def toggle_groupbox(self, button, *things):
     """This is intended to be part of the slot method for clicking on an open/close icon
     of a dialog GroupBox. The arguments should be the button (whose icon will be altered here)
     and the child widgets in the groupbox whose visibility should be toggled.
     """
     if things:
         if things[0].isVisible():
             styleSheet = self.getGroupBoxButtonStyleSheet(bool_expand = False)
             button.setStyleSheet(styleSheet)
             palette = self.getGroupBoxButtonPalette()
             button.setPalette(palette)
             button.setIcon(geticon("ui/actions/Properties Manager/GHOST_ICON"))
             for thing in things:
                 thing.hide()
         else:
             styleSheet = self.getGroupBoxButtonStyleSheet(bool_expand = True)
             button.setStyleSheet(styleSheet)
             palette = self.getGroupBoxButtonPalette()
             button.setPalette(palette)
             button.setIcon(geticon("ui/actions/Properties Manager/GHOST_ICON"))
             for thing in things:
                 thing.show()
     else:
         print "Groupbox has no widgets. Clicking on groupbox button has no effect."
     return

 def toggleExpandCollapse(self):
     """Slot method for the title button to expand/collapse the groupbox.
     """
     if self.expanded: # Collapse groupbox by hiding ahe yellow TextEdit.
         # The styleSheet contains the expand/collapse icon.
         styleSheet = self.getTitleButtonStyleSheet(showExpanded = False)
         self.titleButton.setStyleSheet(styleSheet)
         # Why do we have to keep resetting the palette?
         # Does assigning a new styleSheet reset the button's palette?
         # If yes, we should add the button's color to the styleSheet.
         # Mark 2007-05-20
         self.titleButton.setPalette(self.getTitleButtonPalette())
         self.titleButton.setIcon(
                 geticon("ui/actions/Properties Manager/GHOST_ICON"))
         self.MessageTextEdit.hide()
         self.expanded = False
     else: # Expand groupbox by showing the yellow TextEdit.
         # The styleSheet contains the expand/collapse icon.
         styleSheet = self.getTitleButtonStyleSheet(showExpanded = True)
         self.titleButton.setStyleSheet(styleSheet)
         # Why do we have to keep resetting the palette?
         # Does assigning a new styleSheet reset the button's palette?
         # If yes, we should add the button's color to the styleSheet.
         # Mark 2007-05-20
         self.titleButton.setPalette(self.getTitleButtonPalette())
         self.titleButton.setIcon(
                 geticon("ui/actions/Properties Manager/GHOST_ICON"))
         self.MessageTextEdit.show()
         self.expanded = True

    def setupUi(self, orientationWidget):        
          
        win = self.win
        MainWindow = self.win
        
        # Set the default width and height.
        _width = 150
        _height = 280
        _maxWidth = 400 # 400 should be more than enough. --mark
        
        # "View > Orientation" Dock Widget 
        orientationWidget.setEnabled(True) 
        orientationWidget.setFloating(True)
        orientationWidget.setVisible(False)
        orientationWidget.setWindowTitle("Orientation" )
        orientationWidget.setWindowIcon(
            geticon("ui/actions/View/Modify/Orientation.png"))
        orientationWidget.setGeometry(QRect(0, 0, _width, _height))
        orientationWidget.setMaximumWidth(400)
                
        x = max(0, win.geometry().x())
        y = max(0, win.geometry().y())
       
        orientationWidget.move(x, y)
        
        self.orientationWindowContents = QtGui.QWidget(orientationWidget)
        
        gridlayout = QtGui.QGridLayout(self.orientationWindowContents)
        
        gridlayout.setMargin(4)
        gridlayout.setSpacing(4)
        
        hboxlayout = QtGui.QHBoxLayout()
        hboxlayout.setMargin(0)
        hboxlayout.setSpacing(6)
              
        self.pinOrientationWindowToolButton = QtGui.QToolButton(self.orientationWindowContents)    
        self.pinOrientationWindowToolButton.setCheckable(True)

        self.pinOrientationWindowToolButton.setIcon(
            geticon("ui/dialogs/unpinned.png")) 
        hboxlayout.addWidget(self.pinOrientationWindowToolButton)
        
        self.saveNamedViewToolButton = QtGui.QToolButton(self.orientationWindowContents)    
        self.saveNamedViewToolButton.setIcon(
            geticon("ui/actions/View/Modify/Save_Named_View.png"))  #@@ ninad 061115 dir path will be modified  
        hboxlayout.addWidget(self.saveNamedViewToolButton)
        gridlayout.addLayout(hboxlayout, 0, 0, 1, 1)
        
        self.orientationViewList = QtGui.QListWidget(orientationWidget)
        self.orientationViewList.setFlow(QtGui.QListWidget.TopToBottom)
        self.orientationViewList.setWindowIcon(
            geticon("ui/actions/View/Modify/Orientation.png"))
               
        gridlayout.addWidget(self.orientationViewList, 1, 0, 1, 1)
    
        orientationWidget.setWidget(self.orientationWindowContents)
        
        MainWindow.addDockWidget(Qt.BottomDockWidgetArea, orientationWidget)

 def changePinIcon(self):
     """
     Change the icon of the Pinned button
     """
     if self.pinOrientationWindowToolButton.isChecked():
         self.pinOrientationWindowToolButton.setIcon(
             geticon("ui/dialogs/pinned.png")) 
     else:
         self.pinOrientationWindowToolButton.setIcon(
             geticon("ui/dialogs/unpinned.png")) 

    def _createActions(self, parentWidget):
        """
        Define flyout toolbar actions for this mode.
        """
        #@NOTE: In Build mode, some of the actions defined in this method are also
        #used in Build Atoms PM. (e.g. bond actions) So probably better to rename
        #it as _init_modeActions. Not doing that change in mmkit code cleanup
        #commit(other modes still implement a method by same name)-ninad20070717

        _superclass._createActions(self, parentWidget)

        # The subControlActionGroup is the parent of all flyout QActions.
        self.subControlActionGroup = QActionGroup(parentWidget)
            # Shouldn't the parent be self.win?
            # Isn't parentWidget = BuildAtomsPropertyManager.
            # Ask Bruce about this. --Mark 2008-12-07.

        self.subControlActionGroup.setExclusive(True)

        #Following Actions are added in the Flyout toolbar.
        #Defining them outside that method as those are being used
        #by the subclasses of deposit mode (testmode.py as of 070410) -- ninad

        self.atomsToolAction = \
            NE1_QWidgetAction(self.subControlActionGroup, win = self.win)
        self.atomsToolAction.setText("Atoms Tool")
        self.atomsToolAction.setIcon(geticon(
            "ui/actions/Command Toolbar/BuildAtoms/AtomsTool.png"))
        self.atomsToolAction.setCheckable(True)
        self.atomsToolAction.setChecked(True)
        self.atomsToolAction.setObjectName('ACTION_ATOMS_TOOL')


        self.bondsToolAction = \
            NE1_QWidgetAction(self.subControlActionGroup, win = self.win)
        self.bondsToolAction.setText("Bonds Tool")
        self.bondsToolAction.setIcon(geticon(
            "ui/actions/Command Toolbar/BuildAtoms/BondsTool.png"))
        self.bondsToolAction.setCheckable(True)
        self.bondsToolAction.setObjectName('ACTION_BOND_TOOL')


        self.subControlActionGroup.addAction(self.atomsToolAction)
        self.subControlActionGroup.addAction(self.bondsToolAction)

        self.transmuteAtomsAction = \
            NE1_QWidgetAction(self.subControlActionGroup, win = self.win)
        self.transmuteAtomsAction.setText("Transmute Atoms")
        self.transmuteAtomsAction.setIcon(geticon(
            "ui/actions/Command Toolbar/BuildAtoms/TransmuteAtoms.png"))
        self.transmuteAtomsAction.setCheckable(False)


        self._createBondToolActions(parentWidget)

    def _createActions(self, parentWidget):
        """
        Define flyout toolbar actions for this mode.
        """

        _superclass._createActions(self, parentWidget)

        #Urmi 20080814: show this flyout toolbar only when rosetta plugin path
        # is there
        #Probably only rosetta_enabled_prefs_key check would have sufficed
        plugin_name = "ROSETTA"
        plugin_prefs_keys = (rosetta_enabled_prefs_key, rosetta_path_prefs_key)
        errorcode, errortext_or_path = \
                 checkPluginPreferences(plugin_name, plugin_prefs_keys, ask_for_help = False)
        #print "Error code =", errorcode, errortext_or_path
        if errorcode == 0:
            self.rosetta_enabled = True
        else:
            self.rosetta_enabled = False

        # The subControlActionGroup is the parent of all flyout QActions.
        self.subControlActionGroup = QActionGroup(parentWidget)
            # Shouldn't the parent be self.win?
            # Isn't parentWidget = BuildProteinPropertyManager?
            # Ask Bruce about this. --Mark 2008-12-07.

        self.subControlActionGroup.setExclusive(True)

        self.modelProteinAction = \
            NE1_QWidgetAction(self.subControlActionGroup, win = self.win)
        self.modelProteinAction.setText("Model")
        self.modelProteinAction.setIcon(geticon(
            'ui/actions/Command Toolbar/BuildProtein/ModelProtein.png'))
        self.modelProteinAction.setCheckable(True)
        self.modelProteinAction.setChecked(True)
        self.modelProteinAction.setObjectName('ACTION_MODEL_PROTEINS')

        self.simulateProteinAction = \
            NE1_QWidgetAction(self.subControlActionGroup, win = self.win)
        self.simulateProteinAction.setText("Simulate")
        self.simulateProteinAction.setIcon(geticon(
            "ui/actions/Command Toolbar/BuildProtein/Simulate.png"))
        self.simulateProteinAction.setCheckable(True)
        self.simulateProteinAction.setObjectName('ACTION_SIMULATE_PROTEINS')


        self.subControlActionGroup.addAction(self.modelProteinAction)
        self.subControlActionGroup.addAction(self.simulateProteinAction)

        self._createModelProteinsActions(parentWidget)
        self._createSimulateProteinsActions(parentWidget)

 def _createActions(self, parentWidget):
     self.exitNanotubeAction = NE1_QWidgetAction(parentWidget, 
                                                   win = self.win)
     self.exitNanotubeAction.setText("Exit NT")
     self.exitNanotubeAction.setIcon(
         geticon("ui/actions/Toolbars/Smart/Exit.png"))
     self.exitNanotubeAction.setCheckable(True)
     
     self.insertNanotubeAction = NE1_QWidgetAction(parentWidget,
                                                     win = self.win)
     self.insertNanotubeAction.setText("Insert NT")
     self.insertNanotubeAction.setCheckable(True)        
     self.insertNanotubeAction.setIcon(
         geticon("ui/actions/Tools/Build Structures/InsertNanotube.png"))

    def getGroupBoxTitleButton(self, name, parent = None, bool_expand = True): #Ninad 070206
        """ Return the groupbox title pushbutton. The pushbutton is customized
        such that  it appears as a title bar to the user. If the user clicks on
        this 'titlebar' it sends appropriate signals to open or close the
        groupboxes   'name = string -- title of the groupbox
        'bool_expand' = boolean .. NE1 uses a different background
        image in the button's  Style Sheet depending on the bool.
        (i.e. if bool_expand = True it uses a opened group image  '^')
        See also: getGroupBoxTitleCheckBox , getGroupBoxButtonStyleSheet  methods
        """

        button  = QtGui.QPushButton(name, parent)
        button.setFlat(False)
        button.setAutoFillBackground(True)

        palette = self.getGroupBoxButtonPalette()
        button.setPalette(palette)

        styleSheet = self.getGroupBoxButtonStyleSheet(bool_expand)

        button.setStyleSheet(styleSheet)
        #ninad 070221 set a non existant 'Ghost Icon' for this button
        #By setting such an icon, the button text left aligns!
        #(which what we want :-) )
        #So this might be a bug in Qt4.2.  If we don't use the following kludge,
        #there is no way to left align the push button text but to subclass it.
        #(could mean a lot of work for such a minor thing)  So OK for now

        button.setIcon(geticon("ui/actions/Properties Manager/GHOST_ICON"))

        return button

    def insertItems(self, row, items, setAsDefault = True):
        """
        Insert the <items> specified items in this list widget.
        The list widget shows item name string , as a QListwidgetItem.

        This QListWidgetItem object defines a 'key' of a dictionary
        (self._itemDictionary) and the 'value' of this key is the object
        specified by the 'item' itself.
        Example: self._itemDictionary['C6'] = instance of class Atom.

        @param row: The row number for the item.
        @type row: int

        @param items: A list of objects. These objects are treated as values in
                      the self._itemDictionary
        @type items: list

        @param setAsDefault: Not used here. See PM_ListWidget.insertItems where
                             it is used.

        @see: self.renameItemValue() for a comment about
              self._suppress_itemChanged_signal

        """

        #delete unused argument. Should this be provided as an argument in this
        #class method ?
        del setAsDefault

        #self.__init__ for a comment about this flag
        self._suppress_itemChanged_signal = True

        #Clear the previous contents of the self._itemDictionary
        self._itemDictionary.clear()

        #Clear the contents of this list widget, using QListWidget.clear()
        #See U{<http://doc.trolltech.com/4.2/qlistwidget.html>} for details
        self.clear()

        for item in items:
            if hasattr(item.__class__, 'name'):
                itemName = item.name
            else:
                itemName = str(item)
            listWidgetItem = QListWidgetItem(itemName, self)

            #When we support editing list widget items , uncomment out the
            #following line . See also self.editItems -- Ninad 2008-01-16
            listWidgetItem.setFlags( listWidgetItem.flags()| Qt.ItemIsEditable)

            if hasattr(item.__class__, 'iconPath'):
                try:
                    listWidgetItem.setIcon(geticon(item.iconPath))
                except:
                    print_compact_traceback()

            self._itemDictionary[listWidgetItem] = item

        #Reset the flag that temporarily suppresses itemChange signal.
        self._suppress_itemChanged_signal = False

 def _createToolButton(self, widgetParams):
     """
     Returns a tool button created using the custom parameters. 
             
     @param widgetParams: A list containing tool button parameters. 
     @type  widgetParams: list
     
     @see: L{self._createWidgetUsingParameters} where this method is called.
     """
     
     buttonSize = QSize(32, 32) #@ FOR TEST ONLY
     
     buttonParams = list(widgetParams)
     buttonId       = buttonParams[1]
     buttonText     = buttonParams[2]
     buttonIconPath = buttonParams[3]
     buttonToolTip  = buttonParams[4] 
     buttonShortcut = buttonParams[5]
     
     button = QToolButton(self)
     button.setText(buttonText)
     if buttonIconPath:
         buttonIcon = geticon(buttonIconPath)     
         if not buttonIcon.isNull():       
             button.setIcon(buttonIcon)
             button.setIconSize(QSize(22, 22))
     button.setToolTip(buttonToolTip)
     if buttonShortcut:
         button.setShortcut(buttonShortcut)
         
     button.setFixedSize(buttonSize) #@ Currently fixed to 32 x 32.
     button.setCheckable(True)
     return button

    def _loadBackgroundColorItems(self):
        """
        Load the background color combobox with all the color options and sets
        the current background color
        """
        backgroundIndexes = [bg_BLUE_SKY, bg_EVENING_SKY, bg_SEAGREEN,
                             bg_BLACK, bg_WHITE, bg_GRAY, bg_CUSTOM]

        backgroundNames   = ["Blue Sky (default)", "Evening Sky", "Sea Green",
                             "Black", "White", "Gray", "Custom..."]

        backgroundIcons   = ["Background_BlueSky", "Background_EveningSky",
                             "Background_SeaGreen",
                             "Background_Black",   "Background_White",
                             "Background_Gray",    "Background_Custom"]

        backgroundIconsDict = dict(zip(backgroundNames, backgroundIcons))
        backgroundNamesDict = dict(zip(backgroundIndexes, backgroundNames))

        for backgroundName in backgroundNames:

            basename = backgroundIconsDict[backgroundName] + ".png"
            iconPath = os.path.join("ui/dialogs/Preferences/",
                                    basename)
            self.backgroundColorComboBox.addItem(geticon(iconPath),
                                                 backgroundName)

        self._updateBackgroundColorComboBoxIndex() # Not needed, but OK.
        return

    def __init__(self, jig, glpane):
        """
        Constructor for the class JigProp. 
        @param jig: the jig whose property dialog will be shown
        @type  jig: L{Jig}
        @param glpane: GLPane object
        @type  glpane: L{GLPane}
        """

        QDialog.__init__(self)
        self.setupUi(self)
        self.connect(self.cancel_btn, SIGNAL("clicked()"), self.reject)
        self.connect(self.ok_btn, SIGNAL("clicked()"), self.accept)
        self.connect(self.choose_color_btn,
                     SIGNAL("clicked()"),
                     self.change_jig_color)
        
        # Set the dialog's border icon and caption based on the jig type.
        jigtype_name = jig.__class__.__name__ 
        
        # Fixes bug 1208. mark 060112.  
        self.setWindowIcon(geticon("ui/border/"+ jigtype_name)) 
        
        self.setWindowTitle(jigtype_name + " Properties")
            
        self.jig = jig
        self.glpane = glpane

 def showProgress(self, modal = True):
     """
     Open the progress dialog to show the current job progress.
     """
     #Replace "self.edit_cntl.win" with "None"
     #---Huaicai 7/7/05: To fix bug 751, the "win" may be none.
     #Feel awkward for the design of our code.        
     simProgressDialog = QProgressDialog()
     simProgressDialog.setModal(True)
     simProgressDialog.setObjectName("progressDialog")
     simProgressDialog.setWindowIcon(geticon('ui/border/MainWindow'))
     if self.Calculation == 'Energy':
         simProgressDialog.setWindowTitle("Calculating Energy ...Please Wait")
     else:
         simProgressDialog.setWindowTitle("Optimizing ...Please Wait")
    
     progBar = QProgressBar(simProgressDialog)
     progBar.setMaximum(0)
     progBar.setMinimum(0)
     progBar.setValue(0)
     progBar.setTextVisible(False)
     simProgressDialog.setBar(progBar)
     simProgressDialog.setAutoReset(False)
     simProgressDialog.setAutoClose(False)
     
     return simProgressDialog

    def _createSimulateProteinsActions(self, parentWidget):
        """
        Create the actions to be included in flyout toolbar, when the 'Simulate
        Proteins' is active.

        @see: self._createActions() where this is called.
        """

        self.subControlActionGroupForSimulateProtein = QActionGroup(parentWidget)
            # Shouldn't the parent be self.win?
            # Isn't parentWidget = BuildProteinPropertyManager?
            # Ask Bruce about this. --Mark 2008-12-07.
        self.subControlActionGroupForSimulateProtein.setExclusive(True)

        self.rosetta_fixedbb_design_Action = \
            NE1_QWidgetAction(self.subControlActionGroupForSimulateProtein, win = self.win)
        self.rosetta_fixedbb_design_Action.setText("Fixed BB")
        self.rosetta_fixedbb_design_Action.setCheckable(True)
        self.rosetta_fixedbb_design_Action.setIcon(
            geticon("ui/actions/Command Toolbar/BuildProtein/FixedBackbone.png"))

        self.rosetta_backrub_Action = \
            NE1_QWidgetAction(self.subControlActionGroupForSimulateProtein, win = self.win)
        self.rosetta_backrub_Action.setText("Backrub")
        self.rosetta_backrub_Action.setCheckable(True)
        self.rosetta_backrub_Action.setIcon(
            geticon("ui/actions/Command Toolbar/BuildProtein/Backrub.png"))

        self.editResiduesAction = \
            NE1_QWidgetAction(self.subControlActionGroupForSimulateProtein, win = self.win)
        self.editResiduesAction.setText("Residues")
        self.editResiduesAction.setCheckable(True)
        self.editResiduesAction.setIcon(
            geticon("ui/actions/Command Toolbar/BuildProtein/Residues.png"))

        self.rosetta_score_Action = \
            NE1_QWidgetAction(self.subControlActionGroupForSimulateProtein, win = self.win)
        self.rosetta_score_Action.setText("Score")
        self.rosetta_score_Action.setCheckable(True)
        self.rosetta_score_Action.setIcon(
            geticon("ui/actions/Command Toolbar/BuildProtein/Score.png"))

        self.subControlActionGroupForSimulateProtein.addAction(self.rosetta_fixedbb_design_Action)
        self.subControlActionGroupForSimulateProtein.addAction(self.rosetta_backrub_Action)
        self.subControlActionGroupForSimulateProtein.addAction(self.editResiduesAction)
        self.subControlActionGroupForSimulateProtein.addAction(self.rosetta_score_Action)
        return

    def hideGroupBox(self, groupBoxButton, groupBoxWidget):
        """Hide a groupbox (this is not the same as 'toggle' groupbox)"""

        groupBoxWidget.hide()

        styleSheet = self.getGroupBoxButtonStyleSheet(bool_expand = False)
        groupBoxButton.setStyleSheet(styleSheet)
        palette = self.getGroupBoxButtonPalette()
        groupBoxButton.setPalette(palette)
        groupBoxButton.setIcon(geticon("ui/actions/Properties Manager/GHOST_ICON"))

 def _createFlyoutActions(self):
     self.exitEditCommandAction = NE1_QWidgetAction(self.win, win = self.win)
     if self.editCommand:
         text = "Exit " + self.editCommand.cmdname
     else:
         text = "Exit"
     self.exitEditCommandAction.setText(text)
     self.exitEditCommandAction.setIcon(
         geticon("ui/actions/Toolbars/Smart/Exit.png"))
     self.exitEditCommandAction.setCheckable(True)

    def _loadLayerPropertiesGroupBox(self, inPmGroupBox):
        """
        Load widgets in the Layer Properties group box.
        @param inPmGroupBox: The Layer Properties groupbox in the PM
        @type  inPmGroupBox: L{PM_GroupBox}
        """

        self.currentLayerComboBox = \
            PM_ComboBox( inPmGroupBox,
                         index     = 0,
                         spanWidth = True
                        )

        self.addLayerButton = PM_PushButton(inPmGroupBox)
        self.addLayerButton.setIcon(
            geticon('ui/actions/Properties Manager/addlayer.png'))
        self.addLayerButton.setFixedSize(QSize(26, 26))
        self.addLayerButton.setIconSize(QSize(22, 22))

        # A widget list to create a widget row.
        # Format:
        # - Widget type,
        # - widget object,
        # - column

        firstRowWidgetList = [('PM_ComboBox', self.currentLayerComboBox, 1),
                              ('PM_PushButton', self.addLayerButton, 2)
                              ]

        widgetRow = PM_WidgetRow(inPmGroupBox,
                                 title     = '',
                                 widgetList = firstRowWidgetList,
                                 label = "Layer:",
                                 labelColumn  = 0,
                                 )

        self.layerCellsSpinBox = \
             PM_SpinBox( inPmGroupBox,
                        label         =  "Lattice cells:",
                        labelColumn   =  0,
                        value         =  2,
                        minimum       =  1,
                        maximum       =  25
                      )

        self.layerThicknessLineEdit = PM_LineEdit(inPmGroupBox,
                                         label        = "Thickness:",
                                         text         = "",
                                         setAsDefault = False,
                                         spanWidth    = False )

        #self.layerThicknessLineEdit.setReadOnly(True)
        self.layerThicknessLineEdit.setDisabled(True)
        tooltip = "Thickness of layer in Angstroms"
        self.layerThicknessLineEdit.setToolTip(tooltip)

    def showGroupBox(self, groupBoxButton, groupBoxWidget):
        """Show a groupbox (this is not the same as 'toggle' groupbox)"""

        if not groupBoxWidget.isVisible():
            groupBoxWidget.show()

            styleSheet = self.getGroupBoxButtonStyleSheet(bool_expand = True)
            groupBoxButton.setStyleSheet(styleSheet)
            palette = self.getGroupBoxButtonPalette()
            groupBoxButton.setPalette(palette)
            groupBoxButton.setIcon(geticon("ui/actions/Properties Manager/GHOST_ICON"))

 def __init__(self, parent = None):
     """
     Constructor for Rosetta simulation parameters dialog
     """
     self.parentWidget = parent
     super(RosettaSimulationPopUpDialog, self).__init__(parent)
     self.setWindowIcon(geticon('ui/border/Rosetta.png'))
     self.setWindowTitle("Rosetta Simulation Parameters")
     self._loadWidgets()
     self.connectSignals()
     self.show()
     return

    def __init__(self):
        QWidget.__init__(self)
        self.setupUi(self)
        self.connect(self.help_tab, SIGNAL("currentChanged(int)"), self.setup_current_page)
        self.connect(self.close_btn, SIGNAL("clicked()"), self.close)

        self.setWindowIcon(geticon("ui/border/MainWindow.png"))

        self._setup_mouse_controls_page()
        self.help_tab.setCurrentIndex(0)

        return