenuItem_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.amber.Sander9Frame_jButton1_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.amber.Sander9Frame_jButton2_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.amber.Sander9Frame_jButton3_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.amber.Sander9Frame_jMenuFileExit_ActionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.amber.Sander9Frame_jMenuHelpAbout_ActionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.amber.Sander9Frame_jMenuItem1_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.amber.Sander9Frame_jMenuItem2_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.amber.Sander9Frame_MAXCYC_TextField_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.amber.Sander9Frame_NCYC_TextField_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.amber.Sander9Frame_NSTLIM_TextField_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.amber.Sander9Frame_saveFile_Button_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.amber.SanderJobControlDialog
 
actionPerformed(ActionEvent) - Method in class cct.amber.TextEditorFrame_jMenuItem1_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.amber.TextEditorFrame_jMenuItem2_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.applets.viewer
 
actionPerformed(ActionEvent) - Method in class cct.awtdialogs.AddNewMethodDialog
 
actionPerformed(ActionEvent) - Method in class cct.awtdialogs.AddNewMoleculeDialog
 
actionPerformed(ActionEvent) - Method in class cct.awtdialogs.AddNewStructureDialog
 
actionPerformed(ActionEvent) - Method in class cct.awtdialogs.AtomLabelsDialog
 
actionPerformed(ActionEvent) - Method in class cct.awtdialogs.AtomTypeDialog
 
actionPerformed(ActionEvent) - Method in class cct.awtdialogs.ConnectSQLServer
 
actionPerformed(ActionEvent) - Method in class cct.awtdialogs.GaussianCalcSetupDialog
 
actionPerformed(ActionEvent) - Method in class cct.awtdialogs.GeometrySelectDialog
 
actionPerformed(ActionEvent) - Method in class cct.awtdialogs.MessageWindow
 
actionPerformed(ActionEvent) - Method in class cct.awtdialogs.SelectMethodDialog
 
actionPerformed(ActionEvent) - Method in class cct.awtdialogs.SimpleAtomSelectionDialog
 
actionPerformed(ActionEvent) - Method in class cct.awtdialogs.SingleChoiceDialog
 
actionPerformed(ActionEvent) - Method in class cct.awtdialogs.TextEntryDialog
 
actionPerformed(ActionEvent) - Method in class cct.awtdialogs.YesNoDialog
 
actionPerformed(ActionEvent) - Method in class cct.chart.ChartFrame
 
actionPerformed(ActionEvent) - Method in class cct.chart.jfreechart.JFreeChartPanel
Called when the Timer fires.
actionPerformed(ActionEvent) - Method in class cct.database.ChemistryDatabaseDialog
 
actionPerformed(ActionEvent) - Method in class cct.database.new_ChemistryDatabaseDialog
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.AnimationPanel
Called when the Timer fires.
actionPerformed(ActionEvent) - Method in class cct.dialogs.Frame1_AboutBox
Close the dialog on a button event.
actionPerformed(ActionEvent) - Method in class cct.dialogs.Frame1_helpButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.Frame1_jMenuFileExit_ActionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.Frame1_jMenuHelpAbout_ActionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JAddFragmentDialog.JAddFragmentDialog_addFragButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JAddFragmentDialog.JAddFragmentDialog_jButton1_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JAddMoleculeDialog_cancelButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JAddMoleculeDialog_jTextField1_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JAddMoleculeDialog_okButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JAtomSelectionDialog.JAtomSelectionDialog_All_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JAtomSelectionDialog.JAtomSelectionDialog_Cancel_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JAtomSelectionDialog.JAtomSelectionDialog_Clear_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JAtomSelectionDialog.JAtomSelectionDialog_Invert_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JAtomSelectionDialog.JAtomSelectionDialog_OK_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JAtomTypeDialog
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JChoiceDialog
Close the dialog on a button event.
actionPerformed(ActionEvent) - Method in class cct.dialogs.JEditorFrame
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JEditorFrame.AtomColorScheme_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JEditorFrame.JEditorFrame_deleteMoleculeButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JEditorFrame.JEditorFrame_jButton3_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JEditorFrame.JEditorFrame_jMenuAnalyze_ActionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JEditorFrame.JEditorFrame_jMenuDB_ActionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JEditorFrame.JEditorFrame_jMenuFileEdit_ActionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JEditorFrame.JEditorFrame_jMenuFileExit_ActionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JEditorFrame.JEditorFrame_jMenuFileOpenAs_ActionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JEditorFrame.JEditorFrame_jMenuFileSaveAs_ActionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JEditorFrame.JEditorFrame_jMenuHelpAbout_ActionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JEditorFrame.JEditorFrame_jMenuView_ActionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JEditorFrame.JEditorFrame_openFileButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JEditorFrame_AboutBox
Close the dialog on a button event.
actionPerformed(ActionEvent) - Method in class cct.dialogs.JElementsPanel
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JModifyAngleDialog_currentAngle_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JModifyAngleDialog_Finish_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JModifyAngleDialog_Ok_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JModifyAngleDialog_Reset_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JModifyAngleDialog_undoLastSelection_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JModifyAtomDialog
For listening the JAtomTypesPanel only
actionPerformed(ActionEvent) - Method in class cct.dialogs.JModifyAtomDialog_Cancel_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JModifyAtomDialog_Reset_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JModifyAtomDialog_type_1_Button_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JModifyAtomDialog_type_2_Button_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JModifyAtomDialog_type_3_Button_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JModifyAtomDialog_type_4_Button_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JModifyAtomDialog_type_5_Button_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JModifyAtomDialog_type_6_Button_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JModifyAtomDialog_type_7_Button_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JModifyAtomPanel_Choose_color_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JModifyBondDialog_Cancel_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JModifyBondDialog_currentBondLength_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JModifyBondDialog_Ok_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JModifyBondDialog_Reset_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JModifyBondDialog_undoLastSelection_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JModifyTorsionDialog_angleValue_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JModifyTorsionDialog_Finish_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JModifyTorsionDialog_OK_button_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JModifyTorsionDialog_Reset_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JModifyTorsionDialog_Undo_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JSelectAtomTypesDialog_Cancel_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JSelectAtomTypesDialog_OK_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JSelectMonomersDialog_Cancel_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JSelectMonomersDialog_Help_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JSelectMonomersDialog_OK_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JSelectSubstructureDialog_Cancel_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JSelectSubstructureDialog_Help_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JSelectSubstructureDialog_OK_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JSelectTreeDialog.JSelectTreeDialog_addFragButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JSelectTreeDialog.JSelectTreeDialog_finishButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JSimpleAtomSelectionDialog
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JSolvateShellDialog.JSolvateShellDialog_jTextField1_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.JSolvateShellDialog_browseButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.dialogs.ViewPeriodicImagePanel_resetButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.gaussian.ui.GaussianInputEditorFrame
 
actionPerformed(ActionEvent) - Method in class cct.gaussian.ui.GaussianInputEditorFrame.GaussianInputEditorFrame_insertEntryButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.gaussian.ui.GaussianInputEditorFrame.GaussianInputEditorFrame_jButton6_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.gaussian.ui.GaussianInputEditorFrame.GaussianInputEditorFrame_jMenuFileExit_ActionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.gaussian.ui.GaussianInputEditorFrame.GaussianInputEditorFrame_jMenuHelpAbout_ActionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.gaussian.ui.GaussianInputEditorFrame.GaussianInputEditorFrame_jMenuItem1_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.gaussian.ui.GaussianInputEditorFrame.GaussianInputEditorFrame_nextStepButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.gaussian.ui.GaussianInputEditorFrame.GaussianInputEditorFrame_openFileButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.gaussian.ui.GaussianInputEditorFrame.GaussianInputEditorFrame_openSelectedFileButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.gaussian.ui.GaussianInputEditorFrame.GaussianInputEditorFrame_previousStepButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.gaussian.ui.GaussianInputEditorFrame.GaussianInputEditorFrame_resetButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.gaussian.ui.GaussianInputEditorFrame.GaussianInputEditorFrame_saveFileButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.gaussian.ui.GaussianInputEditorFrame.GaussianInputEditorFrame_saveStepButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.gaussian.ui.GaussianInputEditorFrame_AboutBox
Close the dialog on a button event.
actionPerformed(ActionEvent) - Method in class cct.gaussian.ui.ManageCubesFrame_mappedSurfaceButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.gaussian.ui.SaveG03GJFDialog.SaveG03GJFDialog_cancelButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.gaussian.ui.SaveG03GJFDialog.SaveG03GJFDialog_saveButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.gaussian.ui.SimpleG03EditorPanel_validateGeomButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.grid.TaskProviderPanel_providerComboBox_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.grid.ui.EditScriptDialog
 
actionPerformed(ActionEvent) - Method in class cct.grid.ui.gaussian.SubmitGaussianAppl
 
actionPerformed(ActionEvent) - Method in class cct.grid.ui.gaussian.SubmitGaussianDialog_Cancel_Button_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.grid.ui.gaussian.SubmitGaussianDialog_getProxy_Button_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.grid.ui.gaussian.SubmitGaussianDialog_providerComboBox_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.grid.ui.gaussian.SubmitGaussianDialog_Submit_Button_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.grid.ui.gaussian.SubmitGaussianDialogNew_Cancel_Button_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.grid.ui.gaussian.SubmitGaussianDialogNew_providerComboBox_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.grid.ui.gaussian.SubmitGaussianDialogNew_Submit_Button_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.grid.ui.gaussian.SubmitGaussianFrame_AboutBox
Close the dialog on a button event.
actionPerformed(ActionEvent) - Method in class cct.grid.ui.gaussian.SubmitGaussianFrame_jMenuFileExit_ActionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.grid.ui.gaussian.SubmitGaussianFrame_jMenuHelpAbout_ActionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.grid.ui.JobStatusDialog_downloadButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.grid.ui.JobStatusDialog_HelpButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.grid.ui.JobStatusDialog_hideButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.grid.ui.JobStatusDialog_killButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.grid.ui.JobStatusDialog_removeButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.grid.ui.JobStatusDialog_updateButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.grid.ui.JobStatusPanel
 
actionPerformed(ActionEvent) - Method in class cct.grid.ui.PBS_Panel_ProjectTextField_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.grid.ui.ThreadExec.TimerListener
 
actionPerformed(ActionEvent) - Method in class cct.j3d.InfoPopup
 
actionPerformed(ActionEvent) - Method in class cct.j3d.Java3dUniverse
 
actionPerformed(ActionEvent) - Method in class cct.j3d.MyMouseMotionListener
 
actionPerformed(ActionEvent) - Method in class cct.modelling.ui.CalcButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.modelling.ui.JSetupEnergyDialog_cancelButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.modelling.ui.JSetupEnergyDialog_forceFieldComboBox_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.modelling.ui.JSetupEnergyDialog_helpButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.modelling.ui.JSetupEnergyDialog_nbCutoffTextField_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.modelling.ui.OpenFile
 
actionPerformed(ActionEvent) - Method in class cct.oogl.ui.OOGLViewerFrame_AboutBox
Close the dialog on a button event.
actionPerformed(ActionEvent) - Method in class cct.oogl.ui.OOGLViewerFrame_jMenuFileExit_ActionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.oogl.ui.OOGLViewerFrame_jMenuHelpAbout_ActionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.pdb.ui.PDBFormFrame
 
actionPerformed(ActionEvent) - Method in class cct.tools.filebrowser.ConfirmFileOverwriteDialog
 
actionPerformed(ActionEvent) - Method in class cct.tools.filebrowser.ConnectHostDialog
 
actionPerformed(ActionEvent) - Method in class cct.tools.filebrowser.FileBrowserPanel_deleteButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.tools.filebrowser.FileBrowserPanel_downloadButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.tools.filebrowser.FileBrowserPanel_jComboBox1_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.tools.filebrowser.FileBrowserPanel_mkdirButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.tools.filebrowser.FileBrowserPanel_refreshButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.tools.filebrowser.FileBrowserPanel_upButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.tools.filebrowser.FileChooserDialog
 
actionPerformed(ActionEvent) - Method in class cct.tools.filebrowser.FilePropertiesDialog
 
actionPerformed(ActionEvent) - Method in class cct.tools.filebrowser.FileTransferFrame.HostEditor
 
actionPerformed(ActionEvent) - Method in class cct.tools.filebrowser.FileTransferFrame_connectButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.tools.filebrowser.FileTransferFrame_hostsComboBox_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.tools.filebrowser.PermissionsPanel_modeTextField_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.tools.filebrowser.SFTPBrowser
For processing popup menu items
actionPerformed(ActionEvent) - Method in class cct.tools.filebrowser.SFTPBrowserFrame
 
actionPerformed(ActionEvent) - Method in class cct.tools.filebrowser.SFTPFileChooserDialog
 
actionPerformed(ActionEvent) - Method in class cct.tools.GridProviders
 
actionPerformed(ActionEvent) - Method in class cct.tools.ui.DoubleSpinnerDialog
 
actionPerformed(ActionEvent) - Method in class cct.tools.ui.FontSelectorDialog
 
actionPerformed(ActionEvent) - Method in class cct.tools.ui.JShowText
 
actionPerformed(ActionEvent) - Method in class cct.tools.ui.JShowText.JShowText_jButton1_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.tools.ui.JShowText.JShowText_saveAsMenuItem_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.tools.ui.LogPanel
 
actionPerformed(ActionEvent) - Method in class cct.tools.ui.LogPanel_hideMenuItem_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.tools.ui.LogPanel_saveAsMenuItem_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.tools.ui.PostMessageDialog
 
actionPerformed(ActionEvent) - Method in class cct.tools.ui.SelectFromListDialog
 
actionPerformed(ActionEvent) - Method in class cct.tools.ui.SelectFromListDialog_helpButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.tools.ui.TextToPost
 
actionPerformed(ActionEvent) - Method in class cct.tools.UserPasswordDialog.UserPasswordDialog_cancelButton_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.tools.UserPasswordDialog.UserPasswordDialog_jPasswordField1_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.tools.UserPasswordDialog.UserPasswordDialog_jTextField1_actionAdapter
 
actionPerformed(ActionEvent) - Method in class cct.tools.UserPasswordDialog.UserPasswordDialog_okButton_actionAdapter
 
actionURL - Variable in class cct.amber.AmberSubmitDialog
 
activeButtons - Variable in class cct.dialogs.JAtomTypesPanel
 
adaptee - Variable in class cct.amber.Sander8Frame_jMenuFileExit_ActionAdapter
 
adaptee - Variable in class cct.amber.Sander8Frame_jMenuHelpAbout_ActionAdapter
 
adaptee - Variable in class cct.amber.Sander9Frame_jMenuFileExit_ActionAdapter
 
adaptee - Variable in class cct.amber.Sander9Frame_jMenuHelpAbout_ActionAdapter
 
adaptee - Variable in class cct.dialogs.Frame1_jMenuFileExit_ActionAdapter
 
adaptee - Variable in class cct.dialogs.Frame1_jMenuHelpAbout_ActionAdapter
 
adaptee - Variable in class cct.dialogs.JEditorFrame.JEditorFrame_jMenuAnalyze_ActionAdapter
 
adaptee - Variable in class cct.dialogs.JEditorFrame.JEditorFrame_jMenuDB_ActionAdapter
 
adaptee - Variable in class cct.dialogs.JEditorFrame.JEditorFrame_jMenuFileEdit_ActionAdapter
 
adaptee - Variable in class cct.dialogs.JEditorFrame.JEditorFrame_jMenuFileExit_ActionAdapter
 
adaptee - Variable in class cct.dialogs.JEditorFrame.JEditorFrame_jMenuFileOpenAs_ActionAdapter
 
adaptee - Variable in class cct.dialogs.JEditorFrame.JEditorFrame_jMenuFileSaveAs_ActionAdapter
 
adaptee - Variable in class cct.dialogs.JEditorFrame.JEditorFrame_jMenuHelpAbout_ActionAdapter
 
adaptee - Variable in class cct.dialogs.JEditorFrame.JEditorFrame_jMenuView_ActionAdapter
 
adaptee - Variable in class cct.gaussian.ui.GaussianInputEditorFrame.GaussianInputEditorFrame_jMenuFileExit_ActionAdapter
 
adaptee - Variable in class cct.gaussian.ui.GaussianInputEditorFrame.GaussianInputEditorFrame_jMenuHelpAbout_ActionAdapter
 
adaptee - Variable in class cct.grid.ui.gaussian.SubmitGaussianFrame_jMenuFileExit_ActionAdapter
 
adaptee - Variable in class cct.grid.ui.gaussian.SubmitGaussianFrame_jMenuHelpAbout_ActionAdapter
 
adaptee - Variable in class cct.oogl.ui.OOGLViewerFrame_jMenuFileExit_ActionAdapter
 
adaptee - Variable in class cct.oogl.ui.OOGLViewerFrame_jMenuHelpAbout_ActionAdapter
 
add(FileSize, FileSize) - Static method in class cct.tools.filebrowser.FileSize
 
add(FileSize, int) - Static method in class cct.tools.filebrowser.FileSize
 
add(vPoint3f) - Method in class cct.vecmath.vPoint3f
 
add(Point3fInterface) - Method in class cct.vecmath.vPoint3f
 
add(float, float, float) - Method in class cct.vecmath.vPoint3f
 
addActionListener(ActionListener) - Method in class cct.tools.filebrowser.FileTransferFrame.HostEditor
 
addActionListener(Object, String) - Static method in class cct.tools.GridProviders
 
addActionListenerForTracking(AbstractButton) - Method in class cct.help.JavaHelp
 
addActionListenerForTracking(AbstractButton) - Method in interface cct.interfaces.HelperInterface
 
addAngleBend(AngleBend) - Method in class cct.modelling.AngleBendsArray
 
addArgument(String) - Method in class cct.grid.JobDescription
Adds argument for the executable
addAtom(Object) - Method in class cct.cprocessor.MacroProcessor
 
addAtom(Object) - Method in interface cct.cprocessor.MacroProcessorInterface
 
addAtom(Object) - Method in interface cct.cprocessor.MolProcessorInterface
 
addAtom(GaussianAtom) - Method in class cct.gaussian.GaussianMolecule
 
addAtom(AtomInterface) - Method in interface cct.interfaces.MoleculeInterface
 
addAtom(AtomInterface, int) - Method in interface cct.interfaces.MoleculeInterface
 
addAtom(AtomInterface, int, String) - Method in interface cct.interfaces.MoleculeInterface
 
addAtom(AtomNode) - Method in class cct.j3d.Java3dUniverse
 
addAtom(AtomInterface) - Method in class cct.j3d.Java3dUniverse
 
addAtom(Point3d, Vector3d, float, boolean) - Method in class cct.j3d.Java3dUniverse
 
addAtom(Object) - Method in class cct.j3d.ScriptProcessorWrapper
 
addAtom(AtomInterface) - Method in class cct.modelling.AtomsArray
Adds atom to the last residue in the list
addAtom(AtomInterface, String) - Method in class cct.modelling.AtomsArray
Adds a new monomer and adds an atom to the monomer
addAtom(AtomInterface, int) - Method in class cct.modelling.AtomsArray
Adds atom to the existing nth monomer.
addAtom(AtomInterface, int, String) - Method in class cct.modelling.AtomsArray
 
addAtom(AtomInterface) - Method in class cct.modelling.Molecule
 
addAtom(AtomInterface, int) - Method in class cct.modelling.Molecule
 
addAtom(AtomInterface, String) - Method in class cct.modelling.Molecule
 
addAtom(AtomInterface, int, String) - Method in class cct.modelling.Molecule
 
addAtom(int, float, float, float) - Method in class cct.modelling.Molecule
 
addAtom(AtomInterface) - Method in class cct.modelling.Monomer
 
addAtom(PDBAtom) - Method in class cct.pdb.PDBResidue
 
addAtomImage - Variable in class cct.dialogs.Frame1
 
addBond(Object, Object) - Method in class cct.cprocessor.MacroProcessor
 
addBond(Object, Object) - Method in interface cct.cprocessor.MacroProcessorInterface
 
addBond(Object) - Method in interface cct.cprocessor.MolProcessorInterface
 
addBond(BondInterface) - Method in interface cct.interfaces.MoleculeInterface
 
addBond(BondInterface) - Method in class cct.j3d.Java3dUniverse
 
addBond(Object) - Method in class cct.j3d.ScriptProcessorWrapper
 
addBond(Bond) - Method in class cct.modelling.Molecule
 
addBond(BondInterface) - Method in class cct.modelling.Molecule
 
addBond(int, int) - Method in class cct.pdb.PDBResidue
 
addBond(String, String) - Method in class cct.pdb.PDBResidue
 
addBondBetweenAtoms(int, int) - Method in class cct.modelling.Molecule
 
addBondPair(Object) - Method in class cct.modelling.BondStretchPairs
 
addButton(JButton) - Method in class cct.tools.ui.LogPanel
 
addCheckPoint(CheckPoint) - Method in class cct.grid.ParseCheckpointFile
 
addChoice(String) - Method in class cct.awtdialogs.SingleChoiceDialog
 
addChoices(String[]) - Method in class cct.awtdialogs.SingleChoiceDialog
 
addClient(ShadowClientInterface) - Method in class cct.tools.filebrowser.ShadowSFTPManager
 
addColor(Color3f) - Method in class cct.j3d.color3fPalette
 
AddCommandObjects - Enum in cct.cprocessor
Title:
addCoordinates(vPoint3f) - Method in class cct.modelling.MolecularGeometry
 
addDataSeries(double[], double[], String) - Method in class cct.chart.ChartFrame
 
addDataSeries(double[], double[], int, String) - Method in class cct.chart.ChartFrame
 
addDataSeries(double[], double[], String) - Method in interface cct.chart.ChartInterface
 
addDataSeries(double[], double[], int, String) - Method in interface cct.chart.ChartInterface
 
addDataSeries(double[], double[], String) - Method in class cct.chart.jfreechart.JFreeChartPanel
 
addDataSeries(double[], double[], int, String) - Method in class cct.chart.jfreechart.JFreeChartPanel
 
addedSuccessfully - Variable in class cct.awtdialogs.AddNewMethodDialog
 
addElement(String) - Method in class cct.awtdialogs.AtomTypeDialog
 
addElements(String[]) - Method in class cct.awtdialogs.AtomTypeDialog
 
addEnergyTerm(String, double) - Method in class cct.vasp.VaspSnapshot
 
addExtension(String) - Method in class cct.tools.FileFilterImpl
 
addFragButton - Variable in class cct.dialogs.JAddFragmentDialog
 
addFragButton - Variable in class cct.dialogs.JSelectTreeDialog
 
addFragButton_actionPerformed(ActionEvent) - Method in class cct.dialogs.JAddFragmentDialog
 
addFragButton_actionPerformed(ActionEvent) - Method in class cct.dialogs.JSelectTreeDialog
 
addFragment() - Method in class cct.j3d.Java3dUniverse
 
addFragment(Java3dUniverse) - Method in class cct.j3d.Java3dUniverse
Adds a fragment to a molecule
addFrequencies(ArrayList<ADFFrequency>) - Method in class cct.adf.ADFOutputSection
 
addGaussianData(Gaussian) - Method in class cct.j3d.Java3dUniverse
 
addGeometry(String, MolecularGeometry) - Method in class cct.gaussian.GaussianSnapshot
 
addGraphics(GraphicsObjectInterface) - Method in interface cct.interfaces.GraphicsObjectInterface
 
addGraphics(String, Shape3D) - Method in interface cct.interfaces.GraphicsObjectInterface
 
addGraphics(GraphicsObjectInterface) - Method in class cct.j3d.Java3dUniverse
 
addGraphics(GraphicsObjectInterface) - Method in class cct.j3d.VerticesObject
 
addGraphics(String, Shape3D) - Method in class cct.j3d.VerticesObject
 
addGraphicsToMolecule(BranchGroup, boolean) - Method in class cct.j3d.Java3dUniverse
 
addHost(String, SFTPBrowser) - Static method in class cct.ssh.SSHServiceProvider
 
addItem(String) - Method in class cct.awtdialogs.GeometrySelectDialog
 
addItem(Object) - Method in class cct.dialogs.JChoiceDialog
 
addItem(String) - Method in class cct.dialogs.JChoiceDialog
 
addItems(String[]) - Method in class cct.awtdialogs.GeometrySelectDialog
 
additionalEntries - Variable in class cct.gaussian.ui.GaussianInputEditorFrame
 
addKnownHost(String) - Method in class cct.tools.filebrowser.ShadowSFTPManager
 
addLine(String) - Method in class cct.math.MathExpressionParser
 
addLinkZeroCommands(String) - Method in class cct.gaussian.GaussianMolecule
 
addManyStringItems(String, String, String) - Method in class cct.database.SQLDatabaseAccess
 
addManyStringItems(String, String[], String[]) - Method in class cct.database.SQLDatabaseAccess
 
addMenuItem(String, JMenuItem) - Method in class cct.dialogs.JEditorFrame
 
addMenuItem(String, JMenuItem) - Method in class cct.gaussian.ui.GaussianInputEditorFrame
 
addMeshObject(MeshObject) - Method in class cct.povray.Povray
 
addMessage(String, String) - Method in class cct.tools.MessagePost
 
addMethod - Variable in class cct.awtdialogs.AddNewStructureDialog
 
addMolecule(MoleculeInterface) - Method in class cct.dialogs.J3DTabbedWorld
 
addMolecule(MoleculeInterface, int) - Method in class cct.dialogs.J3DTabbedWorld
 
addMolecule(MoleculeInterface) - Method in interface cct.interfaces.MoleculeRendererInterface
 
addMolecule(MoleculeInterface, int) - Method in interface cct.interfaces.MoleculeRendererInterface
 
addMolecule(Molecule) - Method in class cct.j3d.Java3dUniverse
 
addMolecule(MoleculeInterface, int) - Method in class cct.j3d.Java3dUniverse
 
addMolecule(MoleculeInterface) - Method in class cct.j3d.Java3dUniverse
 
addMolecule(Point3d, Vector3d, float, boolean, Java3dUniverse) - Method in class cct.j3d.Java3dUniverse
Adds a molecule to the main window
addMolecule(Point3f, Java3dUniverse) - Method in class cct.j3d.Java3dUniverse
 
AddMoleculeDialog - Class in cct.dialogs
Title: Jamberoo - Computational Chemistry Toolkit
AddMoleculeDialog(Frame, String) - Constructor for class cct.dialogs.AddMoleculeDialog
 
AddMoleculeDialog(Dialog, String) - Constructor for class cct.dialogs.AddMoleculeDialog
 
AddMoleculeDialog() - Constructor for class cct.dialogs.AddMoleculeDialog
 
addMoleculeSpecsItem(String) - Method in class cct.gaussian.GaussianMolecule
 
addMonomer(String) - Method in interface cct.interfaces.MoleculeInterface
 
addMonomer(String) - Method in class cct.modelling.AtomsArray
 
addMonomer(String) - Method in class cct.modelling.Molecule
 
addMonomer(MoleculeInterface, MonomerInterface) - Static method in class cct.modelling.Molecule
Adds a monomer to a molecule
addMousePicking(Java3dUniverse, BranchGroup, Canvas3D, Bounds) - Method in class cct.j3d.Java3dUniverse
 
addNewMethod(String, String, boolean, boolean, boolean, boolean) - Method in class cct.database.new_SQLChemistryDatabase
 
AddNewMethodDialog - Class in cct.awtdialogs
Title:
AddNewMethodDialog(String, boolean, new_SQLChemistryDatabase) - Constructor for class cct.awtdialogs.AddNewMethodDialog
 
addNewMolecule(String) - Method in class cct.database.new_SQLChemistryDatabase
 
addNewMolecule(String, String, String, boolean, int, int) - Method in class cct.database.new_SQLChemistryDatabase
 
addNewMolecule(String) - Method in class cct.database.SQLChemistryDatabase
 
AddNewMoleculeDialog - Class in cct.awtdialogs
Title:
AddNewMoleculeDialog(String, boolean, String) - Constructor for class cct.awtdialogs.AddNewMoleculeDialog
 
addNewStructure(String, String, String, String, MoleculeInterface) - Method in class cct.database.new_SQLChemistryDatabase
 
addNewStructure(String, String, MoleculeInterface) - Method in class cct.database.SQLChemistryDatabase
 
AddNewStructureDialog - Class in cct.awtdialogs
Title:
AddNewStructureDialog(String, boolean, String, new_SQLChemistryDatabase) - Constructor for class cct.awtdialogs.AddNewStructureDialog
 
addOptions(String) - Method in class cct.gaussian.GaussianKeywords
 
addPreprocessDirective(String) - Method in class cct.grid.JobDescription
 
addProperty(String, double) - Method in class cct.adf.ADFSnapshot
 
addProperty(String, double) - Method in class cct.gaussian.GaussianSnapshot
 
addProperty(String, Object) - Method in interface cct.interfaces.MoleculeInterface
 
addProperty(String, Object) - Method in class cct.modelling.Molecule
Adds molecular property.
addProperty(String, Object) - Method in class cct.modelling.TrajectorySnapshot
 
addRemark(String) - Method in class cct.modelling.MolecularGeometry
 
addRenderingListener(RenderingListener) - Method in class cct.j3d.Java3dUniverse
Add listener for change rendering style events
addResidue(PDBResidue) - Method in class cct.pdb.PDBDictionary
 
ADDRESS - Static variable in class cct.grid.JobDescription
 
addRouteOptions(String) - Method in class cct.gaussian.GaussianMolecule
 
addSnapshot(ADFSnapshot) - Method in class cct.adf.ADFOutputSection
 
addStringItem(String, String, String) - Method in class cct.database.SQLDatabaseAccess
 
addSummary(String) - Method in class cct.adf.ADFOutputSection
 
addTaskProviders(LinkedHashMap) - Static method in class cct.grid.TaskProvider
 
addValue(Sander8VariableValue) - Method in class cct.amber.Sander8Variable
 
addValue(SanderVariableValue) - Method in class cct.amber.SanderVariable
 
addValue(String, String) - Method in class cct.gamess.GamessSwitch
 
addValue(String, String, boolean) - Method in class cct.gamess.GamessSwitch
 
addVector(String, float, float, float) - Method in class cct.adf.ADFFrequency
 
ADF - Class in cct.adf
 
ADF() - Constructor for class cct.adf.ADF
 
ADFAtom - Class in cct.adf
Title: Computational Chemistry Tookit
ADFAtom() - Constructor for class cct.adf.ADFAtom
 
ADFFrequency - Class in cct.adf
Title: Computational Chemistry Tookit
ADFFrequency(double) - Constructor for class cct.adf.ADFFrequency
 
ADFFrequency.ADFVector - Class in cct.adf
 
ADFFrequency.ADFVector() - Constructor for class cct.adf.ADFFrequency.ADFVector
 
adfInput - Static variable in class cct.modelling.MolecularFileFormats
 
ADFOutput - Class in cct.adf
Title: Computational Chemistry Tookit
ADFOutput() - Constructor for class cct.adf.ADFOutput
 
adfOutput - Static variable in class cct.modelling.MolecularFileFormats
 
ADFOutputSection - Class in cct.adf
Title: Computational Chemistry Tookit
ADFOutputSection() - Constructor for class cct.adf.ADFOutputSection
 
ADFSnapshot - Class in cct.adf
Title: Computational Chemistry Tookit
ADFSnapshot() - Constructor for class cct.adf.ADFSnapshot
 
adjustButtons() - Method in class cct.dialogs.JElementsPanel
 
adjustColor(Color) - Method in class cct.oogl.OOGL
 
af - Variable in class cct.oogl.Face
 
af - Variable in class cct.tools.Face
 
aiCubeEdgeFlags - Static variable in class cct.math.polyg.Polygonizer
 
aiTetrahedronEdgeFlags - Variable in class cct.math.polyg.Polygonizer
 
ALF - Variable in class cct.math.LinearSearch
 
aliases - Variable in class cct.awtdialogs.AddNewMoleculeDialog
 
aliases - Variable in class cct.database.ChemistryDatabaseDialog
 
aliases - Variable in class cct.database.new_ChemistryDatabaseDialog
 
All - Variable in class cct.dialogs.JAtomSelectionDialog
 
All - Variable in class cct.dialogs.JQuickSelectionPanel
 
All_actionPerformed(ActionEvent) - Method in class cct.dialogs.JAtomSelectionDialog
 
allBasisSets - Variable in class cct.database.new_ChemistryDatabaseDialog
 
allFormats - Static variable in class cct.modelling.MolecularFileFormats
 
allKeywords - Static variable in class cct.gaussian.GaussianKeywords
 
ALLLORNONE - Static variable in class cct.grid.JobDescription
 
allMethods - Variable in class cct.database.new_ChemistryDatabaseDialog
 
allMolecularExtensions - Static variable in class cct.modelling.MolecularFileFormats
 
allMolecularFormats - Static variable in class cct.modelling.MolecularFileFormats
 
allMolecules - Variable in class cct.database.ChemistryDatabaseDialog
 
allMolecules - Variable in class cct.database.new_ChemistryDatabaseDialog
 
allocateCoordinates(MoleculeInterface) - Method in class cct.dialogs.TrajectoryAnalysisDialog
 
allProviders - Variable in class cct.grid.ui.gaussian.SubmitGaussianDialog
 
allProviders - Variable in class cct.grid.ui.gaussian.SubmitGaussianDialogNew
 
allProviders - Variable in class cct.grid.ui.SubmitTaskDialog
 
allSchedulers - Variable in class cct.grid.ui.SubmitTaskDialog
 
allStructures - Variable in class cct.database.ChemistryDatabaseDialog
 
allStructures - Variable in class cct.database.new_ChemistryDatabaseDialog
 
allVars - Static variable in class cct.amber.Sander8JobControl
 
allVars - Static variable in class cct.amber.Sander9JobControl
 
alpha - Variable in class cct.gamess.GamessAtom
 
alpha - Variable in class cct.j3d.VibrationsRenderer.DVObject
 
alpha - Variable in class cct.mopac.MopacAtom
 
alpha - Variable in class cct.qchem.QChemAtom
 
alphaPar - Variable in class cct.gamess.GamessAtom
 
alphaPar - Variable in class cct.mopac.MopacAtom
 
alphaPar - Variable in class cct.qchem.QChemAtom
 
Amber9JobDialog - Class in cct.amber
Title:
Amber9JobDialog(Frame, String, boolean) - Constructor for class cct.amber.Amber9JobDialog
 
Amber9JobDialog() - Constructor for class cct.amber.Amber9JobDialog
 
amber9JobPanel1 - Variable in class cct.amber.Amber9JobDialog
 
AMBER_NAME - Static variable in interface cct.interfaces.AtomInterface
 
AMBER_TYPE_INDEX - Static variable in interface cct.interfaces.AtomInterface
 
AmberApplet - Class in cct.amber
 
AmberApplet() - Constructor for class cct.amber.AmberApplet
 
AmberAtomFlags - Static variable in class cct.amber.AmberUtilities
 
amberCoordFormat - Static variable in class cct.modelling.MolecularFileFormats
 
AmberLib - Class in cct.amber
 
AmberLib(MoleculeInterface) - Constructor for class cct.amber.AmberLib
 
amberLibFormat - Static variable in class cct.modelling.MolecularFileFormats
 
amberMdcrdFormat - Static variable in class cct.modelling.MolecularFileFormats
 
AmberPrep - Class in cct.amber
Title: Jamberoo - Computational Chemistry Toolkit
AmberPrep() - Constructor for class cct.amber.AmberPrep
 
AmberPrepAtom - Class in cct.amber
 
AmberPrepAtom() - Constructor for class cct.amber.AmberPrepAtom
 
amberPrepFormat - Static variable in class cct.modelling.MolecularFileFormats
 
AmberPrmtop - Class in cct.amber
Title:
AmberPrmtop() - Constructor for class cct.amber.AmberPrmtop
 
amberPrmtopFormat - Static variable in class cct.modelling.MolecularFileFormats
 
AmberSubmit - Variable in class cct.amber.AmberApplet
 
AmberSubmitDialog - Class in cct.amber
 
AmberSubmitDialog(AmberApplet, String, String) - Constructor for class cct.amber.AmberSubmitDialog
 
AmberSubmitMenuHandler - Class in cct.amber
 
AmberSubmitMenuHandler(AmberSubmitDialog) - Constructor for class cct.amber.AmberSubmitMenuHandler
 
AmberUtilities - Class in cct.amber
Title: Picking
AMBIENT_RGB_COLOR - Static variable in interface cct.interfaces.AtomInterface
 
Amoeba - Class in cct.math
Title:
Amoeba() - Constructor for class cct.math.Amoeba
 
amoeba(float[], int, float, MinimizedFunctionInterface) - Method in class cct.math.Amoeba
Multidimensional minimization of the function func(x) where x[ndim] is a vector in ndim dimensions, by the downhill simplex method of Nelder and Mead.
amotry(float[][], float[], float[], int, MinimizedFunctionInterface, int, float) - Method in class cct.math.Amoeba
Extrapolates by a factor fac through the face of the simplex across from the high point, tries it, and replaces the high point if the new point is better.
angle - Variable in class cct.j3d.LabelNode
 
AngleBend - Class in cct.modelling
Title:
AngleBend(int, int, int, float, float) - Constructor for class cct.modelling.AngleBend
 
AngleBendEnergy - Class in cct.modelling
Title:
angleBendEnergy(MoleculeInterface, Object[]) - Static method in class cct.modelling.AngleBendEnergy
 
angleBendEnergy(MoleculeInterface, Object[], vPoint3f[]) - Static method in class cct.modelling.AngleBendEnergy
 
angleBendEnergy - Variable in class cct.modelling.MolecularEnergy
 
AngleBendInteractions - Variable in class cct.modelling.FFMolecule
 
angleBendParams - Static variable in class cct.sff.SimpleForceField
 
angleBends - Variable in class cct.modelling.AngleBendsArray
 
AngleBendsArray - Class in cct.modelling
Title:
AngleBendsArray() - Constructor for class cct.modelling.AngleBendsArray
 
AngleBendsArray(int) - Constructor for class cct.modelling.AngleBendsArray
 
angleBetween(vPoint3f, vPoint3f) - Method in class cct.vecmath.vPoint3f
Angle between atoms "a"-"current"-"b"
angleBetween(Point3fInterface, Point3fInterface, Point3fInterface) - Static method in class cct.vecmath.vPoint3f
Calculate angle a-x-b
angleBetween(Point3fInterface, Point3fInterface) - Static method in class cct.vecmath.vPoint3f
Calculates angle between vectors a & b It's the same as angleBetween(Point3fInterface a, Point3fInterface x, Point3fInterface b) where x=(0,0,0)
anglePanel - Variable in class cct.dialogs.JModifyAngleDialog
 
AngleParam - Class in cct.sff
Title:
AngleParam(float, float) - Constructor for class cct.sff.AngleParam
 
AngleParam() - Constructor for class cct.sff.AngleParam
 
angleUnits - Variable in class cct.adf.ADF
 
angleValue - Variable in class cct.dialogs.JModifyTorsionDialog
 
angleValue_actionPerformed(ActionEvent) - Method in class cct.dialogs.JModifyTorsionDialog
 
ANGSTROM_UNITS - Static variable in class cct.gaussian.GaussianCube
 
angstromRadioButton - Variable in class cct.dialogs.SaveXYZDialog
 
animateCheckBox_itemStateChanged(ItemEvent) - Method in class cct.modelling.ui.VibrationsControlPanel
 
animateCheckBox_stateChanged(ChangeEvent) - Method in class cct.modelling.ui.VibrationsControlPanel
 
animateVibrations(int, boolean) - Method in interface cct.interfaces.VibrationsRendererProvider
 
animateVibrations(int, boolean) - Method in class cct.j3d.VibrationsRenderer
 
animationBranch - Variable in class cct.j3d.VibrationsRenderer.DVObject
 
animationComboBox - Variable in class cct.dialogs.AnimationPanel
 
animationComboBox_itemStateChanged(ItemEvent) - Method in class cct.chart.jfreechart.JFreeChartPanel
 
animationComboBox_itemStateChanged(ItemEvent) - Method in class cct.dialogs.AnimationPanel
 
AnimationPanel - Class in cct.dialogs
Title: Computational Chemistry Tookit
AnimationPanel() - Constructor for class cct.dialogs.AnimationPanel
 
AnimationPanel(StructureManagerInterface) - Constructor for class cct.dialogs.AnimationPanel
 
animationPanel1 - Variable in class cct.dialogs.TrajectoryAnalysisDialog
 
anyValue - Variable in class cct.gamess.GamessSwitch
 
App - Variable in class cct.j3d.ui.VerticesPropertyPanel
 
AppearanceSetup - Class in cct.j3d
 
AppearanceSetup(String[]) - Constructor for class cct.j3d.AppearanceSetup
Creates new form SphereMotion
append(BondInterface) - Method in class cct.modelling.BondsArray
Append an atom to the end of vector
appendMessage(String) - Method in class cct.tools.ui.PostMessagePanel
 
appendMolecule(MoleculeInterface) - Method in interface cct.interfaces.MoleculeInterface
Adds COPIES of atoms from molecule "mol"
appendMolecule(MoleculeInterface, MoleculeInterface, float[][]) - Method in class cct.j3d.Java3dUniverse
 
appendMolecule(MoleculeInterface, boolean) - Method in class cct.j3d.Java3dUniverse
 
appendMolecule(Java3dUniverse) - Method in class cct.j3d.Java3dUniverse
 
appendMolecule(MoleculeInterface) - Method in class cct.modelling.Molecule
 
appendOutput(String) - Method in class cct.grid.ui.gaussian.SubmitGaussianAppl.IOFrame
 
appendOutput(String) - Method in interface cct.grid.ui.JobOutputInterface
 
appendOutputResume(LinkedHashMap<String, String>, String, String) - Method in class cct.gaussian.GaussianOutput
 
appendText(String) - Method in class cct.tools.ui.JShowText
 
appendText(String) - Method in class cct.tools.ui.LogPanel
 
applyForceField(ForceFieldInterface) - Method in class cct.modelling.FFMolecule
 
applySymmetry(String, int, ArrayList<GamessAtom>) - Method in class cct.gamess.Gamess
 
applySymmetry(String, int, ArrayList) - Static method in class cct.math.PointGroup
Not implemented yet....
ArcCos(double) - Static method in class cct.modelling.TorsionEnergy
 
areExtensionsEnabled() - Method in class cct.grid.ui.PBSPanel
 
areLabels() - Method in class cct.j3d.Java3dUniverse
 
areMinimizersSet() - Method in class cct.modelling.ui.JSetupEnergyDialog
 
areOutputFilesLoaded() - Method in class cct.grid.CheckPoint
Informs whether remote output files are downloaded on a local computer
ARGUMENT - Static variable in class cct.grid.JobDescription
 
aromaticBonds - Variable in class cct.modelling.AtomGeometry
 
arrowDown - Variable in class cct.gaussian.ui.GaussianInputEditorFrame
 
arrowDown - Variable in class cct.tools.filebrowser.FileBrowserPanel
 
arrowDownFaded - Variable in class cct.gaussian.ui.GaussianInputEditorFrame
 
ArrowNode - Class in cct.j3d
Title: Computational Chemistry Tookit
ArrowNode() - Constructor for class cct.j3d.ArrowNode
 
ArrowNode(float[], float[]) - Constructor for class cct.j3d.ArrowNode
 
arrowUp - Variable in class cct.gaussian.ui.GaussianInputEditorFrame
 
arrowUp - Variable in class cct.tools.filebrowser.FileBrowserPanel
 
arrowUpFaded - Variable in class cct.gaussian.ui.GaussianInputEditorFrame
 
ASCENDING - Static variable in class cct.tools.filebrowser.TableSorter
 
asCombobox - Variable in class cct.dialogs.JAtomTypeDialog
 
asTable - Variable in class cct.dialogs.JAtomTypeDialog
 
Atom - Variable in class cct.dialogs.JSelectionTypePanel
 
atom - Variable in class cct.j3d.AtomNode
 
ATOM - Static variable in class cct.modelling.AtomGeometry
 
Atom_1 - Variable in class cct.dialogs.JModifyAngleDialog
 
Atom_1 - Variable in class cct.dialogs.JModifyBondDialog
 
Atom_2 - Variable in class cct.dialogs.JModifyAngleDialog
 
Atom_2 - Variable in class cct.dialogs.JModifyBondDialog
 
Atom_2 - Variable in class cct.dialogs.JModifyTorsionDialog
 
Atom_3 - Variable in class cct.dialogs.JModifyAngleDialog
 
ATOM_CCTTYPE_ATTRIBUTE - Static variable in class cct.pdb.PDBDictionary
 
ATOM_COLOR_SCHEME_2 - Static variable in class cct.j3d.ChemicalElementsColors
 
ATOM_COLOR_SCHEME_JMOL - Static variable in class cct.j3d.ChemicalElementsColors
 
ATOM_COLOR_SCHEME_RASMOL - Static variable in class cct.j3d.ChemicalElementsColors
 
ATOM_COLOR_SCHEME_RASMOL_NEW - Static variable in class cct.j3d.ChemicalElementsColors
 
ATOM_ELEMENT - Static variable in class cct.pdb.PDBDictionary
 
ATOM_ELEMENT_ATTRIBUTE - Static variable in class cct.pdb.PDBDictionary
 
ATOM_ICON - Static variable in class cct.modelling.AtomGeometry
 
atom_name - Variable in class cct.adf.ADFFrequency.ADFVector
 
ATOM_NAME_ATTRIBUTE - Static variable in class cct.pdb.PDBDictionary
 
ATOM_NODE - Static variable in class cct.j3d.Java3dUniverse
 
ATOM_TAG - Static variable in class cct.tools.CCTParserEnum
 
atom_types - Variable in class cct.dialogs.JSpecialSelectionPanel
 
atomAppear - Variable in class cct.j3d.Java3dUniverse
 
atomColor - Variable in class cct.j3d.AtomNode
 
atomColor - Variable in class cct.modelling.AtomTypeDef
 
atomColours - Static variable in class cct.j3d.ChemicalElementsColors
 
AtomGenerator - Class in cct.modelling
Title:
AtomGenerator() - Constructor for class cct.modelling.AtomGenerator
 
AtomGeometry - Class in cct.modelling
Title:
AtomGeometry() - Constructor for class cct.modelling.AtomGeometry
 
AtomGeometry(String, int, int, int, int, int, int, ImageIcon) - Constructor for class cct.modelling.AtomGeometry
 
AtomGeometry(AtomGeometry) - Constructor for class cct.modelling.AtomGeometry
 
ATOMIC_CHARGE - Static variable in interface cct.interfaces.AtomInterface
 
AtomicCoordinatesFormat - Enum in cct.siesta
Title: Computational Chemistry Tookit
atomicNumber - Variable in class cct.adf.ADFAtom
 
atomicNumber - Variable in class cct.qchem.QChemAtom
 
atomicNumber - Variable in class cct.siesta.ChemicalSpeciesLabel
 
atomicPositionsType - Variable in class cct.vasp.Vasp
 
atomicSpecies - Variable in class cct.vasp.Vasp
 
atomicSphere - Variable in class cct.j3d.AtomNode
 
atomicWeight - Static variable in class cct.modelling.ChemicalElements
 
atomInfoPopup - Variable in class cct.j3d.Java3dUniverse
 
atomInfoPopupEnabled() - Method in class cct.j3d.Java3dUniverse
 
AtomInterface - Interface in cct.interfaces
Title: Computational Chemsitry Tookit
atomInterface - Variable in class cct.modelling.Molecule
 
atomLabels - Variable in class cct.j3d.Java3dUniverse
 
atomLabelsColor - Variable in class cct.j3d.Java3dUniverse
 
AtomLabelsDialog - Class in cct.awtdialogs
Title:
AtomLabelsDialog(Frame, String, ArrayList, boolean) - Constructor for class cct.awtdialogs.AtomLabelsDialog
 
atomLabelsDialog - Variable in class cct.j3d.Java3dUniverse
 
atomLabelsFont - Variable in class cct.j3d.Java3dUniverse
 
atomLabelsFontName - Variable in class cct.j3d.Java3dUniverse
 
atomLabelsFontSize - Variable in class cct.j3d.Java3dUniverse
 
atomLabelsFontStyle - Variable in class cct.j3d.Java3dUniverse
 
atomMaterial - Variable in class cct.j3d.AtomNode
 
atomName - Variable in class cct.awtdialogs.AtomTypeDialog
 
atomName - Variable in class cct.dialogs.JAtomTypeDialog
 
atomNames - Variable in class cct.dialogs.JSelectAtomTypesDialog
 
AtomNode - Class in cct.j3d
Title:
AtomNode(AtomInterface) - Constructor for class cct.j3d.AtomNode
 
AtomNode(AtomInterface, int) - Constructor for class cct.j3d.AtomNode
 
AtomNode(float, float, float, float, int, Color3f, Material) - Constructor for class cct.j3d.AtomNode
 
atomNodes - Variable in class cct.j3d.Java3dUniverse
 
atomPoint - Variable in class cct.j3d.AtomNode
 
AtomProperties - Interface in cct.modelling
Title:
atomProperties - Static variable in class cct.modelling.CCTAtomTypes
 
Atoms - Variable in class cct.adf.ADF
 
atoms - Variable in class cct.gamess.Gamess
 
atoms - Variable in class cct.gaussian.G03FormCheckpoint
 
Atoms - Variable in class cct.modelling.AtomsArray
 
Atoms - Variable in class cct.modelling.Molecule
 
Atoms - Variable in class cct.mopac.Mopac
 
Atoms - Variable in class cct.qchem.QChem
 
Atoms - Variable in class cct.qchem.QChemOutput
 
atoms - Variable in class cct.tools.CCTParser
 
Atoms - Variable in class cct.vasp.Vasp
 
AtomsArray - Class in cct.modelling
Title: AtomsArray
AtomsArray() - Constructor for class cct.modelling.AtomsArray
Creates a new atom array.
AtomsArray(AtomsArray) - Constructor for class cct.modelling.AtomsArray
Copy constructor
atomsButtonGroup - Variable in class cct.dialogs.SaveXYZDialog
 
atomShape - Variable in class cct.j3d.AtomNode
 
atomType - Variable in class cct.gaussian.GaussianAtom
 
AtomTypeDef - Class in cct.modelling
Title: Molecular Structure Viewer/Editor
AtomTypeDef(String, String, int, int) - Constructor for class cct.modelling.AtomTypeDef
 
AtomTypeDef(String, int, int, int) - Constructor for class cct.modelling.AtomTypeDef
 
AtomTypeDialog - Class in cct.awtdialogs
Title:
AtomTypeDialog(Frame, String, boolean) - Constructor for class cct.awtdialogs.AtomTypeDialog
 
atomTypes - Variable in class cct.dialogs.JAtomSelectionDialog
 
atomTypes - Static variable in class cct.modelling.AtomGeometry
 
AtomTypes - Class in cct.modelling
Title: Molecular Structure Viewer/Editor
AtomTypes() - Constructor for class cct.modelling.AtomTypes
 
atomTypes - Variable in class cct.modelling.AtomTypes
 
atomTypes_actionPerformed(ActionEvent) - Method in class cct.dialogs.JAtomSelectionDialog
 
atomTypesButtons - Variable in class cct.dialogs.JAtomTypeDialog
 
atomTypesPanel - Variable in class cct.dialogs.JAtomTypeDialog
 
atomTypesPanel - Variable in class cct.dialogs.JModifyAtomDialog
 
atomTypesPanel - Variable in class cct.dialogs.SaveXYZDialog
 
atomTypesResolved - Variable in class cct.vasp.ui.ReadPoscarDialog
 
audioFileImage - Static variable in class cct.tools.FileUtilities
 
authenticate(String, char[]) - Method in class cct.tools.filebrowser.SFTPBrowser
Authenticate the user on the remote host.
authenticationMethods - Variable in class cct.tools.filebrowser.SFTPBrowser
 
AuthenticationResult - Variable in class cct.tools.filebrowser.SFTPBrowser
 
AuxNames - Variable in class cct.j3d.VerticesObject
 
available() - Method in class cct.tools.UncompressInputStream
 
availableTransp - Static variable in class cct.j3d.VerticesObjectProperties
 
availableVibrationalSpectra() - Method in class cct.adf.ADFOutput
 
availableVibrationalSpectra() - Method in class cct.gaussian.GaussianFrequency
 
availableVibrationalSpectra() - Method in class cct.gaussian.GaussianOutput
Returns names of available vibrational spectra (if any)
availableVibrationalSpectra() - Method in interface cct.interfaces.OutputResultsInterface
 
AxisOrder - Variable in class cct.gamess.Gamess
 
axisVectors - Variable in class cct.gaussian.java3d.VolumetricData
 

B

b - Variable in class cct.oogl.Color
 
b - Variable in class cct.oogl.Face
 
B - Static variable in class cct.poly.CUBETABLE
 
B - Static variable in class cct.poly.Polygonizer
 
b - Variable in class cct.tools.Crystal
 
b - Variable in class cct.tools.Face
 
backFaceNormalFlip - Variable in class cct.j3d.VerticesObjectProperties
 
backgroundColor - Variable in class cct.povray.Povray
 
BackgroundMinimizer - Class in cct.modelling
Title:
BackgroundMinimizer(Object, ParentInterface, MinimizeStructure) - Constructor for class cct.modelling.BackgroundMinimizer
 
BALL_AND_STICKS - Static variable in interface cct.interfaces.MoleculeInterface
 
BASE_ELEMENT_KEY - Static variable in class cct.modelling.CCTAtomTypes
 
basicButton - Variable in class cct.dialogs.JAddFragmentDialog
 
BasicFragment - Class in cct.modelling
Title:
BasicFragment.CarbonDivalentStr - Class in cct.modelling
 
BasicFragment.CarbonDivalentStr() - Constructor for class cct.modelling.BasicFragment.CarbonDivalentStr
 
basisGroup - Variable in class cct.gamess.Gamess
 
basisSection - Static variable in class cct.gamess.Gamess
 
basisSection - Static variable in class cct.qchem.QChem
 
BasisSet - Variable in class cct.awtdialogs.GaussianCalcSetupDialog
 
basisSet - Variable in class cct.gaussian.GaussianKeywords
 
basisSets - Variable in class cct.awtdialogs.AddNewMethodDialog
 
basisSets - Variable in class cct.awtdialogs.SelectMethodDialog
 
BasisSets - Variable in class cct.database.new_ChemistryDatabaseDialog
 
basisSetsNameKey - Static variable in interface cct.database.TablesDescription
 
basisSetsTable - Variable in class cct.database.new_SQLChemistryDatabase
 
BasisSetsTable - Static variable in interface cct.database.TablesDescription
 
basisSetsTableInfo - Variable in class cct.database.new_SQLChemistryDatabase
 
basisSwitches - Static variable in class cct.gamess.Gamess
 
batchJobTag - Static variable in interface cct.grid.CheckPointInterface
 
batchSeparator - Static variable in class cct.qchem.QChem
 
BathCouplingTime - Variable in class cct.modelling.JobControl
 
BELLYMASK_Label - Variable in class cct.amber.Sander8Frame
 
BELLYMASK_Label - Variable in class cct.amber.Sander9Frame
 
BELLYMASK_Label_mouseEntered(MouseEvent) - Method in class cct.amber.Sander8Frame
 
BELLYMASK_Label_mouseEntered(MouseEvent) - Method in class cct.amber.Sander9Frame
 
BELLYMASK_TextField - Variable in class cct.amber.Sander8Frame
 
BELLYMASK_TextField - Variable in class cct.amber.Sander9Frame
 
BENDED_SINGLE_DOUBLE_ATOM - Static variable in class cct.modelling.AtomGeometry
 
BENDED_SINGLE_DOUBLE_ATOM_ICON - Static variable in class cct.modelling.AtomGeometry
 
beta - Variable in class cct.gamess.GamessAtom
 
beta - Variable in class cct.mopac.MopacAtom
 
beta - Variable in class cct.qchem.QChemAtom
 
betaPar - Variable in class cct.gamess.GamessAtom
 
betaPar - Variable in class cct.mopac.MopacAtom
 
betaPar - Variable in class cct.qchem.QChemAtom
 
bf - Variable in class cct.oogl.Face
 
BF - Static variable in class cct.poly.CUBETABLE
 
bf - Variable in class cct.tools.Face
 
bg - Static variable in class cct.j3d.ui.ColorGradientPanel
 
BICOLOR - Static variable in interface cct.interfaces.BondInterface
 
bigIntValue() - Method in class cct.tools.filebrowser.FileSize
 
BIT(int, int) - Method in class cct.poly.CUBETABLE
 
BIT(int, int) - Method in class cct.poly.Polygonizer
 
BIT(int, int) - Method in class cct.poly.PROCESS
 
black - Variable in class cct.j3d.ui.VerticesPropertyPanel
 
blackColor - Static variable in class cct.gaussian.java3d.GaussianJava3dFactory
 
bLength - Variable in class cct.awtdialogs.AtomTypeDialog
 
BLOCK_TOKEN - Static variable in class cct.siesta.SiestaInput
 
Blue - Variable in class cct.dialogs.JModifyAtomPanel
 
Blue_stateChanged(ChangeEvent) - Method in class cct.dialogs.JModifyAtomPanel
 
blueColor - Static variable in class cct.gaussian.java3d.GaussianJava3dFactory
 
BN - Static variable in class cct.poly.CUBETABLE
 
BOHR_UNITS - Static variable in class cct.gaussian.GaussianCube
 
bohrRadioButton - Variable in class cct.dialogs.SaveXYZDialog
 
Bond - Class in cct.modelling
Title:
Bond() - Constructor for class cct.modelling.Bond
 
Bond(AtomInterface, AtomInterface) - Constructor for class cct.modelling.Bond
 
Bond(Bond) - Constructor for class cct.modelling.Bond
 
Bond(BondInterface) - Constructor for class cct.modelling.Bond
 
BOND_A1_ATTRIBUTE - Static variable in class cct.pdb.PDBDictionary
 
BOND_A2_ATTRIBUTE - Static variable in class cct.pdb.PDBDictionary
 
BOND_ELEMENT - Static variable in class cct.pdb.PDBDictionary
 
BOND_NODE - Static variable in class cct.j3d.Java3dUniverse
 
BOND_TAG - Static variable in class cct.tools.CCTParserEnum
 
bondColoring - Variable in class cct.j3d.BondNode
 
Bonded_to - Variable in class cct.gaussian.GaussianAtom
 
bondedToAtoms - Variable in class cct.modelling.vAtom
 
bondInfoPanel - Variable in class cct.dialogs.JModifyBondDialog
 
BondInterface - Interface in cct.interfaces
Title:
bondInterface - Variable in class cct.modelling.Molecule
 
bondLength - Variable in class cct.awtdialogs.AtomTypeDialog
 
bondLength - Variable in class cct.dialogs.JAtomTypeDialog
 
bondLength - Variable in class cct.gamess.GamessAtom
 
bondLength() - Method in interface cct.interfaces.BondInterface
 
bondLength() - Method in class cct.modelling.Bond
 
bondLength - Variable in class cct.mopac.MopacAtom
 
bondLength - Variable in class cct.qchem.QChemAtom
 
bondLengthPar - Variable in class cct.gamess.GamessAtom
 
bondLengthPar - Variable in class cct.mopac.MopacAtom
 
bondLengthPar - Variable in class cct.qchem.QChemAtom
 
bondLengthSlider - Variable in class cct.dialogs.JModifyBondDialog
 
bondLengthSlider_stateChanged(ChangeEvent) - Method in class cct.dialogs.JModifyBondDialog
 
bondMax - Variable in class cct.dialogs.JModifyBondDialog
 
bondMin - Variable in class cct.dialogs.JModifyBondDialog
 
BondNode - Class in cct.j3d
Title:
BondNode() - Constructor for class cct.j3d.BondNode
 
BondNode(BondInterface) - Constructor for class cct.j3d.BondNode
 
BondNode(BondInterface, int) - Constructor for class cct.j3d.BondNode
 
bondNodes - Variable in class cct.j3d.Java3dUniverse
 
bondPanel - Variable in class cct.dialogs.JModifyBondDialog
 
BondParam - Class in cct.sff
Title:
BondParam(float, float) - Constructor for class cct.sff.BondParam
 
bondRenderingStyle - Variable in class cct.j3d.Java3dUniverse
 
Bonds - Variable in class cct.modelling.Molecule
 
bonds - Variable in class cct.tools.CCTParser
 
BondsArray - Class in cct.modelling
Title: BondsArray
BondsArray() - Constructor for class cct.modelling.BondsArray
 
BondsArray(BondsArray) - Constructor for class cct.modelling.BondsArray
Copy constructor
bondsIndex - Variable in class cct.modelling.vAtom
 
BondStretchEnergy - Class in cct.modelling
Title:
bondStretchEnergy(MoleculeInterface, Object[]) - Static method in class cct.modelling.BondStretchEnergy
 
bondStretchEnergy(MoleculeInterface, Object[], vPoint3f[]) - Static method in class cct.modelling.BondStretchEnergy
 
bondStretchEnergy - Variable in class cct.modelling.MolecularEnergy
 
BondStretchInteractions - Variable in class cct.modelling.FFMolecule
 
BondStretchPairs - Class in cct.modelling
Title:
BondStretchPairs() - Constructor for class cct.modelling.BondStretchPairs
 
BondStretchPairs(int) - Constructor for class cct.modelling.BondStretchPairs
 
bondStretchParams - Static variable in class cct.sff.SimpleForceField
 
border1 - Variable in class cct.dialogs.JModifyAngleDialog
 
border1 - Variable in class cct.dialogs.JQuickSelectionPanel
 
border1 - Variable in class cct.dialogs.JSelectionRulePanel
 
border1 - Variable in class cct.dialogs.JSelectionTypePanel
 
border1 - Variable in class cct.dialogs.TrajectoryAnalysisDialog
 
border1 - Variable in class cct.gaussian.ui.SimpleG03EditorPanel
 
border1 - Variable in class cct.grid.ui.gaussian.SubmitGaussianDialogNew
 
border1 - Variable in class cct.grid.ui.SubmitTaskDialog
 
border1 - Variable in class cct.j3d.ui.VerticesPropertyPanel
 
border1 - Variable in class cct.modelling.ui.JSetupEnergyDialog
 
border2 - Variable in class cct.dialogs.JModifyAngleDialog
 
border2 - Variable in class cct.dialogs.JQuickSelectionPanel
 
border2 - Variable in class cct.dialogs.JSelectionRulePanel
 
border2 - Variable in class cct.dialogs.JSelectionTypePanel
 
border2 - Variable in class cct.dialogs.TrajectoryAnalysisDialog
 
border2 - Variable in class cct.gaussian.ui.SimpleG03EditorPanel
 
border2 - Variable in class cct.grid.ui.gaussian.SubmitGaussianDialogNew
 
border2 - Variable in class cct.grid.ui.SubmitTaskDialog
 
border2 - Variable in class cct.j3d.ui.VerticesPropertyPanel
 
border2 - Variable in class cct.modelling.ui.JSetupEnergyDialog
 
border3 - Variable in class cct.dialogs.JSelectionTypePanel
 
border3 - Variable in class cct.dialogs.TrajectoryAnalysisDialog
 
border4 - Variable in class cct.dialogs.JSelectionTypePanel
 
border4 - Variable in class cct.dialogs.TrajectoryAnalysisDialog
 
borderLayout1 - Variable in class cct.amber.Amber9JobDialog
 
borderLayout1 - Variable in class cct.amber.AmberApplet
 
borderLayout1 - Variable in class cct.amber.Sander8Frame
 
borderLayout1 - Variable in class cct.amber.Sander8Frame_AboutBox
 
borderLayout1 - Variable in class cct.amber.Sander9Frame
 
borderLayout1 - Variable in class cct.amber.Sander9Frame_AboutBox
 
borderLayout1 - Variable in class cct.amber.Sander9JobPanel
 
borderLayout1 - Variable in class cct.amber.TextEditorFrame
 
borderLayout1 - Variable in class cct.applets.viewer
 
borderLayout1 - Variable in class cct.dialogs.AnimationPanel
 
borderLayout1 - Variable in class cct.dialogs.Frame1
 
borderLayout1 - Variable in class cct.dialogs.Frame1_AboutBox
 
borderLayout1 - Variable in class cct.dialogs.JAddFragmentDialog
 
borderLayout1 - Variable in class cct.dialogs.JAddMoleculeDialog
 
borderLayout1 - Variable in class cct.dialogs.JAtomTypeDialog
 
borderLayout1 - Variable in class cct.dialogs.JChoiceDialog
 
borderLayout1 - Variable in class cct.dialogs.JElementsPanel
 
borderLayout1 - Variable in class cct.dialogs.JModifyAngleDialog
 
borderLayout1 - Variable in class cct.dialogs.JModifyAtomDialog
 
borderLayout1 - Variable in class cct.dialogs.JModifyBondDialog
 
borderLayout1 - Variable in class cct.dialogs.JModifyTorsionDialog
 
borderLayout1 - Variable in class cct.dialogs.JSelectAtomTypesDialog
 
borderLayout1 - Variable in class cct.dialogs.JSelectionRulePanel
 
borderLayout1 - Variable in class cct.dialogs.JSelectionTypePanel
 
borderLayout1 - Variable in class cct.dialogs.JSelectMonomersDialog
 
borderLayout1 - Variable in class cct.dialogs.JSelectSubstructureDialog
 
borderLayout1 - Variable in class cct.dialogs.JSelectTreeDialog
 
borderLayout1 - Variable in class cct.dialogs.JSimpleAtomSelectionDialog
 
borderLayout1 - Variable in class cct.dialogs.JSolvateShellDialog
 
borderLayout1 - Variable in class cct.dialogs.SaveXYZDialog
 
borderLayout1 - Variable in class cct.dialogs.TrajectoriesManagerPanel
 
borderLayout1 - Variable in class cct.dialogs.TrajectoryAnalysisDialog
 
borderLayout1 - Variable in class cct.gaussian.ui.GaussianInputEditorFrame
 
borderLayout1 - Variable in class cct.gaussian.ui.GaussianInputEditorFrame_AboutBox
 
borderLayout1 - Variable in class cct.gaussian.ui.ManageCubesFrame
 
borderLayout1 - Variable in class cct.gaussian.ui.SimpleG03EditorPanel
 
borderLayout1 - Variable in class cct.grid.TaskProviderPanel
 
borderLayout1 - Variable in class cct.grid.ui.EditScriptDialog
 
borderLayout1 - Variable in class cct.grid.ui.gaussian.SubmitGaussianDialog
 
borderLayout1 - Variable in class cct.grid.ui.gaussian.SubmitGaussianFrame
 
borderLayout1 - Variable in class cct.grid.ui.gaussian.SubmitGaussianFrame_AboutBox
 
borderLayout1 - Variable in class cct.grid.ui.gaussian.SubmitGaussPanel
 
borderLayout1 - Variable in class cct.grid.ui.JobStatusDialog
 
borderLayout1 - Variable in class cct.grid.ui.JobStatusPanel
 
borderLayout1 - Variable in class cct.grid.ui.NoSchedulerPanel
 
borderLayout1 - Variable in class cct.grid.ui.PBS_Panel
 
borderLayout1 - Variable in class cct.grid.ui.PBSPanel
 
borderLayout1 - Variable in class cct.grid.ui.SubmitTaskDialog
 
borderLayout1 - Variable in class cct.j3d.PopupPanel
 
borderLayout1 - Variable in class cct.j3d.SimpleRenderer
 
borderLayout1 - Variable in class cct.j3d.ui.ColorGradientPanel
 
borderLayout1 - Variable in class cct.j3d.ui.GraphicsObjectPropertiesFrame
 
borderLayout1 - Variable in class cct.j3d.ui.VertexObjectsDialog
 
borderLayout1 - Variable in class cct.modelling.ui.JSetupEnergyDialog
 
borderLayout1 - Variable in class cct.modelling.ui.MinimizationProgressDialog
 
borderLayout1 - Variable in class cct.oogl.ui.OOGLViewerFrame
 
borderLayout1 - Variable in class cct.oogl.ui.OOGLViewerFrame_AboutBox
 
borderLayout1 - Variable in class cct.pdb.ui.PDBBankFormPanel
 
borderLayout1 - Variable in class cct.pdb.ui.PDBFormFrame
 
borderLayout1 - Variable in class cct.tools.filebrowser.ConfirmFileOverwriteDialog
 
borderLayout1 - Variable in class cct.tools.filebrowser.ConnectHostDialog
 
borderLayout1 - Variable in class cct.tools.filebrowser.EditHostsDialog
 
borderLayout1 - Variable in class cct.tools.filebrowser.FileBrowserPanel
 
borderLayout1 - Variable in class cct.tools.filebrowser.FileChooserDialog
 
borderLayout1 - Variable in class cct.tools.filebrowser.FilePropertiesDialog
 
borderLayout1 - Variable in class cct.tools.filebrowser.FilePropertiesPanel
 
borderLayout1 - Variable in class cct.tools.filebrowser.FileTransferFrame
 
borderLayout1 - Variable in class cct.tools.filebrowser.FileTransferPanel
 
borderLayout1 - Variable in class cct.tools.filebrowser.JFileBrowserPanel
 
borderLayout1 - Variable in class cct.tools.filebrowser.SFTPBrowserFrame
 
borderLayout1 - Variable in class cct.tools.filebrowser.SFTPFileChooserDialog
 
borderLayout1 - Variable in class cct.tools.filebrowser.TransferProgressDialog
 
borderLayout1 - Variable in class cct.tools.ui.DoubleSpinnerDialog
 
borderLayout1 - Variable in class cct.tools.ui.FontSelectorDialog
 
borderLayout1 - Variable in class cct.tools.ui.FontSelectorPanel
 
borderLayout1 - Variable in class cct.tools.ui.JPEGOptionsDialog
 
borderLayout1 - Variable in class cct.tools.ui.JPEGOptionsPanel
 
borderLayout1 - Variable in class cct.tools.ui.LogPanel
 
borderLayout1 - Variable in class cct.tools.ui.MemoryMonitorFrame
 
borderLayout1 - Variable in class cct.tools.ui.PostMessageDialog
 
borderLayout1 - Variable in class cct.tools.ui.PostMessagePanel
 
borderLayout1 - Variable in class cct.vasp.ui.ReadPoscarDialog
 
borderLayout2 - Variable in class cct.amber.Sander8Frame
 
borderLayout2 - Variable in class cct.amber.Sander8Frame_AboutBox
 
borderLayout2 - Variable in class cct.amber.Sander9Frame
 
borderLayout2 - Variable in class cct.amber.Sander9Frame_AboutBox
 
borderLayout2 - Variable in class cct.amber.Sander9JobPanel
 
borderLayout2 - Variable in class cct.dialogs.AnimationPanel
 
borderLayout2 - Variable in class cct.dialogs.Frame1_AboutBox
 
borderLayout2 - Variable in class cct.dialogs.JAddFragmentDialog
 
borderLayout2 - Variable in class cct.dialogs.JAtomSelectionDialog
 
borderLayout2 - Variable in class cct.dialogs.JModifyAngleDialog
 
borderLayout2 - Variable in class cct.dialogs.JModifyBondDialog
 
borderLayout2 - Variable in class cct.dialogs.JModifyTorsionDialog
 
borderLayout2 - Variable in class cct.dialogs.TrajectoryAnalysisDialog
 
borderLayout2 - Variable in class cct.gaussian.ui.GaussianInputEditorFrame
 
borderLayout2 - Variable in class cct.gaussian.ui.GaussianInputEditorFrame_AboutBox
 
borderLayout2 - Variable in class cct.gaussian.ui.ManageCubesFrame
 
borderLayout2 - Variable in class cct.grid.ui.gaussian.SubmitGaussianDialog
 
borderLayout2 - Variable in class cct.grid.ui.gaussian.SubmitGaussianDialogNew
 
borderLayout2 - Variable in class cct.grid.ui.gaussian.SubmitGaussianFrame
 
borderLayout2 - Variable in class cct.grid.ui.gaussian.SubmitGaussianFrame_AboutBox
 
borderLayout2 - Variable in class cct.grid.ui.SubmitTaskDialog
 
borderLayout2 - Variable in class cct.j3d.ui.ControlColorGradientPanel
 
borderLayout2 - Variable in class cct.j3d.ui.GraphicsObjectPropertiesFrame
 
borderLayout2 - Variable in class cct.j3d.ui.VerticesPropertyPanel
 
borderLayout2 - Variable in class cct.oogl.ui.OOGLViewerFrame_AboutBox
 
borderLayout2 - Variable in class cct.pdb.ui.PDBFormFrame
 
borderLayout2 - Variable in class cct.tools.filebrowser.FilePropertiesPanel
 
borderLayout2 - Variable in class cct.tools.UserPasswordDialog
 
borderLayout3 - Variable in class cct.amber.Sander8Frame
 
borderLayout3 - Variable in class cct.amber.Sander9Frame
 
borderLayout3 - Variable in class cct.dialogs.JAtomSelectionDialog
 
borderLayout3 - Variable in class cct.dialogs.JModifyBondDialog
 
borderLayout3 - Variable in class cct.dialogs.JModifyTorsionDialog
 
borderLayout3 - Variable in class cct.gaussian.ui.ManageCubesFrame
 
borderLayout3 - Variable in class cct.grid.ui.gaussian.SubmitGaussianDialog
 
borderLayout3 - Variable in class cct.grid.ui.gaussian.SubmitGaussianDialogNew
 
borderLayout3 - Variable in class cct.grid.ui.SubmitTaskDialog
 
borderLayout3 - Variable in class cct.j3d.ui.VerticesPropertyPanel
 
borderLayout4 - Variable in class cct.dialogs.JModifyTorsionDialog
 
borderLayout4 - Variable in class cct.j3d.ui.VerticesPropertyPanel
 
borderLayout5 - Variable in class cct.amber.Sander8Frame
 
borderLayout5 - Variable in class cct.amber.Sander9Frame
 
borderLayout5 - Variable in class cct.j3d.ui.VerticesPropertyPanel
 
borderLayout6 - Variable in class cct.amber.Sander8Frame
 
borderLayout6 - Variable in class cct.amber.Sander9Frame
 
borderLayout6 - Variable in class cct.j3d.ui.VerticesPropertyPanel
 
borderLayout7 - Variable in class cct.j3d.ui.VerticesPropertyPanel
 
borderLayout8 - Variable in class cct.j3d.ui.VerticesPropertyPanel
 
boundary_done - Variable in class cct.modelling.Molecule
 
bounds - Variable in class cct.poly.Polygonizer
 
bounds - Variable in class cct.poly.PROCESS
 
branchGroupLabel - Variable in class cct.j3d.LabelNode
 
browseButton - Variable in class cct.dialogs.JSolvateShellDialog
 
browseButton_actionPerformed(ActionEvent) - Method in class cct.dialogs.JSolvateShellDialog
 
browsePoscarButton - Variable in class cct.vasp.ui.ReadPoscarDialog
 
browsePrmtopButton_actionPerformed(ActionEvent) - Method in class cct.amber.ReadPrmtopDialog
 
browsePrmtopButton_actionPerformed(ActionEvent) - Method in class cct.vasp.ui.ReadPoscarDialog
 
browser - Variable in class cct.tools.filebrowser.SFTPFileChooserDialog
 
browserFrame - Variable in class cct.tools.filebrowser.SFTPObject
 
browserIsBusy - Variable in class cct.tools.filebrowser.FileBrowserPanel
 
browsers - Variable in class cct.tools.filebrowser.FileTransferFrame
 
bs_control - Static variable in class cct.awtdialogs.AddNewMethodDialog
 
bugKey - Static variable in enum cct.tools.PostMessageType
 
buildAnalyzeMenu() - Method in class cct.dialogs.JEditorFrame
 
buildComboxBox() - Method in class cct.dialogs.JElementsPanel
 
buildEditMenu() - Method in class cct.dialogs.JEditorFrame
 
builder - Variable in class cct.modelling.CoordBuilder
 
buildTableForMainElements(JPanel) - Method in class cct.dialogs.JElementsPanel
 
Busy - Variable in class cct.tools.filebrowser.SFTPBrowser
 
button1 - Variable in class cct.amber.Sander8Frame_AboutBox
 
button1 - Variable in class cct.amber.Sander9Frame_AboutBox
 
button1 - Variable in class cct.dialogs.Frame1_AboutBox
 
button1 - Variable in class cct.gaussian.ui.GaussianInputEditorFrame_AboutBox
 
button1 - Variable in class cct.grid.ui.gaussian.SubmitGaussianFrame_AboutBox
 
button1 - Variable in class cct.oogl.ui.OOGLViewerFrame_AboutBox
 
buttonGroup1 - Variable in class cct.dialogs.JAtomSelectionDialog
 
buttonGroup1 - Variable in class cct.dialogs.JAtomTypeDialog
 
buttonGroup1 - Variable in class cct.dialogs.JModifyAngleDialog
 
buttonGroup1 - Variable in class cct.dialogs.JModifyTorsionDialog
 
buttonGroup1 - Variable in class cct.dialogs.JSelectionRulePanel
 
buttonGroup1 - Variable in class cct.dialogs.JSelectionTypePanel
 
buttonGroup1 - Variable in class cct.dialogs.JSolvateShellDialog
 
buttonGroup2 - Variable in class cct.dialogs.JAtomSelectionDialog
 
buttonGroup2 - Variable in class cct.dialogs.JModifyAngleDialog
 
buttonGroup2 - Variable in class cct.dialogs.JModifyTorsionDialog
 
buttonGroup3 - Variable in class cct.dialogs.JModifyAngleDialog
 
buttonPanel - Variable in class cct.dialogs.JAtomSelectionDialog
 
buttonPanel - Variable in class cct.dialogs.JModifyAngleDialog
 
buttonPanel - Variable in class cct.dialogs.JModifyTorsionDialog
 
buttonPanel - Variable in class cct.dialogs.JSelectAtomTypesDialog
 
buttonPanel - Variable in class cct.dialogs.JSelectSubstructureDialog
 
buttonPanel - Variable in class cct.dialogs.JSolvateShellDialog
 
buttonPanel - Variable in class cct.dialogs.TrajectoryAnalysisDialog
 
buttonPanel - Variable in class cct.gaussian.ui.SaveG03GJFDialog
 
ButtonPanel - Variable in class cct.grid.ui.gaussian.SubmitGaussianDialog
 
ButtonPanel - Variable in class cct.grid.ui.SubmitTaskDialog
 
buttonPanel - Variable in class cct.j3d.ui.GraphicsObjectPropertiesFrame
 
buttonPanel - Variable in class cct.j3d.ui.VertexObjectsDialog
 
buttonPanel - Variable in class cct.tools.filebrowser.ConnectHostDialog
 
buttonPanel - Variable in class cct.tools.filebrowser.FilePropertiesDialog
 
buttonPanel - Variable in class cct.tools.UserPasswordDialog
 
buttonPressed - Variable in class cct.tools.filebrowser.ConfirmFileOverwriteDialog
 
buttons - Variable in class cct.dialogs.JAtomTypesPanel
 
Buttons - Variable in class cct.dialogs.JElementsPanel
 
buttons - Variable in class cct.dialogs.JModifyAtomDialog
 
buttonsPanel - Variable in class cct.dialogs.JModifyBondDialog
 
buttonsPanel - Variable in class cct.dialogs.JSelectMonomersDialog
 
buttonsPanel - Variable in class cct.tools.filebrowser.ConfirmFileOverwriteDialog
 
buttonsPanel - Variable in class cct.tools.ui.PostMessageDialog
 
buttonsPanel - Variable in class cct.vasp.ui.ReadPoscarDialog
 
buttonStore - Variable in class cct.dialogs.JElementsPanel
 

C

C - Variable in class cct.modelling.NonbondedPair
 
c - Variable in class cct.tools.Crystal
 
c3dMap - Static variable in class cct.j3d.QueryProperties
 
ca - Variable in class cct.j3d.AtomNode
 
calcAbsoluteCoordinates(ArrayList<GULPAtom>, double[][]) - Method in class cct.gulp.Gulp
 
calcAbsoluteCoordinates(ArrayList<SiestaInput.SiestaAtom>, double[][]) - Method in class cct.siesta.SiestaInput
 
CalcButton - Variable in class cct.modelling.ui.JSetupEnergyDialog
 
CalcButton_actionAdapter - Class in cct.modelling.ui
 
CalcButton_actionAdapter(JSetupEnergyDialog) - Constructor for class cct.modelling.ui.CalcButton_actionAdapter
 
CalcButton_actionPerformed(ActionEvent) - Method in class cct.modelling.ui.JSetupEnergyDialog
 
calcPropertyOnSurface(Object, GaussianCube, int) - Static method in class cct.gaussian.java3d.GaussianJava3dFactory
 
calcPropertyOnSurface(BranchGroup, ImplicitFunctionInterface) - Static method in class cct.gaussian.java3d.GaussianJava3dFactory
 
calcPropertyOnSurface(GraphicsObjectInterface, GaussianCube, int) - Static method in class cct.gaussian.java3d.GaussianJava3dFactory
 
calculate14Energy - Variable in class cct.modelling.MolecularEnergy
 
Calculate_1_4 - Variable in class cct.modelling.FFMolecule
 
calculateAngleBendEnergy - Variable in class cct.modelling.MolecularEnergy
 
calculateBondStretchEnergy - Variable in class cct.modelling.MolecularEnergy
 
calculateElectrostatics - Static variable in class cct.sff.SimpleForceField
 
calculateElsCheckBox - Variable in class cct.modelling.ui.JSetupEnergyDialog
 
calculateElsCheckBox_itemStateChanged(ItemEvent) - Method in class cct.modelling.ui.JSetupEnergyDialog
 
calculateEnergy(boolean) - Method in class cct.modelling.MolecularEnergy
 
calculateIntensity(double[], double[], double, VIBRATIONAL_SPECTRUM_CURVE) - Static method in class cct.modelling.Frequencies
Calculates intensity at point x
calculateNonbondEnergy - Variable in class cct.modelling.MolecularEnergy
 
calculateTorsionEnergy - Variable in class cct.modelling.MolecularEnergy
 
cameraLocation - Variable in class cct.povray.Povray
 
Cancel - Variable in class cct.awtdialogs.AtomLabelsDialog
 
Cancel - Variable in class cct.awtdialogs.AtomTypeDialog
 
Cancel - Variable in class cct.awtdialogs.SimpleAtomSelectionDialog
 
Cancel - Variable in class cct.awtdialogs.SingleChoiceDialog
 
Cancel - Variable in class cct.dialogs.JAtomSelectionDialog
 
Cancel - Variable in class cct.dialogs.JAtomTypeDialog
 
Cancel - Variable in class cct.dialogs.JChoiceDialog
 
Cancel - Variable in class cct.dialogs.JModifyAtomDialog
 
Cancel - Variable in class cct.dialogs.JModifyBondDialog
 
Cancel - Variable in class cct.dialogs.JSelectAtomTypesDialog
 
Cancel - Variable in class cct.dialogs.JSelectMonomersDialog
 
Cancel - Variable in class cct.dialogs.JSelectSubstructureDialog
 
Cancel - Variable in class cct.dialogs.JSimpleAtomSelectionDialog
 
Cancel - Variable in class cct.dialogs.JThreeButtonsPanel
 
cancel() - Method in class cct.grid.ui.gaussian.SubmitGaussianDialog.JobSubProgress
 
cancel() - Method in class cct.grid.ui.gaussian.SubmitGaussianDialog.Task
 
cancel() - Method in class cct.grid.ui.gaussian.SubmitGaussianDialogNew.JobSubProgress
 
cancel() - Method in class cct.grid.ui.gaussian.SubmitGaussianDialogNew.Task
 
cancel() - Method in class cct.grid.ui.JobStatusDialog.Task
 
cancel() - Method in class cct.grid.ui.SubmitTaskDialog.JobSubProgress
 
cancel() - Method in class cct.grid.ui.SubmitTaskDialog.Task
 
cancel - Variable in class cct.grid.ui.ThreadExec
 
cancel() - Method in class cct.grid.ui.ThreadExec
 
CANCEL - Static variable in class cct.tools.filebrowser.ConfirmFileOverwriteDialog
 
CANCEL - Static variable in class cct.tools.filebrowser.ConnectHostDialog
 
CANCEL - Static variable in class cct.tools.filebrowser.FileChooserDialog
 
CANCEL - Static variable in class cct.tools.filebrowser.FilePropertiesDialog
 
Cancel_actionPerformed(ActionEvent) - Method in class cct.dialogs.JAtomSelectionDialog
 
Cancel_actionPerformed(ActionEvent) - Method in class cct.dialogs.JModifyAtomDialog
 
Cancel_actionPerformed(ActionEvent) - Method in class cct.dialogs.JModifyBondDialog
 
Cancel_actionPerformed(ActionEvent) - Method in class cct.dialogs.JSelectAtomTypesDialog
 
Cancel_actionPerformed(ActionEvent) - Method in class cct.dialogs.JSelectMonomersDialog
 
Cancel_actionPerformed(ActionEvent) - Method in class cct.dialogs.JSelectSubstructureDialog
 
Cancel_Button - Variable in class cct.grid.ui.gaussian.SubmitGaussianDialog
 
Cancel_Button - Variable in class cct.grid.ui.SubmitTaskDialog
 
Cancel_Button_actionPerformed(ActionEvent) - Method in class cct.grid.ui.gaussian.SubmitGaussianDialog
 
Cancel_Button_actionPerformed(ActionEvent) - Method in class cct.grid.ui.gaussian.SubmitGaussianDialogNew
 
Cancel_Button_actionPerformed(ActionEvent) - Method in class cct.grid.ui.SubmitTaskDialog
 
cancelButton - Variable in class cct.dialogs.JAddMoleculeDialog
 
cancelButton - Variable in class cct.dialogs.SaveXYZDialog
 
cancelButton - Variable in class cct.gaussian.ui.SaveG03GJFDialog
 
cancelButton - Variable in class cct.grid.ui.EditScriptDialog
 
cancelButton - Variable in class cct.grid.ui.ProgressDialog
 
cancelButton - Variable in class cct.j3d.ui.VertexObjectsDialog
 
cancelButton - Variable in class cct.modelling.ui.JSetupEnergyDialog
 
cancelButton - Variable in class cct.modelling.ui.MinimizationProgressDialog
 
cancelButton - Variable in class cct.pdb.ui.PDBFormFrame
 
cancelButton - Variable in class cct.tools.filebrowser.ConfirmFileOverwriteDialog
 
cancelButton - Variable in class cct.tools.filebrowser.ConnectHostDialog
 
cancelButton - Variable in class cct.tools.filebrowser.EditHostsDialog
 
cancelButton - Variable in class cct.tools.filebrowser.FileChooserDialog
 
cancelButton - Variable in class cct.tools.filebrowser.SFTPFileChooserDialog
 
cancelButton - Variable in class cct.tools.filebrowser.TransferProgressDialog
 
cancelButton - Variable in class cct.tools.ui.DoubleSpinnerDialog
 
cancelButton - Variable in class cct.tools.ui.FontSelectorDialog
 
cancelButton - Variable in class cct.tools.ui.JPEGOptionsDialog
 
cancelButton - Variable in class cct.tools.ui.PostMessageDialog
 
cancelButton - Variable in class cct.tools.UserPasswordDialog
 
cancelButton - Variable in class cct.vasp.ui.ReadPoscarDialog
 
cancelButton_actionPerformed(ActionEvent) - Method in class cct.amber.ReadPrmtopDialog
 
cancelButton_actionPerformed(ActionEvent) - Method in class cct.dialogs.AddMoleculeDialog
 
cancelButton_actionPerformed(ActionEvent) - Method in class cct.dialogs.JAddMoleculeDialog
 
cancelButton_actionPerformed(ActionEvent) - Method in class cct.dialogs.MoleculeSelectorDialog
 
cancelButton_actionPerformed(ActionEvent) - Method in class cct.dialogs.SaveXYZDialog
 
cancelButton_actionPerformed(ActionEvent) - Method in class cct.dialogs.SelectPropShowDialog
 
cancelButton_actionPerformed(ActionEvent) - Method in class cct.gaussian.ui.SaveG03GJFDialog
 
cancelButton_actionPerformed(ActionEvent) - Method in class cct.j3d.ui.VertexObjectsDialog
 
cancelButton_actionPerformed(ActionEvent) - Method in class cct.modelling.ui.EditAndPasteCoordFrame
 
cancelButton_actionPerformed(ActionEvent) - Method in class cct.modelling.ui.EditAndSaveCoordDialog
 
cancelButton_actionPerformed(ActionEvent) - Method in class cct.modelling.ui.JSetupEnergyDialog
 
cancelButton_actionPerformed(ActionEvent) - Method in class cct.siesta.ui.SaveSiestaInputDialog
 
cancelButton_actionPerformed(ActionEvent) - Method in class cct.tools.filebrowser.EditHostsDialog
 
cancelButton_actionPerformed(ActionEvent) - Method in class cct.tools.filebrowser.SFTPFileChooserDialog
 
cancelButton_actionPerformed(ActionEvent) - Method in class cct.tools.ui.JPEGOptionsDialog
 
cancelButton_actionPerformed(ActionEvent) - Method in class cct.tools.UserPasswordDialog
 
cancelButton_actionPerformed(ActionEvent) - Method in class cct.vasp.ui.ReadPoscarDialog
 
cancelButton_keyPressed(KeyEvent) - Method in class cct.tools.UserPasswordDialog
 
cancelMinimization() - Method in class cct.modelling.BackgroundMinimizer
 
cancelSelection() - Method in class cct.j3d.Java3dUniverse
 
cancelSelection() - Method in class cct.modelling.MolecularEditor
 
cancelTranfer() - Method in class cct.tools.filebrowser.SFTPBrowser.FileTranferWorker
Cancels file transfer
cancelTranfer() - Method in class cct.tools.filebrowser.SFTPFileChooserDialog.FileTranferWorker
 
cancelTreeSelection() - Method in interface cct.interfaces.TreeSelectorInterface
 
cancelTreeSelection() - Method in class cct.j3d.Java3dUniverse
 
candidateModification - Variable in class cct.tools.filebrowser.ConfirmFileOverwriteDialog
 
candidateSize - Variable in class cct.tools.filebrowser.ConfirmFileOverwriteDialog
 
canSaveForThisPlatform - Static variable in class cct.tools.ImageTools
 
canvas - Variable in class cct.applets.viewer
 
canvas3D - Variable in class cct.applets.viewer
 
canvas3D - Variable in class cct.dialogs.Frame1
 
canvas3D - Variable in class cct.j3d.GroupToVRML
 
canvas3D - Variable in class cct.j3d.Java3dUniverse
 
canvas3D - Variable in class cct.j3d.PovrayJava3d
 
canvas3D - Variable in class cct.j3d.SimpleRenderer
 
cardLayout1 - Variable in class cct.amber.Sander8Frame
 
cardLayout1 - Variable in class cct.amber.Sander9Frame
 
cardLayout1 - Variable in class cct.gaussian.ui.GaussianInputEditorFrame
 
cardLayout1 - Variable in class cct.grid.TaskProviderPanel
 
cardLayout1 - Variable in class cct.grid.ui.gaussian.SubmitGaussianDialog
 
cardLayout1 - Variable in class cct.grid.ui.gaussian.SubmitGaussianDialogNew
 
cardLayout1 - Variable in class cct.grid.ui.SubmitTaskDialog
 
cardLayout2 - Variable in class cct.grid.ui.SubmitTaskDialog
 
cardPanel - Variable in class cct.gaussian.ui.GaussianInputEditorFrame
 
cardPanel - Variable in class cct.grid.ui.gaussian.SubmitGaussianDialog
 
cardPanel - Variable in class cct.grid.ui.gaussian.SubmitGaussianDialogNew
 
cardPanel - Variable in class cct.grid.ui.SubmitTaskDialog
 
cardsPanel - Variable in class cct.amber.Sander8Frame
 
cardsPanel - Variable in class cct.amber.Sander9Frame
 
caretUpdate(CaretEvent) - Method in class cct.tools.ui.LogPanel_jTextArea1_caretAdapter
 
caretUpdateAdaptor - Variable in class cct.tools.ui.LogPanel
 
CART - Static variable in class cct.gamess.Gamess
 
Cartesian - Variable in class cct.adf.ADFAtom
 
cartesian - Variable in class cct.mopac.MopacAtom
 
CARTESIAN_COORDINATES - Static variable in class cct.vasp.Vasp
 
cartesianCoords - Variable in class cct.qchem.QChem
 
cartesians - Variable in class cct.gaussian.GaussianMolecule
 
Cartesians - Variable in class cct.gulp.GULPAtom
 
caseSensitive - Variable in class cct.math.MathExpressionParser
 
CCSDEnergyProperty - Static variable in interface cct.interfaces.MoleculeInterface
 
CCSDTEnergyProperty - Static variable in interface cct.interfaces.MoleculeInterface
 
cct - package cct
 
cct.adf - package cct.adf
Begin with a one sentence summary about this package.
cct.amber - package cct.amber
Package Specification
cct.applets - package cct.applets
 
cct.awtdialogs - package cct.awtdialogs
 
cct.chart - package cct.chart
 
cct.chart.jfreechart - package cct.chart.jfreechart
 
cct.cprocessor - package cct.cprocessor
 
cct.database - package cct.database
 
cct.dialogs - package cct.dialogs
Begin with a one sentence summary about this package.
cct.gamess - package cct.gamess
 
cct.gaussian - package cct.gaussian
 
cct.gaussian.java3d - package cct.gaussian.java3d
 
cct.gaussian.ui - package cct.gaussian.ui
 
cct.grid - package cct.grid
 
cct.grid.ui - package cct.grid.ui
 
cct.grid.ui.gaussian - package cct.grid.ui.gaussian
 
cct.gromacs - package cct.gromacs
 
cct.gulp - package cct.gulp
 
cct.help - package cct.help
 
cct.interfaces - package cct.interfaces
 
cct.j3d - package cct.j3d
 
cct.j3d.ui - package cct.j3d.ui
 
cct.math - package cct.math
 
cct.math.polyg - package cct.math.polyg
 
cct.math.polyg.java3d - package cct.math.polyg.java3d
 
cct.mdl - package cct.mdl
 
cct.modelling - package cct.modelling
 
cct.modelling.ui - package cct.modelling.ui
 
cct.mopac - package cct.mopac
 
cct.oogl - package cct.oogl
 
cct.oogl.java3d - package cct.oogl.java3d
 
cct.oogl.ui - package cct.oogl.ui
 
cct.pdb - package cct.pdb
 
cct.pdb.ui - package cct.pdb.ui
 
cct.poly - package cct.poly
 
cct.povray - package cct.povray
 
cct.qchem - package cct.qchem
 
cct.resources - package cct.resources
 
cct.resources.images - package cct.resources.images
 
cct.sff - package cct.sff
 
cct.siesta - package cct.siesta
 
cct.siesta.ui - package cct.siesta.ui
 
cct.ssh - package cct.ssh
 
cct.tools - package cct.tools
 
cct.tools.filebrowser - package cct.tools.filebrowser
Begin with a one sentence summary about this package.
cct.tools.ui - package cct.tools.ui
 
cct.tripos - package cct.tripos
 
cct.vasp - package cct.vasp
 
cct.vasp.ui - package cct.vasp.ui
 
cct.vecmath - package cct.vecmath
 
CCT_ATOM_TYPE - Static variable in interface cct.interfaces.AtomInterface
 
CCT_DIRECTORY - Static variable in class cct.tools.Utils
 
CCT_PROPERTY_FILE - Static variable in class cct.GlobalSettings
 
CCT_PROVIDER_PROPERTY_FILE - Static variable in class cct.grid.TaskProvider
 
CCT_TAG - Static variable in class cct.tools.CCTParserEnum
 
cctAtomType - Variable in class cct.pdb.PDBAtom
 
CCTAtomTypes - Class in cct.modelling
Title:
CCTAtomTypes() - Constructor for class cct.modelling.CCTAtomTypes
 
CCTAtomTypes(String) - Constructor for class cct.modelling.CCTAtomTypes
 
cctFileFormat - Static variable in class cct.modelling.MolecularFileFormats
 
CCTParser - Class in cct.tools
Title:
CCTParser(MoleculeInterface) - Constructor for class cct.tools.CCTParser
 
CCTParserEnum - Class in cct.tools
Title:
cd(String) - Method in interface cct.interfaces.FileBrowserInterface
 
cd(String) - Method in class cct.tools.filebrowser.LocalFileBrowser
 
cd(String) - Method in class cct.tools.filebrowser.SFTPBrowser
Changes the working directory on the remote server
CELL_PARAMETER - Enum in cct.modelling
Title: Computational Chemistry Tookit
CellViewManager - Class in cct.j3d
Title: Computational Chemistry Tookit
CellViewManager(Java3dUniverse) - Constructor for class cct.j3d.CellViewManager
 
CellViewManagerInterface - Interface in cct.interfaces
Title: Computational Chemistry Tookit
center - Variable in class cct.j3d.LabelNode
 
centerContentsInCell(double[][], int) - Static method in class cct.siesta.SiestaInput
 
centerContentsInCell() - Method in class cct.siesta.SiestaInput
 
CENTERELEMENT - Class in cct.poly
Title: Molecular Structure Viewer/Editor
CENTERELEMENT(int, int, int) - Constructor for class cct.poly.CENTERELEMENT
 
CENTERLIST - Class in cct.poly
Title: Molecular Structure Viewer/Editor
CENTERLIST() - Constructor for class cct.poly.CENTERLIST
 
CENTERLIST - Variable in class cct.poly.Polygonizer
 
centerMolButton_actionPerformed(ActionEvent) - Method in class cct.siesta.ui.SiestaPanel
 
centerMolecule(Object) - Method in interface cct.cprocessor.MolProcessorInterface
 
centerMolecule(float, float, float) - Method in interface cct.interfaces.MoleculeInterface
 
centerMolecule(MoleculeInterface, float, float, float) - Static method in class cct.j3d.Java3dUniverse
Translates geometric center of a molecule to a point with coordinates x,y,z
centerMolecule(float, float, float) - Method in class cct.j3d.Java3dUniverse
 
centerMolecule(Object) - Method in class cct.j3d.ScriptProcessorWrapper
 
centerMolecule(float, float, float) - Method in class cct.modelling.Molecule
 
centers - Variable in class cct.poly.PROCESS
 
centerScene() - Method in class cct.j3d.Java3dUniverse
 
centerSceneOnScreen() - Method in class cct.j3d.Java3dUniverse
 
centralPanel - Variable in class cct.dialogs.JModifyTorsionDialog
 
centralPanel - Variable in class cct.gaussian.ui.SimpleG03EditorPanel
 
centralPanel - Variable in class cct.tools.filebrowser.FilePropertiesPanel
 
changeAngle - Variable in class cct.dialogs.JModifyAngleDialog
 
changeAngle - Variable in class cct.dialogs.JModifyTorsionDialog
 
changeAngle_stateChanged(ChangeEvent) - Method in class cct.dialogs.JModifyAngleDialog
 
changeAngle_stateChanged(ChangeEvent) - Method in class cct.dialogs.JModifyTorsionDialog
 
changeAngleBetweenSelectedAtoms(float, int, int, int) - Method in class cct.j3d.Java3dUniverse
 
changeAngleBetweenSelectedAtoms(float, int, int, int) - Method in class cct.modelling.MolecularEditor
 
changeAnglePanel - Variable in class cct.dialogs.JModifyAngleDialog
 
changeAtomColorScheme(ActionEvent) - Method in class cct.dialogs.JEditorFrame
 
changeAtomType(ActionEvent) - Method in class cct.dialogs.JAtomTypeDialog
 
changeBondPanel - Variable in class cct.dialogs.JModifyBondDialog
 
changeDihedralForSelectedAtoms(float, int, int) - Method in class cct.j3d.Java3dUniverse
 
changeDihedralForSelectedAtoms(float, int, int) - Method in class cct.modelling.MolecularEditor
 
changeDistanceBetweenSelectedAtoms(float, int, int) - Method in class cct.j3d.Java3dUniverse
Status: 0 - Fixed, 1 - translate Atom; 2 - translate group
changeLookAndFeel(ActionEvent) - Method in class cct.dialogs.JEditorFrame
 
changeMoleculeName(String, String) - Method in class cct.database.new_SQLChemistryDatabase
 
changeMoleculeName(String, String) - Method in class cct.database.SQLChemistryDatabase
 
characters(char[], int, int) - Method in class cct.grid.ParseCheckpointFile.HandleSAXEvents
 
characters(char[], int, int) - Method in class cct.tools.CCTParser
 
characters(char[], int, int) - Method in class cct.tools.FragmentDictionaryParser
 
characters(char[], int, int) - Method in class cct.vasp.VasprunXML
 
Charge - Variable in class cct.awtdialogs.AddNewMoleculeDialog
 
Charge - Variable in class cct.awtdialogs.GaussianCalcSetupDialog
 
charge - Variable in class cct.gaussian.GaussianAtom
 
Charge - Variable in class cct.gaussian.GaussianMolecule
 
charge - Variable in class cct.mopac.MopacAtom
 
chargeAndMultiplicity - Variable in class cct.gaussian.GaussianMolecule
 
ChargeProperty - Static variable in interface cct.interfaces.MoleculeInterface
 
CHARGES_TO_KCAL_AMBER - Static variable in class cct.amber.AmberPrmtop
 
chargeSection - Variable in class cct.gaussian.GaussianMolecule
 
chartChanged(ChartChangeEvent) - Method in class cct.chart.jfreechart.JFreeChartPanel
 
ChartFrame - Class in cct.chart
Title: Computational Chemistry Toolkit
ChartFrame() - Constructor for class cct.chart.ChartFrame
 
ChartInterface - Interface in cct.chart
Title: Computational Chemistry Toolkit
chartProgress(ChartProgressEvent) - Method in class cct.chart.jfreechart.JFreeChartPanel
 
ChartReference - Class in cct.chart
Title: Computational Chemistry Tookit
chartSlider_stateChanged(ChangeEvent) - Method in class cct.chart.jfreechart.JFreeChartPanel
 
charWidth - Variable in class cct.j3d.ui.ColorGradientPanel
 
checkAtomicSymbol(String) - Static method in class cct.modelling.ChemicalElements
 
checkboxesPanel - Variable in class cct.dialogs.JModifyBondDialog
 
checkConnection() - Method in class cct.ssh.SSHPanel
 
checkDataIntegrity() - Method in class cct.amber.AmberSubmitDialog
 
checkedToolTips - Variable in class cct.tools.filebrowser.PermissionsPanel
 
CheckPoint - Class in cct.grid
Title: Molecular Structure Viewer/Editor
CheckPoint() - Constructor for class cct.grid.CheckPoint
 
CheckPoint(String, String) - Constructor for class cct.grid.CheckPoint
 
checkPoint - Variable in class cct.grid.ParseCheckpointFile
 
CHECKPOINT_FILE - Static variable in class cct.grid.ParseCheckpointFile
 
checkPointFile - Static variable in class cct.grid.ParseCheckpointFile
 
CheckPointInterface - Interface in cct.grid
Title: Molecular Structure Viewer/Editor
CheckPointStatus - Class in cct.grid.ui
Title: Molecular Structure Viewer/Editor
CheckPointStatus() - Constructor for class cct.grid.ui.CheckPointStatus
 
CheckPointStatus.FTransferWithProgress - Class in cct.grid.ui
 
CheckPointStatus.FTransferWithProgress(String, String) - Constructor for class cct.grid.ui.CheckPointStatus.FTransferWithProgress
 
ChemicalElements - Class in cct.modelling
Title: ChemicalElements
ChemicalElements() - Constructor for class cct.modelling.ChemicalElements
 
ChemicalElementsColors - Class in cct.j3d
Title:
ChemicalElementsColors() - Constructor for class cct.j3d.ChemicalElementsColors
 
ChemicalSpeciesLabel - Class in cct.siesta
Title: Computational Chemistry Tookit
ChemicalSpeciesLabel(Integer, int, String) - Constructor for class cct.siesta.ChemicalSpeciesLabel
 
CHEMISTRY_FILE_FORMAT - Enum in cct.modelling
Title: Computational Chemistry Tookit
chemistryDatabase - Variable in class cct.modelling.MolecularEditor
 
ChemistryDatabaseDialog - Class in cct.database
Title:
ChemistryDatabaseDialog(Java3dUniverse, SQLChemistryDatabase, String, boolean) - Constructor for class cct.database.ChemistryDatabaseDialog
 
childFinished(Object) - Method in class cct.dialogs.JEditorFrame
 
childFinished(Object) - Method in interface cct.interfaces.ParentInterface
To inform parent that its child process finished its execution
choice - Variable in class cct.awtdialogs.SingleChoiceDialog
 
Choose_color - Variable in class cct.dialogs.JModifyAtomPanel
 
Choose_color_actionPerformed(ActionEvent) - Method in class cct.dialogs.JModifyAtomPanel
 
chooseAtomType - Variable in class cct.j3d.Java3dUniverse
 
chooseFileDialog(String, String, int) - Method in class cct.dialogs.JEditorFrame
 
chooseFileDialog(FileFilter[], Component, String, String, int) - Static method in class cct.tools.IOUtils
 
chooser - Variable in class cct.j3d.GroupToVRML
 
chooser - Variable in class cct.povray.Povray
 
chooser - Variable in class cct.tools.GeomFormat
 
chooser - Variable in class cct.vasp.ui.ReadPoscarDialog
 
CHRG - Variable in class cct.amber.AmberPrepAtom
 
cidetSection - Static variable in class cct.gamess.Gamess
 
cidrtSection - Static variable in class cct.gamess.Gamess
 
ciinpSection - Static variable in class cct.gamess.Gamess
 
cisortSection - Static variable in class cct.gamess.Gamess
 
cleanupMess() - Method in class cct.modelling.ui.VibrationsControlPanel
 
Clear - Variable in class cct.dialogs.JAtomSelectionDialog
 
Clear - Variable in class cct.dialogs.JQuickSelectionPanel
 
clear() - Method in class cct.tools.FortranNamelist
 
Clear_actionPerformed(ActionEvent) - Method in class cct.dialogs.JAtomSelectionDialog
 
clearButton - Variable in class cct.tools.ui.LogPanel
 
clearChoices() - Method in class cct.awtdialogs.SingleChoiceDialog
 
clearElements() - Method in class cct.awtdialogs.AtomTypeDialog
 
clearItems() - Method in class cct.awtdialogs.GeometrySelectDialog
 
clearSelection() - Method in class cct.j3d.Java3dUniverse
 
clearSelection() - Method in class cct.modelling.MolecularEditor
 
clientInterface - Variable in class cct.tools.filebrowser.SFTPObject
 
clientProgram - Variable in class cct.grid.ui.PBSPanel
 
ClientProgram - Variable in class cct.grid.ui.SubmitTaskDialog
 
ClientProgramInterface - Interface in cct.grid
Title:
clone() - Method in class cct.j3d.AtomNode
 
clone() - Method in class cct.j3d.BondNode
 
clone() - Method in class cct.modelling.gAtom
 
clone() - Method in class cct.modelling.vAtom
 
cloneMaterial(Material) - Static method in class cct.j3d.Java3dUniverse
Clones material
cloneMolecule(MoleculeInterface) - Static method in class cct.modelling.Molecule
Duplicates molecule
close() - Method in class cct.tools.ui.JTextAreaOutputStream
Has no effect
closeConnection() - Method in class cct.database.SQLDatabaseAccess
 
CLUSTER_ADDRESS - Static variable in class cct.grid.JobDescription
 
cntrl - Variable in class cct.amber.Sander8Frame
 
cntrl - Variable in class cct.amber.Sander9Frame
 
cntrl_namelist - Variable in class cct.amber.Sander8JobControl
 
cntrl_namelist - Variable in class cct.amber.Sander9JobControl
 
Color - Class in cct.oogl
Title:
Color() - Constructor for class cct.oogl.Color
 
Color(float, float, float, float) - Constructor for class cct.oogl.Color
 
color3fPalette - Class in cct.j3d
 
color3fPalette() - Constructor for class cct.j3d.color3fPalette
 
COLOR_SCHEME - Static variable in interface cct.interfaces.BondInterface
 
colorBuffer - Variable in class cct.dialogs.JModifyAtomPanel
 
colorChooser - Variable in class cct.tools.ui.FontSelectorPanel
 
ColorGradientPanel - Class in cct.j3d.ui
Title: Computational Chemistry Tookit
ColorGradientPanel() - Constructor for class cct.j3d.ui.ColorGradientPanel
 
ColorGradientPanel(float, float, ArrayList<Color3f>) - Constructor for class cct.j3d.ui.ColorGradientPanel
 
colorMap - Static variable in class cct.vasp.Vasp
 
ColorRangeScheme - Class in cct.j3d
Title: Computational Chemistry Tookit
ColorRangeScheme(float, float) - Constructor for class cct.j3d.ColorRangeScheme
 
colors - Variable in class cct.chart.jfreechart.JFreeChartPanel
 
Colors - Variable in class cct.j3d.color3fPalette
 
Colors - Variable in class cct.j3d.ui.ColorGradientPanel
 
colors - Variable in class cct.oogl.OOGL
 
colors - Variable in class cct.tools.OOGL
 
Colors - Variable in class cct.vecmath.MeshObject
 
colorScheme - Variable in class cct.j3d.BondNode
 
colorScheme - Static variable in class cct.j3d.ChemicalElementsColors
 
COLUMN_COUNT - Static variable in interface cct.database.DatabaseAccess
 
COLUMN_NAME - Static variable in interface cct.database.DatabaseAccess
 
COLUMN_TYPE - Static variable in interface cct.database.DatabaseAccess
 
columnNames - Variable in class cct.grid.ui.JobStatusTableModel
 
columnNames - Variable in class cct.tools.filebrowser.FileBrowserTableModel
 
columnNames - Variable in class cct.tools.filebrowser.SFTPBrowser
 
comboBoxAdjusting - Variable in class cct.amber.Sander8Frame
 
comboBoxAdjusting - Variable in class cct.amber.Sander9Frame
 
comboboxPanel - Variable in class cct.dialogs.JElementsPanel
 
comboPanel - Variable in class cct.grid.ui.gaussian.SubmitGaussianDialog
 
comboPanel - Variable in class cct.grid.ui.gaussian.SubmitGaussianDialogNew
 
comboPanel - Variable in class cct.grid.ui.SubmitTaskDialog
 
commandArguments - Variable in class cct.cprocessor.CommandProcessor
 
CommandObject - Enum in cct.cprocessor
Title: Molecular Structure Viewer/Editor
commandObject - Variable in class cct.cprocessor.CommandProcessor
 
CommandProcessor - Class in cct.cprocessor
 
CommandProcessor(MolProcessorInterface) - Constructor for class cct.cprocessor.CommandProcessor
 
commandProcessor - Variable in class cct.cprocessor.MacroProcessor
 
Commands - Enum in cct.cprocessor
Title: Molecular Structure Viewer/Editor
comment - Variable in class cct.mopac.MopacAtom
 
Comment - Variable in class cct.vasp.Vasp
 
Comment_1 - Variable in class cct.mopac.Mopac
 
Comment_2 - Variable in class cct.mopac.Mopac
 
comments - Variable in class cct.amber.Sander8Frame_AboutBox
 
comments - Variable in class cct.amber.Sander9Frame_AboutBox
 
comments - Variable in class cct.dialogs.Frame1_AboutBox
 
comments - Variable in class cct.gaussian.ui.GaussianInputEditorFrame_AboutBox
 
comments - Variable in class cct.grid.ui.gaussian.SubmitGaussianFrame_AboutBox
 
comments - Variable in class cct.oogl.ui.OOGLViewerFrame_AboutBox
 
commentSection - Static variable in class cct.gamess.Gamess
 
commentSection - Static variable in class cct.qchem.QChem
 
commonReadFormatDescription - Static variable in class cct.modelling.MolecularFileFormats
 
commonReadFormats - Static variable in class cct.modelling.MolecularFileFormats
 
comObject - Variable in enum cct.cprocessor.AddCommandObjects
 
comObject - Variable in enum cct.cprocessor.SelectCommandObjects
 
COMP_Label - Variable in class cct.amber.Sander8Frame
 
COMP_Label - Variable in class cct.amber.Sander9Frame
 
COMP_Label_mouseEntered(MouseEvent) - Method in class cct.amber.Sander8Frame
 
COMP_Label_mouseEntered(MouseEvent) - Method in class cct.amber.Sander9Frame
 
COMP_TextField - Variable in class cct.amber.Sander8Frame
 
COMP_TextField - Variable in class cct.amber.Sander9Frame
 
COMPARABLE_COMAPRATOR - Static variable in class cct.tools.filebrowser.TableSorter
 
compare(Object, Object) - Method in class cct.modelling.CCTAtomTypes
 
compare(Object, Object) - Method in class cct.modelling.FormatManager.ParserComparator
Returns a negative integer, zero, or a positive integer as the first argument is less than, equal to, or greater than the second
compareTo(Object) - Method in class cct.modelling.BasicFragment
 
compareTo(String) - Method in class cct.modelling.BasicFragment
 
compareTo(Object) - Method in class cct.tools.CCTParserEnum
 
compareTo(String) - Method in class cct.tools.CCTParserEnum
 
compareTo(Object) - Method in class cct.tools.filebrowser.FileName
 
compareTo(Object) - Method in class cct.tools.filebrowser.FileSize
 
compareToIgnoreCase(String) - Method in class cct.modelling.BasicFragment
 
compareToIgnoreCase(String) - Method in class cct.tools.CCTParserEnum
 
compiledCommands - Variable in class cct.cprocessor.CommandProcessor
 
completed() - Method in class cct.tools.filebrowser.SFTPBrowser.FileTranferWorker
 
completed() - Method in class cct.tools.filebrowser.SFTPFileChooserDialog.FileTranferWorker
 
completionMessages - Static variable in class cct.math.DFPMin
 
component - Variable in class cct.modelling.BackgroundMinimizer
 
compoundPosition - Variable in class cct.mdl.SDCompound
 
Compounds - Variable in class cct.mdl.SDF
 
Compressibility - Variable in class cct.modelling.JobControl
 
computerTag - Static variable in interface cct.grid.CheckPointInterface
 
conditions - Variable in class cct.j3d.MousePickingHandler
 
CONFIRM - Static variable in class cct.tools.filebrowser.FileChooserDialog
 
confirmButton - Variable in class cct.tools.filebrowser.FileChooserDialog
 
confirmChanges() - Method in class cct.j3d.Java3dUniverse
 
confirmChanges() - Method in class cct.modelling.MolecularEditor
 
ConfirmFileOverwriteDialog - Class in cct.tools.filebrowser
Title: Computational Chemistry Tookit
ConfirmFileOverwriteDialog(Frame, String) - Constructor for class cct.tools.filebrowser.ConfirmFileOverwriteDialog
 
ConfirmFileOverwriteDialog() - Constructor for class cct.tools.filebrowser.ConfirmFileOverwriteDialog
 
Conn - Variable in class cct.database.SQLDatabaseAccess
 
connect(String) - Method in interface cct.interfaces.FileBrowserInterface
 
connect(String, String, char[], int) - Method in interface cct.interfaces.FileBrowserInterface
 
CONNECT - Static variable in class cct.tools.filebrowser.ConnectHostDialog
 
connect - Variable in class cct.tools.filebrowser.FileTransferFrame
 
connect(String) - Method in class cct.tools.filebrowser.LocalFileBrowser
 
connect(String, String, char[], int) - Method in class cct.tools.filebrowser.LocalFileBrowser
 
connect(String) - Method in class cct.tools.filebrowser.SFTPBrowser
Connect the client to the server using default connection properties.
connect(String, String) - Method in class cct.tools.filebrowser.SFTPBrowser
 
connect(String, String, char[], int) - Method in class cct.tools.filebrowser.SFTPBrowser
Connect the client to the server using default connection properties.
connectButton - Variable in class cct.ssh.SSHPanel
 
connectButton - Variable in class cct.tools.filebrowser.ConnectHostDialog
 
connectButton - Variable in class cct.tools.filebrowser.FileTransferFrame
 
connectButton_actionPerformed(ActionEvent) - Method in class cct.ssh.SSHPanel
 
connectButton_actionPerformed(ActionEvent) - Method in class cct.tools.filebrowser.FileTransferFrame
 
connectDialog - Variable in class cct.tools.filebrowser.FileTransferFrame
 
connected - Variable in class cct.tools.filebrowser.SFTPObject
 
connectedToDB - Variable in class cct.modelling.MolecularEditor
 
ConnectHostDialog - Class in cct.tools.filebrowser
Title: Computational Chemistry Tookit
ConnectHostDialog(Frame, String, boolean) - Constructor for class cct.tools.filebrowser.ConnectHostDialog
 
ConnectHostDialog() - Constructor for class cct.tools.filebrowser.ConnectHostDialog
 
connectionTable - Variable in class cct.adf.ADF
 
connectMenu - Variable in class cct.tools.filebrowser.SFTPBrowserFrame
 
ConnectSQLServer - Class in cct.awtdialogs
Title:
ConnectSQLServer(String, boolean) - Constructor for class cct.awtdialogs.ConnectSQLServer
 
connectToDatabase() - Method in class cct.j3d.Java3dUniverse
 
connectToHost(String, int) - Method in class cct.tools.filebrowser.SFTPBrowser
Tries to connect to the host
CONSTANT_DIELECTRIC_FUNCTION - Static variable in interface cct.interfaces.ForceFieldInterface
 
Constants - Class in cct
Title: Computational Chemistry Tookit
constraintsCheckBox - Variable in class cct.modelling.ui.JSetupEnergyDialog
 
constraintsCheckBox_itemStateChanged(ItemEvent) - Method in class cct.modelling.ui.JSetupEnergyDialog
 
construct() - Method in class cct.modelling.BackgroundMinimizer
 
construct() - Method in class cct.tools.filebrowser.SFTPBrowser.FileTranferWorker
 
construct() - Method in class cct.tools.filebrowser.SFTPFileChooserDialog.FileTranferWorker
 
construct() - Method in class cct.tools.SwingWorker
Compute the value to be returned by the get method.
constructAngleBendParam(String, String, String, AtomInterface, AtomInterface, AtomInterface, MoleculeInterface) - Static method in class cct.sff.SimpleForceField
 
contentPane - Variable in class cct.amber.Sander8Frame
 
contentPane - Variable in class cct.amber.Sander9Frame
 
contentPane - Variable in class cct.amber.TextEditorFrame
 
contentPane - Variable in class cct.dialogs.Frame1
 
contentPane - Variable in class cct.gaussian.ui.GaussianInputEditorFrame
 
contentPane - Variable in class cct.grid.ui.gaussian.SubmitGaussianAppl.IOFrame
 
contentPane - Variable in class cct.grid.ui.gaussian.SubmitGaussianFrame
 
contentPane - Variable in class cct.j3d.SimpleRenderer
 
contentPane - Variable in class cct.oogl.ui.OOGLViewerFrame
 
controlButtonOK - Static variable in class cct.database.ChemistryDatabaseDialog
 
controlButtonOK - Static variable in class cct.database.new_ChemistryDatabaseDialog
 
ControlColorGradientPanel - Class in cct.j3d.ui
Title: Computational Chemistry Tookit
ControlColorGradientPanel() - Constructor for class cct.j3d.ui.ControlColorGradientPanel
 
controlColorGradientPanel1 - Variable in class cct.j3d.ui.VerticesPropertyPanel
 
ControlData - Variable in class cct.amber.Sander8JobControl
 
ControlData - Variable in class cct.amber.Sander9JobControl
 
controlMolList - Static variable in class cct.database.ChemistryDatabaseDialog
 
controlMolList - Static variable in class cct.database.new_ChemistryDatabaseDialog
 
controlMolName - Static variable in class cct.database.ChemistryDatabaseDialog
 
controlMolName - Static variable in class cct.database.new_ChemistryDatabaseDialog
 
Controls - Variable in class cct.dialogs.JAtomSelectionPanel
 
Controls - Variable in class cct.dialogs.JQuickSelectionPanel
 
Controls - Variable in class cct.dialogs.JSelectionRulePanel
 
Controls - Variable in class cct.dialogs.JSelectionTypePanel
 
Controls - Variable in class cct.dialogs.JSpecialSelectionPanel
 
controls - Variable in class cct.tools.MemoryMonitor
 
controlSection - Static variable in class cct.gamess.Gamess
 
controlsPanel - Variable in class cct.dialogs.JAddMoleculeDialog
 
controlsPanel - Variable in class cct.pdb.ui.PDBBankFormPanel
 
controlsPanel - Variable in class cct.tools.filebrowser.FileBrowserPanel
 
controlsPanel - Variable in class cct.tools.filebrowser.JFileBrowserPanel
 
controlsTable - Variable in class cct.amber.Sander8Frame
 
controlsTable - Variable in class cct.amber.Sander9Frame
 
controlStrList - Static variable in class cct.database.ChemistryDatabaseDialog
 
controlStrList - Static variable in class cct.database.new_ChemistryDatabaseDialog
 
controlSwitches - Static variable in class cct.gamess.Gamess
 
converge(POINT, POINT, float, ImplicitFunctionInterface, POINT) - Static method in class cct.poly.Polygonizer
 
convertImage(BufferedImage, int) - Static method in class cct.tools.ImageTools
 
coord - Variable in class cct.j3d.BondNode
 
CoordBuilder - Class in cct.modelling
Title: Computational Chemistry Tookit
CoordBuilder(String, String, Object) - Constructor for class cct.modelling.CoordBuilder
 
coordButton_actionPerformed(ActionEvent) - Method in class cct.amber.ReadPrmtopDialog
 
coordButton_actionPerformed(ActionEvent) - Method in class cct.vasp.ui.ReadPoscarDialog
 
coordCenter - Variable in class cct.j3d.LabelNode
 
CoordinateBuilderInterface - Interface in cct.interfaces
Title: Computational Chemistry Tookit
CoordinateParserInterface - Interface in cct.interfaces
Title: Computational Chemistry Tookit
coordinates - Variable in class cct.j3d.BondNode
 
coordinatesKey - Variable in class cct.vasp.Vasp
 
COORDINATION_NUMBER_KEY - Static variable in class cct.modelling.CCTAtomTypes
 
coordNumber - Variable in class cct.modelling.AtomGeometry
 
coordOffsets - Variable in class cct.modelling.SingleTrajectory
 
CoordOverTrajectory - Variable in class cct.amber.Sander8JobControl
 
CoordOverTrajectory - Variable in class cct.amber.Sander9JobControl
 
CoordParser - Class in cct.modelling
Title: Computational Chemistry Tookit
CoordParser(String, String, Object) - Constructor for class cct.modelling.CoordParser
 
copyright - Variable in class cct.amber.Sander8Frame_AboutBox
 
copyright - Variable in class cct.amber.Sander9Frame_AboutBox
 
copyright - Variable in class cct.dialogs.Frame1_AboutBox
 
copyright - Variable in class cct.gaussian.ui.GaussianInputEditorFrame_AboutBox
 
copyright - Variable in class cct.grid.ui.gaussian.SubmitGaussianFrame_AboutBox
 
copyright - Variable in class cct.oogl.ui.OOGLViewerFrame_AboutBox
 
CORNER - Class in cct.poly
Title: Molecular Structure Viewer/Editor
CORNER() - Constructor for class cct.poly.CORNER
 
corner1 - Static variable in class cct.poly.CUBETABLE
 
corner2 - Static variable in class cct.poly.CUBETABLE
 
corner_lst - Variable in class cct.poly.PROCESS
 
CORNERELEMENT - Class in cct.poly
Title: Molecular Structure Viewer/Editor
CORNERELEMENT(int, int, int, float) - Constructor for class cct.poly.CORNERELEMENT
 
CORNERELEMENT() - Constructor for class cct.poly.CORNERELEMENT
 
CORNERLIST - Class in cct.poly
Title: Molecular Structure Viewer/Editor
CORNERLIST() - Constructor for class cct.poly.CORNERLIST
 
CORNERLIST - Variable in class cct.poly.Polygonizer
 
corners - Variable in class cct.poly.CUBE
 
corners - Variable in class cct.poly.PROCESS
 
count - Variable in class cct.gaussian.ui.GaussianInputEditorFrame
 
COUNT - Static variable in class cct.grid.JobDescription
 
countAtoms() - Method in class cct.pdb.PDBResidue
 
countBonds() - Method in class cct.pdb.PDBResidue
 
countCubes() - Method in class cct.gaussian.GaussianCube
 
countCubes() - Method in interface cct.interfaces.VolumetricDataInterface
Returns number of volumetric cubes
countFrequencies() - Method in class cct.adf.ADFOutput
 
countFrequencies() - Method in class cct.gaussian.GaussianOutput
 
countFrequencies() - Method in interface cct.interfaces.OutputResultsInterface
 
countMolecules() - Method in class cct.amber.AmberLib
 
countSectionsWithGeometry() - Method in class cct.adf.ADFOutput
 
countSpectra() - Method in class cct.adf.ADFOutput
 
countSpectra() - Method in class cct.gaussian.GaussianOutput
 
countSpectra() - Method in interface cct.interfaces.OutputResultsInterface
 
COVALENT_TO_GRADIUS_FACTOR - Static variable in interface cct.interfaces.AtomInterface
 
covalentBondLength - Variable in class cct.dialogs.JAtomTypeDialog
 
covalentRadii - Static variable in class cct.modelling.ChemicalElements
 
covalentRadius - Variable in class cct.modelling.AtomTypeDef
 
covergLabel - Variable in class cct.amber.Sander8Frame
 
covergLabel - Variable in class cct.amber.Sander9Frame
 
covergLabel_mouseEntered(MouseEvent) - Method in class cct.amber.Sander8Frame
 
covergLabel_mouseEntered(MouseEvent) - Method in class cct.amber.Sander9Frame
 
cphfSection - Static variable in class cct.gamess.Gamess
 
cpinButton - Variable in class cct.amber.Sander9JobPanel
 
cpinCheckBox - Variable in class cct.amber.Sander9JobPanel
 
cpinLabel - Variable in class cct.amber.Sander9JobPanel
 
cpinTextField - Variable in class cct.amber.Sander9JobPanel
 
cpuKey - Static variable in class cct.grid.ui.PBS_Panel
 
cpuKey - Static variable in class cct.grid.ui.PBSPanel
 
cpuLabel - Variable in class cct.grid.ui.PBS_Panel
 
CPUTextField - Variable in class cct.grid.ui.PBS_Panel
 
cpuTextField - Variable in class cct.grid.ui.ResourcesPanel
 
createArrow() - Method in class cct.j3d.ArrowNode
 
createAtom(AtomInterface) - Method in class cct.j3d.Java3dUniverse
 
createBond(int, int) - Method in class cct.j3d.Java3dUniverse
 
createButtons() - Method in class cct.dialogs.JElementsPanel
 
createChart(VIBRATIONAL_SPECTRUM) - Method in class cct.chart.VibrationSpectrumChart
 
CreateCheckpointString(ArrayList) - Static method in class cct.grid.CheckPoint
 
CreateCheckpointString(ArrayList) - Static method in class cct.grid.ParseCheckpointFile
 
createCylinder(float, float, Appearance) - Method in class cct.j3d.BondNode
 
createdCentroidForSelectedAtoms() - Method in class cct.j3d.Java3dUniverse
 
createElements(TransformerHandler, HashMap, HashMap) - Static method in class cct.grid.CheckPoint
 
createElements(TransformerHandler, HashMap) - Static method in class cct.grid.CheckPoint
Prints all tags and their values of "entries"
createElements(TransformerHandler, HashMap, HashMap) - Static method in class cct.grid.ParseCheckpointFile
 
createFolder - Variable in class cct.tools.filebrowser.FileBrowserPanel
 
createFolder - Variable in class cct.tools.filebrowser.JFileBrowserPanel
 
createLabel(Vector3f, String, Color3f, String, int, int) - Method in class cct.j3d.LabelNode
 
createLabel(String, Color3f, String, int, int) - Method in class cct.j3d.LabelNode
 
createLine() - Method in class cct.j3d.BondNode
 
createMaterial(Color3f) - Static method in class cct.j3d.ChemicalElementsColors
 
createMonoCylinder(BondInterface) - Method in class cct.j3d.BondNode
Creates TransformGroup with a cylinder for monocolored bond
createNewBond(AtomInterface, AtomInterface) - Method in class cct.modelling.Molecule
No error check!!!
createNewBrowser(String, String, FileBrowserInterface) - Method in class cct.tools.filebrowser.ShadowSFTPManager
 
createRunScript(GridProviderInterface, SchedulerInterface, ClientProgramInterface) - Static method in class cct.grid.JobDescription
 
createSceneGraph() - Method in class cct.j3d.AppearanceSetup
 
createSceneGraph() - Method in class cct.j3d.Java3dUniverse
 
createUniverse() - Method in class cct.j3d.Java3dUniverse
 
createUnixScript(JobDescription, SchedulerInterface) - Static method in class cct.grid.JobDescription
 
createUnixScript(JobDescription) - Static method in class cct.grid.JobDescription
 
crossProduct(vPoint3f) - Method in class cct.vecmath.vPoint3f
 
crossProduct(Point3fInterface) - Method in class cct.vecmath.vPoint3f
 
crossProduct(Point3fInterface, Point3fInterface, Point3fInterface) - Static method in class cct.vecmath.vPoint3f
Calculate cross vector for vectors v1 and v2 and put result into the crossVector No any memory allocation in the subroutine
crossProduct(Point3fInterface, Point3fInterface) - Method in class cct.vecmath.vPoint3f
 
Crystal - Class in cct.math
Title: Computational Chemistry Tookit
Crystal() - Constructor for class cct.math.Crystal
 
Crystal - Class in cct.tools
Title:
Crystal() - Constructor for class cct.tools.Crystal
 
ctable - Static variable in class cct.poly.CUBETABLE
 
CUBE - Class in cct.poly
Title: Molecular Structure Viewer/Editor
CUBE() - Constructor for class cct.poly.CUBE
 
cubeList - Variable in class cct.gaussian.ui.ManageCubesFrame
 
cubeList_valueChanged(ListSelectionEvent) - Method in class cct.gaussian.ui.ManageCubesFrame
 
Cubes - Variable in class cct.gaussian.ui.ManageCubesFrame
 
cubes - Variable in class cct.poly.PROCESS
 
CUBETABLE - Class in cct.poly
Title: Molecular Structure Viewer/Editor
CUBETABLE() - Constructor for class cct.poly.CUBETABLE
 
cullFace - Variable in class cct.j3d.VerticesObjectProperties
 
current_color - Variable in class cct.dialogs.JModifyAtomDialog
 
currentAngle - Variable in class cct.dialogs.JModifyAngleDialog
 
currentAngle_actionPerformed(ActionEvent) - Method in class cct.dialogs.JModifyAngleDialog
 
currentBond - Variable in class cct.dialogs.JModifyBondDialog
 
currentBondLength - Variable in class cct.dialogs.JModifyBondDialog
 
currentBondLength_actionPerformed(ActionEvent) - Method in class cct.dialogs.JModifyBondDialog
 
currentCheckPoint - Variable in class cct.grid.ui.JobStatusPanel
 
currentColor - Variable in class cct.tools.ui.FontSelectorPanel
 
currentCommand - Variable in class cct.cprocessor.CommandProcessor
 
currentComponent - Variable in class cct.tools.filebrowser.FileBrowserPanel
 
currentElement - Variable in class cct.dialogs.JAtomTypeDialog
 
currentFileList - Variable in class cct.tools.filebrowser.SFTPBrowser
 
currentFrameTextField - Variable in class cct.dialogs.AnimationPanel
 
currentFrameTextField_actionPerformed(ActionEvent) - Method in class cct.dialogs.AnimationPanel
 
currentLocalFile - Variable in class cct.tools.filebrowser.SFTPBrowser.FileTranferWorker
 
currentMacroBlock - Variable in class cct.cprocessor.MacroProcessor
 
currentMacroName - Variable in class cct.cprocessor.MacroProcessor
 
currentMolecule - Variable in class cct.tools.CCTParser
 
currentPlatform - Variable in class cct.amber.SanderResourcesEval
 
currentPWD - Variable in class cct.tools.filebrowser.SFTPBrowser
 
currentTag - Variable in class cct.grid.ParseCheckpointFile
 
currentTag - Variable in class cct.tools.CCTParser
 
currentTag - Variable in class cct.tools.FragmentDictionaryParser
 
currentValueIsNotDefault - Variable in class cct.amber.Sander8Variable
 
currentValueIsNotDefault - Variable in class cct.amber.SanderVariable
 
currentVars - Variable in class cct.gamess.Gamess
 
currentWorkingDirectory - Variable in class cct.dialogs.TrajectoriesManagerPanel
 
currentWorkingDirectory - Variable in class cct.j3d.GroupToVRML
 
currentWorkingDirectory - Variable in class cct.povray.Povray
 
currentWorkingDirectory - Variable in class cct.tools.GeomFormat
 
currentWorkingDirectory - Variable in class cct.vasp.ui.ReadPoscarDialog
 
custom_basis - Variable in class cct.awtdialogs.AddNewMethodDialog
 
CUSTOM_PROPERTY_FILE - Static variable in class cct.grid.ui.PBSPanel
 
CUSTOM_PROPERTY_FILE - Static variable in class cct.ssh.SSHPanel
 
CUSTOM_PROPERTY_FILE - Static variable in class cct.ssh.SSHServiceProvider
 
CUSTOM_PROPERTY_FILE - Static variable in class cct.tools.Utils
 
customObjects - Variable in class cct.dialogs.JSolvateShellDialog
 
CUT - Variable in class cct.amber.Sander8JobControl
 
CUT - Variable in class cct.amber.Sander9JobControl
 
CUT_Button_actionPerformed(ActionEvent) - Method in class cct.amber.Sander8Frame
 
CUT_Button_actionPerformed(ActionEvent) - Method in class cct.amber.Sander9Frame
 
CUT_Label - Variable in class cct.amber.Sander8Frame
 
CUT_Label - Variable in class cct.amber.Sander9Frame
 
CUT_Label_mouseEntered(MouseEvent) - Method in class cct.amber.Sander8Frame
 
CUT_Label_mouseEntered(MouseEvent) - Method in class cct.amber.Sander9Frame
 
CUT_TextField - Variable in class cct.amber.Sander8Frame
 
CUT_TextField - Variable in class cct.amber.Sander9Frame
 
cutImage - Variable in class cct.dialogs.Frame1
 
cutoff - Variable in class cct.amber.SanderJobControlDialog
 
CYLINDER_BICOLOR - Static variable in interface cct.interfaces.BondInterface
 
CYLINDER_MONOCOLOR - Static variable in interface cct.interfaces.BondInterface
 
CYLINDER_RADIUS - Static variable in interface cct.interfaces.BondInterface
 
cylinderRadius - Variable in class cct.j3d.BondNode
 

D

d - Variable in class cct.tools.Crystal
 
D0 - Variable in class cct.math.Minimizer
 
D1 - Variable in class cct.math.Minimizer
 
daddy - Variable in class cct.amber.AmberSubmitDialog
 
daddy - Variable in class cct.amber.SanderJobControlDialog
 
daddy - Variable in class cct.awtdialogs.GeometrySelectDialog
 
daddy - Variable in class cct.awtdialogs.SimpleAtomSelectionDialog
 
daddy - Variable in class cct.dialogs.JAtomSelectionDialog
 
daddy - Variable in class cct.dialogs.JAtomTypeDialog
 
daddy - Variable in class cct.dialogs.JModifyAngleDialog
 
daddy - Variable in class cct.dialogs.JModifyAtomDialog
 
daddy - Variable in class cct.dialogs.JModifyBondDialog
 
daddy - Variable in class cct.dialogs.JModifyTorsionDialog
 
daddy - Variable in class cct.dialogs.JSimpleAtomSelectionDialog
 
daddy - Variable in class cct.j3d.MyMouseMotionListener
 
data - Variable in class cct.gaussian.java3d.VolumetricData
 
data - Variable in class cct.grid.ui.JobStatusTableModel
 
data - Variable in class cct.tools.filebrowser.FileBrowserPanel
 
data - Variable in class cct.tools.filebrowser.FileBrowserTableModel
 
data - Variable in class cct.tools.filebrowser.JFileBrowserPanel
 
data - Variable in class cct.tools.filebrowser.SFTPBrowser
 
database - Variable in class cct.awtdialogs.AddNewMethodDialog
 
database - Variable in class cct.awtdialogs.AddNewStructureDialog
 
database - Variable in class cct.awtdialogs.ConnectSQLServer
 
database - Variable in class cct.database.new_SQLChemistryDatabase
 
database - Variable in class cct.database.SQLChemistryDatabase
 
DatabaseAccess - Interface in cct.database
Title:
databaseAccess - Variable in class cct.modelling.MolecularEditor
 
databaseMenu - Variable in class cct.dialogs.Frame1
 
dataOrigin - Variable in class cct.gaussian.java3d.VolumetricData
 
dataOrigin - Variable in class cct.math.polyg.Polygonizer
 
dataSection - Static variable in class cct.gamess.Gamess
 
dataSource - Variable in class cct.grid.ui.JobStatusPanel
 
dateStampCB - Static variable in class cct.tools.MemoryMonitor
 
db_type - Variable in class cct.awtdialogs.ConnectSQLServer
 
Debug - Variable in class cct.amber.AmberPrmtop
 
debug - Static variable in class cct.chart.jfreechart.JFreeChartPanel
 
Debug - Static variable in class cct.gaussian.Gaussian
 
Debug - Static variable in class cct.gaussian.GaussianMolecule
 
Debug - Static variable in class cct.gaussian.GaussianOutput
 
Debug - Static variable in class cct.grid.CheckPoint
 
debug - Static variable in class cct.grid.ParseCheckpointFile
 
DEBUG - Variable in class cct.grid.ui.JobStatusPanel
 
DEBUG - Variable in class cct.grid.ui.JobStatusTableModel
 
debug - Variable in class cct.math.DFPMin
 
debug - Variable in class cct.math.LinearSearch
 
debug - Static variable in class cct.modelling.FormatManager
 
Debug - Static variable in class cct.pdb.PDB
 
Debug - Static variable in class cct.tools.CCTParser
 
DEBUG - Variable in class cct.tools.filebrowser.FileBrowserTableModel
 
DEBUG - Variable in class cct.tools.filebrowser.SFTPBrowser
 
Debug - Static variable in class cct.tools.FragmentDictionaryParser
 
Debug - Static variable in class cct.tools.ImageTools
 
debug - Variable in class cct.vasp.VasprunXML
 
decreaseFont - Variable in class cct.dialogs.JAtomTypeDialog
 
decreaseFontMenuItem - Variable in class cct.tools.ui.LogPanel
 
decreaseMenuItem - Variable in class cct.gaussian.ui.GaussianInputEditorFrame
 
DEFAULT_ATOM_COLOR_SCHEME - Static variable in class cct.j3d.ChemicalElementsColors
 
DEFAULT_BONDS_AND_STICKS_RADIUS - Static variable in interface cct.interfaces.BondInterface
 
DEFAULT_HOST - Static variable in class cct.ssh.SSHPanel
 
DEFAULT_QUEUE - Static variable in class cct.grid.ui.PBSPanel
 
Default_SFF_File - Static variable in class cct.sff.SimpleForceField
 
DEFAULT_STICKS_RADIUS - Static variable in interface cct.interfaces.BondInterface
 
DEFAULT_TYPE_KEY - Static variable in class cct.modelling.CCTAtomTypes
 
defaultAngleFk - Static variable in class cct.sff.SimpleForceField
 
defaultAtomicRadius - Variable in class cct.povray.Povray
 
defaultAtomicRadius - Variable in class cct.tools.GeomFormat
 
defaultAtomTypeColor - Variable in class cct.dialogs.JAtomTypeDialog
 
defaultAtomTypes - Static variable in class cct.modelling.AtomTypes
 
defaultAtomTypesTableFile - Static variable in class cct.amber.AmberUtilities
 
defaultChargeUsed - Variable in class cct.adf.ADF
 
defaultDictionary - Static variable in class cct.pdb.PDBDictionary
 
defaultElementsTable - Static variable in class cct.amber.AmberUtilities
 
defaultFk - Static variable in class cct.modelling.FFMolecule
 
defaultFontName - Static variable in class cct.gaussian.ui.GaussianInputEditorFrame
 
defaultFontName - Static variable in class cct.grid.ui.EditScriptDialog
 
defaultFontName - Static variable in class cct.tools.ui.LogPanel
 
defaultFragmentDictionary - Static variable in class cct.GlobalSettings
 
DefaultGromacsAtomMapFile - Static variable in class cct.gromacs.Gromacs
 
defaultIsSet - Variable in class cct.amber.Sander8Variable
 
defaultIsSet - Variable in class cct.amber.SanderVariable
 
defaultJPEGQuality - Static variable in class cct.tools.ui.JPEGOptionsPanel
 
defaultMonoColor - Variable in class cct.j3d.BondNode
 
defaultNumberDivisions - Static variable in class cct.j3d.AtomNode
 
defaultOptimizeHuffmanCode - Variable in class cct.tools.ui.JPEGOptionsPanel
 
defaultPalette - Variable in class cct.j3d.ColorRangeScheme
 
defaultPDB_EntryDir - Static variable in class cct.pdb.ui.PDBBankFormPanel
 
defaultPDB_Host - Static variable in class cct.pdb.ui.PDBBankFormPanel
 
defaultProperiesFile - Static variable in class cct.modelling.CCTAtomTypes
 
defaultProperiesFile_16x16 - Static variable in class cct.tools.FileUtilities
 
defaultProperiesFile_32x32 - Static variable in class cct.tools.FileUtilities
 
defaultProtocol - Variable in class cct.tools.filebrowser.ShadowSFTPManager
 
defaultScriptContent - Static variable in class cct.grid.ui.gaussian.SubmitGaussianPanel
 
defaultSolventDictionary - Static variable in class cct.GlobalSettings
 
defaultSolventList - Variable in class cct.j3d.Java3dUniverse
 
defaultValue - Variable in class cct.amber.Sander8VariableValue
 
defaultValue - Variable in class cct.amber.SanderVariableValue
 
defaultValue - Variable in class cct.gamess.GamessSwitch
 
defValues - Static variable in class cct.modelling.CCTAtomTypes
 
DEGREES_TO_RADIANS - Static variable in class cct.adf.ADF
 
DEGREES_TO_RADIANS - Static variable in class cct.Constants
 
DEGREES_TO_RADIANS - Static variable in class cct.gamess.Gamess
 
DEGREES_TO_RADIANS - Variable in class cct.gaussian.Gaussian
 
DEGREES_TO_RADIANS - Static variable in class cct.gaussian.GaussianMolecule
 
DEGREES_TO_RADIANS - Static variable in class cct.gulp.Gulp
 
DEGREES_TO_RADIANS - Static variable in class cct.math.MathExpressionParser
 
DEGREES_TO_RADIANS - Static variable in class cct.mopac.Mopac
 
DEGREES_TO_RADIANS - Static variable in class cct.qchem.QChem
 
DEGREES_TO_RADIANS - Static variable in class cct.vecmath.vPoint3f
 
delAllButton - Variable in class cct.dialogs.TrajectoriesManagerPanel
 
delAllButton_actionPerformed(ActionEvent) - Method in class cct.dialogs.TrajectoriesManagerPanel
 
delete - Variable in class cct.j3d.BondNode
 
delete - Variable in class cct.tools.filebrowser.FileBrowserPanel
 
delete - Variable in class cct.tools.filebrowser.JFileBrowserPanel
 
deleteAllBonds() - Method in class cct.j3d.Java3dUniverse
 
deleteAlltrajectories() - Method in class cct.dialogs.TrajectoriesManagerPanel
 
deleteAllTrajectories() - Method in class cct.modelling.StructureManager
 
deleteAtom(int) - Method in interface cct.interfaces.MoleculeInterface
 
deleteAtom(AtomInterface) - Method in class cct.j3d.Java3dUniverse
 
deleteAtom(int) - Method in class cct.j3d.Java3dUniverse
 
deleteAtom(int) - Method in class cct.modelling.Molecule
Deletes atoms and all associated data
deleteBond(BondInterface) - Method in interface cct.interfaces.MoleculeInterface
 
deleteBond(BondInterface) - Method in class cct.modelling.Molecule
Deletes bond between atoms and all related information
deleteBondBetweenAtoms(AtomInterface, AtomInterface) - Method in class cct.j3d.Java3dUniverse
 
deleteButton - Variable in class cct.dialogs.TrajectoriesManagerPanel
 
deleteButton - Variable in class cct.gaussian.ui.ManageCubesFrame
 
deleteButton - Variable in class cct.j3d.ui.GraphicsObjectPropertiesFrame
 
deleteButton - Variable in class cct.tools.filebrowser.FileBrowserPanel
 
deleteButton - Variable in class cct.tools.filebrowser.JFileBrowserPanel
 
deleteButton_actionPerformed(ActionEvent) - Method in class cct.gaussian.ui.ManageCubesFrame
 
deleteButton_actionPerformed(ActionEvent) - Method in class cct.j3d.ui.GraphicsObjectPropertiesFrame
 
deleteButton_actionPerformed(ActionEvent) - Method in class cct.tools.filebrowser.FileBrowserPanel
 
deleteButton_actionPerformed(ActionEvent) - Method in class cct.tools.filebrowser.JFileBrowserPanel
 
deleteEntryButton - Variable in class cct.gaussian.ui.GaussianInputEditorFrame
 
DeleteItem - Static variable in class cct.tools.filebrowser.SFTPBrowser
 
deleteMolecule(String) - Method in class cct.database.new_SQLChemistryDatabase
 
deleteMolecule(String) - Method in class cct.database.SQLChemistryDatabase
 
deleteMoleculeButton_actionPerformed(ActionEvent) - Method in class cct.dialogs.JEditorFrame
 
deleteObject - Variable in class cct.j3d.ui.GraphicsObjectPropertiesFrame
 
deleteRows(String, String, String) - Method in class cct.database.SQLDatabaseAccess
 
deleteSelectedAtoms() - Method in class cct.j3d.Java3dUniverse
Deletes selected atoms and associated bonds
deleteSelectedAtoms() - Method in class cct.modelling.Molecule
 
deleteSelectedAtoms(MoleculeInterface) - Static method in class cct.modelling.Molecule
 
deleteStep - Variable in class cct.gaussian.ui.GaussianInputEditorFrame
 
deleteStructure(String, String) - Method in class cct.database.new_SQLChemistryDatabase
 
deleteStructure(String, String) - Method in class cct.database.SQLChemistryDatabase
 
deleteStructureFromArray(String, String) - Method in class cct.database.ChemistryDatabaseDialog
 
deleteStructureFromArray(String, String) - Method in class cct.database.new_ChemistryDatabaseDialog
 
Delimiters - Variable in class cct.math.MathExpressionParser
 
delta - Variable in class cct.gaussian.java3d.VolumetricData
 
delta - Variable in class cct.poly.PROCESS
 
DESCENDING - Static variable in class cct.tools.filebrowser.TableSorter
 
Description - Variable in class cct.amber.Sander8Variable
 
Description - Variable in class cct.amber.Sander8VariableValue
 
Description - Variable in class cct.amber.SanderVariable
 
Description - Variable in class cct.amber.SanderVariableValue
 
description - Variable in class cct.gamess.GamessSwitch
 
Description - Variable in class cct.modelling.AtomTypeDef
 
description - Variable in class cct.modelling.CoordBuilder
 
description - Variable in class cct.modelling.CoordParser
 
Description - Variable in class cct.tools.FileFilterImpl
 
descriptionPane - Variable in class cct.amber.Sander8Frame
 
descriptionPane - Variable in class cct.amber.Sander9Frame
 
descrPanel - Variable in class cct.amber.Sander8Frame
 
descrPanel - Variable in class cct.amber.Sander9Frame
 
Destination - Variable in class cct.grid.ui.CheckPointStatus.FTransferWithProgress
 
DESTINATION_URL - Static variable in class cct.grid.JobDescription
 
destroy() - Method in class cct.applets.viewer
 
detSection - Static variable in class cct.gamess.Gamess
 
df - Variable in class cct.tools.filebrowser.SFTPBrowser.FileTranferWorker
 
DFPMin - Class in cct.math
Title:
DFPMin() - Constructor for class cct.math.DFPMin
 
dial - Variable in class cct.modelling.BackgroundMinimizer
 
dialog - Variable in class cct.grid.ui.gaussian.SubmitGaussianDialog.JobSubProgress
 
dialog - Variable in class cct.grid.ui.gaussian.SubmitGaussianDialogNew.JobSubProgress
 
dialog - Variable in class cct.grid.ui.SubmitTaskDialog.JobSubProgress
 
dialog - Variable in class cct.grid.ui.ThreadExec.TimerListener
 
dialog - Variable in class cct.tools.filebrowser.SFTPBrowser.FileTranferWorker
 
dicName - Variable in class cct.pdb.PDBDictionary
 
dicStack - Variable in class cct.tools.FragmentDictionaryParser
 
DICTIONARY_NAME_ATTRIBUTE - Static variable in class cct.pdb.PDBDictionary
 
DICTIONARY_TAG - Static variable in class cct.tools.FragmentDictionaryParser
 
dictionaryTree - Variable in class cct.tools.FragmentDictionaryParser
 
DIELC_Button_actionPerformed(ActionEvent) - Method in class cct.amber.Sander8Frame
 
DIELC_Button_actionPerformed(ActionEvent) - Method in class cct.amber.Sander9Frame
 
DIELC_Label - Variable in class cct.amber.Sander8Frame
 
DIELC_Label - Variable in class cct.amber.Sander9Frame
 
DIELC_Label_mouseEntered(MouseEvent) - Method in class cct.amber.Sander8Frame
 
DIELC_Label_mouseEntered(MouseEvent) - Method in class cct.amber.Sander9Frame
 
DIELC_TextField - Variable in class cct.amber.Sander8Frame
 
DIELC_TextField - Variable in class cct.amber.Sander9Frame
 
dielConstTextField - Variable in class cct.modelling.ui.JSetupEnergyDialog
 
dielectricConstant - Static variable in class cct.sff.SimpleForceField
 
dielectricFunction - Static variable in class cct.sff.SimpleForceField
 
dielFuncComboBox - Variable in class cct.modelling.ui.JSetupEnergyDialog
 
Difference - Variable in class cct.dialogs.JAtomSelectionDialog
 
Difference - Variable in class cct.dialogs.JSelectionRulePanel
 
Difference_stateChanged(ChangeEvent) - Method in class cct.dialogs.JAtomSelectionDialog
 
DIFFUSE_RGB_COLOR - Static variable in interface cct.interfaces.AtomInterface
 
diffuseColorStore - Variable in class cct.j3d.ui.VerticesPropertyPanel
 
dihedralAngle(Point3fInterface, Point3fInterface, Point3fInterface, Point3fInterface) - Static method in class cct.vecmath.vPoint3f
 
dipdrSection - Static variable in class cct.gamess.Gamess
 
DipoleMomentProperty - Static variable in interface cct.interfaces.MoleculeInterface
 
DIRECT_COORDINATES - Static variable in class cct.vasp.Vasp
 
directionTable - Static variable in class cct.dialogs.ViewPeriodicImagePanel
 
directories - Variable in class cct.tools.filebrowser.SFTPBrowser
 
directoriesPanel - Variable in class cct.amber.Sander9JobPanel
 
directory - Variable in class cct.amber.AmberSubmitMenuHandler
 
DIRECTORY - Static variable in class cct.grid.JobDescription
 
disbsSection - Static variable in class cct.gamess.Gamess
 
disconnect() - Method in interface cct.interfaces.FileBrowserInterface
 
disconnect - Variable in class cct.tools.filebrowser.FileTransferFrame
 
disconnect() - Method in class cct.tools.filebrowser.LocalFileBrowser
 
disconnect() - Method in class cct.tools.filebrowser.SFTPBrowser
 
disconnectButton - Variable in class cct.tools.filebrowser.FileTransferFrame
 
Displ_panel - Variable in class cct.dialogs.JModifyBondDialog
 
Displace_1 - Variable in class cct.dialogs.JModifyBondDialog
 
Displace_2 - Variable in class cct.dialogs.JModifyBondDialog
 
displayHelpFromSourceActionListener(AbstractButton) - Method in class cct.help.JavaHelp
 
displayHelpFromSourceActionListener(AbstractButton) - Method in interface cct.interfaces.HelperInterface
 
displaySelectedAtoms(boolean) - Method in class cct.j3d.Java3dUniverse
 
DisplPanel - Variable in class cct.dialogs.JModifyAngleDialog
 
displPanel - Variable in class cct.dialogs.JModifyTorsionDialog
 
dispose() - Method in class cct.math.polyg.Polygonizer
 
dispose() - Method in class cct.tools.filebrowser.SFTPObject
 
disrepSection - Static variable in class cct.gamess.Gamess
 
distance(Point3fInterface, Point3fInterface) - Static method in class cct.vecmath.vPoint3f
 
DISTANCE_DIELECTRIC_FUNCTION - Static variable in interface cct.interfaces.ForceFieldInterface
 
distancesAsString(MoleculeInterface) - Static method in class cct.modelling.Molecule
 
distanceSquared(Point3fInterface, Point3fInterface) - Static method in class cct.vecmath.vPoint3f
 
distanceTo(Point3fInterface) - Method in class cct.gamess.GamessAtom
 
distanceTo(Point3fInterface) - Method in interface cct.interfaces.Point3fInterface
 
distanceTo(gAtom) - Method in class cct.modelling.gAtom
 
distanceTo(vPoint3f) - Method in class cct.modelling.vAtom
 
distanceTo(AtomInterface) - Method in class cct.modelling.vAtom
 
distanceTo(Point3fInterface) - Method in class cct.qchem.QChemAtom
 
distanceTo(Point3fInterface) - Method in class cct.vecmath.vPoint3f
 
distanceTo(float, float, float) - Method in class cct.vecmath.vPoint3f
 
distanceTo(double, double, double) - Method in class cct.vecmath.vPoint3f
 
distanceToLine(vPoint3f, vPoint3f) - Method in class cct.vecmath.vPoint3f
!!! Check out that it works properly!!!
distanceUnits - Variable in class cct.adf.ADF
 
divideIntoMolecules(MoleculeInterface) - Static method in class cct.modelling.Molecule
Divide molecule into submolecules with names R1, R2...
DIVIDER - Static variable in class cct.grid.ui.PBSPanel
 
DIVIDER - Static variable in class cct.ssh.SSHPanel
 
DIVIDER - Static variable in class cct.ssh.SSHServiceProvider
 
DIVIDER - Static variable in class cct.tools.Utils
 
dl - Variable in class cct.amber.AmberPrmtop
 
doAtomSelection(Point3d, Vector3d, BranchGroup, PickResult[]) - Method in class cct.j3d.Java3dUniverse
 
doAtomSelection(int) - Method in class cct.j3d.Java3dUniverse
 
doAtomSelection(BranchGroup, PickResult) - Method in class cct.j3d.Java3dUniverse
 
doControls - Variable in class cct.tools.MemoryMonitor
 
docube(CUBE) - Method in class cct.poly.PROCESS
 
document - Static variable in class cct.tools.filebrowser.FileNameRenderer
 
document - Static variable in class cct.tools.FileUtilities
 
document_32x32 - Static variable in class cct.tools.FileUtilities
 
done - Variable in class cct.grid.ui.ThreadExec
 
doProperSelection(int) - Method in class cct.j3d.Java3dUniverse
 
doRender(int, int) - Method in class cct.j3d.OffScreenCanvas3D
 
dotet - Static variable in class cct.poly.Polygonizer
 
dotet(CUBE, int, int, int, int) - Method in class cct.poly.PROCESS
Tetrahedral Polygonization
dotet2(CUBE, int, int, int, int) - Method in class cct.poly.PROCESS
 
doubleBonds - Variable in class cct.modelling.AtomGeometry
 
DoubleSpinnerDialog - Class in cct.tools.ui
Title:
DoubleSpinnerDialog(Frame, String, boolean, double, double, double, double) - Constructor for class cct.tools.ui.DoubleSpinnerDialog
 
doubleValue() - Method in class cct.tools.filebrowser.FileSize
 
DownhillSimplex(float[], int, float, MinimizedFunctionInterface, int, float) - Method in class cct.math.Simplex
 
downloadButton - Variable in class cct.grid.ui.JobStatusDialog
 
downloadButton - Variable in class cct.tools.filebrowser.FileBrowserPanel
 
downloadButton_actionPerformed(ActionEvent) - Method in class cct.grid.ui.JobStatusDialog
 
downloadButton_actionPerformed(ActionEvent) - Method in class cct.tools.filebrowser.FileBrowserPanel
 
DownloadItem - Static variable in class cct.tools.filebrowser.SFTPBrowser
 
downloadOutputFiles(FileTransferInterface) - Method in class cct.grid.CheckPoint
 
downloadOutputFiles(CheckPoint) - Static method in class cct.grid.TaskProvider
 
downloadOutputFiles() - Method in class cct.grid.ui.JobStatusDialog
 
downloadPrefix - Static variable in class cct.grid.ui.JobStatusPanel
 
downloadRemoteFiles(int[]) - Method in interface cct.grid.JobStatusInterface
 
downloadRemoteFiles(int[]) - Method in class cct.grid.ui.CheckPointStatus
 
downloadSelected() - Method in interface cct.interfaces.FileBrowserInterface
 
downloadSelected() - Method in class cct.tools.filebrowser.LocalFileBrowser
 
downloadSelected() - Method in class cct.tools.filebrowser.SFTPBrowser
Downloads selected items
drawBond - Variable in class cct.awtdialogs.AtomTypeDialog
 
drawBond - Variable in class cct.awtdialogs.GaussianCalcSetupDialog
 
drawBond - Variable in class cct.dialogs.JAtomTypeDialog
 
drawBond - Variable in class cct.dialogs.JModifyBondDialog
 
drawBond_itemStateChanged(ItemEvent) - Method in class cct.dialogs.JModifyBondDialog
 
drawBond_stateChanged(ChangeEvent) - Method in class cct.dialogs.JModifyBondDialog
 
drawBondBetweenSelectedAtoms(boolean) - Method in class cct.j3d.Java3dUniverse
 
drawBonds(MoleculeInterface) - Method in class cct.j3d.Java3dUniverse
 
drawMolecule(MoleculeInterface) - Method in class cct.j3d.Java3dUniverse
 
drcSection - Static variable in class cct.gamess.Gamess
 
DRMS_TextField - Variable in class cct.amber.Sander8Frame
 
DRMS_TextField - Variable in class cct.amber.Sander9Frame
 
DRMS_TextField_actionPerformed(ActionEvent) - Method in class cct.amber.Sander8Frame
 
DRMS_TextField_actionPerformed(ActionEvent) - Method in class cct.amber.Sander9Frame
 
drtSection - Static variable in class cct.gamess.Gamess
 
DT - Variable in class cct.amber.Sander8JobControl
 
DT - Variable in class cct.amber.Sander9JobControl
 
DT_Label - Variable in class cct.amber.Sander8Frame
 
DT_Label - Variable in class cct.amber.Sander9Frame
 
DT_Label_mouseEntered(MouseEvent) - Method in class cct.amber.Sander8Frame
 
DT_Label_mouseEntered(MouseEvent) - Method in class cct.amber.Sander9Frame
 
DT_TextField - Variable in class cct.amber.Sander8Frame
 
DT_TextField - Variable in class cct.amber.Sander9Frame
 
Dummy_MD_Label - Variable in class cct.amber.Sander9Frame
 
duplicateMolecule(MoleculeInterface) - Static method in class cct.modelling.Molecule
Duplicates molecule
DX0_TextField - Variable in class cct.amber.Sander8Frame
 
DX0_TextField - Variable in class cct.amber.Sander9Frame
 
DX0_TextField_actionPerformed(ActionEvent) - Method in class cct.amber.Sander8Frame
 
DX0_TextField_actionPerformed(ActionEvent) - Method in class cct.amber.Sander9Frame
 
dxLabel - Variable in class cct.amber.Sander8Frame
 
dxLabel - Variable in class cct.amber.Sander9Frame
 
dxLabel_mouseEntered(MouseEvent) - Method in class cct.amber.Sander8Frame
 
dxLabel_mouseEntered(MouseEvent) - Method in class cct.amber.Sander9Frame
 
dynamic - Variable in class cct.modelling.vAtom
 
dynamicAtoms - Variable in class cct.modelling.MolecularEnergy
 

E

ecpSection - Static variable in class cct.gamess.Gamess
 
ecpSection - Static variable in class cct.qchem.QChem
 
EDGEELEMENT - Class in cct.poly
Title: Molecular Structure Viewer/Editor
EDGEELEMENT() - Constructor for class cct.poly.EDGEELEMENT
 
EDGELIST - Class in cct.poly
Title: Molecular Structure Viewer/Editor
EDGELIST() - Constructor for class cct.poly.EDGELIST
 
EDGELIST - Variable in class cct.poly.Polygonizer
 
edges - Variable in class cct.poly.PROCESS
 
EDGETABLE - Class in cct.poly
Title: Molecular Structure Viewer/Editor
EDGETABLE() - Constructor for class cct.poly.EDGETABLE
 
Edit_MenuItem - Variable in class cct.amber.Sander8Frame
 
Edit_MenuItem - Variable in class cct.amber.Sander9Frame
 
Edit_MenuItem_actionPerformed(ActionEvent) - Method in class cct.amber.Sander8Frame
 
Edit_MenuItem_actionPerformed(ActionEvent) - Method in class cct.amber.Sander9Frame
 
EditAndPasteCoordFrame - Class in cct.modelling.ui
Title: Computational Chemistry Tookit
EditAndPasteCoordFrame() - Constructor for class cct.modelling.ui.EditAndPasteCoordFrame
 
EditAndSaveCoordDialog - Class in cct.modelling.ui
Title: Computational Chemistry Tookit
EditAndSaveCoordDialog(String) - Constructor for class cct.modelling.ui.EditAndSaveCoordDialog
 
EditAndSaveCoordDialog() - Constructor for class cct.modelling.ui.EditAndSaveCoordDialog
 
editedText - Variable in class cct.amber.TextEditorFrame
 
EditHostsDialog - Class in cct.tools.filebrowser
Title: Computational Chemistry Tookit
EditHostsDialog(Frame, String, boolean) - Constructor for class cct.tools.filebrowser.EditHostsDialog
 
editHostsMenuItem - Variable in class cct.tools.filebrowser.SFTPBrowserFrame
 
editMenu - Variable in class cct.dialogs.Frame1
 
editor - Variable in class cct.j3d.ScriptProcessorWrapper
 
editorPane - Variable in class cct.help.HelpPanel
 
editScriptButton - Variable in class cct.grid.ui.gaussian.SubmitGaussianPanel
 
editScriptButton_actionPerformed(ActionEvent) - Method in class cct.grid.ui.gaussian.SubmitGaussianPanel
 
EditScriptDialog - Class in cct.grid.ui
Title: Molecular Structure Viewer/Editor
EditScriptDialog(Frame, String, boolean) - Constructor for class cct.grid.ui.EditScriptDialog
 
EditScriptDialog() - Constructor for class cct.grid.ui.EditScriptDialog
 
editScriptDialog - Variable in class cct.grid.ui.gaussian.SubmitGaussianDialogNew
 
editScriptDialog - Variable in class cct.grid.ui.SubmitTaskDialog
 
editToolBar - Variable in class cct.dialogs.Frame1
 
EffectiveCorepot - Variable in class cct.awtdialogs.AddNewMethodDialog
 
efieldSection - Static variable in class cct.gamess.Gamess
 
efragSection - Static variable in class cct.gamess.Gamess
 
elButt - Variable in class cct.dialogs.JAtomTypeDialog
 
eldensSection - Static variable in class cct.gamess.Gamess
 
element - Variable in class cct.cprocessor.GenericAtom
 
Element - Variable in class cct.dialogs.JModifyAtomPanel
 
element - Variable in class cct.gamess.GamessAtom
 
element - Variable in class cct.gaussian.GaussianAtom
 
Element - Variable in class cct.gulp.GULPAtom
 
Element - Variable in class cct.modelling.AtomTypeDef
 
element - Variable in class cct.modelling.vAtom
 
element - Variable in class cct.mopac.MopacAtom
 
element - Variable in class cct.pdb.PDBAtom
 
element - Variable in class cct.siesta.SiestaInput.SiestaAtom
 
element - Variable in class cct.vasp.VaspAtom
 
Element_itemStateChanged(ItemEvent) - Method in class cct.dialogs.JModifyAtomPanel
 
elementButtons - Variable in class cct.dialogs.JAtomTypeDialog
 
elementColors - Static variable in class cct.j3d.ChemicalElementsColors
 
elementMapping - Variable in class cct.dialogs.JAtomTypeDialog
 
elementMaterial - Static variable in class cct.j3d.ChemicalElementsColors
 
elementName - Static variable in class cct.modelling.ChemicalElements
 
elements - Variable in class cct.awtdialogs.AtomTypeDialog
 
Elements - Variable in class cct.dialogs.JSelectAtomTypesDialog
 
Elements - Variable in class cct.j3d.VerticesObject
 
ELEMENTS_PRESENTATION - Enum in cct.dialogs
Title: Picking
elementsButton - Variable in class cct.dialogs.JAddFragmentDialog
 
elementsCombobox - Variable in class cct.dialogs.JElementsPanel
 
elementSymbol - Static variable in class cct.modelling.ChemicalElements
 
elfldgSection - Static variable in class cct.gamess.Gamess
 
elmonSection - Static variable in class cct.gamess.Gamess
 
elpotSection - Static variable in class cct.gamess.Gamess
 
els14TextField - Variable in class cct.modelling.ui.JSetupEnergyDialog
 
emailKey - Static variable in class cct.tools.ui.PostMessagePanel
 
emailTextField - Variable in class cct.tools.ui.PostMessagePanel
 
emptyIcon - Static variable in class cct.dialogs.JAtomTypesPanel
 
emptyIcon - Static variable in class cct.dialogs.JModifyAtomDialog
 
emptyIcon - Static variable in class cct.modelling.CCTAtomTypes
 
emptyImage - Static variable in class cct.tools.filebrowser.FilePropertiesPanel
 
emptyLabel - Variable in class cct.grid.ui.JobStatusPopupPanel
 
emptyLabel - Variable in class cct.tools.filebrowser.FilePropertiesPanel
 
emptyLabel2 - Variable in class cct.grid.ui.JobStatusPopupPanel
 
emptyPanel - Variable in class cct.j3d.ui.GraphicsObjectPropertiesFrame
 
enable14Energy(boolean) - Method in class cct.modelling.MolecularEnergy
 
enable1NonbondEnergy(boolean) - Method in class cct.modelling.MolecularEnergy
 
ENABLE_EDIT_EXTENSIONS - Static variable in class cct.grid.ui.PBSPanel
 
ENABLE_EDIT_QUEUE - Static variable in class cct.grid.ui.PBSPanel
 
ENABLE_EXTENSIONS - Static variable in class cct.grid.ui.PBSPanel
 
enableAllControls(boolean) - Method in class cct.j3d.ui.VerticesPropertyPanel
 
enableAngleBendEnergy(boolean) - Method in class cct.modelling.MolecularEnergy
 
enableAnimationPanel(boolean) - Method in class cct.chart.ChartFrame
 
enableAnimationPanel(boolean) - Method in class cct.chart.jfreechart.JFreeChartPanel
 
enableAtomInfoPopup(boolean) - Method in class cct.j3d.Java3dUniverse
 
enableAtomPicking(int, boolean) - Method in class cct.j3d.Java3dUniverse
 
enableBondStretchEnergy(boolean) - Method in class cct.modelling.MolecularEnergy
 
enableCalculateElectrostatics(boolean) - Method in interface cct.interfaces.ForceFieldInterface
 
enableCalculateElectrostatics(boolean) - Method in class cct.sff.SimpleForceField
 
enableCheckBoxes(boolean) - Method in class cct.tools.filebrowser.PermissionsPanel
Enables/disables all checkboxes
enableGASS(boolean) - Method in class cct.grid.JobDescription
 
enableHelpKey(Component, String) - Method in class cct.help.JavaHelp
 
enableHelpKey(Component, String, String, String) - Method in class cct.help.JavaHelp
 
enableHelpKey(Component, String) - Method in interface cct.interfaces.HelperInterface
 
enableHelpKey(Component, String, String, String) - Method in interface cct.interfaces.HelperInterface
 
enableInfraredSpectrum(boolean) - Method in class cct.dialogs.SelectPropShowDialog
 
enableInputFile(boolean) - Method in interface cct.grid.ClientProgramInterface
 
enableInputFile(boolean) - Method in class cct.grid.ui.gaussian.SubmitGaussianDialog
 
enableInputFile(boolean) - Method in class cct.grid.ui.gaussian.SubmitGaussianDialogNew
 
enableInputFile(boolean) - Method in class cct.grid.ui.gaussian.SubmitGaussianPanel
 
enableInputFile(boolean) - Method in class cct.grid.ui.SubmitTaskDialog
 
enableInteractiveChart(boolean) - Method in class cct.dialogs.SelectPropShowDialog
 
enableLabels - Variable in class cct.j3d.Java3dUniverse
 
enableLocalDir(boolean) - Method in interface cct.grid.ClientProgramInterface
 
enableLocalDir(boolean) - Method in class cct.grid.ui.gaussian.SubmitGaussianDialog
 
enableLocalDir(boolean) - Method in class cct.grid.ui.gaussian.SubmitGaussianDialogNew
 
enableLocalDir(boolean) - Method in class cct.grid.ui.gaussian.SubmitGaussianPanel
 
enableLocalDir(boolean) - Method in class cct.grid.ui.SubmitTaskDialog
 
enableMaxGradConvergence(boolean) - Method in class cct.math.DFPMin
 
enableMaxGradConvergence(boolean) - Method in interface cct.math.MinimizerInterface
 
enableMaxGRMSConvergence(boolean) - Method in class cct.math.DFPMin
 
enableMaxGRMSConvergence(boolean) - Method in interface cct.math.MinimizerInterface
 
enableMousePicking(boolean) - Method in class cct.j3d.Java3dUniverse
 
enableMousePicking(boolean) - Method in class cct.modelling.MolecularEditor
 
enableMultipleSelection(boolean) - Method in class cct.tools.ui.SelectFromListDialog
 
EnableNewWindowButton(boolean) - Method in class cct.dialogs.AddMoleculeDialog
 
enableNumericalGradients(boolean) - Method in class cct.modelling.MolecularEnergy
 
enablePDepolSpectrum(boolean) - Method in class cct.dialogs.SelectPropShowDialog
 
enableRamanSpectrum(boolean) - Method in class cct.dialogs.SelectPropShowDialog
 
enableSummary(boolean) - Method in class cct.dialogs.SelectPropShowDialog
 
enableTextEditing(boolean) - Method in class cct.tools.ui.JShowText
 
enableTorsionEnergy(boolean) - Method in class cct.modelling.MolecularEnergy
 
enableUDepolSpectrum(boolean) - Method in class cct.dialogs.SelectPropShowDialog
 
enableUseNBCutoff(boolean) - Method in interface cct.interfaces.ForceFieldInterface
 
enableUseNBCutoff(boolean) - Method in class cct.sff.SimpleForceField
 
enableValidateGeometry(boolean) - Method in class cct.gaussian.ui.SimpleG03EditorPanel
 
enableVCDSpectrum(boolean) - Method in class cct.dialogs.SelectPropShowDialog
 
endDocument() - Method in class cct.grid.ParseCheckpointFile.HandleSAXEvents
 
endDocument() - Method in class cct.tools.CCTParser
 
endDocument() - Method in class cct.tools.FragmentDictionaryParser
 
endDocument() - Method in class cct.vasp.VasprunXML
 
endElement(String, String, String) - Method in class cct.grid.ParseCheckpointFile.HandleSAXEvents
 
endElement(String, String, String) - Method in class cct.tools.CCTParser
 
endElement(String, String, String) - Method in class cct.tools.FragmentDictionaryParser
 
endElement(String, String, String) - Method in class cct.vasp.VasprunXML
 
endProcessingSelectedAtoms() - Method in class cct.j3d.Java3dUniverse
 
endProcessingSelectedAtoms() - Method in class cct.modelling.MolecularEditor
 
endSection - Static variable in class cct.gamess.Gamess
 
endSection - Static variable in class cct.qchem.QChem
 
EnergyOverTrajectory - Variable in class cct.amber.Sander8JobControl
 
EnergyOverTrajectory - Variable in class cct.amber.Sander9JobControl
 
energyPanel - Variable in class cct.modelling.ui.JSetupEnergyDialog
 
energySetupMode() - Method in class cct.modelling.ui.JSetupEnergyDialog
 
EnergyThermCorrProperty - Static variable in interface cct.interfaces.MoleculeInterface
 
EnthalpyThermCorrProperty - Static variable in interface cct.interfaces.MoleculeInterface
 
entryLabels - Variable in class cct.gaussian.ui.GaussianInputEditorFrame
 
enumerated - Variable in class cct.amber.Sander8Variable
 
enumerated - Variable in class cct.amber.SanderVariable
 
ENVIRONMENT - Static variable in class cct.grid.JobDescription
 
ePanel - Variable in class cct.dialogs.JAtomTypeDialog
 
EPS - Variable in class cct.math.DFPMin
 
EPS - Variable in class cct.math.Minimizer
 
equals(AtomsArray) - Method in class cct.modelling.AtomsArray
Compares this AtomArray with another
equals(BondsArray) - Method in class cct.modelling.BondsArray
Compares this AtomVector with another
equals(Object) - Method in class cct.modelling.CCTAtomTypes
 
equals(Object) - Method in class cct.tools.filebrowser.FileSize
 
equalsIgnoreCase(String) - Method in class cct.modelling.BasicFragment
 
equalsIgnoreCase(String) - Method in class cct.tools.CCTParserEnum
 
eraseAtoms(Object) - Method in interface cct.cprocessor.MolProcessorInterface
 
eraseAtoms(Object) - Method in class cct.j3d.ScriptProcessorWrapper
 
EraseCommandObject - Enum in cct.cprocessor
Title: Molecular Structure Viewer/Editor
error - Variable in class cct.database.ChemistryDatabaseDialog
 
error - Variable in class cct.database.new_ChemistryDatabaseDialog
 
errorHappened - Variable in class cct.database.SQLDatabaseAccess
 
errorMessage - Variable in class cct.database.new_SQLChemistryDatabase
 
errorMessage - Variable in class cct.database.SQLChemistryDatabase
 
errorMessage - Variable in class cct.database.SQLDatabaseAccess
 
errorsCount - Variable in class cct.gaussian.java3d.VolumetricData
 
ESPChargesProperty - Static variable in interface cct.interfaces.MoleculeInterface
 
eval - Variable in class cct.amber.AmberSubmitDialog
 
eval(float, float, float) - Method in class cct.gaussian.java3d.VolumetricData
 
eval(float, float, float) - Method in interface cct.interfaces.ImplicitFunctionInterface
 
eval(float, float, float) - Method in class cct.poly.ImplicitFunction
 
eval(float, float, float) - Method in interface cct.poly.ImplicitFunctionInterface
 
eval(float, float, float) - Method in class cct.poly.Torus
 
evaluateCompliance(BufferedReader) - Method in class cct.gaussian.InputOrientationParser
 
evaluateCompliance(BufferedReader) - Method in interface cct.interfaces.CoordinateParserInterface
 
evaluateCompliance(BufferedReader) - Method in class cct.pdb.PDB
 
evaluateCompliance(BufferedReader) - Method in class cct.tools.XMolXYZ
 
evaluateExpression(ArrayList<MathExpressionParser.Type>, ArrayList<TYPE>) - Method in class cct.math.MathExpressionParser
 
evaluateFunction(ArrayList<MathExpressionParser.Type>, ArrayList<TYPE>) - Method in class cct.math.MathExpressionParser
We assume, no functions inside
evaluateMemoryRequirement(Sander8JobControl) - Method in class cct.amber.SanderResourcesEval
 
evaluateTimeRequirement(Sander8JobControl) - Method in class cct.amber.SanderResourcesEval
 
evbinButton - Variable in class cct.amber.Sander9JobPanel
 
evbinCheckBox - Variable in class cct.amber.Sander9JobPanel
 
evbinLabel - Variable in class cct.amber.Sander9JobPanel
 
evbinTextField - Variable in class cct.amber.Sander9JobPanel
 
evt - Variable in class cct.j3d.myKeyNavigatorBehavior
 
ewaldVars - Static variable in class cct.amber.Sander8JobControl
 
ewaldVars - Static variable in class cct.amber.Sander9JobControl
 
exception - Variable in class cct.grid.ui.ThreadExec
 
EXECUTABLE - Static variable in class cct.grid.JobDescription
 
executableButton - Variable in class cct.grid.ui.gaussian.SubmitGaussianPanel
 
executableButton_actionPerformed(ActionEvent) - Method in class cct.grid.ui.gaussian.SubmitGaussianPanel
 
executableKey - Static variable in class cct.grid.ui.gaussian.SubmitGaussianPanel
 
executableLabel - Variable in class cct.grid.ui.gaussian.SubmitGaussianPanel
 
executableLabel - Variable in class cct.grid.ui.JobStatusPopupPanel
 
executableTag - Static variable in interface cct.grid.CheckPointInterface
 
executableTextField - Variable in class cct.grid.ui.gaussian.SubmitGaussianPanel
 
executeAddCommand(AddCommandObjects, Object) - Method in class cct.cprocessor.CommandProcessor
 
executeCenterCommand(Object, Object) - Method in class cct.cprocessor.CommandProcessor
 
executeCommand(SFTPBrowser, String) - Method in class cct.ssh.SSHServiceProvider
 
executeEraseCommand(EraseCommandObject, Object) - Method in class cct.cprocessor.CommandProcessor
 
executeLabel - Variable in class cct.tools.filebrowser.PermissionsPanel
 
executeRenderCommand(RenderCommandObject, Object) - Method in class cct.cprocessor.CommandProcessor
 
executeScript() - Method in class cct.cprocessor.CommandProcessor
 
executeScript(ArrayList<Object[]>) - Method in class cct.cprocessor.CommandProcessor
 
existingModification - Variable in class cct.tools.filebrowser.ConfirmFileOverwriteDialog
 
existingSize - Variable in class cct.tools.filebrowser.ConfirmFileOverwriteDialog
 
exitCode - Variable in class cct.modelling.MinimizeStructure
 
exitMenuItem - Variable in class cct.tools.filebrowser.SFTPBrowserFrame
 
Exp - Variable in class cct.awtdialogs.AddNewMethodDialog
 
Experimental - Class in cct.tools
Title:
Experimental() - Constructor for class cct.tools.Experimental
 
extCheckBox - Variable in class cct.grid.ui.PBS_Panel
 
extCheckBox - Variable in class cct.grid.ui.PBSPanel
 
EXTDIEL_Label - Variable in class cct.amber.Sander8Frame
 
EXTDIEL_Label - Variable in class cct.amber.Sander9Frame
 
EXTDIEL_Label_mouseEntered(MouseEvent) - Method in class cct.amber.Sander8Frame
 
EXTDIEL_Label_mouseEntered(MouseEvent) - Method in class cct.amber.Sander9Frame
 
EXTDIEL_TextField - Variable in class cct.amber.Sander8Frame
 
EXTDIEL_TextField - Variable in class cct.amber.Sander9Frame
 
extension_ADF_Input - Static variable in class cct.modelling.MolecularFileFormats
 
extension_ADF_Output - Static variable in class cct.modelling.MolecularFileFormats
 
extension_All_Formats - Static variable in class cct.modelling.MolecularFileFormats
 
extension_Ambercrd - Static variable in class cct.modelling.MolecularFileFormats
 
extension_AmberLib - Static variable in class cct.modelling.MolecularFileFormats
 
extension_AmberTraj - Static variable in class cct.modelling.MolecularFileFormats
 
extension_CCT - Static variable in class cct.modelling.MolecularFileFormats
 
extension_G03_Cube - Static variable in class cct.modelling.MolecularFileFormats
 
extension_G03_FormCheckpoint - Static variable in class cct.modelling.MolecularFileFormats
 
extension_G03_Fragment - Static variable in class cct.modelling.MolecularFileFormats
 
extension_G03_GJF - Static variable in class cct.modelling.MolecularFileFormats
 
extension_G03_Output - Static variable in class cct.modelling.MolecularFileFormats
 
extension_G03_Trajectory - Static variable in class cct.modelling.MolecularFileFormats
 
extension_GAMESS_Input - Static variable in class cct.modelling.MolecularFileFormats
 
extension_GAMESS_Output - Static variable in class cct.modelling.MolecularFileFormats
 
extension_Geom - Static variable in class cct.modelling.MolecularFileFormats
 
extension_GRO - Static variable in class cct.modelling.MolecularFileFormats
 
extension_GULP_Input - Static variable in class cct.modelling.MolecularFileFormats
 
extension_GULP_Trajectory - Static variable in class cct.modelling.MolecularFileFormats
 
extension_MDL_Molfile - Static variable in class cct.modelling.MolecularFileFormats
 
extension_Mol2 - Static variable in class cct.modelling.MolecularFileFormats
 
extension_MOPAC_Input - Static variable in class cct.modelling.MolecularFileFormats
 
extension_MOPAC_Log - Static variable in class cct.modelling.MolecularFileFormats
 
extension_MOPAC_Output - Static variable in class cct.modelling.MolecularFileFormats
 
extension_PDB - Static variable in class cct.modelling.MolecularFileFormats
 
extension_Povray - Static variable in class cct.modelling.MolecularFileFormats
 
extension_Prep - Static variable in class cct.modelling.MolecularFileFormats
 
extension_Prmtop - Static variable in class cct.modelling.MolecularFileFormats
 
extension_QChem_Input - Static variable in class cct.modelling.MolecularFileFormats
 
extension_QChem_Output - Static variable in class cct.modelling.MolecularFileFormats
 
extension_SIESTA_Input - Static variable in class cct.modelling.MolecularFileFormats
 
extension_VASP_POSCAR - Static variable in class cct.modelling.MolecularFileFormats
 
extension_VASP_Vasprun - Static variable in class cct.modelling.MolecularFileFormats
 
extension_VRML - Static variable in class cct.modelling.MolecularFileFormats
 
extension_XMol_XYZ - Static variable in class cct.modelling.MolecularFileFormats
 
EXTENSIONS - Static variable in class cct.grid.JobDescription
 
Extensions - Variable in class cct.tools.FileFilterImpl
 
extensions16x16 - Static variable in class cct.tools.FileUtilities
 
extensions32x32 - Static variable in class cct.tools.FileUtilities
 
extensionsPanel - Variable in class cct.grid.ui.PBSPanel
 
external_chargesSection - Static variable in class cct.qchem.QChem
 
extractGeometry(String, MoleculeInterface) - Static method in class cct.gaussian.GaussianCube
 
extraParam - Variable in class cct.gaussian.GaussianAtom
 

F

F - Variable in class cct.math.Minimizer
 
F - Static variable in class cct.poly.CUBETABLE
 
F - Static variable in class cct.poly.Polygonizer
 
F0 - Variable in class cct.math.Simplex
 
Face - Class in cct.oogl
Title:
Face() - Constructor for class cct.oogl.Face
 
Face(int[]) - Constructor for class cct.oogl.Face
 
Face - Class in cct.tools
Title: Molecular Structure Viewer/Editor
Face() - Constructor for class cct.tools.Face
 
Face(int[]) - Constructor for class cct.tools.Face
 
facebit - Static variable in class cct.poly.PROCESS
 
FaceIndices - Class in cct.vecmath
Title:
FaceIndices() - Constructor for class cct.vecmath.FaceIndices
 
FaceIndices(int, int, int) - Constructor for class cct.vecmath.FaceIndices
 
faceIndices - Variable in class cct.vecmath.MeshObject
 
faces - Variable in class cct.oogl.OOGL
 
faces - Variable in class cct.tools.OOGL
 
Factor - Static variable in class cct.modelling.AtomGenerator
 
factory - Variable in class cct.grid.ui.JobStatusPanel
 
factory - Variable in class cct.j3d.MyMouseMotionListener
 
FACTORYENDPOINT - Static variable in class cct.grid.JobDescription
 
fastGroup - Variable in class cct.j3d.Java3dUniverse
 
FCAP_Label - Variable in class cct.amber.Sander8Frame
 
FCAP_Label - Variable in class cct.amber.Sander9Frame
 
FCAP_Label_mouseEntered(MouseEvent) - Method in class cct.amber.Sander8Frame
 
FCAP_Label_mouseEntered(MouseEvent) - Method in class cct.amber.Sander9Frame
 
FCAP_TextField - Variable in class cct.amber.Sander8Frame
 
FCAP_TextField - Variable in class cct.amber.Sander9Frame
 
fetchButton - Variable in class cct.pdb.ui.PDBFormFrame
 
Fetcher - Variable in class cct.pdb.ui.PDBFormFrame
 
fetchStructure(String, String, String) - Method in class cct.dialogs.JEditorFrame
 
fetchStructure(String, String, String) - Method in interface cct.pdb.PDBBankFetcherInterface
 
FF_Label - Variable in class cct.adf.ADFAtom
 
FF_LABEL_PROP - Static variable in class cct.adf.ADF
 
ffcalcSection - Static variable in class cct.gamess.Gamess
 
FFMolecule - Class in cct.modelling
Title:
FFMolecule(MoleculeInterface) - Constructor for class cct.modelling.FFMolecule
 
ffMolecule - Variable in class cct.modelling.MinimizeStructure
 
ffMolecule - Variable in class cct.modelling.MolecularEnergy
 
ffName - Static variable in class cct.sff.SimpleForceField
 
fg - Static variable in class cct.j3d.ui.ColorGradientPanel
 
fGetOffset(float, float, float) - Method in class cct.math.polyg.Polygonizer
 
fgrrplSection - Static variable in class cct.gamess.Gamess
 
fieldOfView - Variable in class cct.povray.Povray
 
fieldsEdited - Variable in class cct.gaussian.ui.SimpleG03EditorPanel
 
FILE - Static variable in class cct.tools.filebrowser.FileName
 
fileBrowser - Variable in class cct.tools.filebrowser.FileBrowserPanel
 
fileBrowser - Variable in class cct.tools.filebrowser.JFileBrowserPanel
 
fileBrowser - Variable in class cct.tools.filebrowser.SFTPObject
 
FileBrowserGUIInterface - Interface in cct.interfaces
Title:
FileBrowserInterface - Interface in cct.interfaces
Title:
FileBrowserPanel - Class in cct.tools.filebrowser
Title:
FileBrowserPanel() - Constructor for class cct.tools.filebrowser.FileBrowserPanel
 
FileBrowserPanel(FileBrowserInterface) - Constructor for class cct.tools.filebrowser.FileBrowserPanel
 
fileBrowserPanel1 - Variable in class cct.tools.filebrowser.SFTPFileChooserDialog
 
FileBrowserPanel_deleteButton_actionAdapter - Class in cct.tools.filebrowser
 
FileBrowserPanel_deleteButton_actionAdapter(FileBrowserPanel) - Constructor for class cct.tools.filebrowser.FileBrowserPanel_deleteButton_actionAdapter
 
FileBrowserPanel_downloadButton_actionAdapter - Class in cct.tools.filebrowser
 
FileBrowserPanel_downloadButton_actionAdapter(FileBrowserPanel) - Constructor for class cct.tools.filebrowser.FileBrowserPanel_downloadButton_actionAdapter
 
FileBrowserPanel_jComboBox1_actionAdapter - Class in cct.tools.filebrowser
 
FileBrowserPanel_jComboBox1_actionAdapter(FileBrowserPanel) - Constructor for class cct.tools.filebrowser.FileBrowserPanel_jComboBox1_actionAdapter
 
FileBrowserPanel_jComboBox1_itemAdapter - Class in cct.tools.filebrowser
 
FileBrowserPanel_jComboBox1_itemAdapter(FileBrowserPanel) - Constructor for class cct.tools.filebrowser.FileBrowserPanel_jComboBox1_itemAdapter
 
FileBrowserPanel_mkdirButton_actionAdapter - Class in cct.tools.filebrowser
 
FileBrowserPanel_mkdirButton_actionAdapter(FileBrowserPanel) - Constructor for class cct.tools.filebrowser.FileBrowserPanel_mkdirButton_actionAdapter
 
FileBrowserPanel_refreshButton_actionAdapter - Class in cct.tools.filebrowser
 
FileBrowserPanel_refreshButton_actionAdapter(FileBrowserPanel) - Constructor for class cct.tools.filebrowser.FileBrowserPanel_refreshButton_actionAdapter
 
FileBrowserPanel_upButton_actionAdapter - Class in cct.tools.filebrowser
 
FileBrowserPanel_upButton_actionAdapter(FileBrowserPanel) - Constructor for class cct.tools.filebrowser.FileBrowserPanel_upButton_actionAdapter
 
FileBrowserTableModel - Class in cct.tools.filebrowser
Title: Molecular Structure Viewer/Editor
FileBrowserTableModel(Object[][]) - Constructor for class cct.tools.filebrowser.FileBrowserTableModel
 
FileBrowserTableModel(String[], Object[][]) - Constructor for class cct.tools.filebrowser.FileBrowserTableModel
 
FileBrowserTableModel(ArrayList) - Constructor for class cct.tools.filebrowser.FileBrowserTableModel
 
fileChooser - Variable in class cct.dialogs.TrajectoriesManagerPanel
 
fileChooser - Variable in class cct.gaussian.ui.SaveG03GJFDialog
 
fileChooser - Variable in class cct.tools.filebrowser.SFTPObject
 
fileChooserDialog - Variable in class cct.ssh.SSHPanel
 
FileChooserDialog - Class in cct.tools.filebrowser
Title:
FileChooserDialog(Frame, String, boolean, FileBrowserInterface) - Constructor for class cct.tools.filebrowser.FileChooserDialog
 
FileChooserDialog - Class in cct.tools.ui
Title:
FileChooserDialog(FileFilter[], Component, String, int) - Constructor for class cct.tools.ui.FileChooserDialog
 
FileChooserInterface - Interface in cct.interfaces
Title:
FILECLEANUP - Static variable in class cct.grid.JobDescription
 
fileComboBox - Variable in class cct.gaussian.ui.GaussianInputEditorFrame
 
fileContent - Variable in class cct.amber.AmberSubmitDialog
 
fileContent - Variable in class cct.amber.Sander8Frame
 
fileContent - Variable in class cct.amber.Sander9Frame
 
FileFilterImpl - Class in cct.tools
 
FileFilterImpl() - Constructor for class cct.tools.FileFilterImpl
 
fileFilters - Variable in class cct.tools.filebrowser.SFTPFileChooserDialog
 
fileLocationLabel - Variable in class cct.tools.filebrowser.FilePropertiesPanel
 
fileMenu - Variable in class cct.tools.filebrowser.SFTPBrowserFrame
 
fileMenu - Variable in class cct.tools.ui.LogPanel
 
fileModifiedLabel - Variable in class cct.tools.filebrowser.FilePropertiesPanel
 
fileName - Variable in class cct.amber.AmberSubmitMenuHandler
 
fileName - Variable in class cct.amber.Sander8Frame
 
fileName - Variable in class cct.amber.Sander9Frame
 
fileName - Variable in class cct.amber.TextEditorFrame
 
fileName - Variable in class cct.gaussian.ui.GaussianInputEditorFrame
 
fileName - Variable in class cct.modelling.SingleTrajectory
 
FileName - Class in cct.tools.filebrowser
Title:
FileName(String) - Constructor for class cct.tools.filebrowser.FileName
 
FileName(String, int) - Constructor for class cct.tools.filebrowser.FileName
 
fileName - Variable in class cct.tools.filebrowser.FileName
 
fileNameLabel - Variable in class cct.tools.filebrowser.ConfirmFileOverwriteDialog
 
fileNameLabel - Variable in class cct.tools.filebrowser.FilePropertiesPanel
 
FileNameRenderer - Class in cct.tools.filebrowser
Title:
FileNameRenderer(boolean) - Constructor for class cct.tools.filebrowser.FileNameRenderer
 
filePopup - Variable in class cct.tools.filebrowser.SFTPBrowser
 
fileProperties - Variable in class cct.tools.filebrowser.FilePropertiesDialog
 
FilePropertiesDialog - Class in cct.tools.filebrowser
Title:
FilePropertiesDialog(Frame, String) - Constructor for class cct.tools.filebrowser.FilePropertiesDialog
 
FilePropertiesDialog() - Constructor for class cct.tools.filebrowser.FilePropertiesDialog
 
FilePropertiesPanel - Class in cct.tools.filebrowser
Title:
FilePropertiesPanel() - Constructor for class cct.tools.filebrowser.FilePropertiesPanel
 
fileProps - Variable in class cct.tools.filebrowser.SFTPBrowser
 
fileScrollPane - Variable in class cct.tools.filebrowser.FileBrowserPanel
 
fileScrollPane - Variable in class cct.tools.filebrowser.JFileBrowserPanel
 
FileSize - Class in cct.tools.filebrowser
Title:
FileSize(String) - Constructor for class cct.tools.filebrowser.FileSize
Creates a new FileSize object.
FileSize(byte[]) - Constructor for class cct.tools.filebrowser.FileSize
Creates a new FileSize object.
FileSize(BigInteger) - Constructor for class cct.tools.filebrowser.FileSize
Creates a new FileSize object.
fileSizeLabel - Variable in class cct.tools.filebrowser.FilePropertiesPanel
 
FileSizeRenderer - Class in cct.tools.filebrowser
Title:
FileSizeRenderer() - Constructor for class cct.tools.filebrowser.FileSizeRenderer
 
filesPanel - Variable in class cct.vasp.ui.ReadPoscarDialog
 
FILESTAGEIN - Static variable in class cct.grid.JobDescription
 
fileStageIn(JobDescription, boolean) - Method in class cct.ssh.SFTPFileStaging
 
FILESTAGEOUT - Static variable in class cct.grid.JobDescription
 
filesToDownload - Variable in class cct.tools.filebrowser.SFTPBrowser.FileTranferWorker
 
filesToUpload - Variable in class cct.tools.filebrowser.SFTPBrowser.FileTranferWorker
 
fileTextField - Variable in class cct.dialogs.JSolvateShellDialog
 
fileTextField - Variable in class cct.tools.filebrowser.SFTPFileChooserDialog
 
fileTextField_actionPerformed(ActionEvent) - Method in class cct.tools.filebrowser.SFTPFileChooserDialog
 
FileTransferFrame - Class in cct.tools.filebrowser
Title:
FileTransferFrame(FTPManagerInterface) - Constructor for class cct.tools.filebrowser.FileTransferFrame
 
FileTransferFrame.HostComboBoxRenderer - Class in cct.tools.filebrowser
 
FileTransferFrame.HostComboBoxRenderer() - Constructor for class cct.tools.filebrowser.FileTransferFrame.HostComboBoxRenderer
 
FileTransferFrame.HostEditor - Class in cct.tools.filebrowser
 
FileTransferFrame.HostEditor() - Constructor for class cct.tools.filebrowser.FileTransferFrame.HostEditor
 
FileTransferFrame_connectButton_actionAdapter - Class in cct.tools.filebrowser
 
FileTransferFrame_connectButton_actionAdapter(FileTransferFrame) - Constructor for class cct.tools.filebrowser.FileTransferFrame_connectButton_actionAdapter
 
FileTransferFrame_hostsComboBox_actionAdapter - Class in cct.tools.filebrowser
 
FileTransferFrame_hostsComboBox_actionAdapter(FileTransferFrame) - Constructor for class cct.tools.filebrowser.FileTransferFrame_hostsComboBox_actionAdapter
 
FileTransferInterface - Interface in cct.grid
Title: Molecular Structure Viewer/Editor
FileTransferPanel - Class in cct.tools.filebrowser
Title:
FileTransferPanel() - Constructor for class cct.tools.filebrowser.FileTransferPanel
 
FileTransferPanel(FileBrowserInterface) - Constructor for class cct.tools.filebrowser.FileTransferPanel
 
fileTransferPanel1 - Variable in class cct.tools.filebrowser.FileTransferFrame
 
fileType - Variable in class cct.tools.filebrowser.FileName
 
fileTypeLabel - Variable in class cct.tools.filebrowser.FilePropertiesPanel
 
fileTypesHelpButton - Variable in class cct.tools.filebrowser.SFTPFileChooserDialog
 
fileTypesHelpButton_actionPerformed(ActionEvent) - Method in class cct.tools.filebrowser.SFTPFileChooserDialog
 
FileUsage - Variable in class cct.amber.Sander8JobControl
 
FileUsage - Variable in class cct.amber.Sander9JobControl
 
FileUtilities - Class in cct.tools
Title:
fileViewer - Variable in class cct.grid.ui.JobStatusPanel
 
FileViewerInterface - Interface in cct.grid
Title: Molecular Structure Viewer/Editor
fillEmptyValences(AtomInterface) - Method in class cct.j3d.Java3dUniverse
 
fillEmptyValences(MoleculeInterface, AtomInterface, String, HashMap) - Static method in class cct.modelling.AtomGenerator
 
filter - Variable in class cct.j3d.GroupToVRML
 
filter - Variable in class cct.povray.Povray
 
Filter - Variable in class cct.tools.filebrowser.SFTPBrowser
 
filter - Variable in class cct.tools.GeomFormat
 
filterComboBox - Variable in class cct.tools.filebrowser.SFTPFileChooserDialog
 
filterComboBox_itemStateChanged(ItemEvent) - Method in class cct.tools.filebrowser.SFTPFileChooserDialog
 
final_name - Variable in class cct.awtdialogs.AddNewMethodDialog
 
find - Variable in class cct.j3d.MyMouseMotionListener
 
find(int, float, float, float) - Method in class cct.poly.PROCESS
 
find14Interactions(MoleculeInterface, ArrayList) - Static method in class cct.modelling.FFMolecule
 
find2(int, float[], float[]) - Method in class cct.poly.PROCESS
find: search for point with value of given sign (0: neg, 1: pos)
findAndParseFortranNamelist(String, String) - Method in class cct.tools.FortranNamelist
 
findAndParseFortranNamelist(BufferedReader, String) - Method in class cct.tools.FortranNamelist
 
findBoundaries() - Method in class cct.modelling.Molecule
 
findClosestAtom(Point3d, Vector3d) - Method in class cct.j3d.Java3dUniverse
 
findClosestAtom(int, int) - Method in class cct.j3d.Java3dUniverse
 
findClosestBond(Point3d, Vector3d) - Method in class cct.j3d.Java3dUniverse
 
findClosestBond(int, int) - Method in class cct.j3d.Java3dUniverse
 
findDynamicAngles(MoleculeInterface) - Static method in class cct.modelling.FFMolecule
Finds all valent angles where at least one atom forming angle is dynamic
findDynamicTorsions(MoleculeInterface) - Static method in class cct.modelling.FFMolecule
Finds all regular torsions in molecule
findFragmentSet(ClassLoader, String) - Static method in class cct.tools.IOUtils
 
findNonbondedPairs(MoleculeInterface, Nonbonded15Table) - Static method in class cct.modelling.FFMolecule
 
Finish - Variable in class cct.dialogs.JModifyAngleDialog
 
Finish - Variable in class cct.dialogs.JModifyTorsionDialog
 
Finish_actionPerformed(ActionEvent) - Method in class cct.dialogs.JModifyAngleDialog
 
Finish_actionPerformed(ActionEvent) - Method in class cct.dialogs.JModifyTorsionDialog
 
finish_parsing - Variable in class cct.grid.ParseCheckpointFile
 
finish_parsing - Variable in class cct.tools.CCTParser
 
finish_parsing - Variable in class cct.tools.FragmentDictionaryParser
 
finishButton - Variable in class cct.dialogs.JAddFragmentDialog
 
finishButton - Variable in class cct.dialogs.JSelectTreeDialog
 
finishButton_actionPerformed(ActionEvent) - Method in class cct.dialogs.JSelectTreeDialog
 
finished() - Method in class cct.tools.filebrowser.SFTPBrowser.FileTranferWorker
Called on the event dispatching thread (not on the worker thread) after the construct method has returned.
finished() - Method in class cct.tools.SwingWorker
Called on the event dispatching thread (not on the worker thread) after the construct method has returned.
firstAtom() - Method in class cct.modelling.AtomsArray
Returns first atom in AtomVector
firstBond() - Method in class cct.modelling.BondsArray
Returns first atom in AtomVector
firstLevelTags - Static variable in interface cct.grid.CheckPointInterface
 
Fixed_1 - Variable in class cct.dialogs.JModifyAngleDialog
 
Fixed_1 - Variable in class cct.dialogs.JModifyBondDialog
 
Fixed_1 - Variable in class cct.dialogs.JModifyTorsionDialog
 
Fixed_1_stateChanged(ChangeEvent) - Method in class cct.dialogs.JModifyAngleDialog
 
Fixed_1_stateChanged(ChangeEvent) - Method in class cct.dialogs.JModifyBondDialog
 
Fixed_1_stateChanged(ChangeEvent) - Method in class cct.dialogs.JModifyTorsionDialog
 
Fixed_2 - Variable in class cct.dialogs.JModifyAngleDialog
 
Fixed_2 - Variable in class cct.dialogs.JModifyBondDialog
 
Fixed_2_stateChanged(ChangeEvent) - Method in class cct.dialogs.JModifyAngleDialog
 
Fixed_2_stateChanged(ChangeEvent) - Method in class cct.dialogs.JModifyBondDialog
 
Fixed_3 - Variable in class cct.dialogs.JModifyAngleDialog
 
Fixed_3_stateChanged(ChangeEvent) - Method in class cct.dialogs.JModifyAngleDialog
 
Fixed_4 - Variable in class cct.dialogs.JModifyTorsionDialog
 
Fixed_4_stateChanged(ChangeEvent) - Method in class cct.dialogs.JModifyTorsionDialog
 
FIXED_ATOM - Static variable in interface cct.modelling.OperationsOnAtoms
 
fixedBasis - Variable in class cct.awtdialogs.AddNewMethodDialog
 
Fk - Variable in class cct.modelling.AngleBend
 
Fk - Variable in class cct.modelling.HarmonicBondStretch
 
Fk - Variable in class cct.sff.AngleParam
 
Fk - Variable in class cct.sff.BondParam
 
FK_GRAD_2_RAD_FACTOR - Static variable in class cct.sff.SimpleForceField
 
FLIP(int, int) - Static method in class cct.poly.Polygonizer
 
FLIP(int, int) - Method in class cct.poly.PROCESS
 
floatValue() - Method in class cct.tools.filebrowser.FileSize
 
flowLayout1 - Variable in class cct.amber.Sander8Frame_AboutBox
 
flowLayout1 - Variable in class cct.amber.Sander9Frame_AboutBox
 
flowLayout1 - Variable in class cct.dialogs.Frame1_AboutBox
 
flowLayout1 - Variable in class cct.dialogs.JAddMoleculeDialog
 
flowLayout1 - Variable in class cct.dialogs.JAtomTypeDialog
 
flowLayout1 - Variable in class cct.dialogs.JAtomTypesPanel
 
flowLayout1 - Variable in class cct.dialogs.JChoiceDialog
 
flowLayout1 - Variable in class cct.dialogs.JModifyAngleDialog
 
flowLayout1 - Variable in class cct.dialogs.JModifyAtomDialog
 
flowLayout1 - Variable in class cct.dialogs.JModifyAtomPanel
 
flowLayout1 - Variable in class cct.dialogs.JModifyTorsionDialog
 
flowLayout1 - Variable in class cct.dialogs.JSolvateShellDialog
 
flowLayout1 - Variable in class cct.dialogs.JThreeButtonsPanel
 
flowLayout1 - Variable in class cct.dialogs.SaveXYZDialog
 
flowLayout1 - Variable in class cct.gaussian.ui.GaussianInputEditorFrame_AboutBox
 
flowLayout1 - Variable in class cct.gaussian.ui.ManageCubesFrame
 
flowLayout1 - Variable in class cct.grid.TaskProviderPanel
 
flowLayout1 - Variable in class cct.grid.ui.gaussian.SubmitGaussianDialog
 
flowLayout1 - Variable in class cct.grid.ui.gaussian.SubmitGaussianDialogNew
 
flowLayout1 - Variable in class cct.grid.ui.gaussian.SubmitGaussianFrame_AboutBox
 
flowLayout1 - Variable in class cct.grid.ui.PBSPanel
 
flowLayout1 - Variable in class cct.grid.ui.ResourcesPanel
 
flowLayout1 - Variable in class cct.grid.ui.SubmitTaskDialog
 
flowLayout1 - Variable in class cct.j3d.ui.ControlColorGradientPanel
 
flowLayout1 - Variable in class cct.j3d.ui.GraphicsObjectPropertiesFrame
 
flowLayout1 - Variable in class cct.j3d.ui.VerticesPropertyPanel
 
flowLayout1 - Variable in class cct.modelling.ui.JSetupEnergyDialog
 
flowLayout1 - Variable in class cct.oogl.ui.OOGLViewerFrame_AboutBox
 
flowLayout1 - Variable in class cct.pdb.ui.PDBFormFrame
 
flowLayout1 - Variable in class cct.tools.filebrowser.ConfirmFileOverwriteDialog
 
flowLayout1 - Variable in class cct.tools.filebrowser.FileBrowserPanel
 
flowLayout1 - Variable in class cct.tools.filebrowser.FilePropertiesPanel
 
flowLayout1 - Variable in class cct.tools.filebrowser.JFileBrowserPanel
 
flowLayout1 - Variable in class cct.tools.ui.JPEGOptionsPanel
 
flowLayout2 - Variable in class cct.amber.Sander8Frame
 
flowLayout2 - Variable in class cct.amber.Sander9Frame
 
flowLayout2 - Variable in class cct.dialogs.JAddMoleculeDialog
 
flowLayout2 - Variable in class cct.dialogs.JChoiceDialog
 
flowLayout2 - Variable in class cct.dialogs.JModifyAtomPanel
 
flowLayout2 - Variable in class cct.dialogs.SaveXYZDialog
 
flowLayout2 - Variable in class cct.gaussian.ui.GaussianInputEditorFrame
 
flowLayout2 - Variable in class cct.grid.ui.gaussian.SubmitGaussianDialog
 
flowLayout2 - Variable in class cct.grid.ui.gaussian.SubmitGaussianDialogNew
 
flowLayout2 - Variable in class cct.grid.ui.SubmitTaskDialog
 
flowLayout2 - Variable in class cct.j3d.ui.VerticesPropertyPanel
 
flowLayout2 - Variable in class cct.modelling.ui.JSetupEnergyDialog
 
flowLayout2 - Variable in class cct.tools.ui.FontSelectorPanel
 
flowLayout2 - Variable in class cct.tools.ui.JPEGOptionsPanel
 
flowLayout3 - Variable in class cct.amber.Sander8Frame
 
flowLayout3 - Variable in class cct.amber.Sander9Frame
 
flowLayout3 - Variable in class cct.dialogs.JChoiceDialog
 
flowLayout3 - Variable in class cct.dialogs.JModifyAtomPanel
 
flush() - Method in class cct.tools.ui.JTextAreaOutputStream
Flushes this output stream and forces any buffered output bytes to be written out.
fMax - Variable in class cct.j3d.ColorRangeScheme
 
fMax - Variable in class cct.j3d.ui.ColorGradientPanel
 
fMin - Variable in class cct.j3d.ColorRangeScheme
 
fMin - Variable in class cct.j3d.ui.ColorGradientPanel
 
Fmin - Variable in class cct.math.Amoeba
 
fMin - Variable in class cct.math.LinearSearch
 
focusLost(FocusEvent) - Method in class cct.tools.filebrowser.PermissionsPanel_modeTextField_focusAdapter
 
fog - Variable in class cct.j3d.Java3dUniverse
 
FOLDER - Static variable in class cct.tools.filebrowser.FileName
 
folder - Static variable in class cct.tools.filebrowser.FileNameRenderer
 
folder - Static variable in class cct.tools.FileUtilities
 
folder_32x32 - Static variable in class cct.tools.FileUtilities
 
folderLabel - Variable in class cct.tools.filebrowser.ConfirmFileOverwriteDialog
 
fontChoice - Variable in class cct.tools.ui.FontSelectorPanel
 
fontComboBox - Variable in class cct.tools.ui.FontSelectorPanel
 
fontMenu - Variable in class cct.dialogs.JAtomTypeDialog
 
fontMetrics - Variable in class cct.j3d.ui.ColorGradientPanel
 
fontName - Variable in class cct.gaussian.ui.GaussianInputEditorFrame
 
fontName - Variable in class cct.j3d.LabelNode
 
FontNameKey - Static variable in class cct.gaussian.ui.GaussianInputEditorFrame
 
FontNameKey - Static variable in class cct.grid.ui.EditScriptDialog
 
FontNameKey - Static variable in class cct.tools.ui.LogPanel
 
fontSelector - Variable in class cct.gaussian.ui.GaussianInputEditorFrame
 
fontSelector - Variable in class cct.grid.ui.EditScriptDialog
 
fontSelector - Variable in class cct.tools.ui.LogPanel
 
FontSelectorDialog - Class in cct.tools.ui
Title:
FontSelectorDialog(Frame, String, boolean) - Constructor for class cct.tools.ui.FontSelectorDialog
 
FontSelectorDialog() - Constructor for class cct.tools.ui.FontSelectorDialog
 
FontSelectorPanel - Class in cct.tools.ui
Title:
FontSelectorPanel() - Constructor for class cct.tools.ui.FontSelectorPanel
 
fontSelectorPanel1 - Variable in class cct.tools.ui.FontSelectorDialog
 
fontSize - Variable in class cct.j3d.LabelNode
 
FontSizeKey - Static variable in class cct.gaussian.ui.GaussianInputEditorFrame
 
FontSizeKey - Static variable in class cct.grid.ui.EditScriptDialog
 
FontSizeKey - Static variable in class cct.tools.ui.LogPanel
 
fontStyle - Variable in class cct.j3d.LabelNode
 
FontStyleKey - Static variable in class cct.gaussian.ui.GaussianInputEditorFrame
 
FontStyleKey - Static variable in class cct.grid.ui.EditScriptDialog
 
FontStyleKey - Static variable in class cct.tools.ui.LogPanel
 
forceEvalButton_actionPerformed(ActionEvent) - Method in class cct.amber.Sander8Frame
 
forceEvalButton_actionPerformed(ActionEvent) - Method in class cct.amber.Sander9Frame
 
forceField - Variable in class cct.modelling.MinimizeStructure
 
forceFieldComboBox - Variable in class cct.modelling.ui.JSetupEnergyDialog
 
forceFieldComboBox_actionPerformed(ActionEvent) - Method in class cct.modelling.ui.JSetupEnergyDialog
 
ForceFieldInterface - Interface in cct.interfaces
Title:
forceFields - Variable in class cct.modelling.ui.JSetupEnergyDialog
 
forceSection - Static variable in class cct.gamess.Gamess
 
FORK_SCHEDULER - Static variable in class cct.grid.TaskScheduler
 
formAngleBendInteractions(int, AngleBendsArray) - Method in class cct.modelling.FFMolecule
 
Format - Variable in class cct.modelling.TrajectorySnapshot
 
format_ADF_Input - Static variable in class cct.modelling.MolecularFileFormats
 
format_ADF_Output - Static variable in class cct.modelling.MolecularFileFormats
 
format_AmberCrd - Static variable in class cct.modelling.MolecularFileFormats
 
format_G03_FormCheckpoint - Static variable in class cct.modelling.MolecularFileFormats
 
format_G03_Trajectory - Static variable in class cct.modelling.MolecularFileFormats
 
format_GAMESS_Input - Static variable in class cct.modelling.MolecularFileFormats
 
format_GAMESS_Output - Static variable in class cct.modelling.MolecularFileFormats
 
format_GRO - Static variable in class cct.modelling.MolecularFileFormats
 
format_GULP_Input - Static variable in class cct.modelling.MolecularFileFormats
 
format_GULP_Trajectory - Static variable in class cct.modelling.MolecularFileFormats
 
format_MDL_Molfile - Static variable in class cct.modelling.MolecularFileFormats
 
format_MOPAC_Input - Static variable in class cct.modelling.MolecularFileFormats
 
format_MOPAC_Log - Static variable in class cct.modelling.MolecularFileFormats
 
format_MOPAC_Output - Static variable in class cct.modelling.MolecularFileFormats
 
format_Povray - Static variable in class cct.modelling.MolecularFileFormats
 
format_Prmtop - Static variable in class cct.modelling.MolecularFileFormats
 
format_QChem_Input - Static variable in class cct.modelling.MolecularFileFormats
 
format_QChem_Output - Static variable in class cct.modelling.MolecularFileFormats
 
format_SIESTA_Input - Static variable in class cct.modelling.MolecularFileFormats
 
format_VASP_Poscar - Static variable in class cct.modelling.MolecularFileFormats
 
format_VASP_Vasprun - Static variable in class cct.modelling.MolecularFileFormats
 
format_XMol_XYZ - Static variable in class cct.modelling.MolecularFileFormats
 
formatCCT - Static variable in class cct.modelling.MolecularFileFormats
 
formatComboBox_actionPerformed(ActionEvent) - Method in class cct.siesta.ui.SiestaPanel
 
formatG03_Cube - Static variable in class cct.modelling.MolecularFileFormats
 
formatG03_Fragment - Static variable in class cct.modelling.MolecularFileFormats
 
formatG03_GJF - Static variable in class cct.modelling.MolecularFileFormats
 
formatG03_Output - Static variable in class cct.modelling.MolecularFileFormats
 
FormatManager - Class in cct.modelling
Title: Computational Chemistry Tookit
FormatManager() - Constructor for class cct.modelling.FormatManager
 
FormatManager.ParserComparator - Class in cct.modelling
 
FormatManager.ParserComparator() - Constructor for class cct.modelling.FormatManager.ParserComparator
 
FormatManager.ParserScore - Class in cct.modelling
 
FormatManager.ParserScore(CoordParser, double) - Constructor for class cct.modelling.FormatManager.ParserScore
 
formatPDB - Static variable in class cct.modelling.MolecularFileFormats
 
FORMATS_XML_FILE - Static variable in class cct.GlobalSettings
 
formatTripos_Mol2 - Static variable in class cct.modelling.MolecularFileFormats
 
formatUnknown - Static variable in class cct.modelling.MolecularFileFormats
 
formBondStretchInteractions(int, int) - Method in class cct.modelling.FFMolecule
 
formChemicalSpeciesLabels(MoleculeInterface) - Static method in class cct.siesta.Siesta
Creates a new set of ChemicalSpeciesLabels
formFFParameters() - Method in class cct.modelling.FFMolecule
 
formTorsionInteractions(int, ArrayList) - Method in class cct.modelling.FFMolecule
 
formTrajectoryFileFilters() - Static method in class cct.modelling.MolecularFileFormats
 
formTrajectoryFileRef() - Static method in class cct.modelling.MolecularFileFormats
 
formula - Variable in class cct.database.ChemistryDatabaseDialog
 
formula - Variable in class cct.database.new_ChemistryDatabaseDialog
 
FortranNamelist - Class in cct.tools
 
FortranNamelist() - Constructor for class cct.tools.FortranNamelist
 
fpsModel - Variable in class cct.dialogs.AnimationPanel
 
fpsSpinner - Variable in class cct.dialogs.AnimationPanel
 
fpsSpinner_stateChanged(ChangeEvent) - Method in class cct.chart.jfreechart.JFreeChartPanel
 
fpsSpinner_stateChanged(ChangeEvent) - Method in class cct.dialogs.AnimationPanel
 
Fractional - Variable in class cct.gulp.GULPAtom
 
fragContext - Variable in class cct.j3d.Java3dUniverse
 
FRAGMENT_TAG - Static variable in class cct.tools.FragmentDictionaryParser
 
fragmentDictionary - Variable in class cct.j3d.Java3dUniverse
 
FragmentDictionaryParser - Class in cct.tools
Title:
FragmentDictionaryParser() - Constructor for class cct.tools.FragmentDictionaryParser
 
fragmentsReferences - Variable in class cct.j3d.Java3dUniverse
 
fragmentsTree - Variable in class cct.dialogs.JAddFragmentDialog
 
fragmentsTree - Variable in class cct.dialogs.JSelectTreeDialog
 
fragnameSection - Static variable in class cct.gamess.Gamess
 
Frame1 - Class in cct.dialogs
Title: Molecular Structure Viewer/Editor
Frame1() - Constructor for class cct.dialogs.Frame1
 
Frame1.testFrame - Class in cct.dialogs
 
Frame1.testFrame() - Constructor for class cct.dialogs.Frame1.testFrame
 
Frame1_AboutBox - Class in cct.dialogs
Title: Molecular Structure Viewer/Editor
Frame1_AboutBox(Frame) - Constructor for class cct.dialogs.Frame1_AboutBox
 
Frame1_AboutBox() - Constructor for class cct.dialogs.Frame1_AboutBox
 
Frame1_helpButton_actionAdapter - Class in cct.dialogs
 
Frame1_helpButton_actionAdapter(Frame1) - Constructor for class cct.dialogs.Frame1_helpButton_actionAdapter
 
Frame1_jMenuFileExit_ActionAdapter - Class in cct.dialogs
 
Frame1_jMenuFileExit_ActionAdapter(Frame1) - Constructor for class cct.dialogs.Frame1_jMenuFileExit_ActionAdapter
 
Frame1_jMenuHelpAbout_ActionAdapter - Class in cct.dialogs
 
Frame1_jMenuHelpAbout_ActionAdapter(Frame1) - Constructor for class cct.dialogs.Frame1_jMenuHelpAbout_ActionAdapter
 
FrameGroupProperty - Static variable in interface cct.interfaces.MoleculeInterface
 
freeAll() - Method in class cct.math.DFPMin
 
freq - Variable in class cct.dialogs.SelectPropShowDialog
 
freqOptions - Static variable in class cct.gaussian.GaussianKeywords
 
Frequencies - Class in cct.modelling
Title: Computational Chemistry Tookit
Frequencies() - Constructor for class cct.modelling.Frequencies
 
frequencyUpdate_for_variables - Variable in class cct.modelling.BackgroundMinimizer
 
fret - Variable in class cct.math.DFPMin
 
fromArchiveFormat(InputStream) - Method in class cct.modelling.Molecule
 
fromArchiveFormat(byte[]) - Method in class cct.modelling.Molecule
 
fromInternalToCartesians(ArrayList) - Static method in class cct.gaussian.GaussianMolecule
 
fromInternalToCartesians(vPoint3f, double, double, double, vPoint3f, vPoint3f, vPoint3f) - Static method in class cct.vecmath.VecmathTools
 
fromLabel - Variable in class cct.tools.filebrowser.TransferProgressDialog
 
fromZMatrixToCartesians(ArrayList<ADFAtom>) - Static method in class cct.adf.ADF
 
fromZMatrixToCartesians(ArrayList<GamessAtom>) - Static method in class cct.gamess.Gamess
Expects bond length in angstroms
fromZMatrixToCartesians(ArrayList<MopacAtom>) - Static method in class cct.mopac.Mopac
 
fromZMatrixToCartesians(ArrayList<QChemAtom>) - Static method in class cct.qchem.QChem
Expects bond length in angstroms
frozen - Variable in class cct.gaussian.GaussianAtom
 
frozenParameters - Variable in class cct.adf.ADF
 
fStepSize - Variable in class cct.math.polyg.Polygonizer
 
fTargetValue - Variable in class cct.math.polyg.Polygonizer
 
FTP_OBJECT - Enum in cct.tools.filebrowser
Title: Computational Chemistry Tookit
FTP_Protocols - Static variable in class cct.tools.filebrowser.FTPManager
 
ftpBrowsers - Static variable in class cct.tools.filebrowser.FTPManager
 
ftpManager - Variable in class cct.tools.filebrowser.FileTransferFrame
 
FTPManager - Class in cct.tools.filebrowser
Title:
FTPManager() - Constructor for class cct.tools.filebrowser.FTPManager
 
FTPManagerInterface - Interface in cct.interfaces
Title:
fullString - Variable in class cct.tools.CCTParser
 
fun - Variable in class cct.gaussian.java3d.VolumetricData
 
fun_and_grad - Variable in class cct.math.Minimizer
 
func - Variable in class cct.poly.Polygonizer
 
function(int, double[], double[]) - Method in interface cct.math.MinimizedFunctionInterface
 
function(int, float[], float[]) - Method in interface cct.math.MinimizedFunctionInterface
 
function(int, double[]) - Method in interface cct.math.MinimizedFunctionInterface
 
function(int, float[]) - Method in interface cct.math.MinimizedFunctionInterface
 
function - Variable in class cct.math.polyg.Polygonizer
 
function(int, double[], double[]) - Method in class cct.modelling.MolecularEnergy
 
function(int, float[], float[]) - Method in class cct.modelling.MolecularEnergy
 
function(int, double[]) - Method in class cct.modelling.MolecularEnergy
 
function(int, float[]) - Method in class cct.modelling.MolecularEnergy
 
function - Variable in class cct.poly.PROCESS
 
fv - Variable in class cct.gaussian.java3d.VolumetricData
 
fX - Variable in class cct.math.polyg.GLvector
 
fY - Variable in class cct.math.polyg.GLvector
 
fZ - Variable in class cct.math.polyg.GLvector
 

G

g - Variable in class cct.oogl.Color
 
g - Variable in class cct.oogl.Face
 
g - Variable in class cct.tools.Face
 
G03_CHECKPOINT_KEY_WORDS - Enum in cct.gaussian
 
G03FormCheckpoint - Class in cct.gaussian
 
G03FormCheckpoint() - Constructor for class cct.gaussian.G03FormCheckpoint
 
G03MDTrajectory - Class in cct.gaussian
Title: Computational Chemistry Tookit
G03MDTrajectory() - Constructor for class cct.gaussian.G03MDTrajectory
 
Gamess - Class in cct.gamess
Title:
Gamess() - Constructor for class cct.gamess.Gamess
 
GamessAtom - Class in cct.gamess
Title:
GamessAtom() - Constructor for class cct.gamess.GamessAtom
 
GamessAtom(float, float, float) - Constructor for class cct.gamess.GamessAtom
 
gamessInput - Static variable in class cct.modelling.MolecularFileFormats
 
GamessOutput - Class in cct.gamess
Title:
GamessOutput() - Constructor for class cct.gamess.GamessOutput
 
gamessOutput - Static variable in class cct.modelling.MolecularFileFormats
 
GamessSwitch - Class in cct.gamess
Title:
GamessSwitch(String, String) - Constructor for class cct.gamess.GamessSwitch
 
GamessSwitch(String, String, boolean) - Constructor for class cct.gamess.GamessSwitch
 
gamma - Variable in class cct.math.Amoeba
 
GAMMA_LN_Label - Variable in class cct.amber.Sander8Frame
 
GAMMA_LN_Label - Variable in class cct.amber.Sander9Frame
 
GAMMA_LN_Label_mouseEntered(MouseEvent) - Method in class cct.amber.Sander8Frame
 
GAMMA_LN_Label_mouseEntered(MouseEvent) - Method in class cct.amber.Sander9Frame
 
GAMMA_LN_TextField - Variable in class cct.amber.Sander8Frame
 
GAMMA_LN_TextField - Variable in class cct.amber.Sander9Frame
 
gatekeeperPanel1 - Variable in class cct.grid.ui.gaussian.SubmitGaussPanel
 
gAtom - Class in cct.modelling
Title:
gAtom() - Constructor for class cct.modelling.gAtom
 
gAtom(gAtom) - Constructor for class cct.modelling.gAtom
 
gAtom(AtomInterface) - Constructor for class cct.modelling.gAtom
 
gAtom(int, float, float, float) - Constructor for class cct.modelling.gAtom
 
Gaussian - Class in cct.gaussian
Title:
Gaussian() - Constructor for class cct.gaussian.Gaussian
 
gaussian03Cube - Static variable in class cct.modelling.MolecularFileFormats
 
gaussian03GJF - Static variable in class cct.modelling.MolecularFileFormats
 
gaussian03Output - Static variable in class cct.modelling.MolecularFileFormats
 
GaussianAtom - Class in cct.gaussian
Title:
GaussianAtom() - Constructor for class cct.gaussian.GaussianAtom
 
GaussianAtom(AtomInterface) - Constructor for class cct.gaussian.GaussianAtom
 
GaussianCalcSetupDialog - Class in cct.awtdialogs
Title:
GaussianCalcSetupDialog(Frame, String, boolean) - Constructor for class cct.awtdialogs.GaussianCalcSetupDialog
 
GaussianCube - Class in cct.gaussian
Title:
GaussianCube() - Constructor for class cct.gaussian.GaussianCube
 
gaussianData - Variable in class cct.modelling.MolecularEditor
 
gaussianData - Variable in class cct.modelling.ui.OpenFile
 
gaussianElementColors - Static variable in class cct.j3d.ChemicalElementsColors
 
gaussianExecutable - Static variable in class cct.grid.ui.gaussian.SubmitGaussianPanel
 
gaussianFormCheckpoint - Static variable in class cct.modelling.MolecularFileFormats
 
GaussianFragment - Class in cct.gaussian
Title:
GaussianFragment() - Constructor for class cct.gaussian.GaussianFragment
 
gaussianFragment - Static variable in class cct.modelling.MolecularFileFormats
 
GaussianFrequency - Class in cct.gaussian
Title: Computational Chemistry Tookit
GaussianFrequency(int) - Constructor for class cct.gaussian.GaussianFrequency
 
gaussianImage - Static variable in class cct.tools.filebrowser.FileNameRenderer
 
gaussianImage - Static variable in class cct.tools.FileUtilities
 
gaussianInput - Variable in class cct.mopac.Mopac
 
GaussianInputEditorFrame - Class in cct.gaussian.ui
Title: Gasussian Utility Classes
GaussianInputEditorFrame(GJFParserInterface) - Constructor for class cct.gaussian.ui.GaussianInputEditorFrame
 
gaussianInputEditorFrame - Variable in class cct.j3d.Java3dUniverse
 
gaussianInputEditorFrame - Variable in class cct.modelling.ui.OpenFile
 
GaussianInputEditorFrame.GaussianInputEditorFrame_insertEntryButton_actionAdapter - Class in cct.gaussian.ui
 
GaussianInputEditorFrame.GaussianInputEditorFrame_insertEntryButton_actionAdapter(GaussianInputEditorFrame) - Constructor for class cct.gaussian.ui.GaussianInputEditorFrame.GaussianInputEditorFrame_insertEntryButton_actionAdapter
 
GaussianInputEditorFrame.GaussianInputEditorFrame_jButton6_actionAdapter - Class in cct.gaussian.ui
 
GaussianInputEditorFrame.GaussianInputEditorFrame_jButton6_actionAdapter(GaussianInputEditorFrame) - Constructor for class cct.gaussian.ui.GaussianInputEditorFrame.GaussianInputEditorFrame_jButton6_actionAdapter
 
GaussianInputEditorFrame.GaussianInputEditorFrame_jMenuFileExit_ActionAdapter - Class in cct.gaussian.ui
 
GaussianInputEditorFrame.GaussianInputEditorFrame_jMenuFileExit_ActionAdapter(GaussianInputEditorFrame) - Constructor for class cct.gaussian.ui.GaussianInputEditorFrame.GaussianInputEditorFrame_jMenuFileExit_ActionAdapter
 
GaussianInputEditorFrame.GaussianInputEditorFrame_jMenuHelpAbout_ActionAdapter - Class in cct.gaussian.ui
 
GaussianInputEditorFrame.GaussianInputEditorFrame_jMenuHelpAbout_ActionAdapter(GaussianInputEditorFrame) - Constructor for class cct.gaussian.ui.GaussianInputEditorFrame.GaussianInputEditorFrame_jMenuHelpAbout_ActionAdapter
 
GaussianInputEditorFrame.GaussianInputEditorFrame_jMenuItem1_actionAdapter - Class in cct.gaussian.ui
 
GaussianInputEditorFrame.GaussianInputEditorFrame_jMenuItem1_actionAdapter(GaussianInputEditorFrame) - Constructor for class cct.gaussian.ui.GaussianInputEditorFrame.GaussianInputEditorFrame_jMenuItem1_actionAdapter
 
GaussianInputEditorFrame.GaussianInputEditorFrame_nextStepButton_actionAdapter - Class in cct.gaussian.ui
 
GaussianInputEditorFrame.GaussianInputEditorFrame_nextStepButton_actionAdapter(GaussianInputEditorFrame) - Constructor for class cct.gaussian.ui.GaussianInputEditorFrame.GaussianInputEditorFrame_nextStepButton_actionAdapter
 
GaussianInputEditorFrame.GaussianInputEditorFrame_openFileButton_actionAdapter - Class in cct.gaussian.ui
 
GaussianInputEditorFrame.GaussianInputEditorFrame_openFileButton_actionAdapter(GaussianInputEditorFrame) - Constructor for class cct.gaussian.ui.GaussianInputEditorFrame.GaussianInputEditorFrame_openFileButton_actionAdapter
 
GaussianInputEditorFrame.GaussianInputEditorFrame_openSelectedFileButton_actionAdapter - Class in cct.gaussian.ui
 
GaussianInputEditorFrame.GaussianInputEditorFrame_openSelectedFileButton_actionAdapter(GaussianInputEditorFrame) - Constructor for class cct.gaussian.ui.GaussianInputEditorFrame.GaussianInputEditorFrame_openSelectedFileButton_actionAdapter
 
GaussianInputEditorFrame.GaussianInputEditorFrame_previousStepButton_actionAdapter - Class in cct.gaussian.ui
 
GaussianInputEditorFrame.GaussianInputEditorFrame_previousStepButton_actionAdapter(GaussianInputEditorFrame) - Constructor for class cct.gaussian.ui.GaussianInputEditorFrame.GaussianInputEditorFrame_previousStepButton_actionAdapter
 
GaussianInputEditorFrame.GaussianInputEditorFrame_resetButton_actionAdapter - Class in cct.gaussian.ui
 
GaussianInputEditorFrame.GaussianInputEditorFrame_resetButton_actionAdapter(GaussianInputEditorFrame) - Constructor for class cct.gaussian.ui.GaussianInputEditorFrame.GaussianInputEditorFrame_resetButton_actionAdapter
 
GaussianInputEditorFrame.GaussianInputEditorFrame_saveFileButton_actionAdapter - Class in cct.gaussian.ui
 
GaussianInputEditorFrame.GaussianInputEditorFrame_saveFileButton_actionAdapter(GaussianInputEditorFrame) - Constructor for class cct.gaussian.ui.GaussianInputEditorFrame.GaussianInputEditorFrame_saveFileButton_actionAdapter
 
GaussianInputEditorFrame.GaussianInputEditorFrame_saveStepButton_actionAdapter - Class in cct.gaussian.ui
 
GaussianInputEditorFrame.GaussianInputEditorFrame_saveStepButton_actionAdapter(GaussianInputEditorFrame) - Constructor for class cct.gaussian.ui.GaussianInputEditorFrame.GaussianInputEditorFrame_saveStepButton_actionAdapter
 
GaussianInputEditorFrame.GaussianInputEditorFrame_stepsComboBox_itemAdapter - Class in cct.gaussian.ui
 
GaussianInputEditorFrame.GaussianInputEditorFrame_stepsComboBox_itemAdapter(GaussianInputEditorFrame) - Constructor for class cct.gaussian.ui.GaussianInputEditorFrame.GaussianInputEditorFrame_stepsComboBox_itemAdapter
 
GaussianInputEditorFrame_AboutBox - Class in cct.gaussian.ui
Title: Gasussian Utility Classes
GaussianInputEditorFrame_AboutBox(Frame) - Constructor for class cct.gaussian.ui.GaussianInputEditorFrame_AboutBox
 
GaussianInputEditorFrame_AboutBox() - Constructor for class cct.gaussian.ui.GaussianInputEditorFrame_AboutBox
 
GaussianInputEditorImpl - Class in cct.gaussian.ui
Title: Gasussian Utility Classes
GaussianInputEditorImpl() - Constructor for class cct.gaussian.ui.GaussianInputEditorImpl
Construct and show the application.
GaussianJava3dFactory - Class in cct.gaussian.java3d
Title:
GaussianKeywords - Class in cct.gaussian
Title:
GaussianKeywords() - Constructor for class cct.gaussian.GaussianKeywords
 
GaussianMolecule - Class in cct.gaussian
 
GaussianMolecule() - Constructor for class cct.gaussian.GaussianMolecule
 
GaussianOutput - Class in cct.gaussian
Title:
GaussianOutput() - Constructor for class cct.gaussian.GaussianOutput
 
gaussianOutputFileTag - Static variable in class cct.grid.ui.gaussian.SubmitGaussianPanel
 
GaussianSnapshot - Class in cct.gaussian
Title: Computational Chemistry Tookit
GaussianSnapshot() - Constructor for class cct.gaussian.GaussianSnapshot
 
gaussianTrajectory - Static variable in class cct.modelling.MolecularFileFormats
 
gaussOutMenuItem - Variable in class cct.dialogs.Frame1
 
GB_Dummy_Label - Variable in class cct.amber.Sander8Frame
 
GB_Dummy_Label - Variable in class cct.amber.Sander9Frame
 
GB_Panel - Variable in class cct.amber.Sander8Frame
 
GB_Panel - Variable in class cct.amber.Sander9Frame
 
GBSA_ComboBox - Variable in class cct.amber.Sander8Frame
 
GBSA_ComboBox - Variable in class cct.amber.Sander9Frame
 
GBSA_ComboBox_itemStateChanged(ItemEvent) - Method in class cct.amber.Sander8Frame
 
GBSA_ComboBox_itemStateChanged(ItemEvent) - Method in class cct.amber.Sander9Frame
 
GBSA_ComboBox_mouseEntered(MouseEvent) - Method in class cct.amber.Sander8Frame
 
GBSA_ComboBox_mouseEntered(MouseEvent) - Method in class cct.amber.Sander9Frame
 
GBSA_Label - Variable in class cct.amber.Sander8Frame
 
GBSA_Label - Variable in class cct.amber.Sander9Frame
 
GBSA_Label_mouseEntered(MouseEvent) - Method in class cct.amber.Sander8Frame
 
GBSA_Label_mouseEntered(MouseEvent) - Method in class cct.amber.Sander9Frame
 
GENERAL_MESH_OBJECT - Static variable in class cct.vecmath.MeshObject
 
generalPopup - Variable in class cct.tools.filebrowser.SFTPBrowser
 
generalTorsionParams - Static variable in class cct.sff.SimpleForceField
 
generateAtom(Point3fInterface, float, float, Point3fInterface) - Static method in class cct.modelling.AtomGenerator
 
generateFileContents(String) - Method in class cct.amber.Sander8Frame
 
generateFileContents(String) - Method in class cct.amber.Sander9Frame
 
generatePoints(String, int, Point3fInterface) - Static method in class cct.math.PointGroup
 
generateSolventShell(MoleculeInterface, MoleculeInterface, float, float, int) - Static method in class cct.modelling.Molecule
Generates solvation shell(s) of radius "radius" around a molecule using solvent "solvent"
GenericAtom - Class in cct.cprocessor
Title: Molecular Structure Viewer/Editor
GenericAtom() - Constructor for class cct.cprocessor.GenericAtom
 
GenericAtom(float, float, float, int, String) - Constructor for class cct.cprocessor.GenericAtom
 
GenericBond - Class in cct.cprocessor
Title: Molecular Structure Viewer/Editor
GenericBond(int, int) - Constructor for class cct.cprocessor.GenericBond
 
Geometries - Variable in class cct.gamess.GamessOutput
 
Geometries - Variable in class cct.j3d.Java3dUniverse
 
Geometries - Variable in class cct.mopac.MopacOutput
 
geometry - Variable in class cct.modelling.AtomGeometry
 
Geometry - Variable in class cct.modelling.AtomTypeDef
 
Geometry3d - Class in cct.vecmath
Title: Picking
GEOMETRY_KEY - Static variable in class cct.modelling.CCTAtomTypes
 
GEOMETRY_LINEAR - Static variable in interface cct.modelling.AtomProperties
 
GEOMETRY_TETRAHEDRAL - Static variable in interface cct.modelling.AtomProperties
 
GEOMETRY_TRIGONAL - Static variable in interface cct.modelling.AtomProperties
 
geometryAsString(MoleculeInterface) - Static method in class cct.modelling.Molecule
 
GeometrySelectDialog - Class in cct.awtdialogs
Title:
GeometrySelectDialog(Java3dUniverse, String, boolean) - Constructor for class cct.awtdialogs.GeometrySelectDialog
 
geometrySelectioDialog - Variable in class cct.j3d.Java3dUniverse
 
geometrySelection - Variable in class cct.j3d.Java3dUniverse
 
geomFormat - Static variable in class cct.modelling.MolecularFileFormats
 
GeomFormat - Class in cct.tools
Title: Jamberoo - Computational Chemistry Toolkit
GeomFormat() - Constructor for class cct.tools.GeomFormat
 
geomOptions - Static variable in class cct.gaussian.GaussianKeywords
 
get(String, String) - Method in interface cct.interfaces.FileBrowserInterface
 
get(String, String, FileTransferProgress) - Method in interface cct.interfaces.FileBrowserInterface
 
get(String, String) - Method in class cct.tools.filebrowser.LocalFileBrowser
 
get(String, String, FileTransferProgress) - Method in class cct.tools.filebrowser.LocalFileBrowser
 
get(String, String) - Method in class cct.tools.filebrowser.SFTPBrowser
 
get(String, String, FileTransferProgress) - Method in class cct.tools.filebrowser.SFTPBrowser
 
get() - Method in class cct.tools.SwingWorker
Return the value created by the construct method.
get14ElsScale() - Method in interface cct.interfaces.ForceFieldInterface
 
get14ElsScale() - Method in class cct.sff.SimpleForceField
 
get14Interactions() - Method in class cct.modelling.FFMolecule
 
get14NBScale() - Method in interface cct.interfaces.ForceFieldInterface
 
get14NBScale() - Method in class cct.sff.SimpleForceField
 
get15(int, int) - Method in class cct.modelling.Nonbonded15Table
 
get_cubetable_entry(int) - Static method in class cct.poly.CUBETABLE
 
get_cubetable_entry(int) - Method in class cct.poly.Polygonizer
 
get_i1() - Method in class cct.gamess.GamessAtom
 
get_i1() - Method in class cct.mopac.MopacAtom
 
get_i1() - Method in class cct.qchem.QChemAtom
 
get_i2() - Method in class cct.gamess.GamessAtom
 
get_i2() - Method in class cct.mopac.MopacAtom
 
get_i2() - Method in class cct.qchem.QChemAtom
 
get_i3() - Method in class cct.gamess.GamessAtom
 
get_i3() - Method in class cct.mopac.MopacAtom
 
get_i3() - Method in class cct.qchem.QChemAtom
 
get_lists(int) - Static method in class cct.poly.CUBETABLE
 
get_normal(int) - Method in class cct.poly.Polygonizer
 
GET_PSUM(int) - Method in class cct.math.Amoeba
 
get_triangle(int) - Method in class cct.poly.Polygonizer
 
get_vertex(int) - Method in class cct.poly.Polygonizer
 
getAbsRange() - Method in class cct.j3d.ColorRangeScheme
 
getActionListener() - Static method in class cct.tools.GridProviders
 
getActualIterNum() - Method in class cct.math.DFPMin
 
getAddCommandObject(String) - Method in class cct.cprocessor.CommandProcessor
 
getAliases() - Method in class cct.awtdialogs.AddNewMoleculeDialog
 
getAllElements() - Static method in class cct.modelling.ChemicalElements
 
getAllTerms(String) - Method in class cct.adf.ADFOutput
 
getAllTerms(String) - Method in class cct.gaussian.G03MDTrajectory
 
getAllTerms(String) - Method in class cct.gaussian.GaussianOutput
 
getAllTerms(String) - Method in class cct.vasp.VasprunXML
Returns all values for (energy) term "term"
getAllVariablesInfo() - Method in class cct.amber.Sander8JobControl
 
getAllVariablesInfo() - Method in class cct.amber.Sander9JobControl
 
getAlpha() - Method in class cct.gamess.GamessAtom
 
getAlpha() - Method in class cct.mopac.MopacAtom
 
getAlpha() - Method in class cct.qchem.QChemAtom
 
getAlphaPar() - Method in class cct.gamess.GamessAtom
 
getAlphaPar() - Method in class cct.mopac.MopacAtom
 
getAlphaPar() - Method in class cct.qchem.QChemAtom
 
getAngle() - Method in class cct.adf.ADFAtom
 
getAngleBend(int) - Method in class cct.modelling.AngleBendsArray
 
getAngleBendInteractions() - Method in class cct.modelling.FFMolecule
 
getAngleBendParams(MoleculeInterface, AngleBendsArray) - Static method in class cct.sff.SimpleForceField
 
getAngleBends() - Method in class cct.modelling.AngleBendsArray
 
getAppearance(AtomInterface) - Method in class cct.j3d.BondNode
 
getAppearance(Appearance, OutputStream) - Method in class cct.j3d.GroupToVRML
 
getAppearence(Color3f) - Method in class cct.j3d.VerticesObjectProperties
 
getAppletInfo() - Method in class cct.amber.AmberApplet
 
getAppletInfo() - Method in class cct.applets.viewer
 
getArgument(int) - Method in class cct.grid.JobDescription
Returns n-th argument
getArgumentCount() - Method in class cct.grid.JobDescription
Returns number of arguments
getAtom(int) - Method in class cct.gaussian.GaussianMolecule
 
getAtom(int) - Method in interface cct.interfaces.MonomerInterface
 
getAtom(int) - Method in class cct.modelling.AtomsArray
Returns ith atom
getAtom(int) - Method in class cct.modelling.Molecule
 
getAtom(int) - Method in class cct.modelling.Monomer
 
getAtom(int) - Method in class cct.pdb.PDBResidue
 
getAtom(String) - Method in class cct.pdb.PDBResidue
 
getAtomColor(AtomInterface) - Static method in class cct.j3d.AtomNode
 
getAtomColorSchemeNames() - Static method in class cct.j3d.ChemicalElementsColors
 
getAtomColorSchemeNumber() - Static method in class cct.j3d.ChemicalElementsColors
Returns number of available atom color schemes
getAtomGeometry(String) - Static method in class cct.modelling.AtomGeometry
 
getAtomicCoordinatesAsString() - Method in class cct.siesta.SiestaInput
 
getAtomicCoordinatesAsString(MoleculeInterface) - Method in class cct.siesta.SiestaInput
 
getAtomicMass() - Method in interface cct.interfaces.AtomInterface
 
getAtomicMass() - Method in class cct.modelling.vAtom
 
getAtomicNumber(String) - Static method in class cct.gamess.Gamess
 
getAtomicNumber() - Method in class cct.gamess.GamessAtom
 
getAtomicNumber() - Method in interface cct.interfaces.AtomInterface
 
getAtomicNumber(String) - Static method in class cct.modelling.ChemicalElements
 
getAtomicNumber() - Method in class cct.modelling.vAtom
 
getAtomicNumber() - Method in class cct.mopac.MopacAtom
 
getAtomicNumber(String) - Static method in class cct.qchem.QChem
 
getAtomicNumber() - Method in class cct.qchem.QChemAtom
 
getAtomicNumber() - Method in class cct.siesta.ChemicalSpeciesLabel
 
getAtomicNumber() - Method in class cct.vasp.VaspAtom
 
getAtomicSphere() - Method in class cct.j3d.AtomNode
 
getAtomicSphereRadius(AtomInterface) - Static method in class cct.j3d.AtomNode
returns sphere radius for drawing an atom
getAtomicSphereRadius() - Method in class cct.j3d.AtomNode
 
getAtomicSphereScale(BranchGroup) - Static method in class cct.j3d.Java3dUniverse
Finds TransformGroup which scales sphere's redius
getAtomicTranformGroup(BranchGroup) - Method in class cct.j3d.Java3dUniverse
 
getAtomicWeight(String) - Static method in class cct.modelling.ChemicalElements
 
getAtomicWeight(int) - Static method in class cct.modelling.ChemicalElements
 
getAtomIndex(AtomInterface) - Method in interface cct.interfaces.MoleculeInterface
 
getAtomIndex(AtomInterface) - Method in interface cct.interfaces.MonomerInterface
 
getAtomIndex(AtomInterface) - Method in class cct.modelling.AtomsArray
Returns atom number in the list.
getAtomIndex(AtomInterface) - Method in class cct.modelling.Molecule
 
getAtomIndex(AtomInterface) - Method in class cct.modelling.Monomer
 
getAtomInterface(int) - Method in interface cct.interfaces.MoleculeInterface
 
getAtomInterface() - Method in class cct.j3d.AtomNode
 
getAtomInterface(int) - Method in class cct.modelling.AtomsArray
 
getAtomInterface(int) - Method in class cct.modelling.Molecule
 
getAtomLabel(String) - Method in class cct.mopac.Mopac
 
getAtomLabelsColor() - Method in class cct.j3d.Java3dUniverse
 
getAtomLabelsFont() - Method in class cct.j3d.Java3dUniverse
 
getAtomLabelsFont(Font) - Method in class cct.j3d.Java3dUniverse
 
getAtomName() - Method in class cct.dialogs.JAtomTypeDialog
 
getAtomNamesInMolecule() - Method in class cct.j3d.Java3dUniverse
 
getAtomNamesInMolecule() - Method in class cct.modelling.MolecularEditor
 
getAtomNamesInMolecule() - Method in class cct.modelling.Molecule
Returns set of all unique atomic names presented in molecule
getAtomNamesInMolecule(MoleculeInterface) - Static method in class cct.modelling.Molecule
Returns set of all unique atomic names presented in molecule
getAtomNumber(String) - Static method in class cct.gaussian.Gaussian
Defines element of an atom
getAtomProperties() - Method in class cct.modelling.gAtom
 
getAtoms() - Method in class cct.adf.ADFSnapshot
 
getAtoms() - Method in class cct.j3d.SuperCell.CellObject
 
getAtoms() - Method in class cct.vasp.VaspSnapshot
 
getAtomType() - Method in class cct.dialogs.JAtomTypeDialog
 
getAtomTypeInfo(String) - Static method in class cct.modelling.CCTAtomTypes
 
getAtomTypeName() - Method in class cct.modelling.CCTAtomTypes
 
getAtomTypes() - Static method in class cct.modelling.CCTAtomTypes
 
getAtomTypesCount() - Static method in class cct.modelling.CCTAtomTypes
 
getAtomTypesForElement(int) - Static method in class cct.modelling.CCTAtomTypes
 
getAtomTypesForElement(String) - Static method in class cct.modelling.CCTAtomTypes
 
getAvailableAtomicProperties(MoleculeInterface) - Static method in class cct.modelling.Molecule
 
getAvailableAuthMethods(String) - Method in class cct.tools.filebrowser.SFTPBrowser
Returns the list of available authentication methods for a given user.
getAvailableBasisSets() - Method in class cct.database.new_SQLChemistryDatabase
 
getAvailableFTPProtocols() - Method in interface cct.interfaces.FTPManagerInterface
 
getAvailableFTPProtocols() - Method in class cct.tools.filebrowser.FTPManager
 
getAvailableLookAndFeels() - Static method in class cct.tools.SwingLookAndFeel
 
getAvailableMethods() - Method in class cct.database.new_SQLChemistryDatabase
 
getAvailablePolygonModes() - Static method in class cct.j3d.VerticesObjectProperties
 
getAvailableScriptSubmitters() - Static method in class cct.tools.GridProviders
 
getAvailableTaskProviders() - Static method in class cct.grid.TaskProvider
 
getAvailableTaskSchedulers() - Static method in class cct.grid.TaskScheduler
 
getAvailableTrajectories() - Method in class cct.modelling.StructureManager
 
getAvailableTranspModes() - Static method in class cct.j3d.VerticesObjectProperties
 
getAvailPropToChart() - Method in class cct.adf.ADFOutput
 
getAvailPropToChart() - Method in class cct.gaussian.G03MDTrajectory
 
getAvailPropToChart() - Method in class cct.gaussian.GaussianOutput
 
getAxisVectors() - Method in class cct.gaussian.GaussianCube
 
getAxisVectors() - Method in interface cct.interfaces.VolumetricDataInterface
 
getBackground(Background, OutputStream) - Method in class cct.j3d.GroupToVRML
 
getBackgroundColor() - Method in class cct.j3d.Java3dUniverse
 
getBackgroundColor3f() - Method in class cct.j3d.Java3dUniverse
 
getBasisSet() - Method in class cct.gaussian.GaussianKeywords
 
getBasisSets() - Method in class cct.database.new_SQLChemistryDatabase
 
getBeta() - Method in class cct.gamess.GamessAtom
 
getBeta() - Method in class cct.mopac.MopacAtom
 
getBeta() - Method in class cct.qchem.QChemAtom
 
getBetaPar() - Method in class cct.gamess.GamessAtom
 
getBetaPar() - Method in class cct.mopac.MopacAtom
 
getBetaPar() - Method in class cct.qchem.QChemAtom
 
getBicolorLine(BondInterface) - Method in class cct.j3d.BondNode
 
getBlob(String, String, String, String) - Method in class cct.database.SQLDatabaseAccess
 
getBond() - Method in class cct.j3d.BondNode
 
getBond() - Method in class cct.modelling.Bond
 
getBond(int) - Method in class cct.modelling.BondsArray
Returns atom at specified index
getBond(int) - Method in class cct.modelling.Molecule
 
getBond(BondInterface) - Method in class cct.modelling.Molecule
 
getBond(int) - Method in class cct.pdb.PDBResidue
 
getBondedToAtoms() - Method in interface cct.interfaces.AtomInterface
 
getBondedToAtoms() - Method in class cct.modelling.vAtom
 
getBondIndex() - Method in interface cct.interfaces.AtomInterface
 
getBondIndex(BondInterface) - Method in interface cct.interfaces.MoleculeInterface
 
getBondIndex(BondInterface) - Method in class cct.modelling.Molecule
 
getBondIndex() - Method in class cct.modelling.vAtom
 
getBondInterface(int) - Method in interface cct.interfaces.MoleculeInterface
 
getBondInterface(int) - Method in class cct.modelling.Molecule
 
getBondLength() - Method in class cct.adf.ADFAtom
 
getBondLength() - Method in class cct.awtdialogs.AtomTypeDialog
 
getBondLength() - Method in class cct.dialogs.JAtomTypeDialog
 
getBondLength() - Method in class cct.gamess.GamessAtom
 
getBondLength() - Method in class cct.mopac.MopacAtom
 
getBondLength() - Method in class cct.qchem.QChemAtom
 
getBondLengthPar() - Method in class cct.gamess.GamessAtom
 
getBondLengthPar() - Method in class cct.mopac.MopacAtom
 
getBondLengthPar() - Method in class cct.qchem.QChemAtom
 
getBondStretchInteractions() - Method in class cct.modelling.FFMolecule
 
getBondStretchPairs() - Method in class cct.modelling.BondStretchPairs
 
getBondStretchPairsAsArray() - Method in class cct.modelling.BondStretchPairs
 
getBondStretchParam(String, String) - Static method in class cct.sff.SimpleForceField
 
getBondToAtom(AtomInterface) - Method in interface cct.interfaces.AtomInterface
 
getBondToAtom(AtomInterface) - Method in class cct.modelling.vAtom
 
getBoundingSphere() - Method in class cct.j3d.Java3dUniverse
 
getBranchGroup(BranchGroup, OutputStream) - Method in class cct.j3d.GroupToVRML
 
getButtons() - Method in class cct.dialogs.JElementsPanel
 
getBytes(String, String, String, String) - Method in class cct.database.SQLDatabaseAccess
 
getCancelButton() - Method in class cct.grid.ui.SubmitTaskDialog
 
getCancelButton() - Method in class cct.modelling.ui.MinimizationProgressDialog
 
getCanvas3D() - Method in class cct.j3d.Java3dUniverse
 
getCartesianFromFractional(double[][], int, double[][]) - Static method in class cct.math.Crystal
 
getCartesians() - Method in class cct.gaussian.GaussianMolecule
 
getCartesianToFractionalTransMatrix(double[]) - Static method in class cct.math.Crystal
 
getCCTDirectory() - Static method in class cct.tools.Utils
Checks if the ~/CCT_DIRECTORY (~/.cct) directory exists.
getCellGraphicsObject(double[][]) - Method in class cct.j3d.UnitCellGraphics
 
getCellGraphicsObject(float[][]) - Method in class cct.j3d.UnitCellGraphics
 
getCenterCoord(Vector3f) - Method in class cct.j3d.LabelNode
 
getCenterCoord(Point3f) - Method in class cct.j3d.LabelNode
 
getCharge() - Method in class cct.awtdialogs.AddNewMoleculeDialog
 
getChargeAndMultiplicity() - Method in class cct.gaussian.GaussianMolecule
 
getChargeSection(int) - Method in class cct.gaussian.Gaussian
 
getChargeSection() - Method in class cct.gaussian.GaussianMolecule
 
getChargeSection(int) - Method in interface cct.gaussian.GJFParserInterface
 
getChargeSection() - Method in class cct.gaussian.ui.SimpleG03EditorPanel
 
getCheckPoint(int) - Method in interface cct.grid.JobStatusInterface
 
getCheckPoint(int) - Method in class cct.grid.ui.CheckPointStatus
 
getCheckPointFile() - Static method in class cct.grid.ParseCheckpointFile
 
getCheckPointSpecifications() - Static method in class cct.grid.CheckPoint
Returns all possible specifications of checkpoint
getChemicalElement(String, String) - Static method in class cct.gromacs.Gromacs
 
getChemicalFormula(MoleculeInterface) - Static method in class cct.modelling.Molecule
Returns chemical formula
getChemicalSpeciesLabels() - Method in class cct.siesta.SiestaInput
 
getChemicalSpeciesLabels() - Method in interface cct.siesta.SiestaInterface
 
getChoice() - Method in class cct.awtdialogs.SingleChoiceDialog
 
getChoiceIndex() - Method in class cct.awtdialogs.SingleChoiceDialog
 
getClipboardContents() - Method in class cct.tools.TextClipboard
Get the String residing on the clipboard.
getClipMax() - Method in class cct.j3d.ColorRangeScheme
 
getClipMin() - Method in class cct.j3d.ColorRangeScheme
 
getClob(String, String, String, String) - Method in class cct.database.SQLDatabaseAccess
 
getCloseness() - Method in class cct.dialogs.JSolvateShellDialog
 
getClosenessAsText() - Method in class cct.dialogs.JSolvateShellDialog
 
getClusterAddress() - Method in class cct.grid.JobDescription
 
getColor3f() - Method in class cct.j3d.AtomNode
 
getColor3f(AtomInterface) - Method in class cct.j3d.BondNode
 
getColor3f(float, Color3f) - Method in class cct.j3d.ColorRangeScheme
 
getColor3fInRange(float) - Method in class cct.j3d.color3fPalette
 
getColor3fPalette() - Method in class cct.j3d.color3fPalette
 
getColor3fPalette() - Method in class cct.j3d.ColorRangeScheme
 
getColor4f(float, Color4f) - Method in class cct.j3d.ColorRangeScheme
 
getColorHash(Integer, Integer, Integer) - Method in class cct.povray.Povray
 
getColorHash(int, int, int) - Method in class cct.povray.Povray
 
getColorHash(float, float, float) - Method in class cct.povray.Povray
 
getColorHash(Float, Float, Float) - Method in class cct.povray.Povray
 
getColors() - Method in class cct.oogl.OOGL
 
getColors() - Method in class cct.tools.OOGL
 
getColorsAsArray() - Method in class cct.vecmath.MeshObject
 
getColumnClass(int) - Method in class cct.grid.ui.JobStatusTableModel
 
getColumnClass(int) - Method in class cct.tools.filebrowser.FileBrowserTableModel
 
getColumnClass(int) - Method in class cct.tools.filebrowser.TableSorter
 
getColumnCount() - Method in class cct.chart.jfreechart.JFreeChartPanel.ChartTableModel
Returns the column count.
getColumnCount() - Method in class cct.grid.ui.JobStatusTableModel
 
getColumnCount() - Method in class cct.modelling.ui.VibrationsControlPanel.ChartTableModel
Returns the column count.
getColumnCount() - Method in class cct.tools.filebrowser.FileBrowserTableModel
 
getColumnCount() - Method in class cct.tools.filebrowser.TableSorter
 
getColumnName(int) - Method in class cct.chart.jfreechart.JFreeChartPanel.ChartTableModel
Returns the column name.
getColumnName(int) - Method in class cct.grid.ui.JobStatusTableModel
 
getColumnName(int) - Method in class cct.modelling.ui.VibrationsControlPanel.ChartTableModel
Returns the column name.
getColumnName(int) - Method in class cct.tools.filebrowser.FileBrowserTableModel
 
getColumnName(int) - Method in class cct.tools.filebrowser.TableSorter
 
getColumnNames() - Method in interface cct.grid.JobStatusInterface
 
getColumnNames() - Method in class cct.grid.ui.CheckPointStatus
 
getColumnsFromTable(String, String) - Method in class cct.database.SQLDatabaseAccess
 
getCommand(String) - Method in class cct.cprocessor.CommandProcessor
 
getCommand(String) - Method in enum cct.cprocessor.Commands
 
getCommandObject(String) - Method in enum cct.cprocessor.CommandObject
 
getCommandObject(String) - Method in enum cct.vasp.VasprunTags
 
getCommandsAsString() - Method in interface cct.grid.ClientProgramInterface
 
getCommandsAsString() - Method in interface cct.grid.GridProviderInterface
 
getCommandsAsString() - Method in class cct.grid.LocalServiceProvider
 
getCommandsAsString() - Method in interface cct.grid.SchedulerInterface
 
getCommandsAsString() - Method in class cct.grid.ui.gaussian.SubmitGaussianPanel
 
getCommandsAsString() - Method in class cct.grid.ui.NoSchedulerPanel
 
getCommandsAsString() - Method in class cct.grid.ui.PBSPanel
 
getCommandsAsString() - Method in class cct.ssh.SSHServiceProvider
 
getComparator(int) - Method in class cct.tools.filebrowser.TableSorter
 
getComponent() - Method in class cct.dialogs.J3DTabbedWorld
 
getComponent() - Method in class cct.dialogs.JEditorFrame
 
getComponent() - Method in interface cct.interfaces.FileBrowserInterface
 
getComponent() - Method in interface cct.interfaces.ParentInterface
Gets parent component (if any)
getComponent() - Method in class cct.tools.filebrowser.LocalFileBrowser
 
getComponent() - Method in class cct.tools.filebrowser.SFTPBrowser
 
getComponent() - Method in class cct.tools.filebrowser.SFTPFileChooserDialog
 
getComponent() - Method in class cct.tools.filebrowser.SFTPObject
 
getComponent() - Method in interface cct.tools.filebrowser.ShadowClientInterface
 
getComputer() - Method in class cct.grid.CheckPoint
 
getCone(Cone, OutputStream) - Method in class cct.j3d.GroupToVRML
 
getConnection(String, String, String) - Method in class cct.database.SQLDatabaseAccess
 
getConnection() - Method in class cct.database.SQLDatabaseAccess
 
getConnection(String) - Static method in class cct.ssh.SSHServiceProvider
 
getControls() - Method in class cct.dialogs.JAtomSelectionPanel
 
getControls() - Method in class cct.dialogs.JQuickSelectionPanel
 
getControls() - Method in class cct.dialogs.JSelectionRulePanel
 
getControls() - Method in class cct.dialogs.JSelectionTypePanel
 
getControls() - Method in class cct.dialogs.JSpecialSelectionPanel
 
getControlSection() - Method in class cct.gamess.Gamess
 
getCoordinateBuilder(String) - Static method in class cct.modelling.FormatManager
 
getCoordinateBuilders() - Static method in class cct.modelling.FormatManager
 
getCoordinateParser(String) - Static method in class cct.modelling.FormatManager
 
getCoordinateParsers() - Static method in class cct.modelling.FormatManager
 
getCoordinates(MoleculeInterface, boolean, Writer) - Method in interface cct.interfaces.CoordinateBuilderInterface
 
getCoordinates() - Method in class cct.modelling.gAtom
 
getCoordinates(int, float[]) - Method in class cct.modelling.MinimizeStructure
 
getCoordinates(int, float[]) - Method in class cct.modelling.MolecularEnergy
 
getCoordinates(int) - Method in class cct.modelling.MolecularGeometry
 
getCoordinates(MoleculeInterface, vPoint3f[]) - Static method in class cct.modelling.Molecule
Fills array with atomic coordinates.
getCoordinates() - Method in class cct.siesta.SiestaInput.SiestaAtom
 
getCoordinates(MoleculeInterface, boolean, Writer) - Method in class cct.tools.XMolXYZ
 
getCoordinatesAsString(MoleculeInterface, boolean) - Method in interface cct.interfaces.CoordinateBuilderInterface
 
getCoordinatesAsString(MoleculeInterface, boolean) - Method in class cct.tools.XMolXYZ
 
getCoordinationNumber() - Method in class cct.modelling.AtomGeometry
 
getCoordOffset() - Method in class cct.modelling.SingleTrajectory
 
getCovalentRadius() - Method in class cct.modelling.CCTAtomTypes
 
getCovalentRadius(int) - Static method in class cct.modelling.ChemicalElements
 
getCovalentRadius(String) - Static method in class cct.modelling.ChemicalElements
 
getCrystalToCartesianMatrix(double, double, double, double, double, double) - Method in class cct.gulp.Gulp
 
getCubeDescription() - Method in class cct.gaussian.GaussianCube
 
getCubeDescription() - Method in interface cct.interfaces.VolumetricDataInterface
Returns description of the whole volumetric data
getCubeLabel(int) - Method in class cct.gaussian.GaussianCube
 
getCubeLabel(int) - Method in interface cct.interfaces.VolumetricDataInterface
Returns description of nth cube
getCurrentAtomColorScheme() - Static method in class cct.j3d.ChemicalElementsColors
 
getCustomObjects() - Method in class cct.dialogs.JSolvateShellDialog
 
getCustomPropertiesFile() - Static method in class cct.tools.Utils
 
getCustomSolventFile() - Method in class cct.dialogs.JSolvateShellDialog
 
getCutoff() - Method in class cct.amber.Sander8JobControl
 
getCutoff() - Method in class cct.amber.Sander9JobControl
 
getCylinder(int) - Method in class cct.j3d.BondNode
 
getCylinder(Cylinder, OutputStream) - Method in class cct.j3d.GroupToVRML
 
getCylinderRadius() - Method in class cct.j3d.BondNode
 
getData() - Method in interface cct.grid.JobStatusInterface
 
getData() - Method in class cct.grid.ui.CheckPointStatus
 
getDatabase() - Method in class cct.awtdialogs.ConnectSQLServer
 
getDataCollection() - Method in class cct.chart.jfreechart.JFreeChartPanel.DataSet
 
getDataOrigin() - Method in class cct.gaussian.GaussianCube
 
getDataOrigin() - Method in interface cct.interfaces.VolumetricDataInterface
Data origin of a cube, i.e.
getDefaultAtomicCoordinatesFormat() - Static method in class cct.siesta.Siesta
 
getDefaultFragmentDictionary() - Static method in class cct.GlobalSettings
 
getDefaultIsovalue() - Method in class cct.gaussian.GaussianCube
 
getDefaultLatticeParameters(MoleculeInterface, double) - Static method in class cct.math.Crystal
 
getDefaultPolygonMode() - Static method in class cct.j3d.VerticesObjectProperties
 
getDefaultSolventDictionary() - Static method in class cct.GlobalSettings
 
getDefaultTranspMode() - Static method in class cct.j3d.VerticesObjectProperties
 
getDescription() - Method in class cct.amber.Sander8Variable
 
getDescription() - Method in class cct.amber.Sander8VariableValue
 
getDescription() - Method in class cct.amber.SanderVariable
 
getDescription() - Method in class cct.amber.SanderVariableValue
 
getDescription() - Method in class cct.tools.FileFilterImpl
 
getDialog() - Method in interface cct.grid.ScriptSubmitterDialogInterface
 
getDialog() - Method in class cct.grid.ui.gaussian.SubmitGaussianDialog
 
getDialog() - Method in class cct.grid.ui.gaussian.SubmitGaussianDialogNew
 
getDialog() - Method in class cct.grid.ui.SubmitTaskDialog
 
getDictionaryTree() - Method in class cct.tools.FragmentDictionaryParser
 
getDielectricConstant() - Method in interface cct.interfaces.ForceFieldInterface
 
getDielectricConstant() - Method in class cct.sff.SimpleForceField
 
getDielectricFunction() - Method in interface cct.interfaces.ForceFieldInterface
 
getDielectricFunction() - Method in class cct.sff.SimpleForceField
 
getDirectionalLight(DirectionalLight, OutputStream) - Method in class cct.j3d.GroupToVRML
 
getDirectionTo(vPoint3f) - Method in class cct.modelling.gAtom
 
getDirectories() - Method in interface cct.interfaces.FileChooserInterface
 
getDirectories() - Method in class cct.ssh.SSHPanel
 
getDirectory() - Method in interface cct.interfaces.FileChooserInterface
 
getDirectory() - Method in class cct.ssh.SSHPanel
 
getDisplacementVectors() - Method in class cct.adf.ADFFrequency
 
getDisplacementVectors(int) - Method in class cct.adf.ADFOutput
 
getDisplacementVectors() - Method in class cct.gaussian.GaussianFrequency
 
getDisplacementVectors(int) - Method in class cct.gaussian.GaussianOutput
 
getDisplacementVectors(int) - Method in interface cct.interfaces.OutputResultsInterface
 
getDuration() - Method in interface cct.interfaces.VibrationsRendererProvider
 
getDuration() - Method in class cct.j3d.VibrationsRenderer
 
getedge(int, int, int, int, int, int) - Method in class cct.poly.EDGETABLE
 
getEditorComponent() - Method in class cct.tools.filebrowser.FileTransferFrame.HostEditor
 
getElement(String) - Static method in class cct.amber.AmberUtilities
 
getElement() - Method in class cct.awtdialogs.AtomTypeDialog
 
getElement() - Method in class cct.dialogs.JAtomTypeDialog
 
getElement() - Method in class cct.gaussian.GaussianAtom
 
getElement() - Method in class cct.modelling.CCTAtomTypes
 
getElementColor(int) - Static method in class cct.j3d.ChemicalElementsColors
 
getElementCount(MoleculeInterface) - Static method in class cct.modelling.Molecule
Count number of each element in molecule
getElementMapping() - Static method in class cct.modelling.CCTAtomTypes
 
getElementMaterial(int) - Static method in class cct.j3d.ChemicalElementsColors
 
getElementName(int) - Static method in class cct.modelling.ChemicalElements
 
getElementNumber() - Method in class cct.awtdialogs.AtomTypeDialog
 
getElementsFont() - Method in class cct.dialogs.JElementsPanel
 
getElementsInMolecule() - Method in class cct.j3d.Java3dUniverse
 
getElementsInMolecule() - Method in class cct.modelling.MolecularEditor
 
getElementsInMolecule() - Method in class cct.modelling.Molecule
Returns a set of chemical elements presented in molecule
getElementsInMolecule(MoleculeInterface) - Static method in class cct.modelling.Molecule
Returns a set of chemical elements presented in molecule
getElementSymbol(int) - Static method in class cct.modelling.ChemicalElements
 
getEnergyTerm(String) - Method in class cct.vasp.VaspSnapshot
 
getEnergyTerms() - Method in class cct.vasp.VasprunXML
 
getEntryDirectory() - Method in class cct.pdb.ui.PDBBankFormPanel
 
getEnum() - Method in class cct.modelling.BasicFragment
 
getEnum() - Method in class cct.tools.CCTParserEnum
 
getEraseCommandObject(String) - Method in class cct.cprocessor.CommandProcessor
 
getErrorMessage() - Method in class cct.amber.Sander8JobControl
 
getErrorMessage() - Method in class cct.amber.Sander9JobControl
 
getErrorMessage() - Method in class cct.database.new_SQLChemistryDatabase
 
getErrorMessage() - Method in class cct.database.SQLChemistryDatabase
 
getErrorMessage() - Method in class cct.database.SQLDatabaseAccess
 
getErrorMessage() - Method in class cct.gaussian.Gaussian
 
getException() - Method in class cct.grid.ui.gaussian.SubmitGaussianDialog.Task
 
getException() - Method in class cct.grid.ui.gaussian.SubmitGaussianDialogNew.Task
 
getException() - Method in class cct.grid.ui.JobStatusDialog.Task
 
getException() - Method in class cct.grid.ui.SubmitTaskDialog.Task
 
getException() - Method in class cct.grid.ui.ThreadExec
 
getExecutable() - Method in class cct.grid.CheckPoint
 
getExecutable() - Method in class cct.grid.JobDescription
 
getExecutable() - Method in class cct.grid.ui.gaussian.SubmitGaussianPanel
 
getExitCodeDescription(int) - Method in class cct.math.DFPMin
 
getExitCodeDescription(int) - Method in interface cct.math.MinimizerInterface
 
getExtension(File) - Static method in class cct.tools.FileFilterImpl
 
getExtension(String) - Static method in class cct.tools.FileFilterImpl
 
getFaceIndices() - Method in class cct.vecmath.MeshObject
 
getFaces() - Method in class cct.oogl.OOGL
 
getFaces() - Method in class cct.tools.OOGL
 
getFile() - Method in interface cct.interfaces.FileChooserInterface
 
getFile() - Method in class cct.modelling.TrajectorySnapshot
 
getFile() - Method in class cct.ssh.SSHPanel
 
getFile() - Method in class cct.tools.ui.FileChooserDialog
 
getFileBrowserInterface() - Method in class cct.tools.filebrowser.JFileBrowserPanel
 
getFileCount() - Method in interface cct.interfaces.FileBrowserInterface
 
getFileCount() - Method in class cct.tools.filebrowser.LocalFileBrowser
 
getFileCount() - Method in class cct.tools.filebrowser.SFTPBrowser
 
getFileExtension(String) - Static method in class cct.tools.FileUtilities
Returns file extension
getFileFilters(LinkedHashMap) - Static method in class cct.tools.FileFilterImpl
Builds file filter implementations using HaspMap
getFileMenu() - Method in class cct.gaussian.ui.GaussianInputEditorFrame
 
getFileName() - Method in class cct.modelling.ui.OpenFile
 
getFileName() - Method in class cct.tools.filebrowser.FileName
 
getFileName(Object) - Method in class cct.tools.filebrowser.SFTPBrowser
 
getFileName(String) - Static method in class cct.tools.FileUtilities
 
getFileNames() - Method in interface cct.interfaces.FileBrowserInterface
 
getFileNames() - Method in class cct.tools.filebrowser.LocalFileBrowser
 
getFileNames() - Method in class cct.tools.filebrowser.SFTPBrowser
 
getFiles() - Method in interface cct.interfaces.FileChooserInterface
 
getFiles() - Method in class cct.ssh.SSHPanel
 
getFileStageIn(int) - Method in class cct.grid.JobDescription
Returns source and destination files
getFileStageInCount() - Method in class cct.grid.JobDescription
Returns number of files for staging in
getFileType() - Method in class cct.tools.filebrowser.FileName
 
getFirstCylinder(BondInterface) - Method in class cct.j3d.BondNode
 
getFloat(String) - Method in class cct.dialogs.JSolvateShellDialog
 
getFMin() - Method in class cct.math.LinearSearch
 
getFog(Fog, OutputStream) - Method in class cct.j3d.GroupToVRML
 
getFolderIcon32x32() - Static method in class cct.tools.FileUtilities
 
getFontForText() - Method in class cct.gaussian.ui.Link0Panel
 
getFontForText() - Method in class cct.gaussian.ui.MoleculeSpecsPanel
 
getFontForText() - Method in class cct.gaussian.ui.RouteSectionPanel
 
getFontForText() - Method in class cct.gaussian.ui.SimpleG03EditorPanel
 
getFontForText() - Method in class cct.gaussian.ui.TitleSectionPanel
 
getFontName() - Method in class cct.tools.ui.FontSelectorDialog
 
getFontSize() - Method in class cct.tools.ui.FontSelectorDialog
 
getFontSize() - Method in class cct.tools.ui.FontSelectorPanel
 
getFontStyle() - Method in class cct.tools.ui.FontSelectorDialog
 
getFontStyle() - Method in class cct.tools.ui.FontSelectorPanel
 
getFontStyleAsString() - Method in class cct.tools.ui.FontSelectorPanel
 
getFormat() - Method in class cct.modelling.TrajectorySnapshot
 
getFractionalCoordinates(double[][]) - Method in class cct.siesta.SiestaInput
 
getFractionalCoordinates(float, float, float, float[][]) - Static method in class cct.siesta.SiestaInput
 
getFrequencies() - Method in class cct.adf.ADFOutputSection
 
getFrequency(int) - Method in class cct.adf.ADFOutput
 
getFrequency(int) - Method in class cct.gaussian.GaussianOutput
 
getFrequency(int) - Method in interface cct.interfaces.OutputResultsInterface
 
getFrequencyValue() - Method in class cct.adf.ADFFrequency
 
getFTPBrowser(String) - Method in interface cct.interfaces.FTPManagerInterface
 
getFTPBrowser(String) - Method in class cct.tools.filebrowser.FTPManager
 
getFullLocalPath(String) - Method in class cct.grid.CheckPoint
 
getGatekeeper() - Method in interface cct.grid.GridProviderInterface
 
getGatekeeper() - Method in class cct.grid.LocalServiceProvider
 
getGatekeeper() - Method in class cct.ssh.SSHServiceProvider
 
getGaussianData() - Method in class cct.j3d.Java3dUniverse
 
getGaussianMolecule(int) - Method in class cct.gaussian.Gaussian
 
getGeneralParameters(String, int) - Method in class cct.amber.Sander8JobControl
 
getGeneralParameters(String, int, FortranNamelist, String) - Static method in class cct.amber.Sander8JobControl
 
getGeneralParameters(String, int) - Method in class cct.amber.Sander9JobControl
 
getGeneralParameters(String, int, FortranNamelist, String) - Static method in class cct.amber.Sander9JobControl
 
getGeometries() - Method in class cct.j3d.Java3dUniverse
 
getGeometry(String) - Method in class cct.gaussian.GaussianSnapshot
 
getGeometry(Geometry, int, OutputStream) - Method in class cct.j3d.GroupToVRML
Geometry is an abstract class that specifies the geometry component information required by a Shape3D node.
getGeometry() - Method in class cct.modelling.AtomGeometry
 
getGeometryArray(GeometryArray, int, OutputStream) - Method in class cct.j3d.GroupToVRML
The GeometryArray object contains separate arrays of positional coordinates, colors, normals, texture coordinates, and vertex attributes that describe point, line, or polygon geometry.
getGeometryStripArray(GeometryStripArray, OutputStream) - Method in class cct.j3d.GroupToVRML
 
getGJFAsString() - Method in class cct.gaussian.ui.GaussianInputEditorFrame
 
getGradients() - Method in class cct.math.DFPMin
 
getGradients() - Method in interface cct.math.MinimizerInterface
 
getGradients() - Method in class cct.modelling.MolecularEnergy
 
getGraphicsElement(int) - Method in interface cct.interfaces.GraphicsObjectInterface
 
getGraphicsElement(int) - Method in class cct.j3d.VerticesObject
 
getGraphicsObject(GaussianCube, int, float, boolean) - Static method in class cct.gaussian.java3d.GaussianJava3dFactory
 
getGraphicsObject(int) - Method in class cct.j3d.Java3dUniverse
 
getGraphicsObject(OOGL) - Static method in class cct.oogl.java3d.OoglJava3d
 
getGraphicsObjects() - Method in class cct.j3d.Java3dUniverse
 
getGridAsLines(GaussianCube) - Static method in class cct.gaussian.java3d.GaussianJava3dFactory
 
getGridAsPoints(GaussianCube) - Static method in class cct.gaussian.java3d.GaussianJava3dFactory
 
getGromacsAtomType(String, String) - Static method in class cct.gromacs.Gromacs
 
getGroup(Group, OutputStream) - Method in class cct.j3d.GroupToVRML
Converts Group into VRML String
getHashMap() - Method in class cct.grid.CheckPoint
Returns checkpoint as a HashMap
getHeaderRendererIcon(int, int) - Method in class cct.tools.filebrowser.TableSorter
 
getHelp() - Method in class cct.grid.ui.JobStatusPanel
 
getHelpButton() - Method in class cct.dialogs.JAddFragmentDialog
 
getHelpButton() - Method in class cct.dialogs.JAddMoleculeDialog
 
getHelpButton() - Method in class cct.dialogs.JAtomSelectionDialog
 
getHelpButton() - Method in class cct.dialogs.JAtomTypeDialog
 
getHelpButton() - Method in class cct.dialogs.JModifyAngleDialog
 
getHelpButton() - Method in class cct.dialogs.JModifyAtomDialog
 
getHelpButton() - Method in class cct.dialogs.JModifyTorsionDialog
 
getHelpButton() - Method in class cct.dialogs.JSolvateShellDialog
 
getHelpButton() - Method in class cct.gaussian.ui.ManageCubesFrame
 
getHelpButton() - Method in class cct.gaussian.ui.SaveG03GJFDialog
 
getHelpButton() - Method in class cct.j3d.ui.GraphicsObjectPropertiesFrame
 
getHighlightColor3f() - Static method in class cct.j3d.ChemicalElementsColors
 
getHighlightMaterial() - Static method in class cct.j3d.ChemicalElementsColors
 
getHost() - Method in class cct.pdb.ui.PDBBankFormPanel
 
getHost() - Method in class cct.ssh.SSHPanel
 
getHost() - Method in class cct.tools.filebrowser.ConnectHostDialog
 
getHost() - Method in class cct.tools.filebrowser.SFTPBrowser
 
getHostname() - Method in class cct.awtdialogs.ConnectSQLServer
 
getI() - Method in class cct.modelling.AngleBend
 
getI() - Method in class cct.modelling.Bond
 
getI() - Method in class cct.modelling.NonbondedPair
 
getI() - Method in class cct.modelling.Torsion
 
getI() - Method in class cct.modelling.TorsionParameter
 
getIAtomInterface() - Method in interface cct.interfaces.BondInterface
 
getIAtomInterface() - Method in class cct.modelling.Bond
 
getIcon() - Method in class cct.modelling.AtomGeometry
 
getIcon16x16(String) - Static method in class cct.tools.FileUtilities
Returns image icon
getIcon32x32(String) - Static method in class cct.tools.FileUtilities
Returns image icon
getImageCapture() - Method in class cct.j3d.Java3dUniverse
 
getImageIcon(CCTAtomTypes) - Static method in class cct.modelling.CCTAtomTypes
 
getInputAsString() - Method in class cct.siesta.SiestaInput
 
getInputAsString() - Method in class cct.siesta.ui.SiestaPanel
 
getInputFile() - Method in interface cct.grid.ClientProgramInterface
 
getInputFile() - Method in class cct.grid.ui.gaussian.SubmitGaussianPanel
 
getInputFileName() - Method in class cct.grid.ui.gaussian.SubmitGaussianPanel
 
getInstance() - Method in class cct.gamess.GamessAtom
 
getInstance(Point3fInterface) - Method in class cct.gamess.GamessAtom
 
getInstance(float, float, float) - Method in class cct.gamess.GamessAtom
 
getInstance() - Method in interface cct.interfaces.MoleculeInterface
 
getInstance() - Method in interface cct.interfaces.Point3fInterface
 
getInstance(Point3fInterface) - Method in interface cct.interfaces.Point3fInterface
 
getInstance(float, float, float) - Method in interface cct.interfaces.Point3fInterface
 
getInstance() - Method in class cct.modelling.Molecule
 
getInstance(float, float, float) - Method in class cct.vecmath.vPoint3f
 
getInstance() - Method in class cct.vecmath.vPoint3f
 
getInstance(Point3fInterface) - Method in class cct.vecmath.vPoint3f
 
getItem() - Method in class cct.tools.filebrowser.FileTransferFrame.HostEditor
 
getJ() - Method in class cct.modelling.AngleBend
 
getJ() - Method in class cct.modelling.Bond
 
getJ() - Method in class cct.modelling.NonbondedPair
 
getJ() - Method in class cct.modelling.Torsion
 
getJ() - Method in class cct.modelling.TorsionParameter
 
getJ3DUniverse() - Method in class cct.dialogs.JEditorFrame
 
getJAtomInterface() - Method in interface cct.interfaces.BondInterface
 
getJAtomInterface() - Method in class cct.modelling.Bond
 
getJava3dPropsAsString() - Static method in class cct.j3d.QueryProperties
 
getJobFS() - Method in class cct.grid.JobDescription
 
getJobFS() - Method in class cct.grid.ui.PBS_Panel
 
getJobFS() - Method in class cct.grid.ui.PBSPanel
 
getJobHandle() - Method in class cct.grid.CheckPoint
 
getJobHandle() - Method in class cct.grid.LocalServiceProvider
 
getJobHandle() - Method in class cct.grid.TaskProvider
 
getJobHandle() - Method in class cct.ssh.SSHServiceProvider
Returns job handle of a submitted job (in the case of success)
getJobName() - Method in class cct.grid.CheckPoint
 
getJobName() - Method in interface cct.grid.ClientProgramInterface
 
getJobName() - Method in class cct.grid.JobDescription
 
getJobName() - Method in class cct.grid.ui.gaussian.SubmitGaussianPanel
 
getJobStatus() - Method in class cct.grid.CheckPoint
 
getJobStatus(CheckPoint) - Method in interface cct.grid.GridProviderInterface
 
getJobStatus(CheckPoint) - Method in class cct.grid.LocalServiceProvider
 
getJobStatus(CheckPoint) - Static method in class cct.grid.TaskProvider
Returns job status as a string for a given checkpoint
getJobStatus(CheckPoint) - Method in class cct.ssh.SSHServiceProvider
Returns current job status of a job
getJobStatuses() - Method in class cct.grid.ParseCheckpointFile
 
getJobStatusInterface() - Method in class cct.grid.ui.JobStatusTableModel
 
getJobSubmitTime() - Method in class cct.grid.CheckPoint
 
getJobType() - Method in class cct.gaussian.GaussianKeywords
 
getJobType() - Method in class cct.modelling.MolecularEditor
 
getJPEGQuality() - Method in class cct.tools.ui.JPEGOptionsDialog
 
getJPEGQuality() - Method in class cct.tools.ui.JPEGOptionsPanel
 
getJToolBar() - Method in class cct.dialogs.JEditorFrame
 
getK() - Method in class cct.modelling.AngleBend
 
getK() - Method in class cct.modelling.Torsion
 
getK() - Method in class cct.modelling.TorsionParameter
 
getKeyPressed() - Method in class cct.tools.filebrowser.ConnectHostDialog
 
getKeywords() - Method in class cct.awtdialogs.AddNewMoleculeDialog
 
getKnownHosts() - Method in interface cct.tools.filebrowser.ShadowManagerInterface
 
getKnownHosts() - Method in class cct.tools.filebrowser.ShadowSFTPManager
 
getL() - Method in class cct.modelling.Torsion
 
getL() - Method in class cct.modelling.TorsionParameter
 
getLabel() - Method in class cct.siesta.SiestaInput.SiestaAtom
 
getLastInsertId(String) - Method in class cct.database.SQLDatabaseAccess
 
getLastSelectedAtom() - Method in class cct.j3d.Java3dUniverse
 
getLatticeVectors() - Method in class cct.gaussian.GaussianSnapshot
 
getLatticeVectors() - Method in class cct.siesta.SiestaInput
 
getLatticeVectors() - Method in class cct.vasp.ui.ReadPoscarDialog
 
getLatticeVectors() - Method in class cct.vasp.Vasp
 
getLatticeVectors() - Method in class cct.vasp.VasprunXML
 
getLatticeVectors() - Method in class cct.vasp.VaspSnapshot
 
getLeaf(Leaf, OutputStream) - Method in class cct.j3d.GroupToVRML
 
getLight(Light, OutputStream) - Method in class cct.j3d.GroupToVRML
 
getLinearFog(LinearFog, OutputStream) - Method in class cct.j3d.GroupToVRML
 
getLinkZeroCommandbject(String) - Method in class cct.gaussian.GaussianMolecule
Command should be without initial "%"
getLinkZeroCommands(int) - Method in class cct.gaussian.Gaussian
 
getLinkZeroCommands() - Method in class cct.gaussian.GaussianMolecule
 
getLinkZeroCommands(int) - Method in interface cct.gaussian.GJFParserInterface
 
getLinkZeroCommands() - Method in class cct.gaussian.ui.SimpleG03EditorPanel
 
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class cct.tools.filebrowser.FileTransferFrame.HostComboBoxRenderer
 
getLoadMode() - Method in class cct.dialogs.AddMoleculeDialog
 
getLocalDirectory() - Method in class cct.grid.CheckPoint
 
getLocalDirectory() - Method in interface cct.grid.ClientProgramInterface
 
getLocalDirectory() - Method in class cct.grid.JobDescription
 
getLocalDirectory() - Method in class cct.grid.ui.gaussian.SubmitGaussianPanel
 
getLocale(Locale, OutputStream) - Method in class cct.j3d.GroupToVRML
Writes Locale into OutputStream
getLocale() - Method in class cct.j3d.Java3dUniverse
 
getLocalFile() - Method in class cct.tools.filebrowser.SFTPFileChooserDialog
 
getLookAndFeel() - Static method in class cct.tools.SwingLookAndFeel
 
getMaterial() - Method in class cct.j3d.AtomNode
 
getMaxAbsValue(float[]) - Static method in class cct.vecmath.VecmathTools
Returns element of the vector (signed) with the largest absolute value
getMaxCpuTime() - Method in class cct.grid.JobDescription
 
getMaxFunValue() - Method in class cct.gaussian.GaussianCube
 
getMaxFunValue() - Method in interface cct.interfaces.VolumetricDataInterface
Returns maximum function value
getMaxFunValue() - Method in class cct.j3d.ColorRangeScheme
 
getMaxGradientConv() - Method in class cct.math.DFPMin
 
getMaxGradientConv() - Method in interface cct.math.MinimizerInterface
 
getMaximumDuration() - Method in interface cct.interfaces.VibrationsRendererProvider
 
getMaximumDuration() - Method in class cct.j3d.VibrationsRenderer
 
getMaximumSize() - Method in class cct.tools.MemoryMonitor.Surface
 
getMaxIterations() - Method in class cct.math.DFPMin
 
getMaxIterations() - Method in interface cct.math.MinimizerInterface
 
getMaxMemory() - Method in class cct.grid.JobDescription
 
getMaxMemory() - Method in class cct.grid.ui.PBS_Panel
 
getMaxMemoryInMb() - Method in interface cct.grid.ResourcesProviderInterface
 
getMaxMemoryInMb() - Method in class cct.grid.ui.ResourcesPanel
 
getMaxRMSGradientConv() - Method in class cct.math.DFPMin
 
getMaxRMSGradientConv() - Method in interface cct.math.MinimizerInterface
 
getMaxSingleBonds() - Method in class cct.modelling.AtomGeometry
 
getMaxTime() - Method in class cct.grid.JobDescription
 
getMaxTime() - Method in class cct.grid.ui.PBS_Panel
 
getMaxWallTime() - Method in class cct.grid.JobDescription
 
getMaxWallTimeFormatted() - Method in class cct.grid.JobDescription
Returns time in the format [[hours:]minutes:]seconds
getMaxWallTimeFormatted(int) - Static method in class cct.grid.ui.PBSPanel
Returns time in the format [[hours:]minutes:]seconds
getMemory() - Method in class cct.gaussian.Gaussian
Returns memory in KB
getMemory() - Method in class cct.gaussian.GaussianMolecule
Returns memory in KB.
getMenuItem(String, String) - Method in class cct.dialogs.JEditorFrame
Gets menu item with ActionCommand name "menuItemName" from the menu with ActionCommand name "menuName"
getMessage() - Method in class cct.grid.CheckPoint
 
getMessage() - Method in class cct.tools.ui.PostMessagePanel
 
getMethod() - Method in class cct.awtdialogs.AddNewStructureDialog
 
getMethod() - Method in class cct.gaussian.GaussianKeywords
 
getMethods() - Method in class cct.database.new_SQLChemistryDatabase
 
getMinFunValue() - Method in class cct.gaussian.GaussianCube
 
getMinFunValue() - Method in interface cct.interfaces.VolumetricDataInterface
Returns minimum function value
getMinFunValue() - Method in class cct.j3d.ColorRangeScheme
 
getMinimumDuration() - Method in interface cct.interfaces.VibrationsRendererProvider
 
getMinimumDuration() - Method in class cct.j3d.VibrationsRenderer
 
getMinimumSize() - Method in class cct.tools.MemoryMonitor.Surface
 
getMinimumValue() - Method in class cct.math.Simplex
 
getMolecularInterface(MoleculeInterface) - Method in class cct.adf.ADF
 
getMolecularInterface(MoleculeInterface, int) - Method in class cct.adf.ADFOutput
 
getMolecularInterface(MoleculeInterface) - Method in class cct.amber.AmberPrep
 
getMolecularInterface(MoleculeInterface) - Method in class cct.gamess.Gamess
 
getMolecularInterface(MoleculeInterface) - Method in class cct.gamess.GamessOutput
 
getMolecularInterface(MoleculeInterface) - Method in class cct.gaussian.G03MDTrajectory
Contrary to any similar subroutines it returns the FIRST snapshot
getMolecularInterface(MoleculeInterface) - Method in class cct.gulp.Gulp
 
getMolecularInterface(MoleculeInterface) - Method in class cct.mopac.Mopac
 
getMolecularInterface(MoleculeInterface) - Method in class cct.mopac.MopacOutput
 
getMolecularInterface(MoleculeInterface) - Method in class cct.qchem.QChem
 
getMolecularInterface(MoleculeInterface) - Method in class cct.qchem.QChemOutput
 
getMolecularInterface(MoleculeInterface) - Method in class cct.siesta.SiestaInput
 
getMolecularInterface(MoleculeInterface) - Method in class cct.vasp.Vasp
 
getMolecularInterface(MoleculeInterface) - Method in class cct.vasp.VasprunXML
Takes the last snapshot from the bunch
getMolecularSubstructure() - Method in interface cct.interfaces.MoleculeInterface
 
getMolecularSubstructure() - Method in class cct.modelling.MolecularEditor
 
getMolecularSubstructure() - Method in class cct.modelling.Molecule
 
getMolecularWeight(MoleculeInterface) - Static method in class cct.modelling.Molecule
Calculates molecular weight
getMolecule(String) - Method in class cct.amber.AmberLib
 
getMolecule() - Method in class cct.amber.ReadPrmtopDialog
 
getMolecule() - Method in class cct.dialogs.JEditorFrame
 
getMolecule(MoleculeInterface) - Method in class cct.gaussian.G03FormCheckpoint
 
getMolecule(MoleculeInterface, int) - Method in class cct.gaussian.Gaussian
 
getMolecule(MoleculeInterface) - Method in class cct.gaussian.GaussianCube
 
getMolecule(MoleculeInterface) - Method in class cct.gaussian.GaussianMolecule
 
getMolecule(MoleculeInterface) - Method in interface cct.interfaces.VolumetricDataInterface
Returns molecular goemetry (if any).
getMolecule() - Method in class cct.j3d.Java3dUniverse
 
getMolecule() - Method in class cct.modelling.BackgroundMinimizer
 
getMolecule() - Method in class cct.modelling.BasicFragment.CarbonDivalentStr
 
getMolecule() - Method in class cct.modelling.FFMolecule
 
getMolecule() - Method in class cct.modelling.MinimizeStructure
 
getMolecule() - Method in class cct.vasp.ui.ReadPoscarDialog
 
getMoleculeAtomBelongsTo(AtomInterface) - Static method in class cct.modelling.Molecule
 
getMoleculeBranchGroup() - Method in class cct.j3d.Java3dUniverse
Returns BranchGroup of a molecule
getMoleculeInterface() - Method in interface cct.interfaces.GraphicsRendererInterface
 
getMoleculeInterface() - Method in class cct.j3d.Java3dUniverse
 
getMoleculeInterface() - Method in class cct.j3d.SimpleRenderer
 
getMoleculeNames() - Method in class cct.amber.AmberLib
 
getMolecules() - Method in class cct.amber.AmberLib
 
getMolecules() - Method in class cct.database.new_SQLChemistryDatabase
 
getMolecules() - Method in class cct.database.SQLChemistryDatabase
 
getMolecules() - Method in class cct.tools.CCTParser
 
getMoleculesCount() - Method in class cct.tools.CCTParser
 
getMoleculeSpecs(int) - Method in class cct.gaussian.Gaussian
 
getMoleculeSpecsAsString(MoleculeInterface) - Static method in class cct.gaussian.Gaussian
Returns molecule specifications (coordinates) as a String
getMoleculeSpecsSection(int) - Method in class cct.gaussian.Gaussian
 
getMoleculeSpecsSection() - Method in class cct.gaussian.GaussianMolecule
 
getMoleculeSpecsSection(int) - Method in interface cct.gaussian.GJFParserInterface
 
getMoleculeSpecsSection() - Method in class cct.gaussian.ui.SimpleG03EditorPanel
 
getMoleculeSpecsSectionAsString() - Method in class cct.gaussian.GaussianMolecule
 
getMonocolorLine(BondInterface) - Method in class cct.j3d.BondNode
 
getMonomer(int) - Method in class cct.modelling.AtomsArray
Returns nth monomer from the list.
getMonomer(int) - Method in class cct.modelling.Molecule
 
getMonomerInterface(int) - Method in interface cct.interfaces.MoleculeInterface
 
getMonomerInterface(int) - Method in class cct.modelling.Molecule
 
getMousePickingStatus() - Method in class cct.j3d.Java3dUniverse
 
getMousePickingStatus() - Method in class cct.modelling.MolecularEditor
 
getMultipleItemsIcon32x32() - Static method in class cct.tools.FileUtilities
 
getMultiplicity() - Method in class cct.awtdialogs.AddNewMoleculeDialog
 
getName() - Method in class cct.awtdialogs.AddNewStructureDialog
 
getName() - Method in class cct.gamess.GamessAtom
 
getName() - Method in class cct.gamess.GamessSwitch
 
getName() - Method in interface cct.grid.GridProviderInterface
 
getName() - Method in class cct.grid.LocalServiceProvider
 
getName() - Method in interface cct.interfaces.AtomInterface
 
getName() - Method in interface cct.interfaces.ForceFieldInterface
 
getName() - Method in interface cct.interfaces.GraphicsObjectInterface
 
getName() - Method in interface cct.interfaces.MoleculeInterface
 
getName() - Method in interface cct.interfaces.MonomerInterface
 
getName() - Method in class cct.j3d.VerticesObject
 
getName() - Method in class cct.math.DFPMin
 
getName() - Method in interface cct.math.MinimizerInterface
 
getName() - Method in class cct.modelling.AtomTypeDef
Get name (mnemonic) of atom type
getName() - Method in class cct.modelling.MolecularGeometry
 
getName() - Method in class cct.modelling.Molecule
 
getName() - Method in class cct.modelling.Monomer
 
getName() - Method in class cct.modelling.vAtom
 
getName() - Method in class cct.mopac.MopacAtom
 
getName() - Method in class cct.qchem.QChemAtom
 
getName() - Method in class cct.sff.SimpleForceField
 
getName() - Method in class cct.ssh.SSHServiceProvider
 
getName() - Method in class cct.vasp.VaspAtom
 
getNAtomsFromCoordFile(String) - Static method in class cct.amber.AmberUtilities
 
getNBCutoff() - Method in interface cct.interfaces.ForceFieldInterface
 
getNBCutoff() - Method in class cct.sff.SimpleForceField
 
getNCPU() - Method in class cct.grid.JobDescription
 
getNCPUs() - Method in interface cct.grid.ResourcesProviderInterface
 
getNCPUs() - Method in class cct.grid.ui.PBS_Panel
 
getNCPUs() - Method in class cct.grid.ui.ResourcesPanel
 
getNewAtom() - Method in class cct.modelling.gAtom
 
getNewAtomInstance() - Method in interface cct.interfaces.AtomInterface
 
getNewAtomInstance(AtomInterface) - Method in interface cct.interfaces.AtomInterface
 
getNewAtomInstance() - Method in interface cct.interfaces.MoleculeInterface
 
getNewAtomInstance() - Method in class cct.modelling.gAtom
 
getNewAtomInstance(AtomInterface) - Method in class cct.modelling.gAtom
 
getNewAtomInstance() - Method in class cct.modelling.Molecule
 
getNewAtomInstance() - Method in class cct.modelling.vAtom
 
getNewAtomInstance(AtomInterface) - Method in class cct.modelling.vAtom
 
getNewBondInstance() - Method in interface cct.interfaces.BondInterface
 
getNewBondInstance(BondInterface) - Method in interface cct.interfaces.BondInterface
 
getNewBondInstance(AtomInterface, AtomInterface) - Method in interface cct.interfaces.BondInterface
 
getNewBondInstance() - Method in interface cct.interfaces.MoleculeInterface
 
getNewBondInstance(AtomInterface, AtomInterface) - Method in interface cct.interfaces.MoleculeInterface
 
getNewBondInstance() - Method in class cct.modelling.Bond
 
getNewBondInstance(AtomInterface, AtomInterface) - Method in class cct.modelling.Bond
 
getNewBondInstance(BondInterface) - Method in class cct.modelling.Bond
 
getNewBondInstance() - Method in class cct.modelling.Molecule
 
getNewBondInstance(AtomInterface, AtomInterface) - Method in class cct.modelling.Molecule
 
getNewInstance() - Static method in class cct.modelling.Molecule
 
getNewMethod() - Method in class cct.awtdialogs.AddNewMethodDialog
 
getNFaces() - Method in class cct.oogl.OOGL
 
getNFaces() - Method in class cct.tools.OOGL
 
getNGraphicsElements() - Method in interface cct.interfaces.GraphicsObjectInterface
 
getNGraphicsElements() - Method in class cct.j3d.VerticesObject
 
getNode(Node, OutputStream) - Method in class cct.j3d.GroupToVRML
 
getNonbondInteractions() - Method in class cct.modelling.FFMolecule
 
getNormal(GLvector, float, float, float) - Method in class cct.math.polyg.Polygonizer
 
getNormal(Point3f, Point3f, Point3f) - Static method in class cct.oogl.java3d.OoglJava3d
Normal points toward the side from which the vertices p1, p2, and p3 appear in counterclockwise order.
getNormals() - Method in class cct.math.polyg.Polygonizer
 
getNormals() - Method in class cct.oogl.OOGL
 
getNormals() - Method in class cct.tools.OOGL
 
getNormals() - Method in class cct.vecmath.MeshObject
 
getNotes() - Method in class cct.awtdialogs.AddNewMoleculeDialog
 
getNotes() - Method in class cct.awtdialogs.AddNewStructureDialog
 
getNuclearCharge() - Method in class cct.gamess.GamessAtom
 
getNumber(JTextField) - Method in class cct.grid.ui.ResourcesPanel
 
getNumberOfAtoms() - Method in class cct.amber.AmberPrmtop
 
getNumberOfAtoms() - Method in class cct.amber.Sander8JobControl
 
getNumberOfAtoms() - Method in class cct.amber.Sander9JobControl
 
getNumberOfAtoms() - Method in class cct.amber.SanderResourcesEval
 
getNumberOfAtoms() - Method in interface cct.interfaces.MoleculeInterface
 
getNumberOfAtoms() - Method in interface cct.interfaces.MonomerInterface
 
getNumberOfAtoms() - Method in class cct.modelling.Molecule
 
getNumberOfAtoms() - Method in class cct.modelling.Monomer
 
getNumberOfAtoms() - Method in class cct.vasp.Vasp
 
getNumberOfBondedAtoms() - Method in interface cct.interfaces.AtomInterface
 
getNumberOfBondedAtoms() - Method in class cct.modelling.vAtom
 
getNumberOfBonds() - Method in interface cct.interfaces.MoleculeInterface
 
getNumberOfBonds() - Method in class cct.modelling.Molecule
 
getNumberOfElements() - Static method in class cct.modelling.ChemicalElements
 
getNumberOfGraphicsObjects() - Method in class cct.j3d.Java3dUniverse
 
getNumberOfMolecules() - Method in class cct.gaussian.Gaussian
 
getNumberOfMonomers() - Method in interface cct.interfaces.MoleculeInterface
 
getNumberOfMonomers() - Method in class cct.modelling.AtomsArray
Returns number of monomers
getNumberOfMonomers() - Method in class cct.modelling.Molecule
 
getNumberOfProcessors() - Method in class cct.gaussian.Gaussian
Returns the maximum number of processors from all molecules
getNumberOfProcessors() - Method in class cct.gaussian.GaussianMolecule
 
getNumberOfSteps() - Method in class cct.gaussian.Gaussian
 
getNumberOfSteps() - Method in interface cct.gaussian.GJFParserInterface
 
getNumberOfValues() - Method in class cct.amber.Sander8Variable
 
getNumberOfValues() - Method in class cct.amber.SanderVariable
 
getNumberOfVoxels() - Method in class cct.gaussian.GaussianCube
 
getNumberOfVoxels() - Method in interface cct.interfaces.VolumetricDataInterface
Number of voxels along every axis (x,y,z)
getNVertices() - Method in class cct.oogl.Face
 
getNVertices() - Method in class cct.oogl.OOGL
 
getNVertices() - Method in class cct.tools.OOGL
 
getObjectAsString(Object) - Static method in class cct.tools.CCTParser
 
getObjectClass(String, String) - Static method in class cct.tools.CCTParser
 
getObjectType() - Method in class cct.vecmath.MeshObject
 
getOffset() - Method in class cct.gaussian.GaussianSnapshot
 
getOffset() - Method in class cct.modelling.TrajectorySnapshot
 
getOpacity() - Method in class cct.vecmath.MeshObject
 
getOption(String) - Method in class cct.gaussian.GaussianKeywords
 
getOption(String) - Method in interface cct.grid.SchedulerInterface
 
getOption(String) - Method in class cct.grid.ui.NoSchedulerPanel
 
getOption(String) - Method in class cct.grid.ui.PBSPanel
 
getOptions() - Method in class cct.gaussian.GaussianKeywords
 
getOS() - Method in interface cct.grid.GridProviderInterface
 
getOS() - Method in class cct.grid.LocalServiceProvider
 
getOS() - Method in class cct.ssh.SSHServiceProvider
 
getOtherOptions() - Method in class cct.siesta.SiestaInput
 
getOtherOptions() - Method in interface cct.siesta.SiestaInterface
 
getOtherOptionsAsString() - Method in class cct.siesta.SiestaInput
 
getOutputFile() - Method in interface cct.grid.ClientProgramInterface
 
getOutputFile() - Method in class cct.grid.ui.gaussian.SubmitGaussianPanel
 
getOutputFileName() - Method in class cct.grid.ui.gaussian.SubmitGaussianPanel
 
getOutputFilesEntry() - Method in class cct.grid.CheckPoint
 
getOutputFileType(String) - Method in class cct.grid.CheckPoint
 
getOutputResume() - Method in class cct.gaussian.GaussianOutput
 
getOutputResume() - Method in class cct.mopac.MopacOutput
 
getOutputResume() - Method in class cct.qchem.QChemOutput
 
getOverallJobStatus() - Method in class cct.grid.CheckPoint
 
getParameter(String, String) - Method in class cct.amber.AmberApplet
 
getParameter(String, String) - Method in class cct.applets.viewer
 
getParameterInfo() - Method in class cct.amber.AmberApplet
 
getParameterInfo() - Method in class cct.applets.viewer
 
getParentFrame() - Method in class cct.dialogs.JEditorFrame
 
getParentFrame() - Method in interface cct.interfaces.ParentInterface
 
getParsedValue() - Method in class cct.amber.Sander8Variable
 
getParsedValue() - Method in class cct.amber.Sander8VariableValue
 
getParsedValue() - Method in class cct.amber.SanderVariable
 
getParsedValue() - Method in class cct.amber.SanderVariableValue
 
getPassword() - Method in class cct.awtdialogs.ConnectSQLServer
 
getPassword() - Method in class cct.tools.filebrowser.ConnectHostDialog
 
getPassword() - Method in class cct.tools.filebrowser.SFTPBrowser
 
getPassword() - Method in class cct.tools.UserPasswordDialog
 
getPBSOther() - Method in class cct.grid.JobDescription
 
getPermissions() - Method in class cct.tools.filebrowser.FilePropertiesDialog
 
getPermissions() - Method in class cct.tools.filebrowser.PermissionsPanel
 
getPickMode() - Method in class cct.j3d.MousePicking
Return the pickMode component of this PickRotateBehavior.
getPictureMapping(int) - Static method in class cct.modelling.CCTAtomTypes
 
getPolygonMode() - Method in class cct.j3d.VerticesObjectProperties
 
getPort() - Method in class cct.ssh.SSHPanel
 
getPort() - Method in class cct.tools.filebrowser.ConnectHostDialog
 
getPort() - Method in class cct.tools.filebrowser.SFTPBrowser
 
getPredefinedDistance() - Method in class cct.dialogs.JAddMoleculeDialog
 
getPreference(Object, String) - Static method in class cct.tools.Utils
 
getPreferredSize() - Method in class cct.tools.MemoryMonitor.Surface
 
getPreprocessDir(int) - Method in class cct.grid.JobDescription
 
getPreprocessDirCount() - Method in class cct.grid.JobDescription
Returns number of preprocess directives
getPressedKey() - Method in class cct.tools.filebrowser.FileChooserDialog
 
getPrimitive(Primitive, OutputStream) - Method in class cct.j3d.GroupToVRML
 
getProgram() - Method in class cct.grid.CheckPoint
 
getProgramName() - Method in interface cct.grid.ClientProgramInterface
 
getProgramName() - Method in class cct.grid.ui.gaussian.SubmitGaussianPanel
 
getProject() - Method in class cct.grid.JobDescription
 
getProject() - Method in interface cct.grid.SchedulerInterface
 
getProject() - Method in class cct.grid.ui.NoSchedulerPanel
 
getProject() - Method in class cct.grid.ui.PBS_Panel
 
getProject() - Method in class cct.grid.ui.PBSPanel
 
getProjectionMode() - Method in class cct.j3d.Java3dUniverse
 
getProjectionModeAsString() - Method in class cct.j3d.Java3dUniverse
 
getProjectionModes() - Method in class cct.j3d.Java3dUniverse
 
getProperties() - Method in interface cct.interfaces.AtomInterface
 
getProperties() - Method in interface cct.interfaces.BondInterface
 
getProperties() - Method in interface cct.interfaces.MoleculeInterface
 
getProperties() - Method in class cct.modelling.Bond
 
getProperties() - Method in class cct.modelling.Molecule
 
getProperties() - Method in class cct.modelling.vAtom
 
getProperty(String) - Method in class cct.adf.ADFSnapshot
 
getProperty(VIBRATIONAL_SPECTRUM) - Method in class cct.gaussian.GaussianFrequency
 
getProperty(String) - Method in class cct.gaussian.GaussianFrequency
 
getProperty(String) - Method in class cct.gaussian.GaussianSnapshot
 
getProperty(String) - Method in interface cct.interfaces.AtomInterface
 
getProperty(String) - Method in interface cct.interfaces.BondInterface
 
getProperty(String) - Method in interface cct.interfaces.MoleculeInterface
 
getProperty(String) - Method in class cct.modelling.Bond
 
getProperty(String) - Method in class cct.modelling.Molecule
 
getProperty(String) - Method in class cct.modelling.TrajectorySnapshot
 
getProperty(String) - Method in class cct.modelling.vAtom
 
getProvider(String) - Static method in class cct.grid.TaskProvider
 
getProviders() - Method in class cct.tools.GridProviders
 
getProxy_Button - Variable in class cct.grid.ui.gaussian.SubmitGaussianDialog
 
getProxy_Button_actionPerformed(ActionEvent) - Method in class cct.grid.ui.gaussian.SubmitGaussianDialog
 
getProxy_Button_actionPerformed(ActionEvent) - Method in class cct.grid.ui.gaussian.SubmitGaussianDialogNew
 
getProxy_Button_actionPerformed(ActionEvent) - Method in class cct.grid.ui.SubmitTaskDialog
 
getProxyItem - Variable in class cct.grid.ui.gaussian.SubmitGaussianAppl
 
getPWD() - Method in class cct.tools.filebrowser.FileBrowserPanel
 
getQueue() - Method in class cct.grid.JobDescription
 
getQueue() - Method in class cct.grid.ui.PBS_Panel
 
getQueue() - Method in class cct.grid.ui.PBSPanel
 
getRadius() - Method in class cct.dialogs.JSolvateShellDialog
 
getRadiusAsText() - Method in class cct.dialogs.JSolvateShellDialog
 
getReadCoordFormats() - Static method in class cct.modelling.MolecularFileFormats
 
getReadFileType(String) - Static method in class cct.modelling.MolecularFileFormats
 
getReferenceMolecule() - Method in class cct.modelling.StructureManager
 
getRemoteDirectory() - Method in class cct.grid.CheckPoint
 
getRemoteDirectory() - Method in interface cct.grid.ClientProgramInterface
 
getRemoteDirectory() - Method in class cct.grid.JobDescription
 
getRemoteDirectory() - Method in class cct.grid.ui.gaussian.SubmitGaussianPanel
 
getRemoteFileChooser() - Method in interface cct.grid.GridProviderInterface
 
getRemoteFileChooser() - Method in class cct.grid.LocalServiceProvider
 
getRemoteFileChooser(String) - Static method in class cct.grid.TaskProvider
 
getRemoteFileChooser() - Method in class cct.ssh.SSHServiceProvider
 
getRemoteHost() - Method in interface cct.grid.GridProviderInterface
 
getRemoteHost() - Method in class cct.grid.JobDescription
 
getRemoteHost() - Method in class cct.grid.LocalServiceProvider
 
getRemoteHost() - Method in class cct.ssh.SSHServiceProvider
 
getRenderCommandObject(String) - Method in class cct.cprocessor.CommandProcessor
 
getRenderingMode(String) - Static method in class cct.j3d.VerticesObjectProperties
 
getRenderingModeAsString(int) - Static method in class cct.j3d.VerticesObjectProperties
 
getRenderingStyle(AtomInterface) - Static method in class cct.j3d.AtomNode
 
getRenderingStyles() - Method in class cct.j3d.Java3dUniverse
 
getResourceAsString(String) - Static method in class cct.tools.Utils
 
getResourcesUsed() - Method in class cct.grid.CheckPoint
 
getResourcesUsed() - Method in class cct.grid.PBSJobStatus
 
getResponseMessage() - Method in class cct.tools.MessagePost
 
getRMS(int, float[]) - Method in class cct.math.DFPMin
 
getRMS(float[]) - Static method in class cct.vecmath.VecmathTools
Calculates root-mean-square of the vector
getRootBranch() - Method in class cct.j3d.BondNode
 
getRootBranchGroup() - Method in class cct.j3d.Java3dUniverse
 
getRootDirectory(Object) - Static method in class cct.tools.IOUtils
 
getRouteSection(int) - Method in class cct.gaussian.Gaussian
 
getRouteSection() - Method in class cct.gaussian.GaussianMolecule
 
getRouteSection(int) - Method in interface cct.gaussian.GJFParserInterface
 
getRouteSection() - Method in class cct.gaussian.ui.SimpleG03EditorPanel
 
getRowCount() - Method in class cct.chart.jfreechart.JFreeChartPanel.ChartTableModel
Returns the row count.
getRowCount() - Method in class cct.grid.ui.JobStatusTableModel
 
getRowCount() - Method in class cct.modelling.ui.VibrationsControlPanel.ChartTableModel
Returns the row count.
getRowCount() - Method in class cct.tools.filebrowser.FileBrowserTableModel
 
getRowCount() - Method in class cct.tools.filebrowser.TableSorter
 
getSaveCoordFormats() - Static method in class cct.modelling.MolecularFileFormats
 
getSaveImageFormatNames() - Static method in class cct.tools.ImageTools
 
getScheduler() - Method in class cct.grid.JobDescription
 
getScreenRefreshRate() - Method in class cct.modelling.ui.JSetupEnergyDialog
 
getScriptContents() - Method in class cct.grid.ui.gaussian.SubmitGaussianPanel
 
getScriptFile() - Method in interface cct.grid.ClientProgramInterface
 
getScriptFile() - Method in class cct.grid.ui.gaussian.SubmitGaussianPanel
 
getScriptName() - Method in class cct.grid.ui.gaussian.SubmitGaussianPanel
 
getScriptSubmitter(String) - Static method in class cct.tools.GridProviders
 
getSecondCylinder(BondInterface) - Method in class cct.j3d.BondNode
 
getSection(int) - Method in class cct.adf.ADFOutput
 
getSectionsWithGeometry() - Method in class cct.adf.ADFOutput
 
getSelectedAtomNames() - Method in class cct.dialogs.JSelectAtomTypesDialog
 
getSelectedAtomNumber(BranchGroup, Sphere) - Method in class cct.j3d.Java3dUniverse
 
getSelectedAtomNumber(BranchGroup, Sphere) - Method in class cct.j3d.MousePicking
Register the class @param callback to be called each time the picked object moves
getSelectedAtomType() - Method in class cct.dialogs.JAtomTypeDialog
 
getSelectedBranch(String) - Method in interface cct.interfaces.TreeSelectorInterface
 
getSelectedBranch(String) - Method in class cct.j3d.Java3dUniverse
 
getSelectedColumnsFromTable(String, String, String) - Method in class cct.database.SQLDatabaseAccess
 
getSelectedElements() - Method in class cct.dialogs.JSelectAtomTypesDialog
 
getSelectedFF() - Method in class cct.modelling.ui.JSetupEnergyDialog
 
getSelectedFFIndex() - Method in class cct.modelling.ui.JSetupEnergyDialog
 
getSelectedFiles() - Method in interface cct.interfaces.FileBrowserInterface
 
getSelectedFiles() - Method in class cct.tools.filebrowser.FileBrowserPanel
 
getSelectedFiles() - Method in class cct.tools.filebrowser.FileChooserDialog
 
getSelectedFiles() - Method in class cct.tools.filebrowser.JFileBrowserPanel
 
getSelectedFiles() - Method in class cct.tools.filebrowser.LocalFileBrowser
 
getSelectedFiles() - Method in class cct.tools.filebrowser.SFTPBrowser
Returns selected files (ignores selected directories, if any)
getSelectedFolders() - Method in interface cct.interfaces.FileBrowserInterface
 
getSelectedFolders() - Method in class cct.tools.filebrowser.FileBrowserPanel
 
getSelectedFolders() - Method in class cct.tools.filebrowser.FileChooserDialog
 
getSelectedFolders() - Method in class cct.tools.filebrowser.LocalFileBrowser
 
getSelectedFolders() - Method in class cct.tools.filebrowser.SFTPBrowser
Returns selected directories (ignores selected files, if any)
getSelectedGeometry() - Method in class cct.j3d.Java3dUniverse
 
getSelectedGraphicsObjects() - Method in class cct.j3d.ui.VertexObjectsDialog
 
getSelectedIndex() - Method in class cct.amber.Sander8Variable
 
getSelectedIndex() - Method in class cct.amber.SanderVariable
 
getSelectedIndex() - Method in class cct.awtdialogs.AtomLabelsDialog
 
getSelectedIndex() - Method in class cct.awtdialogs.GeometrySelectDialog
 
getSelectedIndex() - Method in class cct.dialogs.JChoiceDialog
 
getSelectedIndex() - Method in class cct.dialogs.JSolvateShellDialog
 
getSelectedIndices() - Method in class cct.tools.filebrowser.EditHostsDialog
 
getSelectedItem() - Method in class cct.awtdialogs.AtomLabelsDialog
 
getSelectedItem() - Method in class cct.awtdialogs.GeometrySelectDialog
 
getSelectedItem() - Method in class cct.dialogs.JSolvateShellDialog
 
getSelectedItem() - Method in class cct.tools.ui.SelectFromListDialog
 
getSelectedItems() - Method in class cct.tools.filebrowser.SFTPBrowser
Returns absolute paths of all selected items
getSelectedItems() - Method in class cct.tools.ui.SelectFromListDialog
 
getSelectedMethod() - Method in class cct.awtdialogs.SelectMethodDialog
 
getSelectedMinimizer() - Method in class cct.modelling.ui.JSetupEnergyDialog
 
getSelectedMonomers() - Method in class cct.dialogs.JSelectMonomersDialog
 
getSelectedMonomers() - Method in class cct.dialogs.JSelectSubstructureDialog
 
getSelectedRowFromQuery(ArrayList, String, String) - Method in class cct.database.new_SQLChemistryDatabase
 
getSelectedStep() - Method in class cct.gaussian.ui.GaussianInputEditorFrame
 
getSelectionPaths() - Method in class cct.j3d.ui.VertexObjectsDialog
 
getSelectionType() - Method in class cct.modelling.MolecularEditor
 
getSeletedFilterDescription() - Method in class cct.tools.filebrowser.SFTPFileChooserDialog
 
getSeletedFilterIndex() - Method in class cct.tools.filebrowser.SFTPFileChooserDialog
 
getSerie() - Method in class cct.modelling.TorsionParameter
 
getServiceTag(String) - Method in class cct.grid.CheckPoint
Query spesific "service" tags
getSftpClient() - Method in class cct.tools.filebrowser.SFTPBrowser
 
getShape3D(Shape3D, OutputStream) - Method in class cct.j3d.GroupToVRML
The Shape3D leaf node specifies all geometric objects.
getShape3D(Object) - Method in class cct.j3d.PovrayJava3d
 
getShape3DElements() - Method in interface cct.interfaces.GraphicsObjectInterface
 
getShape3DElements() - Method in class cct.j3d.VerticesObject
 
getShell() - Method in class cct.grid.JobDescription
 
getShift() - Method in class cct.j3d.LabelNode
 
getSimpleCoordinateBuilders() - Static method in class cct.modelling.FormatManager
 
getSimpleCoordinateBuilders(String) - Static method in class cct.modelling.FormatManager
 
getSimpleCoordinateParsers() - Static method in class cct.modelling.FormatManager
 
getSimpleCoordinateParsers(String) - Static method in class cct.modelling.FormatManager
 
getSimpleEditor(int) - Method in class cct.gaussian.ui.GaussianInputEditorFrame
 
getSize() - Method in class cct.modelling.AngleBendsArray
 
getSize() - Method in class cct.modelling.BondStretchPairs
 
getSnapshots() - Method in class cct.adf.ADFOutputSection
 
getSnapshotsCount() - Method in class cct.gaussian.G03MDTrajectory
 
getSnapshotsCount() - Method in class cct.gaussian.GaussianOutput
 
getSnapshotsCount() - Method in class cct.modelling.StructureManager
 
getSoftware() - Method in class cct.grid.JobDescription
 
getSoftware() - Method in class cct.grid.ui.PBS_Panel
 
getSoftware() - Method in class cct.grid.ui.PBSPanel
 
getSoftwareName() - Method in interface cct.grid.ClientProgramInterface
 
getSoftwareName() - Method in class cct.grid.ui.gaussian.SubmitGaussianPanel
 
getSortingStatus(int) - Method in class cct.tools.filebrowser.TableSorter
 
getSpecies() - Method in class cct.siesta.SiestaInput.SiestaAtom
 
getSpeciesLabel() - Method in class cct.siesta.ChemicalSpeciesLabel
 
getSpeciesLabelsAsString() - Method in class cct.siesta.SiestaInput
 
getSpeciesType() - Method in class cct.gulp.GULPAtom
 
getSpectrum(double[], double[], int, VIBRATIONAL_SPECTRUM) - Method in class cct.adf.ADFOutput
 
getSpectrum(double[], double[], int, VIBRATIONAL_SPECTRUM) - Method in class cct.gaussian.GaussianOutput
 
getSpectrum(double[], double[], int, String) - Method in class cct.gaussian.GaussianOutput
 
getSpectrum(double[], double[], int, VIBRATIONAL_SPECTRUM) - Method in interface cct.interfaces.OutputResultsInterface
 
getSpectrumName(VIBRATIONAL_SPECTRUM) - Static method in enum cct.modelling.VIBRATIONAL_SPECTRUM
 
getSpectrumValue(int, VIBRATIONAL_SPECTRUM) - Method in class cct.adf.ADFOutput
 
getSpectrumValue(int, VIBRATIONAL_SPECTRUM) - Method in class cct.gaussian.GaussianOutput
 
getSpectrumValue(int, VIBRATIONAL_SPECTRUM) - Method in interface cct.interfaces.OutputResultsInterface
 
getSphere(Sphere, OutputStream) - Method in class cct.j3d.GroupToVRML
 
getSQLHostName() - Method in class cct.j3d.Java3dUniverse
 
getSshClient() - Method in class cct.tools.filebrowser.SFTPBrowser
 
getSSHProvider() - Method in class cct.ssh.SSHPanel
 
getStderr() - Method in class cct.grid.JobDescription
 
getStderrFileName() - Method in interface cct.grid.ClientProgramInterface
 
getStderrFileName() - Method in class cct.grid.ui.gaussian.SubmitGaussianPanel
 
getStdout() - Method in class cct.grid.JobDescription
 
getStdoutFileName() - Method in interface cct.grid.ClientProgramInterface
 
getStdoutFileName() - Method in class cct.grid.ui.gaussian.SubmitGaussianPanel
 
getStepAsString() - Method in class cct.gaussian.ui.SimpleG03EditorPanel
 
getStringLength(String) - Method in class cct.j3d.ui.ColorGradientPanel
 
getStructure(int) - Method in class cct.adf.ADFOutput
 
getStructure(int, String) - Method in class cct.adf.ADFOutput
 
getStructure(int) - Method in class cct.chart.ChartFrame
 
getStructure(int, String) - Method in class cct.chart.ChartFrame
 
getStructure(int) - Method in class cct.dialogs.TrajectoryAnalysisDialog
 
getStructure(int, String) - Method in class cct.dialogs.TrajectoryAnalysisDialog
 
getStructure(int) - Method in class cct.gaussian.G03MDTrajectory
 
getStructure(int, String) - Method in class cct.gaussian.G03MDTrajectory
 
getStructure(int) - Method in class cct.gaussian.GaussianOutput
 
getStructure(int, String) - Method in class cct.gaussian.GaussianOutput
 
getStructure(int, float[][]) - Method in class cct.modelling.StructureManager
 
getStructure(int) - Method in interface cct.modelling.StructureManagerInterface
 
getStructure(int, String) - Method in interface cct.modelling.StructureManagerInterface
 
getStructure(int) - Method in class cct.vasp.VasprunXML
 
getStructure(int, String) - Method in class cct.vasp.VasprunXML
 
getStructureManager() - Method in class cct.dialogs.TrajectoriesManagerPanel
 
getStructures() - Method in class cct.database.new_SQLChemistryDatabase
 
getStructures() - Method in class cct.database.SQLChemistryDatabase
 
getStructuresForMolecule(String) - Method in class cct.database.new_SQLChemistryDatabase
 
getStyle() - Method in class cct.j3d.VerticesObjectProperties
 
getStyleAsString() - Method in class cct.j3d.VerticesObjectProperties
 
getSubstructureNumber() - Method in interface cct.interfaces.AtomInterface
 
getSubstructureNumber() - Method in class cct.modelling.vAtom
 
getSurface(GaussianCube, int, float) - Static method in class cct.gaussian.java3d.GaussianJava3dFactory
Creates surface as a TriangleArray
getSurface() - Method in class cct.math.polyg.java3d.j3dPolygonizer
 
getSurface(OOGL) - Static method in class cct.oogl.java3d.OoglJava3d
 
getSurface2(GaussianCube, int, float) - Static method in class cct.gaussian.java3d.GaussianJava3dFactory
 
getSymmetricSurfaces(GaussianCube, int, float) - Static method in class cct.gaussian.java3d.GaussianJava3dFactory
Creates two surfaces for values delta and -delta and returns them as a Shape3D
getSystemInfoAsString() - Static method in class cct.tools.Utils
 
getSystemLabel() - Method in class cct.siesta.SiestaInput
 
getSystemLabel() - Method in interface cct.siesta.SiestaInterface
 
getTable(String, ArrayList) - Method in class cct.database.new_SQLChemistryDatabase
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class cct.tools.filebrowser.FileNameRenderer
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class cct.tools.filebrowser.FileSizeRenderer
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class cct.tools.filebrowser.UnsignedInteger64Renderer
 
getTableHeader() - Method in class cct.tools.filebrowser.TableSorter
 
getTableMetaData(String) - Method in class cct.database.SQLDatabaseAccess
 
getTableModel() - Method in class cct.tools.filebrowser.TableSorter
 
getTaskProvider() - Method in class cct.grid.CheckPoint
 
getTaskProvider() - Method in class cct.grid.JobDescription
 
getTaskProvider() - Method in class cct.grid.TaskProviderPanel
 
getTaskProviderObject() - Method in class cct.grid.JobDescription
 
getTasks() - Method in class cct.grid.ParseCheckpointFile
 
getText() - Method in class cct.gaussian.ui.Link0Panel
 
getText() - Method in class cct.gaussian.ui.MoleculeSpecsPanel
 
getText() - Method in class cct.gaussian.ui.RouteSectionPanel
 
getText(ArrayList) - Method in class cct.gaussian.ui.SimpleG03EditorPanel
 
getText() - Method in class cct.gaussian.ui.TitleSectionPanel
 
getText() - Method in class cct.tools.ui.LogPanel
 
getTextArea() - Method in class cct.tools.ui.LogPanel
 
getTimeInSeconds() - Method in interface cct.grid.ResourcesProviderInterface
 
getTimeInSeconds() - Method in class cct.grid.ui.ResourcesPanel
 
getTitle(VIBRATIONAL_SPECTRUM) - Static method in class cct.chart.ChartReference
 
getTitle() - Method in class cct.gaussian.GaussianCube
 
getTitleSection(int) - Method in class cct.gaussian.Gaussian
 
getTitleSection() - Method in class cct.gaussian.GaussianMolecule
 
getTitleSection(int) - Method in interface cct.gaussian.GJFParserInterface
 
getTitleSection() - Method in class cct.gaussian.ui.SimpleG03EditorPanel
 
getToken(ArrayList<MathExpressionParser.Type>, int) - Method in class cct.math.MathExpressionParser
 
getToolBar() - Method in class cct.gaussian.ui.GaussianInputEditorFrame
 
getTorsion() - Method in class cct.adf.ADFAtom
 
getTorsionInteractions() - Method in class cct.modelling.FFMolecule
 
getTorsionParams(MoleculeInterface, ArrayList) - Static method in class cct.sff.SimpleForceField
 
getTotalEnergies() - Method in class cct.vasp.VasprunXML
Returns all total energies ("total" key) It's the same as getAllTerms(TOTAL_ENERGY_KEY)
getTrajectoryCount() - Method in class cct.modelling.StructureManager
 
getTrajectoryReadFormatDescription() - Static method in class cct.modelling.MolecularFileFormats
 
getTrajectoryReadFormats() - Static method in class cct.modelling.MolecularFileFormats
 
getTransformGroup(TransformGroup, OutputStream) - Method in class cct.j3d.GroupToVRML
 
getTransparency() - Method in class cct.j3d.VerticesObjectProperties
 
getTransparency() - Method in class cct.vecmath.MeshObject
 
getTransparencyMode() - Method in class cct.j3d.VerticesObjectProperties
 
getTransparencyMode(String) - Static method in class cct.j3d.VerticesObjectProperties
 
getTransparencyModeAsString(int) - Static method in class cct.j3d.VerticesObjectProperties
 
getTriangleArray(TriangleArray, int, OutputStream) - Method in class cct.j3d.GroupToVRML
The TriangleArray object draws the array of vertices as individual triangles.
getTriangleArray() - Method in class cct.math.polyg.java3d.j3dPolygonizer
 
getTriangleStripArray(TriangleStripArray, OutputStream) - Method in class cct.j3d.GroupToVRML
Note that only one additional vertex is needed to draw the second triangle.
getType() - Method in class cct.amber.Sander8Variable
 
getType() - Method in class cct.amber.SanderVariable
 
getUFFDistance(int) - Static method in class cct.modelling.ChemicalElements
 
getUFFWellDepth(int) - Static method in class cct.modelling.ChemicalElements
 
getUniqueMonomersInMolecule() - Method in class cct.modelling.AtomsArray
 
getUniqueMonomersInMolecule() - Method in class cct.modelling.MolecularEditor
 
getUniqueMonomersInMolecule() - Method in class cct.modelling.Molecule
 
getUniqueMonomersInMolecule(MoleculeInterface) - Static method in class cct.modelling.Molecule
 
getUpdateCoordFormats() - Static method in class cct.modelling.MolecularFileFormats
 
getURL(String, Object, String, String) - Static method in class cct.tools.IOUtils
 
getUser() - Method in class cct.database.SQLDatabaseAccess
 
getUsername() - Method in class cct.awtdialogs.ConnectSQLServer
 
getUserName() - Method in class cct.ssh.SSHPanel
 
getUsername() - Method in class cct.tools.filebrowser.ConnectHostDialog
 
getUsername() - Method in class cct.tools.filebrowser.SFTPBrowser
 
getUsername() - Method in class cct.tools.UserPasswordDialog
 
getValue() - Method in class cct.amber.Sander8Variable
 
getValue(int) - Method in class cct.amber.Sander8Variable
 
getValue() - Method in class cct.amber.Sander8VariableValue
 
getValue() - Method in class cct.amber.SanderVariable
 
getValue(int) - Method in class cct.amber.SanderVariable
 
getValue() - Method in class cct.amber.SanderVariableValue
 
getValue() - Method in class cct.awtdialogs.TextEntryDialog
 
getValue(String) - Method in class cct.grid.PBSJobStatus
Parsing line of a PBS full display output, for example: job_state = R and returning "R"
getValue(int, int, int) - Method in class cct.j3d.SuperCell.SuperCube
 
getValue() - Method in class cct.tools.SwingWorker
Get the value produced by the worker thread, or null if it hasn't been constructed yet.
getValue() - Method in class cct.tools.ui.DoubleSpinnerDialog
 
getValueAt(int, int) - Method in class cct.chart.jfreechart.JFreeChartPanel.ChartTableModel
Returns the value at the specified cell in the table.
getValueAt(int, int) - Method in class cct.grid.ui.JobStatusTableModel
 
getValueAt(int, int) - Method in class cct.modelling.ui.VibrationsControlPanel.ChartTableModel
Returns the value at the specified cell in the table.
getValueAt(int, int) - Method in class cct.tools.filebrowser.FileBrowserTableModel
 
getValueAt(int, int) - Method in class cct.tools.filebrowser.TableSorter
 
getVanDerWaalsRadius(int) - Static method in class cct.modelling.ChemicalElements
Returns van-der-Waals radius of element (from Bondi, J.Phys.Chem., 68, 441, 1964)
getVanDerWaalsRadius(String) - Static method in class cct.modelling.ChemicalElements
Returns van-der-Waals radius of element (from Bondi, J.Phys.Chem., 68, 441, 1964)
getVariables() - Method in class cct.tools.FortranNamelist
 
getVariablesFrequencyUpdate() - Method in interface cct.interfaces.MinimizeProgressInterface
Frequency for updating optimized variables
getVariablesFrequencyUpdate() - Method in class cct.modelling.BackgroundMinimizer
 
getVDWDIstance() - Method in class cct.modelling.CCTAtomTypes
 
getVDWWellDepth() - Method in class cct.modelling.CCTAtomTypes
 
getVDWWellDepth(String) - Static method in class cct.modelling.ChemicalElements
 
getVertices() - Method in class cct.math.polyg.Polygonizer
 
getVertices() - Method in class cct.oogl.OOGL
 
getVertices() - Method in class cct.tools.OOGL
 
getVerticesAsArray() - Method in class cct.vecmath.MeshObject
 
getView() - Method in class cct.j3d.Java3dUniverse
 
getViewPlatform(OutputStream) - Method in class cct.j3d.GroupToVRML
 
getVirtualWorldCoordinates(MoleculeInterface) - Method in class cct.dialogs.JEditorFrame
Transforms coordinates of atoms of the arbitrary molecule into current virtual world space
getVirtualWorldCoordinates(MoleculeInterface) - Method in class cct.j3d.Java3dUniverse
Transforms coordinates of atoms of the arbitrary molecule into current virtual world space
getVirtualWorldCoordinates(AtomInterface) - Method in class cct.j3d.Java3dUniverse
Returns Virtual World coordinates of an atom
getVisualComponent() - Method in interface cct.grid.ClientProgramInterface
 
getVisualComponent() - Method in interface cct.grid.GridProviderInterface
 
getVisualComponent() - Method in class cct.grid.LocalServiceProvider
 
getVisualComponent() - Method in interface cct.grid.SchedulerInterface
 
getVisualComponent() - Method in class cct.grid.ui.gaussian.SubmitGaussianPanel
 
getVisualComponent() - Method in class cct.grid.ui.NoSchedulerPanel
 
getVisualComponent() - Method in class cct.grid.ui.PBSPanel
 
getVisualComponent() - Method in interface cct.interfaces.GraphicsObjectInterface
 
getVisualComponent(int) - Method in interface cct.interfaces.GraphicsObjectInterface
 
getVisualComponent() - Method in class cct.j3d.VerticesObject
 
getVisualComponent(int) - Method in class cct.j3d.VerticesObject
 
getVisualComponent() - Method in class cct.ssh.SSHServiceProvider
 
getVolumetricData() - Method in class cct.gaussian.GaussianCube
 
getVolumetricData(int) - Method in class cct.gaussian.GaussianCube
 
getVolumetricData() - Method in interface cct.interfaces.VolumetricDataInterface
Returns 3d array of volumetric data
getVolumetricData(int) - Method in interface cct.interfaces.VolumetricDataInterface
Returns 3d array of volumetric data for n-th cube
getVWTransform() - Method in class cct.j3d.Java3dUniverse
 
getX() - Method in class cct.adf.ADFAtom
 
getX() - Method in class cct.gamess.GamessAtom
 
getX() - Method in class cct.gaussian.GaussianAtom
 
getX() - Method in interface cct.interfaces.Point3fInterface
 
getX() - Method in class cct.modelling.gAtom
 
getX() - Method in class cct.mopac.MopacAtom
 
getX() - Method in class cct.qchem.QChemAtom
 
getX() - Method in class cct.siesta.SiestaInput.SiestaAtom
 
getX() - Method in class cct.vasp.VaspAtom
 
getX() - Method in class cct.vecmath.vPoint3f
 
getXAxisTitle(VIBRATIONAL_SPECTRUM) - Static method in class cct.chart.ChartReference
 
getXFactor() - Method in class cct.j3d.MyMouseRotate
Return the x-axis movement multipler.
getXmax() - Method in interface cct.interfaces.MoleculeInterface
 
getXmax() - Method in class cct.modelling.Molecule
 
getXmin() - Method in interface cct.interfaces.MoleculeInterface
 
getXmin() - Method in class cct.modelling.Molecule
 
getXTitle(String) - Method in class cct.gaussian.GaussianFrequency
 
getXTitle(String) - Method in class cct.gaussian.GaussianOutput
 
getXYZ() - Method in class cct.vecmath.vPoint3f
 
getY() - Method in class cct.adf.ADFAtom
 
getY() - Method in class cct.gamess.GamessAtom
 
getY() - Method in class cct.gaussian.GaussianAtom
 
getY() - Method in interface cct.interfaces.Point3fInterface
 
getY() - Method in class cct.modelling.gAtom
 
getY() - Method in class cct.mopac.MopacAtom
 
getY() - Method in class cct.qchem.QChemAtom
 
getY() - Method in class cct.siesta.SiestaInput.SiestaAtom
 
getY() - Method in class cct.vasp.VaspAtom
 
getY() - Method in class cct.vecmath.vPoint3f
 
getYAxisTitle(VIBRATIONAL_SPECTRUM) - Static method in class cct.chart.ChartReference
 
getYFactor() - Method in class cct.j3d.MyMouseRotate
Return the y-axis movement multipler.
getYMax() - Method in class cct.chart.jfreechart.JFreeChartPanel.DataSet
 
getYmax() - Method in interface cct.interfaces.MoleculeInterface
 
getYmax() - Method in class cct.modelling.Molecule
 
getYMin() - Method in class cct.chart.jfreechart.JFreeChartPanel.DataSet
 
getYmin() - Method in interface cct.interfaces.MoleculeInterface
 
getYmin() - Method in class cct.modelling.Molecule
 
getYTitle(String) - Method in class cct.gaussian.GaussianFrequency
 
getYTitle(String) - Method in class cct.gaussian.GaussianOutput
 
getZ() - Method in class cct.adf.ADFAtom
 
getZ() - Method in class cct.gamess.GamessAtom
 
getZ() - Method in class cct.gaussian.GaussianAtom
 
getZ() - Method in interface cct.interfaces.Point3fInterface
 
getZ() - Method in class cct.modelling.gAtom
 
getZ() - Method in class cct.mopac.MopacAtom
 
getZ() - Method in class cct.qchem.QChemAtom
 
getZ() - Method in class cct.siesta.SiestaInput.SiestaAtom
 
getZ() - Method in class cct.vasp.VaspAtom
 
getZ() - Method in class cct.vecmath.vPoint3f
 
getZmax() - Method in interface cct.interfaces.MoleculeInterface
 
getZmax() - Method in class cct.modelling.Molecule
 
getZmin() - Method in interface cct.interfaces.MoleculeInterface
 
getZmin() - Method in class cct.modelling.Molecule
 
gf - Variable in class cct.oogl.Face
 
gf - Variable in class cct.tools.Face
 
GibbsThermCorrProperty - Static variable in interface cct.interfaces.MoleculeInterface
 
gjfMenuItem - Variable in class cct.dialogs.Frame1
 
gjfParser - Variable in class cct.gaussian.ui.GaussianI