class InsertNanotube_PropertyManager(DnaOrCnt_PropertyManager): """ The InsertNanotube_PropertyManager class provides a Property Manager for the B{Build > Nanotube > CNT} command. @ivar title: The title that appears in the property manager header. @type title: str @ivar pmName: The name of this property manager. This is used to set the name of the PM_Dialog object via setObjectName(). @type name: str @ivar iconPath: The relative path to the PNG file that contains a 22 x 22 icon image that appears in the PM header. @type iconPath: str """ title = "Insert Nanotube" pmName = title iconPath = "ui/actions/Tools/Build Structures/InsertNanotube.png" def __init__(self, win, editCommand): """ Constructor for the Nanotube property manager. """ self.endPoint1 = None self.endPoint2 = None self.nanotube = Nanotube() # A 5x5 CNT. _superclass.__init__(self, win, editCommand) self.showTopRowButtons( PM_DONE_BUTTON | \ PM_CANCEL_BUTTON | \ PM_WHATS_THIS_BUTTON) def connect_or_disconnect_signals(self, isConnect): """ Connect or disconnect widget signals sent to their slot methods. This can be overridden in subclasses. By default it does nothing. @param isConnect: If True the widget will send the signals to the slot method. @type isConnect: boolean """ if isConnect: change_connect = self.win.connect else: change_connect = self.win.disconnect change_connect(self.ntTypeComboBox, SIGNAL("currentIndexChanged(const QString&)"), self._ntTypeComboBoxChanged) change_connect(self.chiralityNSpinBox, SIGNAL("valueChanged(int)"), self._chiralityFixup) change_connect(self.chiralityMSpinBox, SIGNAL("valueChanged(int)"), self._chiralityFixup) change_connect(self.endingsComboBox, SIGNAL("currentIndexChanged(const QString&)"), self._endingsComboBoxChanged) # This spin box is currently hidden. change_connect(self.bondLengthDoubleSpinBox, SIGNAL("valueChanged(double)"), self._bondLengthChanged) change_connect(self.showCursorTextCheckBox, SIGNAL('stateChanged(int)'), self._update_state_of_cursorTextGroupBox) def ok_btn_clicked(self): """ Slot for the OK button """ if self.editCommand: self.editCommand.preview_or_finalize_structure(previewing=False) ##env.history.message(self.editCommand.logMessage) self.win.toolsDone() def cancel_btn_clicked(self): """ Slot for the Cancel button. """ if self.editCommand: self.editCommand.cancelStructure() self.win.toolsCancel() def _update_widgets_in_PM_before_show(self): """ Update various widgets in this Property manager. Overrides MotorPropertyManager._update_widgets_in_PM_before_show. The various widgets , (e.g. spinboxes) will get values from the structure for which this propMgr is constructed for (self.editcCntroller.struct) @see: MotorPropertyManager._update_widgets_in_PM_before_show @see: self.show where it is called. """ pass def getFlyoutActionList(self): """ Returns custom actionlist that will be used in a specific mode or editing a feature etc Example: while in movie mode, the _createFlyoutToolBar method calls this. """ #'allActionsList' returns all actions in the flyout toolbar #including the subcontrolArea actions allActionsList = [] #Action List for subcontrol Area buttons. #In this mode there is really no subcontrol area. #We will treat subcontrol area same as 'command area' #(subcontrol area buttons will have an empty list as their command area #list). We will set the Comamnd Area palette background color to the #subcontrol area. subControlAreaActionList = [] self.exitEditCommandAction.setChecked(True) subControlAreaActionList.append(self.exitEditCommandAction) separator = QAction(self.w) separator.setSeparator(True) subControlAreaActionList.append(separator) allActionsList.extend(subControlAreaActionList) #Empty actionlist for the 'Command Area' commandActionLists = [] #Append empty 'lists' in 'commandActionLists equal to the #number of actions in subControlArea for i in range(len(subControlAreaActionList)): lst = [] commandActionLists.append(lst) params = (subControlAreaActionList, commandActionLists, allActionsList) return params def _addGroupBoxes(self): """ Add the Insert Nanotube Property Manager group boxes. """ self._pmGroupBox1 = PM_GroupBox(self, title="Endpoints") self._loadGroupBox1(self._pmGroupBox1) self._pmGroupBox1.hide() self._pmGroupBox2 = PM_GroupBox(self, title="Parameters") self._loadGroupBox2(self._pmGroupBox2) self._displayOptionsGroupBox = PM_GroupBox(self, title="Display Options") self._loadDisplayOptionsGroupBox(self._displayOptionsGroupBox) self._pmGroupBox3 = PM_GroupBox(self, title="Nanotube Distortion") self._loadGroupBox3(self._pmGroupBox3) self._pmGroupBox3.hide() #@ Temporary. self._pmGroupBox4 = PM_GroupBox(self, title="Multi-Walled CNTs") self._loadGroupBox4(self._pmGroupBox4) self._pmGroupBox4.hide() #@ Temporary. self._pmGroupBox5 = PM_GroupBox(self, title="Advanced Options") self._loadGroupBox5(self._pmGroupBox5) self._pmGroupBox5.hide() #@ Temporary. def _loadGroupBox1(self, pmGroupBox): """ Load widgets in group box 1. """ #Following toolbutton facilitates entering a temporary NanotubeLineMode #to create a CNT using endpoints of the specified line. self.specifyCntLineButton = PM_ToolButton( pmGroupBox, text="Specify Endpoints", iconPath="ui/actions/Properties Manager/Pencil.png", spanWidth=True) self.specifyCntLineButton.setCheckable(True) self.specifyCntLineButton.setAutoRaise(True) self.specifyCntLineButton.setToolButtonStyle( Qt.ToolButtonTextBesideIcon) #EndPoint1 and endPoint2 coordinates. These widgets are hidden # as of 2007- 12 - 05 self._endPoint1SpinBoxes = PM_CoordinateSpinBoxes(pmGroupBox, label="End Point 1") self.x1SpinBox = self._endPoint1SpinBoxes.xSpinBox self.y1SpinBox = self._endPoint1SpinBoxes.ySpinBox self.z1SpinBox = self._endPoint1SpinBoxes.zSpinBox self._endPoint2SpinBoxes = PM_CoordinateSpinBoxes(pmGroupBox, label="End Point 2") self.x2SpinBox = self._endPoint2SpinBoxes.xSpinBox self.y2SpinBox = self._endPoint2SpinBoxes.ySpinBox self.z2SpinBox = self._endPoint2SpinBoxes.zSpinBox self._endPoint1SpinBoxes.hide() self._endPoint2SpinBoxes.hide() def _loadGroupBox2(self, pmGroupBox): """ Load widgets in group box 2. """ _ntTypeChoices = ['Carbon', 'Boron Nitride'] self.ntTypeComboBox = \ PM_ComboBox( pmGroupBox, label = "Type:", choices = _ntTypeChoices, setAsDefault = True) self.ntRiseDoubleSpinBox = \ PM_DoubleSpinBox( pmGroupBox, label = "Rise:", value = self.nanotube.getRise(), setAsDefault = True, minimum = 2.0, maximum = 4.0, decimals = 3, singleStep = 0.01 ) self.ntRiseDoubleSpinBox.hide() # Nanotube Length self.ntLengthLineEdit = \ PM_LineEdit( pmGroupBox, label = "Nanotube Length: ", text = "0.0 Angstroms", setAsDefault = False) self.ntLengthLineEdit.setDisabled(True) self.ntLengthLineEdit.hide() # Nanotube diameter self.ntDiameterLineEdit = \ PM_LineEdit( pmGroupBox, label = "Diameter: ", setAsDefault = False) self.ntDiameterLineEdit.setDisabled(True) self.updateNanotubeDiameter() self.chiralityNSpinBox = \ PM_SpinBox( pmGroupBox, label = "Chirality (n):", value = self.nanotube.getChiralityN(), minimum = 2, maximum = 100, setAsDefault = True ) self.chiralityMSpinBox = \ PM_SpinBox( pmGroupBox, label = "Chirality (m):", value = self.nanotube.getChiralityM(), minimum = 0, maximum = 100, setAsDefault = True ) # How about having user prefs for CNT and BNNT bond lengths? # I'm guessing that if the user wants to set these values, they will # do it once and would like those bond length values persist forever. # Need to discuss with others to determine if this spinbox comes out. # --Mark 2008-03-29 self.bondLengthDoubleSpinBox = \ PM_DoubleSpinBox( pmGroupBox, label = "Bond length:", value = self.nanotube.getBondLength(), setAsDefault = True, minimum = 1.0, maximum = 3.0, singleStep = 0.1, decimals = 3, suffix = " Angstroms" ) #self.bondLengthDoubleSpinBox.hide() endingChoices = ["Hydrogen", "None"] # Removed:, "Nitrogen"] self.endingsComboBox= \ PM_ComboBox( pmGroupBox, label = "Endings:", choices = endingChoices, index = 0, setAsDefault = True, spanWidth = False ) def _loadGroupBox3(self, inPmGroupBox): """ Load widgets in group box 3. """ self.zDistortionDoubleSpinBox = \ PM_DoubleSpinBox( inPmGroupBox, label = "Z-distortion:", value = 0.0, setAsDefault = True, minimum = 0.0, maximum = 10.0, singleStep = 0.1, decimals = 3, suffix = " Angstroms" ) self.xyDistortionDoubleSpinBox = \ PM_DoubleSpinBox( inPmGroupBox, label = "XY-distortion:", value = 0.0, setAsDefault = True, minimum = 0.0, maximum = 2.0, singleStep = 0.1, decimals = 3, suffix = " Angstroms" ) self.twistSpinBox = \ PM_SpinBox( inPmGroupBox, label = "Twist:", value = 0, setAsDefault = True, minimum = 0, maximum = 100, # What should maximum be? suffix = " deg/A" ) self.bendSpinBox = \ PM_SpinBox( inPmGroupBox, label = "Bend:", value = 0, setAsDefault = True, minimum = 0, maximum = 360, suffix = " deg" ) def _loadGroupBox4(self, inPmGroupBox): """ Load widgets in group box 4. """ # "Number of Nanotubes" SpinBox self.mwntCountSpinBox = \ PM_SpinBox( inPmGroupBox, label = "Number:", value = 1, setAsDefault = True, minimum = 1, maximum = 10, suffix = " nanotubes" ) self.mwntCountSpinBox.setSpecialValueText("SWNT") # "Spacing" lineedit. self.mwntSpacingDoubleSpinBox = \ PM_DoubleSpinBox( inPmGroupBox, label = "Spacing:", value = 2.46, setAsDefault = True, minimum = 1.0, maximum = 10.0, singleStep = 0.1, decimals = 3, suffix = " Angstroms" ) def _loadGroupBox5(self, pmGroupBox): """ Load widgets in group box 5. """ self._rubberbandLineGroupBox = PM_GroupBox(pmGroupBox, title='Rubber band Line:') ntLineChoices = ['Ladder'] self.ntRubberBandLineDisplayComboBox = \ PM_ComboBox( self._rubberbandLineGroupBox , label = " Display as:", choices = ntLineChoices, setAsDefault = True) self.lineSnapCheckBox = \ PM_CheckBox(self._rubberbandLineGroupBox , text = 'Enable line snap' , widgetColumn = 1, state = Qt.Checked ) def _connect_showCursorTextCheckBox(self): """ Connect the show cursor text checkbox with user prefs_key. Overrides DnaOrCnt_PropertyManager._connect_showCursorTextCheckBox """ connect_checkbox_with_boolean_pref( self.showCursorTextCheckBox, insertNanotubeEditCommand_showCursorTextCheckBox_prefs_key) def _params_for_creating_cursorTextCheckBoxes(self): """ Returns params needed to create various cursor text checkboxes connected to prefs_keys that allow custom cursor texts. @return: A list containing tuples in the following format: ('checkBoxTextString' , preference_key). PM_PrefsCheckBoxes uses this data to create checkboxes with the the given names and connects them to the provided preference keys. (Note that PM_PrefsCheckBoxes puts thes within a GroupBox) @rtype: list @see: PM_PrefsCheckBoxes @see: self._loadDisplayOptionsGroupBox where this list is used. @see: Superclass method which is overridden here -- DnaOrCnt_PropertyManager._params_for_creating_cursorTextCheckBoxes() """ params = \ [ #Format: (" checkbox text", prefs_key) ("Nanotube length", insertNanotubeEditCommand_cursorTextCheckBox_length_prefs_key ), ("Angle", insertNanotubeEditCommand_cursorTextCheckBox_angle_prefs_key ) ] return params def _addToolTipText(self): """ Tool Tip text for widgets in the Insert Nanotube Property Manager. """ pass def _setEndPoints(self): """ Set the two endpoints of the nanotube using the values from the X, Y, Z coordinate spinboxes in the property manager. @note: The group box containing the 2 sets of XYZ spin boxes are currently hidden. """ # First endpoint (origin) of nanotube x1 = self.x1SpinBox.value() y1 = self.y1SpinBox.value() z1 = self.z1SpinBox.value() # Second endpoint (direction vector/axis) of nanotube. x2 = self.x2SpinBox.value() y2 = self.y2SpinBox.value() z2 = self.z2SpinBox.value() if not self.endPoint1: self.endPoint1 = V(x1, y1, z1) if not self.endPoint2: self.endPoint2 = V(x2, y2, z2) self.nanotube.setEndPoints(self.endPoint1, self.endPoint2) # Need arg "recompute=True", which will recompute the second # endpoint (endPoint2) using the nanotube rise. def getParameters(self): """ Return the parameters from this property manager to be used to create the nanotube. @return: A nanotube instance with its attrs set to the current parameters in the property manager. @rtype: L{Nanotube} @see: L{InsertNanotube_EditCommand._gatherParameters} where this is used """ self._setEndPoints() return (self.nanotube) def _ntTypeComboBoxChanged(self, type): """ Slot for the Type combobox. It is called whenever the Type choice is changed. @param inIndex: The new index. @type inIndex: int """ self.nanotube.setType(str(type)) print "Bond Length =", self.nanotube.getBondLength() self.bondLengthDoubleSpinBox.setValue(self.nanotube.getBondLength()) #self.bondLengthDoubleSpinBox.setValue(ntBondLengths[inIndex]) def _bondLengthChanged(self, bondLength): """ Slot for the B{Bond Length} spinbox. """ self.nanotube.setBondLength(bondLength) self.updateNanotubeDiameter() return def _chiralityFixup(self, spinBoxValueJunk=None): """ Slot for several validators for different parameters. This gets called whenever the user changes the n, m chirality values. @param spinBoxValueJunk: This is the Spinbox value from the valueChanged signal. It is not used. We just want to know that the spinbox value has changed. @type spinBoxValueJunk: double or None """ _n, _m = self.nanotube.setChirality(self.chiralityNSpinBox.value(), self.chiralityMSpinBox.value()) #self.n, self.m = self.nanotube.getChirality() self.connect_or_disconnect_signals(isConnect=False) self.chiralityNSpinBox.setValue(_n) self.chiralityMSpinBox.setValue(_m) self.connect_or_disconnect_signals(isConnect=True) self.updateNanotubeDiameter() def updateNanotubeDiameter(self): """ Update the nanotube Diameter lineEdit widget. """ diameterText = "%-7.4f Angstroms" % (self.nanotube.getDiameter()) self.ntDiameterLineEdit.setText(diameterText) # ntRiseDoubleSpinBox is currently hidden. self.ntRiseDoubleSpinBox.setValue(self.nanotube.getRise()) def _endingsComboBoxChanged(self, endings): """ Slot for the B{Ending} combobox. @param endings: The option's text. @type endings: string """ self.nanotube.setEndings(str(endings)) return def _addWhatsThisText(self): """ What's This text for widgets in this Property Manager. """ whatsThis_InsertNanotube_PropertyManager(self) return
class OrderDna_PropertyManager(Command_PropertyManager): """ The OrderDna_PropertyManager class provides a Property Manager for the B{Order Dna} command on the flyout toolbar in the Build > Dna mode. @ivar title: The title that appears in the property manager header. @type title: str @ivar pmName: The name of this property manager. This is used to set the name of the PM_Dialog object via setObjectName(). @type name: str @ivar iconPath: The relative path to the PNG file that contains a 22 x 22 icon image that appears in the PM header. @type iconPath: str """ title = "Order DNA" pmName = title iconPath = "ui/actions/Command Toolbar/BuildDna/OrderDna.png" def __init__(self, command): """ Constructor for the property manager. """ _superclass.__init__(self, command) self.assy = self.win.assy self.showTopRowButtons( PM_DONE_BUTTON | \ PM_WHATS_THIS_BUTTON) self.update_includeStrands() # Updates the message box. return def connect_or_disconnect_signals(self, isConnect): """ Connect or disconnect widget signals sent to their slot methods. This can be overridden in subclasses. By default it does nothing. @param isConnect: If True the widget will send the signals to the slot method. @type isConnect: boolean """ if isConnect: change_connect = self.win.connect else: change_connect = self.win.disconnect change_connect(self.viewDnaOrderFileButton, SIGNAL("clicked()"), self.viewDnaOrderFile) change_connect(self.includeStrandsComboBox, SIGNAL("activated(int)"), self.update_includeStrands) return def _addGroupBoxes(self): """ Add the Property Manager group boxes. """ self._pmGroupBox1 = PM_GroupBox(self, title="Options") self._loadGroupBox1(self._pmGroupBox1) def _loadGroupBox1(self, pmGroupBox): """ Load widgets in group box. """ includeStrandsChoices = [ "All strands in model", "Selected strands only" ] self.includeStrandsComboBox = \ PM_ComboBox( pmGroupBox, label = "Include strands:", choices = includeStrandsChoices, setAsDefault = True) self.numberOfBasesLineEdit = \ PM_LineEdit( pmGroupBox, label = "Total nucleotides:", text = str(self.getNumberOfBases())) self.numberOfBasesLineEdit.setEnabled(False) self.numberOfXBasesLineEdit = \ PM_LineEdit( pmGroupBox, label = "Unassigned:", text = str(self.getNumberOfBases(unassignedOnly = True))) self.numberOfXBasesLineEdit.setEnabled(False) self.viewDnaOrderFileButton = \ PM_PushButton( pmGroupBox, label = "", text = "View DNA Order File...", spanWidth = True) return def _addWhatsThisText(self): """ What's This text for widgets in this Property Manager. """ whatsThis_OrderDna_PropertyManager(self) return def _addToolTipText(self): """ Tool Tip text for widgets in the DNA Property Manager. """ pass # Ask Bruce where this should live (i.e. class Part?) --Mark def getAllDnaStrands(self, selectedOnly=False): """ Returns a list of all the DNA strands in the current part, or only the selected strands if I{selectedOnly} is True. @param selectedOnly: If True, return only the selected DNA strands. @type selectedOnly: bool """ dnaStrandList = [] def func(node): if isinstance(node, DnaStrand): if selectedOnly: if node.picked: dnaStrandList.append(node) else: dnaStrandList.append(node) self.win.assy.part.topnode.apply2all(func) return dnaStrandList def getNumberOfBases(self, selectedOnly=False, unassignedOnly=False): """ Returns the number of bases count for all the DNA strands in the current part, or only the selected strand if I{selectedOnly} is True. @param selectedOnly: If True, return only the number of bases in the selected DNA strands. @type selectedOnly: bool @param unassignedOnly: If True, return only the number of unassigned bases (i.e. base letters = X). @type unassignedOnly: bool """ dnaSequenceString = '' selectedOnly = self.includeStrandsComboBox.currentIndex() strandList = self.getAllDnaStrands(selectedOnly) for strand in strandList: strandSequenceString = str(strand.getStrandSequence()) dnaSequenceString += strandSequenceString if unassignedOnly: return dnaSequenceString.count("X") return len(dnaSequenceString) def _update_UI_do_updates(self): """ Overrides superclass method. """ self.update_includeStrands() return def getDnaSequence(self, format='CSV'): """ Return the complete Dna sequence information string (i.e. all strand sequences) in the specified format. @return: The Dna sequence string @rtype: string """ if format == 'CSV': #comma separated values. separator = ',' dnaSequenceString = '' selectedOnly = self.includeStrandsComboBox.currentIndex() strandList = self.getAllDnaStrands(selectedOnly) for strand in strandList: dnaSequenceString = dnaSequenceString + strand.name + separator strandSequenceString = str(strand.getStrandSequence()) if strandSequenceString: strandSequenceString = strandSequenceString.upper() strandLength = str(len(strandSequenceString)) + separator dnaSequenceString = dnaSequenceString + strandLength + strandSequenceString dnaSequenceString = dnaSequenceString + "\n" return dnaSequenceString def viewDnaOrderFile(self, openFileInEditor=True): """ Writes a DNA Order file in comma-separated values (CSV) format and opens it in a text editor. The user must save the file to a permanent location using the text editor. @see: Ui_DnaFlyout.orderDnaCommand @see: writeDnaOrderFile() @TODO: assy.getAllDnaObjects(). """ dnaSequence = self.getDnaSequence(format='CSV') if dnaSequence: tmpdir = find_or_make_Nanorex_subdir('temp') fileBaseName = 'DnaOrder' temporaryFile = os.path.join(tmpdir, "%s.csv" % fileBaseName) writeDnaOrderFile(temporaryFile, self.assy, self.getNumberOfBases(), self.getNumberOfBases(unassignedOnly=True), dnaSequence) if openFileInEditor: open_file_in_editor(temporaryFile) return def update_includeStrands(self, ignoreVal=0): """ Slot method for "Include (strands)" combobox. """ idx = self.includeStrandsComboBox.currentIndex() includeType = ["model", "selection"] _numberOfBases = self.getNumberOfBases() self.numberOfBasesLineEdit.setText(str(_numberOfBases) + " bases") _numberOfXBases = self.getNumberOfBases(unassignedOnly=True) self.numberOfXBasesLineEdit.setText(str(_numberOfXBases) + " bases") # Make the background color red if there are any unassigned bases. if _numberOfXBases: self.numberOfXBasesLineEdit.setStyleSheet(\ "QLineEdit {"\ "background-color: rgb(255, 0, 0)"\ "}") else: self.numberOfXBasesLineEdit.setStyleSheet(\ "QLineEdit {"\ "background-color: rgb(255, 255, 255)"\ "}") if _numberOfBases > 0: self.viewDnaOrderFileButton.setEnabled(True) msg = "Click on <b>View DNA Order File...</b> to preview a " \ "DNA order for all DNA strands in the current %s." \ % includeType[idx] else: self.viewDnaOrderFileButton.setEnabled(False) msg = "<font color=red>" \ "There are no DNA strands in the current %s." \ % includeType[idx] self.updateMessage(msg) return
class DnaStrand_PropertyManager( DnaOrCnt_PropertyManager): """ The DnaStrand_PropertyManager class provides a Property Manager for the DnaStrand_EditCommand. @ivar title: The title that appears in the property manager header. @type title: str @ivar pmName: The name of this property manager. This is used to set the name of the PM_Dialog object via setObjectName(). @type name: str @ivar iconPath: The relative path to the PNG file that contains a 22 x 22 icon image that appears in the PM header. @type iconPath: str """ title = "DnaStrand Properties" iconPath = "ui/actions/Properties Manager/Strand.png" def __init__( self, command ): """ Constructor for the Build DNA property manager. """ self.sequenceEditor = None self._numberOfBases = 0 self._conformation = 'B-DNA' self.dnaModel = 'PAM3' _superclass.__init__( self, command) self.showTopRowButtons( PM_DONE_BUTTON | \ PM_WHATS_THIS_BUTTON) return def _addGroupBoxes( self ): """ Add group boxes to this PM. """ self._pmGroupBox1 = PM_GroupBox( self, title = "Parameters" ) self._loadGroupBox1( self._pmGroupBox1 ) self._displayOptionsGroupBox = PM_GroupBox( self, title = "Display Options" ) self._loadDisplayOptionsGroupBox( self._displayOptionsGroupBox ) #Sequence Editor. This is NOT a groupbox, needs cleanup. Doing it here #so that the sequence editor gets connected! Perhaps #superclass should define _loadAdditionalWidgets. -- Ninad2008-10-03 self._loadSequenceEditor() return def _loadGroupBox1(self, pmGroupBox): """ Load widgets in group box 1. """ self.nameLineEdit = PM_LineEdit( pmGroupBox, label = "Name:", text = "", setAsDefault = False) self.numberOfBasesSpinBox = \ PM_SpinBox( pmGroupBox, label = "Number of bases:", value = self._numberOfBases, setAsDefault = False, minimum = 2, maximum = 10000 ) self.disableStructHighlightingCheckbox = \ PM_CheckBox( pmGroupBox, text = "Don't highlight while editing DNA", widgetColumn = 0, state = Qt.Unchecked, setAsDefault = True, spanWidth = True ) #As of 2008-03-31, the properties such as number of bases will be #editable only by using the resize handles. self.numberOfBasesSpinBox.setEnabled(False) return def _loadSequenceEditor(self): """ Temporary code that shows the Sequence editor ..a doc widget docked at the bottom of the mainwindow. The implementation is going to change before 'rattleSnake' product release. As of 2007-11-20: This feature (sequence editor) is waiting for the ongoing dna model work to complete. """ self.sequenceEditor = self.win.createDnaSequenceEditorIfNeeded() self.sequenceEditor.hide() return def _loadDisplayOptionsGroupBox(self, pmGroupBox): """ Overrides superclass method. Also loads the color chooser widget. """ self._loadColorChooser(pmGroupBox) _superclass._loadDisplayOptionsGroupBox(self, pmGroupBox) return def _connect_showCursorTextCheckBox(self): """ Connect the show cursor text checkbox with user prefs_key. Overrides DnaOrCnt_PropertyManager._connect_showCursorTextCheckBox """ connect_checkbox_with_boolean_pref( self.showCursorTextCheckBox , dnaStrandEditCommand_showCursorTextCheckBox_prefs_key) return def _params_for_creating_cursorTextCheckBoxes(self): """ Returns params needed to create various cursor text checkboxes connected to prefs_keys that allow custom cursor texts. @return: A list containing tuples in the following format: ('checkBoxTextString' , preference_key). PM_PrefsCheckBoxes uses this data to create checkboxes with the the given names and connects them to the provided preference keys. (Note that PM_PrefsCheckBoxes puts thes within a GroupBox) @rtype: list @see: PM_PrefsCheckBoxes @see: self._loadDisplayOptionsGroupBox where this list is used. @see: Superclass method which is overridden here -- DnaOrCnt_PropertyManager._params_for_creating_cursorTextCheckBoxes() """ params = \ [ #Format: (" checkbox text", prefs_key) ("Number of bases", dnaStrandEditCommand_cursorTextCheckBox_numberOfBases_prefs_key), ("Number of bases to be changed", dnaStrandEditCommand_cursorTextCheckBox_changedBases_prefs_key) ] return params def getParameters(self): name = self.nameLineEdit.text() numberOfBases = self.numberOfBasesSpinBox.value() dnaForm = self._conformation dnaModel = self.dnaModel color = self._colorChooser.getColor() return (numberOfBases, dnaForm, dnaModel, color, name ) def setParameters(self, params): """ This is usually called when you are editing an existing structure. It also gets called when selecting a new strand (within this command). Some property manager ui elements then display the information obtained from the object being edited. TODO: - Make this a EditCommand_PM API method? - See also the routines GraphicsMode.setParams or object.setProps ..better to name them all in one style? """ numberOfBases, \ dnaForm, \ dnaModel, \ color, \ name = params if numberOfBases is not None: self.numberOfBasesSpinBox.setValue(numberOfBases) if dnaForm is not None: self._conformation = dnaForm if dnaModel is not None: self.dnaModel = dnaModel if color is not None: self._colorChooser.setColor(color) if name: # Minimal test. Should add a validator. --Mark 2008-12-16 self.nameLineEdit.setText(name) # This gets called when we enter the command *and* when selecting a new # strand. In either case, we must update the sequence in the sequenece # editor. Fixes bug 2951. --Mark 2008-12-16 if self.command and self.command.hasValidStructure(): #print "setParameters(): loading sequence in sequence editor for ", name self.updateSequence(strand = self.command.struct) return def connect_or_disconnect_signals(self, isConnect): """ Connect or disconnect widget signals sent to their slot methods. This can be overridden in subclasses. By default it does nothing. @param isConnect: If True the widget will send the signals to the slot method. @type isConnect: boolean """ #TODO: This is a temporary fix for a bug. When you invoke a temporary # mode Entering such a temporary mode keeps the signals of #PM from the previous mode connected ( #but while exiting that temporary mode and reentering the #previous mode, it atucally reconnects the signal! This gives rise to #lots of bugs. This needs more general fix in Temporary mode API. # -- Ninad 2008-01-09 (similar comment exists in MovePropertyManager.py if isConnect and self.isAlreadyConnected: if debug_flags.atom_debug: print_compact_stack("warning: attempt to connect widgets"\ "in this PM that are already connected." ) return if not isConnect and self.isAlreadyDisconnected: if debug_flags.atom_debug: print_compact_stack("warning: attempt to disconnect widgets"\ "in this PM that are already disconnected.") return self.isAlreadyConnected = isConnect self.isAlreadyDisconnected = not isConnect if isConnect: change_connect = self.win.connect else: change_connect = self.win.disconnect if self.sequenceEditor: self.sequenceEditor.connect_or_disconnect_signals(isConnect) _superclass.connect_or_disconnect_signals(self, isConnect) change_connect(self.disableStructHighlightingCheckbox, SIGNAL('stateChanged(int)'), self.change_struct_highlightPolicy) change_connect(self.showCursorTextCheckBox, SIGNAL('stateChanged(int)'), self._update_state_of_cursorTextGroupBox) change_connect(self.nameLineEdit, SIGNAL("editingFinished()"), self._nameChanged) return def _update_UI_do_updates(self): """ @see: Command_PropertyManager. _update_UI_do_updates() @see: DnaStrand_EditCommand.command_update_UI() @see: DnaStrand_EditCommand.hasResizableStructure() """ if not self.command.hasValidStructure(): print "DnaStrand not a valid structure." self._pmGroupBox1.setEnabled(False) self._displayOptionsGroupBox.setEnabled(False) self.sequenceEditor.updateSequence(strand = " ") self.sequenceEditor.setEnabled(False) self.nameLineEdit.setText("") self.numberOfBasesSpinBox.setValue(0) return else: self._pmGroupBox1.setEnabled(True) self._displayOptionsGroupBox.setEnabled(True) self.sequenceEditor.setEnabled(True) isStructResizable, why_not = self.command.hasResizableStructure() if not isStructResizable: #disable all widgets if self._pmGroupBox1.isEnabled(): self._pmGroupBox1.setEnabled(False) msg1 = ("Attention: ") % (self.command.struct.name) msg2 = redmsg("DnaStrand <b>%s</b> is not resizable. Reason: %s" % \ (self.command.struct.name, why_not)) self.updateMessage(msg1 + msg2) else: if not self._pmGroupBox1.isEnabled(): self._pmGroupBox1.setEnabled(True) msg1 = ("Editing <b>%s</b>. ") % (self.command.struct.name) msg2 = "Use resize handles to resize the strand. "\ "Use the <i>Sequence Editor</i> to edit the sequence." self.updateMessage(msg1 + msg2) return def close(self): """ Close this property manager. Also sets the name of the self.command's structure to the one displayed in the line edit field. @see self.show() @see: DnaSegment_EditCommand.setStructureName """ if self.command is not None: name = str(self.nameLineEdit.text()) self.command.setStructureName(name) if self.sequenceEditor: self.sequenceEditor.close() _superclass.close(self) return def updateSequence(self, strand = None): """ Public method provided for convenience. If any callers outside of this command need to update the sequence in the sequence editor, they can simply do DnaStrand_ProprtyManager.updateSequence() rather than DnaStrand_ProprtyManager.sequenceEditor.updateSequence() @see: Ui_DnaSequenceEditor.updateSequence() """ if self.sequenceEditor: self.sequenceEditor.updateSequence(strand = strand) return def change_struct_highlightPolicy(self,checkedState = False): """ Change the 'highlight policy' of the structure being edited (i.e. self.command.struct) . @param checkedState: The checked state of the checkbox that says 'Don't highlight while editing DNA'. So, it its True, the structure being edited won't get highlighted. @see: DnaStrand.setHighlightPolicy for more comments """ if self.command and self.command.hasValidStructure(): highlight = not checkedState self.command.struct.setHighlightPolicy(highlight = highlight) return def _addWhatsThisText(self): """ Add what's this text. Abstract method. """ pass def _nameChanged(self): # Added by Mark. 2008-12-16 """ Slot for "Name" field. Changes the name of the strand if the user types in a new name. @warning: this lacks a validator. User can type in a name with invalid characters. """ if not self.command.hasValidStructure(): return name = str(self.nameLineEdit.text()) if not name: # Minimal test. Should add a validator. Ask Bruce for example validator code somewhere. --Mark 2008-12-16 if self.command.hasValidStructure(): self.nameLineEdit.setText(self.command.getStructureName()) return self.command.setStructureName(name) self._update_UI_do_updates() # Updates the message box. return
class DnaStrand_PropertyManager( DnaOrCnt_PropertyManager): """ The DnaStrand_PropertyManager class provides a Property Manager for the DnaStrand_EditCommand. @ivar title: The title that appears in the property manager header. @type title: str @ivar pmName: The name of this property manager. This is used to set the name of the PM_Dialog object via setObjectName(). @type name: str @ivar iconPath: The relative path to the PNG file that contains a 22 x 22 icon image that appears in the PM header. @type iconPath: str """ title = "DnaStrand Properties" pmName = title iconPath = "ui/actions/Properties Manager/Strand.png" def __init__( self, win, editCommand ): """ Constructor for the Build DNA property manager. """ #For model changed signal self.previousSelectionParams = None #see self.connect_or_disconnect_signals for comment about this flag self.isAlreadyConnected = False self.isAlreadyDisconnected = False self.sequenceEditor = None self._numberOfBases = 0 self._conformation = 'B-DNA' self.duplexRise = 3.18 self.basesPerTurn = 10 self.dnaModel = 'PAM3' _superclass.__init__( self, win, editCommand) self.showTopRowButtons( PM_DONE_BUTTON | \ PM_WHATS_THIS_BUTTON) self._loadSequenceEditor() msg = "Use resize handles to resize the strand. Use sequence editor"\ "to assign a new sequence or the current one to a file." self.updateMessage(msg) def _addGroupBoxes( self ): """ Add the DNA Property Manager group boxes. """ self._pmGroupBox1 = PM_GroupBox( self, title = "Parameters" ) self._loadGroupBox1( self._pmGroupBox1 ) self._displayOptionsGroupBox = PM_GroupBox( self, title = "Display Options" ) self._loadDisplayOptionsGroupBox( self._displayOptionsGroupBox ) def _loadGroupBox1(self, pmGroupBox): """ Load widgets in group box 4. """ self.nameLineEdit = PM_LineEdit( pmGroupBox, label = "Strand name:", text = "", setAsDefault = False) self.numberOfBasesSpinBox = \ PM_SpinBox( pmGroupBox, label = "Number of bases:", value = self._numberOfBases, setAsDefault = False, minimum = 2, maximum = 10000 ) self.basesPerTurnDoubleSpinBox = \ PM_DoubleSpinBox( pmGroupBox, label = "Bases per turn:", value = self.basesPerTurn, setAsDefault = True, minimum = 8.0, maximum = 20.0, decimals = 2, singleStep = 0.1 ) self.duplexRiseDoubleSpinBox = \ PM_DoubleSpinBox( pmGroupBox, label = "Rise:", value = self.duplexRise, setAsDefault = True, minimum = 2.0, maximum = 4.0, decimals = 3, singleStep = 0.01 ) self.disableStructHighlightingCheckbox = \ PM_CheckBox( pmGroupBox, text = "Don't highlight while editing DNA", widgetColumn = 0, state = Qt.Unchecked, setAsDefault = True, spanWidth = True ) #As of 2008-03-31, the properties such as number of bases will be #editable only by using the resize handles. post FNANO we will support #the self.numberOfBasesSpinBox.setEnabled(False) self.basesPerTurnDoubleSpinBox.setEnabled(False) self.duplexRiseDoubleSpinBox.setEnabled(False) def _loadSequenceEditor(self): """ Temporary code that shows the Sequence editor ..a doc widget docked at the bottom of the mainwindow. The implementation is going to change before 'rattleSnake' product release. As of 2007-11-20: This feature (sequence editor) is waiting for the ongoing dna model work to complete. """ self.sequenceEditor = self.win.createDnaSequenceEditorIfNeeded() self.sequenceEditor.hide() def _loadDisplayOptionsGroupBox(self, pmGroupBox): """ Overrides superclass method. Also loads the color chooser widget. """ self._loadColorChooser(pmGroupBox) _superclass._loadDisplayOptionsGroupBox(self, pmGroupBox) def _connect_showCursorTextCheckBox(self): """ Connect the show cursor text checkbox with user prefs_key. Overrides DnaOrCnt_PropertyManager._connect_showCursorTextCheckBox """ connect_checkbox_with_boolean_pref( self.showCursorTextCheckBox , dnaStrandEditCommand_showCursorTextCheckBox_prefs_key) def _params_for_creating_cursorTextCheckBoxes(self): """ Returns params needed to create various cursor text checkboxes connected to prefs_keys that allow custom cursor texts. @return: A list containing tuples in the following format: ('checkBoxTextString' , preference_key). PM_PrefsCheckBoxes uses this data to create checkboxes with the the given names and connects them to the provided preference keys. (Note that PM_PrefsCheckBoxes puts thes within a GroupBox) @rtype: list @see: PM_PrefsCheckBoxes @see: self._loadDisplayOptionsGroupBox where this list is used. @see: Superclass method which is overridden here -- DnaOrCnt_PropertyManager._params_for_creating_cursorTextCheckBoxes() """ params = \ [ #Format: (" checkbox text", prefs_key) ("Number of bases", dnaStrandEditCommand_cursorTextCheckBox_numberOfBases_prefs_key), ("Number of bases to be changed", dnaStrandEditCommand_cursorTextCheckBox_changedBases_prefs_key) ] return params def getParameters(self): numberOfBases = self.numberOfBasesSpinBox.value() dnaForm = self._conformation dnaModel = self.dnaModel basesPerTurn = self.basesPerTurn duplexRise = self.duplexRise color = self._colorChooser.getColor() return (numberOfBases, dnaForm, dnaModel, basesPerTurn, duplexRise, color ) def setParameters(self, params): """ This is usually called when you are editing an existing structure. Some property manager ui elements then display the information obtained from the object being edited. TODO: - Make this a EditCommand_PM API method? - See also the routines GraphicsMode.setParams or object.setProps ..better to name them all in one style? """ #Set the duplex rise and bases per turn spinbox values. numberOfBases, \ dnaForm, \ dnaModel, \ basesPerTurn, \ duplexRise, \ color = params if numberOfBases is not None: self.numberOfBasesSpinBox.setValue(numberOfBases) if dnaForm is not None: self._conformation = dnaForm if dnaModel is not None: self.dnaModel = dnaModel if duplexRise is not None: self.duplexRiseDoubleSpinBox.setValue(duplexRise) if basesPerTurn is not None: self.basesPerTurnDoubleSpinBox.setValue(basesPerTurn) if color is not None: self._colorChooser.setColor(color) def connect_or_disconnect_signals(self, isConnect): """ Connect or disconnect widget signals sent to their slot methods. This can be overridden in subclasses. By default it does nothing. @param isConnect: If True the widget will send the signals to the slot method. @type isConnect: boolean """ #TODO: This is a temporary fix for a bug. When you invoke a temporary # mode Entering such a temporary mode keeps the signals of #PM from the previous mode connected ( #but while exiting that temporary mode and reentering the #previous mode, it atucally reconnects the signal! This gives rise to #lots of bugs. This needs more general fix in Temporary mode API. # -- Ninad 2008-01-09 (similar comment exists in MovePropertyManager.py if isConnect and self.isAlreadyConnected: if debug_flags.atom_debug: print_compact_stack("warning: attempt to connect widgets"\ "in this PM that are already connected." ) return if not isConnect and self.isAlreadyDisconnected: if debug_flags.atom_debug: print_compact_stack("warning: attempt to disconnect widgets"\ "in this PM that are already disconnected.") return self.isAlreadyConnected = isConnect self.isAlreadyDisconnected = not isConnect if isConnect: change_connect = self.win.connect else: change_connect = self.win.disconnect if self.sequenceEditor: self.sequenceEditor.connect_or_disconnect_signals(isConnect) _superclass.connect_or_disconnect_signals(self, isConnect) change_connect(self.disableStructHighlightingCheckbox, SIGNAL('stateChanged(int)'), self.change_struct_highlightPolicy) change_connect(self.showCursorTextCheckBox, SIGNAL('stateChanged(int)'), self._update_state_of_cursorTextGroupBox) def model_changed(self): """ @see: DnaStrand_EditCommand.model_changed() @see: DnaStrand_EditCommand.hasResizableStructure() """ isStructResizable, why_not = self.editCommand.hasResizableStructure() if not isStructResizable: #disable all widgets if self._pmGroupBox1.isEnabled(): self._pmGroupBox1.setEnabled(False) msg1 = ("Viewing properties of %s <br>") %(self.editCommand.struct.name) msg2 = redmsg("DnaStrand is not resizable. Reason: %s"%(why_not)) self.updateMessage(msg1 + msg2) else: if not self._pmGroupBox1.isEnabled(): self._pmGroupBox1.setEnabled(True) msg1 = ("Viewing properties of %s <br>") %(self.editCommand.struct.name) msg2 = "Use resize handles to resize the strand. Use sequence editor"\ "to assign a new sequence or the current one to a file." self.updateMessage(msg1 + msg2) def show(self): """ Show this PM As of 2007-11-20, it also shows the Sequence Editor widget and hides the history widget. This implementation may change in the near future This method also retrives the name information from the editCommand's structure for its name line edit field. @see: DnaStrand_EditCommand.getStructureName() @see: self.close() """ _superclass.show(self) self._showSequenceEditor() if self.editCommand is not None: name = self.editCommand.getStructureName() if name is not None: self.nameLineEdit.setText(name) def close(self): """ Close this property manager. Also sets the name of the self.editCommand's structure to the one displayed in the line edit field. @see self.show() @see: DnaSegment_EditCommand.setStructureName """ if self.editCommand is not None: name = str(self.nameLineEdit.text()) self.editCommand.setStructureName(name) if self.sequenceEditor: self.sequenceEditor.close() _superclass.close(self) def _showSequenceEditor(self): if self.sequenceEditor: if not self.sequenceEditor.isVisible(): #Show the sequence editor #ATTENTION: the sequence editor also closes (temporarily) the #reports dockwidget (if visible) Its state is later restored when #the sequuence Editor is closed. self.sequenceEditor.show() self.updateSequence() def updateSequence(self): """ Update the sequence string in the sequence editor @see: DnaSequenceEditor.setSequence() @see DnaSequenceEditor._determine_complementSequence() @see: DnaSequenceEditor.setComplementSequence() @see: DnaStrand.getStrandSequenceAndItsComplement() """ #Read in the strand sequence of the selected strand and #show it in the text edit in the sequence editor. ##strand = self.strandListWidget.getPickedItem() if not self.editCommand.hasValidStructure(): return strand = self.editCommand.struct titleString = 'Sequence Editor for ' + strand.name self.sequenceEditor.setWindowTitle(titleString) sequenceString, complementSequenceString = strand.getStrandSequenceAndItsComplement() if sequenceString: sequenceString = QString(sequenceString) sequenceString = sequenceString.toUpper() #Set the initial sequence (read in from the file) self.sequenceEditor.setSequence(sequenceString) #Set the initial complement sequence for DnaSequence editor. #do this independently because 'complementSequenceString' may have #some characters (such as * ) that denote a missing base on the #complementary strand. this information is used by the sequence #editor. See DnaSequenceEditor._determine_complementSequence() #for more details. See also bug 2787 self.sequenceEditor.setComplementSequence(complementSequenceString) def change_struct_highlightPolicy(self,checkedState = False): """ Change the 'highlight policy' of the structure being edited (i.e. self.editCommand.struct) . @param checkedState: The checked state of the checkbox that says 'Don't highlight while editing DNA'. So, it its True, the structure being edited won't get highlighted. @see: DnaStrand.setHighlightPolicy for more comments """ if self.editCommand and self.editCommand.hasValidStructure(): highlight = not checkedState self.editCommand.struct.setHighlightPolicy(highlight = highlight) def _addWhatsThisText(self): """ Add what's this text. Abstract method. """ pass
class EditNanotube_PropertyManager( DnaOrCnt_PropertyManager ): """ The NanotubeSegmenta_PropertyManager class provides a Property Manager for the EditNanotube_EditCommand. @ivar title: The title that appears in the property manager header. @type title: str @ivar pmName: The name of this property manager. This is used to set the name of the PM_Dialog object via setObjectName(). @type name: str @ivar iconPath: The relative path to the PNG file that contains a 22 x 22 icon image that appears in the PM header. @type iconPath: str """ title = "Nanotube Properties" pmName = title iconPath = "ui/actions/Command Toolbar/BuildNanotube/EditNanotube.png" def __init__( self, command ): """ Constructor for the Cnt Segment Properties property manager. """ #For model changed signal self.previousSelectionParams = None #see self.connect_or_disconnect_signals for comment about this flag self.isAlreadyConnected = False self.isAlreadyDisconnected = False # Initialized here. Their values will be set in # _update_widgets_in_PM_before_show() self.endPoint1 = V(0, 0, 0) self.endPoint2 = V(0, 0, 0) _superclass.__init__( self, command) self.showTopRowButtons( PM_DONE_BUTTON | \ PM_CANCEL_BUTTON | \ PM_WHATS_THIS_BUTTON) def connect_or_disconnect_signals(self, isConnect): """ Connect or disconnect widget signals sent to their slot methods. This can be overridden in subclasses. By default it does nothing. @param isConnect: If True the widget will send the signals to the slot method. @type isConnect: boolean """ if isConnect: change_connect = self.win.connect else: change_connect = self.win.disconnect change_connect(self.nameLineEdit, SIGNAL("editingFinished()"), self._nameChanged) change_connect(self.showCursorTextCheckBox, SIGNAL('stateChanged(int)'), self._update_state_of_cursorTextGroupBox) return def show(self): """ Show this property manager. Overrides EditCommand_PM.show() This method also retrives the name information from the command's structure for its name line edit field. @see: EditNanotube_EditCommand.getStructureName() @see: self.close() """ _superclass.show(self) #if self.command is not None: #name = self.command.getStructureName() #if name is not None: #self.nameLineEdit.setText(name) def close(self): """ Close this property manager. Also sets the name of the self.command's structure to the one displayed in the line edit field. @see self.show() @see: EditNanotube_EditCommand.setStructureName """ if self.command is not None: name = str(self.nameLineEdit.text()) self.command.setStructureName(name) _superclass.close(self) def _connect_showCursorTextCheckBox(self): """ Connect the show cursor text checkbox with user prefs_key. Overrides DnaOrCnt_PropertyManager._connect_showCursorTextCheckBox """ connect_checkbox_with_boolean_pref( self.showCursorTextCheckBox , editNanotubeEditCommand_showCursorTextCheckBox_prefs_key) def _params_for_creating_cursorTextCheckBoxes(self): """ Returns params needed to create various cursor text checkboxes connected to prefs_keys that allow custom cursor texts. @return: A list containing tuples in the following format: ('checkBoxTextString' , preference_key). PM_PrefsCheckBoxes uses this data to create checkboxes with the the given names and connects them to the provided preference keys. (Note that PM_PrefsCheckBoxes puts thes within a GroupBox) @rtype: list @see: PM_PrefsCheckBoxes @see: self._loadDisplayOptionsGroupBox where this list is used. @see: Superclass method which is overridden here -- DnaOrCnt_PropertyManager._params_for_creating_cursorTextCheckBoxes() """ params = \ [ #Format: (" checkbox text", prefs_key) ("Nanotube length", editNanotubeEditCommand_cursorTextCheckBox_length_prefs_key) ] return params def setParameters(self, params): """ This is called when entering "Nanotube Segment Properties (i.e. "Edit properties...") to retrieve and set parameters of the nanotube segment that might be modified during this command and are needed to regenerate the nanotube segment. @param params: The parameters of the nanotube segment. These parameters are retreived via L{NanotubeSegment.getProps()}, called from L{EditNanotube_EditCommand.editStructure()}. Parameters: - n, m (chirality) - type (i.e. carbon or boron nitride) - endings (none, hydrogen, nitrogen) - endpoints (endPoint1, endPoint2) @type params: list (n, m), type, endings, (endPoint1, endPoint2) @note: Any widgets in the property manager that display these parameters should be updated here. @see: L{NanotubeSegment.getProps()} TODO: - Make this a EditCommand_PM API method? - See also the routines GraphicsMode.setParams or object.setProps ..better to name them all in one style? """ (self.n, self.m), self.type, self.endings,\ (self.endPoint1, self.endPoint2) = params # This is needed to update the endpoints since the Nanotube segment # may have been moved (i.e. translated or rotated). In that case, # the endpoints are not updated, so we recompute them here. nanotubeChunk = self.command.struct.members[0] self.endPoint1, self.endPoint2, radius = \ self.command.struct.nanotube.computeEndPointsFromChunk(nanotubeChunk) if 0: print "\n--------------" print "setParameters():" print "Struct=", self.command.struct print "N, M:", self.n, self.m print "type:", self.type print "endings:", self.endings print "pt1, pt2:", self.endPoint1, self.endPoint2 def getParameters(self): """ Get the parameters that the edit command will use to determine if any have changed. If any have, then the nanotube will be modified. """ if 0: print "\n--------------" print "getParameters():" print "Struct=", self.command.struct print "N, M:", self.n, self.m print "type:", self.type print "endings:", self.endings print "pt1, pt2:", self.endPoint1, self.endPoint2 return (self.n, self.m, self.type, self.endings, self.endPoint1, self.endPoint2) def _update_widgets_in_PM_before_show(self): """ This is called only when user is editing an existing structure. Its different than self.update_widgets_in_pm_before_show. (that method is called just before showing the property manager) @see: EditNanotube_EditCommand.editStructure() """ if self.command and self.command.hasValidStructure(): self.nanotube = self.command.struct.nanotube self.n, self.m = self.nanotube.getChirality() self.type = self.nanotube.getType() self.endings = self.nanotube.getEndings() self.endPoint1, self.endPoint2 = self.nanotube.getEndPoints() pass # Note that _update_widgets_in_PM_before_show() is called in # self.show, before you connect the signals. So, for the # 'first show' we will need to manually set the value of any # widgets that need updated. But later, when a different # NanotubeSegment is clicked, (while still in # EditNanotube_EditCommand, the propMgr will already be connected # so any calls in that case is redundant. self.updateNameField() self.updateLength() self.updateNanotubeDiameter() self.updateChirality() return def _update_UI_do_updates(self): """ Overrides superclass method. @see: Command_PropertyManager._update_UI_do_updates() """ self._update_widgets_in_PM_before_show() if self.command.struct: msg = "Editing structure <b>%s</b>." % \ self.command.getStructureName() else: msg = "Select a nanotube to edit." self.updateMessage(msg) return def _addGroupBoxes( self ): """ Add the Property Manager group boxes. """ self._pmGroupBox1 = PM_GroupBox( self, title = "Parameters" ) self._loadGroupBox1( self._pmGroupBox1 ) self._displayOptionsGroupBox = PM_GroupBox( self, title = "Display Options" ) self._loadDisplayOptionsGroupBox( self._displayOptionsGroupBox ) def _loadGroupBox1(self, pmGroupBox): """ Load widgets in group box 4. """ self.nameLineEdit = PM_LineEdit( pmGroupBox, label = "Name:", text = "", setAsDefault = False) # Nanotube Length self.ntLengthLineEdit = \ PM_LineEdit( pmGroupBox, label = "Length: ", text = "0.0 Angstroms", setAsDefault = False) self.ntLengthLineEdit.setDisabled(True) # Nanotube Radius self.ntDiameterLineEdit = \ PM_LineEdit( pmGroupBox, label = "Nanotube Diameter: ", setAsDefault = False) self.ntDiameterLineEdit.setDisabled(True) # Nanotube chirality. These are disabled (read-only) for now. --Mark self.chiralityNSpinBox = \ PM_SpinBox( pmGroupBox, label = "Chirality (n) :", minimum = 2, maximum = 100, setAsDefault = True ) self.chiralityNSpinBox.setDisabled(True) self.chiralityMSpinBox = \ PM_SpinBox( pmGroupBox, label = "Chirality (m) :", minimum = 0, maximum = 100, setAsDefault = True ) self.chiralityMSpinBox.setDisabled(True) def _addWhatsThisText(self): """ Add what's this text. """ pass def _addToolTipText(self): """ Add Tooltip text """ pass def _nameChanged(self): """ Slot for "Name" field. @TODO: Include a validator for the name field. """ _name = str(self.nameLineEdit.text()) if not _name: # Minimal test. Need to implement a validator. self.updateNameField() return self.command.setStructureName(_name) msg = "Editing structure <b>%s</b>." % _name self.updateMessage(msg) return def updateNameField(self): """ Update the name field showing the name of the currently selected protein. clear the combobox list. """ if self.command.hasValidStructure(): self.nameLineEdit.setEnabled(True) self.nameLineEdit.setText(self.command.getStructureName()) else: self.nameLineEdit.setDisabled(True) self.nameLineEdit.setText("") return def updateLength( self ): """ Update the nanotube Length lineEdit widget. """ if self.command.hasValidStructure(): _nanotubeLength = vlen(self.endPoint1 - self.endPoint2) _lengthText = "%-7.4f Angstroms" % (_nanotubeLength) else: _lengthText = "" self.ntLengthLineEdit.setText(_lengthText) return def updateNanotubeDiameter(self): """ Update the nanotube Diameter lineEdit widget. """ if self.command.hasValidStructure(): _diameterText = "%-7.4f Angstroms" % (self.nanotube.getDiameter()) else: _diameterText = "" self.ntDiameterLineEdit.setText(_diameterText) return def updateChirality( self ): """ Update the nanotube chirality spinboxes (read-only). """ if self.command.hasValidStructure(): n, m = self.nanotube.getChirality() else: n = 0 m = 0 self.chiralityNSpinBox.setValue(n) self.chiralityMSpinBox.setValue(m) return pass # End of EditNanotube_PropertyManager class
class InsertDna_PropertyManager(DnaOrCnt_PropertyManager): """ The InsertDna_PropertyManager class provides a Property Manager for the B{Insert Dna} command. @ivar title: The title that appears in the property manager header. @type title: str @ivar pmName: The name of this property manager. This is used to set the name of the PM_Dialog object via setObjectName(). @type name: str @ivar iconPath: The relative path to the PNG file that contains a 22 x 22 icon image that appears in the PM header. @type iconPath: str """ title = "Insert DNA" pmName = title iconPath = "ui/actions/Command Toolbar/BuildDna/InsertDna.png" def __init__(self, command): """ Constructor for the DNA Duplex property manager. """ self.endPoint1 = None self.endPoint2 = None self._conformation = "B-DNA" self._numberOfBases = 0 self._basesPerTurn = getDuplexBasesPerTurn(self._conformation) self._duplexRise = getDuplexRise(self._conformation) self._duplexLength = getDuplexLength(self._conformation, self._numberOfBases) _superclass.__init__(self, command) self.showTopRowButtons( PM_DONE_BUTTON | \ PM_CANCEL_BUTTON | \ PM_WHATS_THIS_BUTTON) def connect_or_disconnect_signals(self, isConnect): """ Connect or disconnect widget signals sent to their slot methods. This can be overridden in subclasses. By default it does nothing. @param isConnect: If True the widget will send the signals to the slot method. @type isConnect: boolean """ if isConnect: change_connect = self.win.connect else: change_connect = self.win.disconnect change_connect(self._placementOptions.buttonGroup, SIGNAL("buttonClicked(int)"), self.activateSpecifyReferencePlaneTool) change_connect(self.conformationComboBox, SIGNAL("currentIndexChanged(int)"), self.conformationComboBoxChanged) change_connect(self.numberOfBasePairsSpinBox, SIGNAL("valueChanged(int)"), self.numberOfBasesChanged) change_connect(self.basesPerTurnDoubleSpinBox, SIGNAL("valueChanged(double)"), self.basesPerTurnChanged) change_connect(self.duplexRiseDoubleSpinBox, SIGNAL("valueChanged(double)"), self.duplexRiseChanged) change_connect(self.showCursorTextCheckBox, SIGNAL('stateChanged(int)'), self._update_state_of_cursorTextGroupBox) self.duplexRiseDoubleSpinBox.connectWithState( Preferences_StateRef_double(bdnaRise_prefs_key, env.prefs[bdnaRise_prefs_key])) self.basesPerTurnDoubleSpinBox.connectWithState( Preferences_StateRef_double(bdnaBasesPerTurn_prefs_key, env.prefs[bdnaBasesPerTurn_prefs_key])) def show(self): _superclass.show(self) self.updateMessage("Specify the DNA parameters below, then click "\ "two endpoints in the graphics area to insert a DNA duplex.") def _addGroupBoxes(self): """ Add the DNA Property Manager group boxes. """ self._pmReferencePlaneGroupBox = PM_GroupBox(self, title="Placement Options") self._loadReferencePlaneGroupBox(self._pmReferencePlaneGroupBox) self._pmGroupBox1 = PM_GroupBox(self, title="Endpoints") self._loadGroupBox1(self._pmGroupBox1) self._pmGroupBox1.hide() self._pmGroupBox2 = PM_GroupBox(self, title="Parameters") self._loadGroupBox2(self._pmGroupBox2) self._displayOptionsGroupBox = PM_GroupBox(self, title="Display Options") self._loadDisplayOptionsGroupBox(self._displayOptionsGroupBox) def _loadGroupBox1(self, pmGroupBox): """ Load widgets in group box 3. """ #Folllowing toolbutton facilitates entering a temporary DnaLineMode #to create a DNA using endpoints of the specified line. self.specifyDnaLineButton = PM_ToolButton( pmGroupBox, text="Specify Endpoints", iconPath="ui/actions/Properties Manager/Pencil.png", spanWidth=True) self.specifyDnaLineButton.setCheckable(True) self.specifyDnaLineButton.setAutoRaise(True) self.specifyDnaLineButton.setToolButtonStyle( Qt.ToolButtonTextBesideIcon) #EndPoint1 and endPoint2 coordinates. These widgets are hidden # as of 2007- 12 - 05 self._endPoint1SpinBoxes = PM_CoordinateSpinBoxes(pmGroupBox, label="End Point 1") self.x1SpinBox = self._endPoint1SpinBoxes.xSpinBox self.y1SpinBox = self._endPoint1SpinBoxes.ySpinBox self.z1SpinBox = self._endPoint1SpinBoxes.zSpinBox self._endPoint2SpinBoxes = PM_CoordinateSpinBoxes(pmGroupBox, label="End Point 2") self.x2SpinBox = self._endPoint2SpinBoxes.xSpinBox self.y2SpinBox = self._endPoint2SpinBoxes.ySpinBox self.z2SpinBox = self._endPoint2SpinBoxes.zSpinBox self._endPoint1SpinBoxes.hide() self._endPoint2SpinBoxes.hide() def _loadGroupBox2(self, pmGroupBox): """ Load widgets in group box 4. """ self.conformationComboBox = \ PM_ComboBox( pmGroupBox, label = "Conformation:", choices = ["B-DNA"], setAsDefault = True) dnaModelChoices = ['PAM3', 'PAM5'] self.dnaModelComboBox = \ PM_ComboBox( pmGroupBox, label = "Model:", choices = dnaModelChoices, setAsDefault = True) self.basesPerTurnDoubleSpinBox = \ PM_DoubleSpinBox( pmGroupBox, label = "Bases per turn:", value = env.prefs[bdnaBasesPerTurn_prefs_key], setAsDefault = True, minimum = 8.0, maximum = 20.0, decimals = 2, singleStep = 0.1 ) self.duplexRiseDoubleSpinBox = \ PM_DoubleSpinBox( pmGroupBox, label = "Rise:", value = env.prefs[bdnaRise_prefs_key], setAsDefault = True, minimum = 2.0, maximum = 4.0, decimals = 3, singleStep = 0.01 ) # Strand Length (i.e. the number of bases) self.numberOfBasePairsSpinBox = \ PM_SpinBox( pmGroupBox, label = "Base pairs:", value = self._numberOfBases, setAsDefault = False, minimum = 0, maximum = 10000 ) self.numberOfBasePairsSpinBox.setDisabled(True) # Duplex Length self.duplexLengthLineEdit = \ PM_LineEdit( pmGroupBox, label = "Duplex length: ", text = "0.0 Angstroms", setAsDefault = False) self.duplexLengthLineEdit.setDisabled(True) def _loadDisplayOptionsGroupBox(self, pmGroupBox): """ Load widgets in the Display Options GroupBox @see: DnaOrCnt_PropertyManager. _loadDisplayOptionsGroupBox """ #Call the superclass method that loads the cursor text checkboxes. #Note, as of 2008-05-19, the superclass, DnaOrCnt_PropertyManager #only loads the cursor text groupboxes. Subclasses like this can #call custom methods like self._loadCursorTextCheckBoxes etc if they #don't need all groupboxes that the superclass loads. _superclass._loadDisplayOptionsGroupBox(self, pmGroupBox) self._rubberbandLineGroupBox = PM_GroupBox(pmGroupBox, title='Rubber band line:') dnaLineChoices = ['Ribbons', 'Ladder'] self.dnaRubberBandLineDisplayComboBox = \ PM_ComboBox( self._rubberbandLineGroupBox , label = " Display as:", choices = dnaLineChoices, setAsDefault = True) self.lineSnapCheckBox = \ PM_CheckBox(self._rubberbandLineGroupBox , text = 'Enable line snap' , widgetColumn = 1, state = Qt.Checked ) def _connect_showCursorTextCheckBox(self): """ Connect the show cursor text checkbox with user prefs_key. Overrides DnaOrCnt_PropertyManager._connect_showCursorTextCheckBox """ connect_checkbox_with_boolean_pref( self.showCursorTextCheckBox, dnaDuplexEditCommand_showCursorTextCheckBox_prefs_key) def _params_for_creating_cursorTextCheckBoxes(self): """ Returns params needed to create various cursor text checkboxes connected to prefs_keys that allow custom cursor texts. @return: A list containing tuples in the following format: ('checkBoxTextString' , preference_key). PM_PrefsCheckBoxes uses this data to create checkboxes with the the given names and connects them to the provided preference keys. (Note that PM_PrefsCheckBoxes puts thes within a GroupBox) @rtype: list @see: PM_PrefsCheckBoxes @see: self._loadDisplayOptionsGroupBox where this list is used. @see: Superclass method which is overridden here -- DnaOrCnt_PropertyManager._params_for_creating_cursorTextCheckBoxes() """ params = \ [ #Format: (" checkbox text", prefs_key) ("Number of base pairs", dnaDuplexEditCommand_cursorTextCheckBox_numberOfBasePairs_prefs_key), ("Number of turns", dnaDuplexEditCommand_cursorTextCheckBox_numberOfTurns_prefs_key), ("Duplex length", dnaDuplexEditCommand_cursorTextCheckBox_length_prefs_key), ("Angle", dnaDuplexEditCommand_cursorTextCheckBox_angle_prefs_key) ] return params def _addToolTipText(self): """ Tool Tip text for widgets in the DNA Property Manager. """ pass def conformationComboBoxChanged(self, inIndex): """ Slot for the Conformation combobox. It is called whenever the Conformation choice is changed. @param inIndex: The new index. @type inIndex: int """ conformation = self.conformationComboBox.currentText() if conformation == "B-DNA": self.basesPerTurnDoubleSpinBox.setValue("10.0") elif conformation == "Z-DNA": self.basesPerTurnDoubleSpinBox.setValue("12.0") else: msg = redmsg("conformationComboBoxChanged(): \ Error - unknown DNA conformation. Index = " + inIndex) env.history.message(msg) self.duplexLengthSpinBox.setSingleStep(getDuplexRise(conformation)) def numberOfBasesChanged(self, numberOfBases): """ Slot for the B{Number of Bases} spinbox. """ # Update the Duplex Length lineEdit widget. text = str(getDuplexLength(self._conformation, numberOfBases, self._duplexRise)) \ + " Angstroms" self.duplexLengthLineEdit.setText(text) return def basesPerTurnChanged(self, basesPerTurn): """ Slot for the B{Bases per turn} spinbox. """ self.command.basesPerTurn = basesPerTurn self._basesPerTurn = basesPerTurn return def duplexRiseChanged(self, rise): """ Slot for the B{Rise} spinbox. """ self.command.duplexRise = rise self._duplexRise = rise return def getParameters(self): """ Return the parameters from this property manager to be used to create the DNA duplex. @return: A tuple containing the parameters @rtype: tuple @see: L{InsertDna_EditCommand._gatherParameters} where this is used """ numberOfBases = self.numberOfBasePairsSpinBox.value() dnaForm = str(self.conformationComboBox.currentText()) basesPerTurn = self.basesPerTurnDoubleSpinBox.value() duplexRise = self.duplexRiseDoubleSpinBox.value() dnaModel = str(self.dnaModelComboBox.currentText()) # First endpoint (origin) of DNA duplex x1 = self.x1SpinBox.value() y1 = self.y1SpinBox.value() z1 = self.z1SpinBox.value() # Second endpoint (direction vector/axis) of DNA duplex. x2 = self.x2SpinBox.value() y2 = self.y2SpinBox.value() z2 = self.z2SpinBox.value() if not self.endPoint1: self.endPoint1 = V(x1, y1, z1) if not self.endPoint2: self.endPoint2 = V(x2, y2, z2) return (numberOfBases, dnaForm, dnaModel, basesPerTurn, duplexRise, self.endPoint1, self.endPoint2) def _addWhatsThisText(self): """ What's This text for widgets in this Property Manager. """ whatsThis_InsertDna_PropertyManager(self)
class OrderDna_PropertyManager( PM_Dialog, DebugMenuMixin ): """ The OrderDna_PropertyManager class provides a Property Manager for the B{Order Dna} command on the flyout toolbar in the Build > Dna mode. @ivar title: The title that appears in the property manager header. @type title: str @ivar pmName: The name of this property manager. This is used to set the name of the PM_Dialog object via setObjectName(). @type name: str @ivar iconPath: The relative path to the PNG file that contains a 22 x 22 icon image that appears in the PM header. @type iconPath: str """ title = "Order Dna" pmName = title iconPath = "ui/actions/Command Toolbar/Order_DNA.png" def __init__( self, parentCommand ): """ Constructor for the property manager. """ self.parentMode = parentCommand self.w = self.parentMode.w self.win = self.parentMode.w self.pw = self.parentMode.pw self.o = self.win.glpane self.assy = self.win.assy PM_Dialog.__init__(self, self.pmName, self.iconPath, self.title) DebugMenuMixin._init1( self ) self.showTopRowButtons( PM_DONE_BUTTON | \ PM_WHATS_THIS_BUTTON) self.update_includeStrands() # Updates the message box. """ if self.getNumberOfBases(): msg = "Click on <b>View DNA Order File...</b> to preview a "\ "DNA order for all DNA strands in the current model." else: msg = "<font color=red>There is no DNA in the current model." self.updateMessage(msg) """ def connect_or_disconnect_signals(self, isConnect): """ Connect or disconnect widget signals sent to their slot methods. This can be overridden in subclasses. By default it does nothing. @param isConnect: If True the widget will send the signals to the slot method. @type isConnect: boolean """ if isConnect: change_connect = self.win.connect else: change_connect = self.win.disconnect change_connect( self.viewDnaOrderFileButton, SIGNAL("clicked()"), self.viewDnaOrderFile) change_connect( self.includeStrandsComboBox, SIGNAL("activated(int)"), self.update_includeStrands ) def ok_btn_clicked(self): """ Slot for the OK button """ self.win.toolsDone() def show(self): """ Shows the Property Manager. Overrides PM_Dialog.show. """ PM_Dialog.show(self) self.connect_or_disconnect_signals(isConnect = True) def close(self): """ Closes the Property Manager. Overrides PM_Dialog.close. """ self.connect_or_disconnect_signals(False) PM_Dialog.close(self) def _addGroupBoxes( self ): """ Add the Property Manager group boxes. """ self._pmGroupBox1 = PM_GroupBox( self, title = "Options" ) self._loadGroupBox1( self._pmGroupBox1 ) def _loadGroupBox1(self, pmGroupBox): """ Load widgets in group box. """ includeStrandsChoices = ["All strands in model", "Selected strands only"] self.includeStrandsComboBox = \ PM_ComboBox( pmGroupBox, label = "Include strands:", choices = includeStrandsChoices, setAsDefault = True) self.numberOfBasesLineEdit = \ PM_LineEdit( pmGroupBox, label = "Number of bases:", text = str(self.getNumberOfBases())) self.numberOfBasesLineEdit.setEnabled(False) self.viewDnaOrderFileButton = \ PM_PushButton( pmGroupBox, label = "", text = "View DNA Order File...", spanWidth = True) def _addWhatsThisText( self ): """ What's This text for widgets in the DNA Property Manager. """ pass def _addToolTipText(self): """ Tool Tip text for widgets in the DNA Property Manager. """ pass # Ask Bruce where this should live (i.e. class Part?) --Mark def getAllDnaStrands(self, selectedOnly = False): """ Returns a list of all the DNA strands in the current part, or only the selected strands if I{selectedOnly} is True. @param selectedOnly: If True, return only the selected DNA strands. @type selectedOnly: bool """ dnaStrandList = [] def func(node): if isinstance(node, DnaStrand): if selectedOnly: if node.picked: dnaStrandList.append(node) else: dnaStrandList.append(node) self.win.assy.part.topnode.apply2all(func) return dnaStrandList def getNumberOfBases(self, selectedOnly = False): """ Returns the number of bases count for all the DNA strands in the current part, or only the selected strand if I{selectedOnly} is True. @param selectedOnly: If True, return only the selected DNA strands. @type selectedOnly: bool """ dnaSequenceString = '' selectedOnly = self.includeStrandsComboBox.currentIndex() strandList = self.getAllDnaStrands(selectedOnly) for strand in strandList: strandSequenceString = str(strand.getStrandSequence()) dnaSequenceString += strandSequenceString return len(dnaSequenceString) def getDnaSequence(self, format = 'CSV'): """ Return the complete Dna sequence information string (i.e. all strand sequences) in the specified format. @return: The Dna sequence string @rtype: string """ if format == 'CSV': #comma separated values. separator = ',' dnaSequenceString = '' selectedOnly = self.includeStrandsComboBox.currentIndex() strandList = self.getAllDnaStrands(selectedOnly) for strand in strandList: dnaSequenceString = dnaSequenceString + strand.name + separator strandSequenceString = str(strand.getStrandSequence()) if strandSequenceString: strandSequenceString = strandSequenceString.upper() dnaSequenceString = dnaSequenceString + strandSequenceString dnaSequenceString = dnaSequenceString + "\n" return dnaSequenceString def viewDnaOrderFile(self, openFileInEditor = True): """ Opens a text editor and loads a temporary text file containing all the DNA strand names and their sequences in the current DNA object. It will look something like this: Strand1,ATCAGCTACGCATCGCT Strand2,TAGTCGATGCGTAGCGA ... Strandn, ... The user can then save the file to a permanent location using the text editor the file is loaded (and displayed) in. @see: Ui_DnaFlyout.orderDnaCommand @see: writeDnaOrderFile() @TODO: assy.getAllDnaObjects(). """ dnaSequence = self.getDnaSequence(format = 'CSV') if dnaSequence: tmpdir = find_or_make_Nanorex_subdir('temp') fileBaseName = 'DnaOrder' temporaryFile = os.path.join(tmpdir, "%s.csv" % fileBaseName) writeDnaOrderFile(temporaryFile, self.assy, dnaSequence) if openFileInEditor: open_file_in_editor(temporaryFile) def update_includeStrands(self, ignoreVal = 0): """ Slot method for "Include (strands)" combobox. """ idx = self.includeStrandsComboBox.currentIndex() includeType = ["model", "selection"] _numberOfBases = self.getNumberOfBases() self.numberOfBasesLineEdit.setText(str(_numberOfBases)) if _numberOfBases > 0: self.viewDnaOrderFileButton.setEnabled(True) msg = "Click on <b>View DNA Order File...</b> to preview a " \ "DNA order for all DNA strands in the current %s." \ % includeType[idx] else: self.viewDnaOrderFileButton.setEnabled(False) msg = "<font color=red>" \ "There are no DNA strands in the current %s." \ % includeType[idx] self.updateMessage(msg)
class CompareProteins_PropertyManager(Command_PropertyManager): """ The CompareProteins_PropertyManager class provides a Property Manager for the B{Compare Proteins} command on the Build Protein flyout toolbar. @ivar title: The title that appears in the property manager header. @type title: str @ivar pmName: The name of this property manager. This is used to set the name of the PM_Dialog object via setObjectName(). @type name: str @ivar iconPath: The relative path to the PNG file that contains a 22 x 22 icon image that appears in the PM header. @type iconPath: str @ivar proteinChunk1: The first currently selected protein to be compared. @type proteinChunk1: protein chunk @ivar proteinChunk2: The second currently selected protein to be compared. @type proteinChunk2: protein chunk """ title = "Compare Proteins" pmName = title iconPath = "ui/actions/Command Toolbar/BuildProtein/Compare.png" proteinChunk1 = None proteinChunk2 = None def __init__(self, command): """ Constructor for the property manager. """ self.threshold = 10.0 _superclass.__init__(self, command) self.showTopRowButtons(PM_DONE_BUTTON | PM_WHATS_THIS_BUTTON) return def connect_or_disconnect_signals(self, isConnect=True): if isConnect: change_connect = self.win.connect else: change_connect = self.win.disconnect change_connect(self.comparePushButton, SIGNAL("clicked()"), self._compareProteins) change_connect(self.thresholdDoubleSpinBox, SIGNAL("valueChanged(double)"), self._thresholdChanged) change_connect(self.hidePushButton, SIGNAL("clicked()"), self._hideDifferences) return def close(self): """ Closes the Property Manager. Overrides EditCommand_PM.close() """ env.history.statusbar_msg("") self._resetAminoAcids() _superclass.close(self) # Restore the original global display style. self.o.setGlobalDisplayStyle(self.originalDisplayStyle) return def show(self): """ Show the PM. Extends superclass method. @note: _update_UI_do_updates() gets called immediately after this and updates PM widgets with their correct values/settings. """ _superclass.show(self) env.history.statusbar_msg("") # Force the Global Display Style to "Protein" since this is the only way # to see comparisons. The global display style will be restored when leaving # this command (via self.close()). self.originalDisplayStyle = self.o.displayMode self.o.setGlobalDisplayStyle(diPROTEIN) return def _addGroupBoxes(self): """ Add the Property Manager group boxes. """ self._pmGroupBox1 = PM_GroupBox(self, title="Compare") self._loadGroupBox1(self._pmGroupBox1) return def _addWhatsThisText(self): """ What's This text for widgets in this Property Manager. """ pass def _addToolTipText(self): """ Tool Tip text for widgets in this Property Manager. """ pass def _loadGroupBox1(self, pmGroupBox): """ Load widgets in group box. """ self.structure1LineEdit = PM_LineEdit(pmGroupBox, label="First structure:", setAsDefault=False) self.structure1LineEdit.setEnabled(False) self.structure2LineEdit = PM_LineEdit(pmGroupBox, label="Second structure:", setAsDefault=False) self.structure2LineEdit.setEnabled(False) self.thresholdDoubleSpinBox = PM_DoubleSpinBox( pmGroupBox, label="Threshold:", value=self.threshold, setAsDefault=True, minimum=0.0, maximum=360.0, decimals=1, singleStep=30.0, suffix=" deg", spanWidth=False, ) self.comparePushButton = PM_PushButton(pmGroupBox, text="Compare", setAsDefault=True) self.hidePushButton = PM_PushButton(pmGroupBox, text="Hide differences", setAsDefault=True) return def _compareProteins(self): """ Slot for Compare button. Compares two selected proteins of the same length. Amino acids that differ greater than the "threshold" value are displayed in two colors (red for the first protein and yellow for the second protein) and are only visible when the two proteins are displayed in the reduced display style. """ from utilities.constants import red, orange, green, cyan if not self.proteinChunk1 or not self.proteinChunk2: return protein_1 = self.proteinChunk1.protein protein_2 = self.proteinChunk2.protein if protein_1 and protein_2: aa_list_1 = protein_1.get_amino_acids() aa_list_2 = protein_2.get_amino_acids() protein_1.collapse_all_rotamers() protein_2.collapse_all_rotamers() if len(aa_list_1) == len(aa_list_2): for aa1, aa2 in zip(aa_list_1, aa_list_2): aa1.color = None aa2.color = None # aa1.collapse() # aa2.collapse() if aa1.get_one_letter_code() != aa2.get_one_letter_code(): aa1.set_color(red) aa1.expand() aa2.set_color(yellow) aa2.expand() else: max = 0.0 for chi in range(0, 3): angle1 = aa1.get_chi_angle(chi) angle2 = aa2.get_chi_angle(chi) if angle1 and angle2: if angle1 < 0.0: angle1 += 360.0 if angle2 < 0.0: angle2 += 360.0 diff = abs(angle1 - angle2) if diff > max: max = diff if max >= self.threshold: # This be a parameter. aa1.set_color(green) aa1.expand() aa2.set_color(cyan) aa2.expand() self.win.glpane.gl_update() else: msg = "The lengths of compared proteins are not equal." self.updateMessage(msg) env.history.redmsg(msg) return def _hideDifferences(self): """ Slot for the "Hide differences" button. Hides amino acids that differ greater than the "threshold" value. @warning: Untested. Code looks suspicious. """ if not self.proteinChunk1 or not self.proteinChunk2: return protein_1 = self.proteinChunk1.protein protein_2 = self.proteinChunk2.protein if protein_1 and protein_2: aa_list_1 = protein_1.get_amino_acids() aa_list_2 = protein_2.get_amino_acids() if len(aa_list_1) == len(aa_list_2): protein_1.collapse_all_rotamers() # @@@ protein_2.collapse_all_rotamers() # @@@ for aa1, aa2 in zip(aa_list_1, aa_list_2): aa1.color = None aa2.color = None aa1.collapse() aa2.collapse() self.win.glpane.gl_update() return def _thresholdChanged(self, value): """ Slot for Threshold spinbox. """ self.threshold = value self._compareProteins() return def _resetAminoAcids(self): """ Resets the color and collapse all amino acids of all proteins. """ proteinChunkList = getAllProteinChunksInPart(self.win.assy) for proteinChunk in proteinChunkList: proteinChunk.protein.collapse_all_rotamers() aa_list = proteinChunk.protein.get_amino_acids() for aa in aa_list: aa.color = None aa.collapse() self.win.glpane.gl_update() return def _update_UI_do_updates(self): """ Overrides superclass method. @see: Command_PropertyManager._update_UI_do_updates() """ self.proteinChunk1 = None self.proteinChunk2 = None self.comparePushButton.setEnabled(False) self.hidePushButton.setEnabled(False) selectedProteinList = self.win.assy.getSelectedProteinChunks() if len(selectedProteinList) == 0: self.structure1LineEdit.setText("") self.structure2LineEdit.setText("") msg = ( "Select two structures of the same length in the graphics area, " "then click the <b>Compare</b> button to compare them." ) elif len(selectedProteinList) == 1: self.proteinChunk1 = selectedProteinList[0] aa1_count = " (%d)" % self.proteinChunk1.protein.count_amino_acids() self.structure1LineEdit.setText(self.proteinChunk1.name + aa1_count) self.structure2LineEdit.setText("") msg = ( "Select one more structure in the graphics area that is the same " "length as <b>" + self.proteinChunk1.name + "</b>. " "Then click the <b>Compare</b> button to compare them." ) elif len(selectedProteinList) == 2: self.proteinChunk1 = selectedProteinList[0] aa1_count = " (%d)" % self.proteinChunk1.protein.count_amino_acids() self.structure1LineEdit.setText(self.proteinChunk1.name + aa1_count) self.proteinChunk2 = selectedProteinList[1] aa2_count = " (%d)" % self.proteinChunk2.protein.count_amino_acids() self.structure2LineEdit.setText(self.proteinChunk2.name + aa2_count) if aa1_count == aa2_count: self.comparePushButton.setEnabled(True) self.hidePushButton.setEnabled(True) msg = "Click the <b>Compare</b> button to compare the two selected structures." else: msg = "<b>%s</b> and <b>%s</b> are not the same length." % ( self.proteinChunk1.name, self.proteinChunk2.name, ) msg = redmsg(msg) else: self.structure1LineEdit.setText("") self.structure2LineEdit.setText("") msg = redmsg("Too many proteins selected.") self.updateMessage(msg) env.history.redmsg(msg) return
class InsertNanotube_PropertyManager( DnaOrCnt_PropertyManager): """ The InsertNanotube_PropertyManager class provides a Property Manager for the B{Build > Nanotube > CNT} command. @ivar title: The title that appears in the property manager header. @type title: str @ivar pmName: The name of this property manager. This is used to set the name of the PM_Dialog object via setObjectName(). @type name: str @ivar iconPath: The relative path to the PNG file that contains a 22 x 22 icon image that appears in the PM header. @type iconPath: str """ title = "Insert Nanotube" pmName = title iconPath = "ui/actions/Tools/Build Structures/InsertNanotube.png" def __init__( self, win, editCommand ): """ Constructor for the Nanotube property manager. """ self.endPoint1 = None self.endPoint2 = None self.nanotube = Nanotube() # A 5x5 CNT. _superclass.__init__( self, win, editCommand) self.showTopRowButtons( PM_DONE_BUTTON | \ PM_CANCEL_BUTTON | \ PM_WHATS_THIS_BUTTON) def connect_or_disconnect_signals(self, isConnect): """ Connect or disconnect widget signals sent to their slot methods. This can be overridden in subclasses. By default it does nothing. @param isConnect: If True the widget will send the signals to the slot method. @type isConnect: boolean """ if isConnect: change_connect = self.win.connect else: change_connect = self.win.disconnect change_connect( self.ntTypeComboBox, SIGNAL("currentIndexChanged(const QString&)"), self._ntTypeComboBoxChanged ) change_connect(self.chiralityNSpinBox, SIGNAL("valueChanged(int)"), self._chiralityFixup) change_connect(self.chiralityMSpinBox, SIGNAL("valueChanged(int)"), self._chiralityFixup) change_connect(self.endingsComboBox, SIGNAL("currentIndexChanged(const QString&)"), self._endingsComboBoxChanged ) # This spin box is currently hidden. change_connect(self.bondLengthDoubleSpinBox, SIGNAL("valueChanged(double)"), self._bondLengthChanged) change_connect(self.showCursorTextCheckBox, SIGNAL('stateChanged(int)'), self._update_state_of_cursorTextGroupBox) def ok_btn_clicked(self): """ Slot for the OK button """ if self.editCommand: self.editCommand.preview_or_finalize_structure(previewing = False) ##env.history.message(self.editCommand.logMessage) self.win.toolsDone() def cancel_btn_clicked(self): """ Slot for the Cancel button. """ if self.editCommand: self.editCommand.cancelStructure() self.win.toolsCancel() def _update_widgets_in_PM_before_show(self): """ Update various widgets in this Property manager. Overrides MotorPropertyManager._update_widgets_in_PM_before_show. The various widgets , (e.g. spinboxes) will get values from the structure for which this propMgr is constructed for (self.editcCntroller.struct) @see: MotorPropertyManager._update_widgets_in_PM_before_show @see: self.show where it is called. """ pass def getFlyoutActionList(self): """ Returns custom actionlist that will be used in a specific mode or editing a feature etc Example: while in movie mode, the _createFlyoutToolBar method calls this. """ #'allActionsList' returns all actions in the flyout toolbar #including the subcontrolArea actions allActionsList = [] #Action List for subcontrol Area buttons. #In this mode there is really no subcontrol area. #We will treat subcontrol area same as 'command area' #(subcontrol area buttons will have an empty list as their command area #list). We will set the Comamnd Area palette background color to the #subcontrol area. subControlAreaActionList =[] self.exitEditCommandAction.setChecked(True) subControlAreaActionList.append(self.exitEditCommandAction) separator = QAction(self.w) separator.setSeparator(True) subControlAreaActionList.append(separator) allActionsList.extend(subControlAreaActionList) #Empty actionlist for the 'Command Area' commandActionLists = [] #Append empty 'lists' in 'commandActionLists equal to the #number of actions in subControlArea for i in range(len(subControlAreaActionList)): lst = [] commandActionLists.append(lst) params = (subControlAreaActionList, commandActionLists, allActionsList) return params def _addGroupBoxes( self ): """ Add the Insert Nanotube Property Manager group boxes. """ self._pmGroupBox1 = PM_GroupBox( self, title = "Endpoints" ) self._loadGroupBox1( self._pmGroupBox1 ) self._pmGroupBox1.hide() self._pmGroupBox2 = PM_GroupBox( self, title = "Parameters" ) self._loadGroupBox2( self._pmGroupBox2 ) self._displayOptionsGroupBox = PM_GroupBox( self, title = "Display Options" ) self._loadDisplayOptionsGroupBox( self._displayOptionsGroupBox ) self._pmGroupBox3 = PM_GroupBox( self, title = "Nanotube Distortion" ) self._loadGroupBox3( self._pmGroupBox3 ) self._pmGroupBox3.hide() #@ Temporary. self._pmGroupBox4 = PM_GroupBox( self, title = "Multi-Walled CNTs" ) self._loadGroupBox4( self._pmGroupBox4 ) self._pmGroupBox4.hide() #@ Temporary. self._pmGroupBox5 = PM_GroupBox( self, title = "Advanced Options" ) self._loadGroupBox5( self._pmGroupBox5 ) self._pmGroupBox5.hide() #@ Temporary. def _loadGroupBox1(self, pmGroupBox): """ Load widgets in group box 1. """ #Following toolbutton facilitates entering a temporary NanotubeLineMode #to create a CNT using endpoints of the specified line. self.specifyCntLineButton = PM_ToolButton( pmGroupBox, text = "Specify Endpoints", iconPath = "ui/actions/Properties Manager/Pencil.png", spanWidth = True ) self.specifyCntLineButton.setCheckable(True) self.specifyCntLineButton.setAutoRaise(True) self.specifyCntLineButton.setToolButtonStyle( Qt.ToolButtonTextBesideIcon) #EndPoint1 and endPoint2 coordinates. These widgets are hidden # as of 2007- 12 - 05 self._endPoint1SpinBoxes = PM_CoordinateSpinBoxes(pmGroupBox, label = "End Point 1") self.x1SpinBox = self._endPoint1SpinBoxes.xSpinBox self.y1SpinBox = self._endPoint1SpinBoxes.ySpinBox self.z1SpinBox = self._endPoint1SpinBoxes.zSpinBox self._endPoint2SpinBoxes = PM_CoordinateSpinBoxes(pmGroupBox, label = "End Point 2") self.x2SpinBox = self._endPoint2SpinBoxes.xSpinBox self.y2SpinBox = self._endPoint2SpinBoxes.ySpinBox self.z2SpinBox = self._endPoint2SpinBoxes.zSpinBox self._endPoint1SpinBoxes.hide() self._endPoint2SpinBoxes.hide() def _loadGroupBox2(self, pmGroupBox): """ Load widgets in group box 2. """ _ntTypeChoices = ['Carbon', 'Boron Nitride'] self.ntTypeComboBox = \ PM_ComboBox( pmGroupBox, label = "Type:", choices = _ntTypeChoices, setAsDefault = True) self.ntRiseDoubleSpinBox = \ PM_DoubleSpinBox( pmGroupBox, label = "Rise:", value = self.nanotube.getRise(), setAsDefault = True, minimum = 2.0, maximum = 4.0, decimals = 3, singleStep = 0.01 ) self.ntRiseDoubleSpinBox.hide() # Nanotube Length self.ntLengthLineEdit = \ PM_LineEdit( pmGroupBox, label = "Nanotube Length: ", text = "0.0 Angstroms", setAsDefault = False) self.ntLengthLineEdit.setDisabled(True) self.ntLengthLineEdit.hide() # Nanotube diameter self.ntDiameterLineEdit = \ PM_LineEdit( pmGroupBox, label = "Diameter: ", setAsDefault = False) self.ntDiameterLineEdit.setDisabled(True) self.updateNanotubeDiameter() self.chiralityNSpinBox = \ PM_SpinBox( pmGroupBox, label = "Chirality (n):", value = self.nanotube.getChiralityN(), minimum = 2, maximum = 100, setAsDefault = True ) self.chiralityMSpinBox = \ PM_SpinBox( pmGroupBox, label = "Chirality (m):", value = self.nanotube.getChiralityM(), minimum = 0, maximum = 100, setAsDefault = True ) # How about having user prefs for CNT and BNNT bond lengths? # I'm guessing that if the user wants to set these values, they will # do it once and would like those bond length values persist forever. # Need to discuss with others to determine if this spinbox comes out. # --Mark 2008-03-29 self.bondLengthDoubleSpinBox = \ PM_DoubleSpinBox( pmGroupBox, label = "Bond length:", value = self.nanotube.getBondLength(), setAsDefault = True, minimum = 1.0, maximum = 3.0, singleStep = 0.1, decimals = 3, suffix = " Angstroms" ) #self.bondLengthDoubleSpinBox.hide() endingChoices = ["Hydrogen", "None"] # Removed:, "Nitrogen"] self.endingsComboBox= \ PM_ComboBox( pmGroupBox, label = "Endings:", choices = endingChoices, index = 0, setAsDefault = True, spanWidth = False ) def _loadGroupBox3(self, inPmGroupBox): """ Load widgets in group box 3. """ self.zDistortionDoubleSpinBox = \ PM_DoubleSpinBox( inPmGroupBox, label = "Z-distortion:", value = 0.0, setAsDefault = True, minimum = 0.0, maximum = 10.0, singleStep = 0.1, decimals = 3, suffix = " Angstroms" ) self.xyDistortionDoubleSpinBox = \ PM_DoubleSpinBox( inPmGroupBox, label = "XY-distortion:", value = 0.0, setAsDefault = True, minimum = 0.0, maximum = 2.0, singleStep = 0.1, decimals = 3, suffix = " Angstroms" ) self.twistSpinBox = \ PM_SpinBox( inPmGroupBox, label = "Twist:", value = 0, setAsDefault = True, minimum = 0, maximum = 100, # What should maximum be? suffix = " deg/A" ) self.bendSpinBox = \ PM_SpinBox( inPmGroupBox, label = "Bend:", value = 0, setAsDefault = True, minimum = 0, maximum = 360, suffix = " deg" ) def _loadGroupBox4(self, inPmGroupBox): """ Load widgets in group box 4. """ # "Number of Nanotubes" SpinBox self.mwntCountSpinBox = \ PM_SpinBox( inPmGroupBox, label = "Number:", value = 1, setAsDefault = True, minimum = 1, maximum = 10, suffix = " nanotubes" ) self.mwntCountSpinBox.setSpecialValueText("SWNT") # "Spacing" lineedit. self.mwntSpacingDoubleSpinBox = \ PM_DoubleSpinBox( inPmGroupBox, label = "Spacing:", value = 2.46, setAsDefault = True, minimum = 1.0, maximum = 10.0, singleStep = 0.1, decimals = 3, suffix = " Angstroms" ) def _loadGroupBox5(self, pmGroupBox): """ Load widgets in group box 5. """ self._rubberbandLineGroupBox = PM_GroupBox( pmGroupBox, title = 'Rubber band Line:') ntLineChoices = ['Ladder'] self.ntRubberBandLineDisplayComboBox = \ PM_ComboBox( self._rubberbandLineGroupBox , label = " Display as:", choices = ntLineChoices, setAsDefault = True) self.lineSnapCheckBox = \ PM_CheckBox(self._rubberbandLineGroupBox , text = 'Enable line snap' , widgetColumn = 1, state = Qt.Checked ) def _connect_showCursorTextCheckBox(self): """ Connect the show cursor text checkbox with user prefs_key. Overrides DnaOrCnt_PropertyManager._connect_showCursorTextCheckBox """ connect_checkbox_with_boolean_pref( self.showCursorTextCheckBox , insertNanotubeEditCommand_showCursorTextCheckBox_prefs_key ) def _params_for_creating_cursorTextCheckBoxes(self): """ Returns params needed to create various cursor text checkboxes connected to prefs_keys that allow custom cursor texts. @return: A list containing tuples in the following format: ('checkBoxTextString' , preference_key). PM_PrefsCheckBoxes uses this data to create checkboxes with the the given names and connects them to the provided preference keys. (Note that PM_PrefsCheckBoxes puts thes within a GroupBox) @rtype: list @see: PM_PrefsCheckBoxes @see: self._loadDisplayOptionsGroupBox where this list is used. @see: Superclass method which is overridden here -- DnaOrCnt_PropertyManager._params_for_creating_cursorTextCheckBoxes() """ params = \ [ #Format: (" checkbox text", prefs_key) ("Nanotube length", insertNanotubeEditCommand_cursorTextCheckBox_length_prefs_key ), ("Angle", insertNanotubeEditCommand_cursorTextCheckBox_angle_prefs_key ) ] return params def _addToolTipText(self): """ Tool Tip text for widgets in the Insert Nanotube Property Manager. """ pass def _setEndPoints(self): """ Set the two endpoints of the nanotube using the values from the X, Y, Z coordinate spinboxes in the property manager. @note: The group box containing the 2 sets of XYZ spin boxes are currently hidden. """ # First endpoint (origin) of nanotube x1 = self.x1SpinBox.value() y1 = self.y1SpinBox.value() z1 = self.z1SpinBox.value() # Second endpoint (direction vector/axis) of nanotube. x2 = self.x2SpinBox.value() y2 = self.y2SpinBox.value() z2 = self.z2SpinBox.value() if not self.endPoint1: self.endPoint1 = V(x1, y1, z1) if not self.endPoint2: self.endPoint2 = V(x2, y2, z2) self.nanotube.setEndPoints(self.endPoint1, self.endPoint2) # Need arg "recompute=True", which will recompute the second # endpoint (endPoint2) using the nanotube rise. def getParameters(self): """ Return the parameters from this property manager to be used to create the nanotube. @return: A nanotube instance with its attrs set to the current parameters in the property manager. @rtype: L{Nanotube} @see: L{InsertNanotube_EditCommand._gatherParameters} where this is used """ self._setEndPoints() return (self.nanotube) def _ntTypeComboBoxChanged( self, type ): """ Slot for the Type combobox. It is called whenever the Type choice is changed. @param inIndex: The new index. @type inIndex: int """ self.nanotube.setType(str(type)) print "Bond Length =", self.nanotube.getBondLength() self.bondLengthDoubleSpinBox.setValue(self.nanotube.getBondLength()) #self.bondLengthDoubleSpinBox.setValue(ntBondLengths[inIndex]) def _bondLengthChanged(self, bondLength): """ Slot for the B{Bond Length} spinbox. """ self.nanotube.setBondLength(bondLength) self.updateNanotubeDiameter() return def _chiralityFixup(self, spinBoxValueJunk = None): """ Slot for several validators for different parameters. This gets called whenever the user changes the n, m chirality values. @param spinBoxValueJunk: This is the Spinbox value from the valueChanged signal. It is not used. We just want to know that the spinbox value has changed. @type spinBoxValueJunk: double or None """ _n, _m = self.nanotube.setChirality(self.chiralityNSpinBox.value(), self.chiralityMSpinBox.value()) #self.n, self.m = self.nanotube.getChirality() self.connect_or_disconnect_signals(isConnect = False) self.chiralityNSpinBox.setValue(_n) self.chiralityMSpinBox.setValue(_m) self.connect_or_disconnect_signals(isConnect = True) self.updateNanotubeDiameter() def updateNanotubeDiameter(self): """ Update the nanotube Diameter lineEdit widget. """ diameterText = "%-7.4f Angstroms" % (self.nanotube.getDiameter()) self.ntDiameterLineEdit.setText(diameterText) # ntRiseDoubleSpinBox is currently hidden. self.ntRiseDoubleSpinBox.setValue(self.nanotube.getRise()) def _endingsComboBoxChanged(self, endings): """ Slot for the B{Ending} combobox. @param endings: The option's text. @type endings: string """ self.nanotube.setEndings(str(endings)) return def _addWhatsThisText(self): """ What's This text for widgets in this Property Manager. """ whatsThis_InsertNanotube_PropertyManager(self) return
class DnaStrand_PropertyManager(DnaOrCnt_PropertyManager): """ The DnaStrand_PropertyManager class provides a Property Manager for the DnaStrand_EditCommand. @ivar title: The title that appears in the property manager header. @type title: str @ivar pmName: The name of this property manager. This is used to set the name of the PM_Dialog object via setObjectName(). @type name: str @ivar iconPath: The relative path to the PNG file that contains a 22 x 22 icon image that appears in the PM header. @type iconPath: str """ title = "DnaStrand Properties" iconPath = "ui/actions/Properties Manager/Strand.png" def __init__(self, command): """ Constructor for the Build DNA property manager. """ self.sequenceEditor = None self._numberOfBases = 0 self._conformation = 'B-DNA' self.dnaModel = 'PAM3' _superclass.__init__(self, command) self.showTopRowButtons( PM_DONE_BUTTON | \ PM_WHATS_THIS_BUTTON) return def _addGroupBoxes(self): """ Add group boxes to this PM. """ self._pmGroupBox1 = PM_GroupBox(self, title="Parameters") self._loadGroupBox1(self._pmGroupBox1) self._displayOptionsGroupBox = PM_GroupBox(self, title="Display Options") self._loadDisplayOptionsGroupBox(self._displayOptionsGroupBox) #Sequence Editor. This is NOT a groupbox, needs cleanup. Doing it here #so that the sequence editor gets connected! Perhaps #superclass should define _loadAdditionalWidgets. -- Ninad2008-10-03 self._loadSequenceEditor() return def _loadGroupBox1(self, pmGroupBox): """ Load widgets in group box 1. """ self.nameLineEdit = PM_LineEdit(pmGroupBox, label="Name:", text="", setAsDefault=False) self.numberOfBasesSpinBox = \ PM_SpinBox( pmGroupBox, label = "Number of bases:", value = self._numberOfBases, setAsDefault = False, minimum = 2, maximum = 10000 ) self.disableStructHighlightingCheckbox = \ PM_CheckBox( pmGroupBox, text = "Don't highlight while editing DNA", widgetColumn = 0, state = Qt.Unchecked, setAsDefault = True, spanWidth = True ) #As of 2008-03-31, the properties such as number of bases will be #editable only by using the resize handles. self.numberOfBasesSpinBox.setEnabled(False) return def _loadSequenceEditor(self): """ Temporary code that shows the Sequence editor ..a doc widget docked at the bottom of the mainwindow. The implementation is going to change before 'rattleSnake' product release. As of 2007-11-20: This feature (sequence editor) is waiting for the ongoing dna model work to complete. """ self.sequenceEditor = self.win.createDnaSequenceEditorIfNeeded() self.sequenceEditor.hide() return def _loadDisplayOptionsGroupBox(self, pmGroupBox): """ Overrides superclass method. Also loads the color chooser widget. """ self._loadColorChooser(pmGroupBox) _superclass._loadDisplayOptionsGroupBox(self, pmGroupBox) return def _connect_showCursorTextCheckBox(self): """ Connect the show cursor text checkbox with user prefs_key. Overrides DnaOrCnt_PropertyManager._connect_showCursorTextCheckBox """ connect_checkbox_with_boolean_pref( self.showCursorTextCheckBox, dnaStrandEditCommand_showCursorTextCheckBox_prefs_key) return def _params_for_creating_cursorTextCheckBoxes(self): """ Returns params needed to create various cursor text checkboxes connected to prefs_keys that allow custom cursor texts. @return: A list containing tuples in the following format: ('checkBoxTextString' , preference_key). PM_PrefsCheckBoxes uses this data to create checkboxes with the the given names and connects them to the provided preference keys. (Note that PM_PrefsCheckBoxes puts thes within a GroupBox) @rtype: list @see: PM_PrefsCheckBoxes @see: self._loadDisplayOptionsGroupBox where this list is used. @see: Superclass method which is overridden here -- DnaOrCnt_PropertyManager._params_for_creating_cursorTextCheckBoxes() """ params = \ [ #Format: (" checkbox text", prefs_key) ("Number of bases", dnaStrandEditCommand_cursorTextCheckBox_numberOfBases_prefs_key), ("Number of bases to be changed", dnaStrandEditCommand_cursorTextCheckBox_changedBases_prefs_key) ] return params def getParameters(self): name = self.nameLineEdit.text() numberOfBases = self.numberOfBasesSpinBox.value() dnaForm = self._conformation dnaModel = self.dnaModel color = self._colorChooser.getColor() return (numberOfBases, dnaForm, dnaModel, color, name) def setParameters(self, params): """ This is usually called when you are editing an existing structure. It also gets called when selecting a new strand (within this command). Some property manager ui elements then display the information obtained from the object being edited. TODO: - Make this a EditCommand_PM API method? - See also the routines GraphicsMode.setParams or object.setProps ..better to name them all in one style? """ numberOfBases, \ dnaForm, \ dnaModel, \ color, \ name = params if numberOfBases is not None: self.numberOfBasesSpinBox.setValue(numberOfBases) if dnaForm is not None: self._conformation = dnaForm if dnaModel is not None: self.dnaModel = dnaModel if color is not None: self._colorChooser.setColor(color) if name: # Minimal test. Should add a validator. --Mark 2008-12-16 self.nameLineEdit.setText(name) # This gets called when we enter the command *and* when selecting a new # strand. In either case, we must update the sequence in the sequenece # editor. Fixes bug 2951. --Mark 2008-12-16 if self.command and self.command.hasValidStructure(): #print "setParameters(): loading sequence in sequence editor for ", name self.updateSequence(strand=self.command.struct) return def connect_or_disconnect_signals(self, isConnect): """ Connect or disconnect widget signals sent to their slot methods. This can be overridden in subclasses. By default it does nothing. @param isConnect: If True the widget will send the signals to the slot method. @type isConnect: boolean """ #TODO: This is a temporary fix for a bug. When you invoke a temporary # mode Entering such a temporary mode keeps the signals of #PM from the previous mode connected ( #but while exiting that temporary mode and reentering the #previous mode, it atucally reconnects the signal! This gives rise to #lots of bugs. This needs more general fix in Temporary mode API. # -- Ninad 2008-01-09 (similar comment exists in MovePropertyManager.py if isConnect and self.isAlreadyConnected: if debug_flags.atom_debug: print_compact_stack("warning: attempt to connect widgets"\ "in this PM that are already connected." ) return if not isConnect and self.isAlreadyDisconnected: if debug_flags.atom_debug: print_compact_stack("warning: attempt to disconnect widgets"\ "in this PM that are already disconnected.") return self.isAlreadyConnected = isConnect self.isAlreadyDisconnected = not isConnect if isConnect: change_connect = self.win.connect else: change_connect = self.win.disconnect if self.sequenceEditor: self.sequenceEditor.connect_or_disconnect_signals(isConnect) _superclass.connect_or_disconnect_signals(self, isConnect) change_connect(self.disableStructHighlightingCheckbox, SIGNAL('stateChanged(int)'), self.change_struct_highlightPolicy) change_connect(self.showCursorTextCheckBox, SIGNAL('stateChanged(int)'), self._update_state_of_cursorTextGroupBox) change_connect(self.nameLineEdit, SIGNAL("editingFinished()"), self._nameChanged) return def _update_UI_do_updates(self): """ @see: Command_PropertyManager. _update_UI_do_updates() @see: DnaStrand_EditCommand.command_update_UI() @see: DnaStrand_EditCommand.hasResizableStructure() """ if not self.command.hasValidStructure(): print "DnaStrand not a valid structure." self._pmGroupBox1.setEnabled(False) self._displayOptionsGroupBox.setEnabled(False) self.sequenceEditor.updateSequence(strand=" ") self.sequenceEditor.setEnabled(False) self.nameLineEdit.setText("") self.numberOfBasesSpinBox.setValue(0) return else: self._pmGroupBox1.setEnabled(True) self._displayOptionsGroupBox.setEnabled(True) self.sequenceEditor.setEnabled(True) isStructResizable, why_not = self.command.hasResizableStructure() if not isStructResizable: #disable all widgets if self._pmGroupBox1.isEnabled(): self._pmGroupBox1.setEnabled(False) msg1 = ("Attention: ") % (self.command.struct.name) msg2 = redmsg("DnaStrand <b>%s</b> is not resizable. Reason: %s" % \ (self.command.struct.name, why_not)) self.updateMessage(msg1 + msg2) else: if not self._pmGroupBox1.isEnabled(): self._pmGroupBox1.setEnabled(True) msg1 = ("Editing <b>%s</b>. ") % (self.command.struct.name) msg2 = "Use resize handles to resize the strand. "\ "Use the <i>Sequence Editor</i> to edit the sequence." self.updateMessage(msg1 + msg2) return def close(self): """ Close this property manager. Also sets the name of the self.command's structure to the one displayed in the line edit field. @see self.show() @see: DnaSegment_EditCommand.setStructureName """ if self.command is not None: name = str(self.nameLineEdit.text()) self.command.setStructureName(name) if self.sequenceEditor: self.sequenceEditor.close() _superclass.close(self) return def updateSequence(self, strand=None): """ Public method provided for convenience. If any callers outside of this command need to update the sequence in the sequence editor, they can simply do DnaStrand_ProprtyManager.updateSequence() rather than DnaStrand_ProprtyManager.sequenceEditor.updateSequence() @see: Ui_DnaSequenceEditor.updateSequence() """ if self.sequenceEditor: self.sequenceEditor.updateSequence(strand=strand) return def change_struct_highlightPolicy(self, checkedState=False): """ Change the 'highlight policy' of the structure being edited (i.e. self.command.struct) . @param checkedState: The checked state of the checkbox that says 'Don't highlight while editing DNA'. So, it its True, the structure being edited won't get highlighted. @see: DnaStrand.setHighlightPolicy for more comments """ if self.command and self.command.hasValidStructure(): highlight = not checkedState self.command.struct.setHighlightPolicy(highlight=highlight) return def _addWhatsThisText(self): """ Add what's this text. Abstract method. """ pass def _nameChanged(self): # Added by Mark. 2008-12-16 """ Slot for "Name" field. Changes the name of the strand if the user types in a new name. @warning: this lacks a validator. User can type in a name with invalid characters. """ if not self.command.hasValidStructure(): return name = str(self.nameLineEdit.text()) if not name: # Minimal test. Should add a validator. Ask Bruce for example validator code somewhere. --Mark 2008-12-16 if self.command.hasValidStructure(): self.nameLineEdit.setText(self.command.getStructureName()) return self.command.setStructureName(name) self._update_UI_do_updates() # Updates the message box. return
class DnaStrand_PropertyManager(DnaOrCnt_PropertyManager): """ The DnaStrand_PropertyManager class provides a Property Manager for the DnaStrand_EditCommand. @ivar title: The title that appears in the property manager header. @type title: str @ivar pmName: The name of this property manager. This is used to set the name of the PM_Dialog object via setObjectName(). @type name: str @ivar iconPath: The relative path to the PNG file that contains a 22 x 22 icon image that appears in the PM header. @type iconPath: str """ title = "DnaStrand Properties" pmName = title iconPath = "ui/actions/Properties Manager/Strand.png" def __init__(self, win, editCommand): """ Constructor for the Build DNA property manager. """ #For model changed signal self.previousSelectionParams = None #see self.connect_or_disconnect_signals for comment about this flag self.isAlreadyConnected = False self.isAlreadyDisconnected = False self.sequenceEditor = None self._numberOfBases = 0 self._conformation = 'B-DNA' self.duplexRise = 3.18 self.basesPerTurn = 10 self.dnaModel = 'PAM3' _superclass.__init__(self, win, editCommand) self.showTopRowButtons( PM_DONE_BUTTON | \ PM_WHATS_THIS_BUTTON) self._loadSequenceEditor() msg = "Use resize handles to resize the strand. Use sequence editor"\ "to assign a new sequence or the current one to a file." self.updateMessage(msg) def _addGroupBoxes(self): """ Add the DNA Property Manager group boxes. """ self._pmGroupBox1 = PM_GroupBox(self, title="Parameters") self._loadGroupBox1(self._pmGroupBox1) self._displayOptionsGroupBox = PM_GroupBox(self, title="Display Options") self._loadDisplayOptionsGroupBox(self._displayOptionsGroupBox) def _loadGroupBox1(self, pmGroupBox): """ Load widgets in group box 4. """ self.nameLineEdit = PM_LineEdit(pmGroupBox, label="Strand name:", text="", setAsDefault=False) self.numberOfBasesSpinBox = \ PM_SpinBox( pmGroupBox, label = "Number of bases:", value = self._numberOfBases, setAsDefault = False, minimum = 2, maximum = 10000 ) self.basesPerTurnDoubleSpinBox = \ PM_DoubleSpinBox( pmGroupBox, label = "Bases per turn:", value = self.basesPerTurn, setAsDefault = True, minimum = 8.0, maximum = 20.0, decimals = 2, singleStep = 0.1 ) self.duplexRiseDoubleSpinBox = \ PM_DoubleSpinBox( pmGroupBox, label = "Rise:", value = self.duplexRise, setAsDefault = True, minimum = 2.0, maximum = 4.0, decimals = 3, singleStep = 0.01 ) self.disableStructHighlightingCheckbox = \ PM_CheckBox( pmGroupBox, text = "Don't highlight while editing DNA", widgetColumn = 0, state = Qt.Unchecked, setAsDefault = True, spanWidth = True ) #As of 2008-03-31, the properties such as number of bases will be #editable only by using the resize handles. post FNANO we will support #the self.numberOfBasesSpinBox.setEnabled(False) self.basesPerTurnDoubleSpinBox.setEnabled(False) self.duplexRiseDoubleSpinBox.setEnabled(False) def _loadSequenceEditor(self): """ Temporary code that shows the Sequence editor ..a doc widget docked at the bottom of the mainwindow. The implementation is going to change before 'rattleSnake' product release. As of 2007-11-20: This feature (sequence editor) is waiting for the ongoing dna model work to complete. """ self.sequenceEditor = self.win.createDnaSequenceEditorIfNeeded() self.sequenceEditor.hide() def _loadDisplayOptionsGroupBox(self, pmGroupBox): """ Overrides superclass method. Also loads the color chooser widget. """ self._loadColorChooser(pmGroupBox) _superclass._loadDisplayOptionsGroupBox(self, pmGroupBox) def _connect_showCursorTextCheckBox(self): """ Connect the show cursor text checkbox with user prefs_key. Overrides DnaOrCnt_PropertyManager._connect_showCursorTextCheckBox """ connect_checkbox_with_boolean_pref( self.showCursorTextCheckBox, dnaStrandEditCommand_showCursorTextCheckBox_prefs_key) def _params_for_creating_cursorTextCheckBoxes(self): """ Returns params needed to create various cursor text checkboxes connected to prefs_keys that allow custom cursor texts. @return: A list containing tuples in the following format: ('checkBoxTextString' , preference_key). PM_PrefsCheckBoxes uses this data to create checkboxes with the the given names and connects them to the provided preference keys. (Note that PM_PrefsCheckBoxes puts thes within a GroupBox) @rtype: list @see: PM_PrefsCheckBoxes @see: self._loadDisplayOptionsGroupBox where this list is used. @see: Superclass method which is overridden here -- DnaOrCnt_PropertyManager._params_for_creating_cursorTextCheckBoxes() """ params = \ [ #Format: (" checkbox text", prefs_key) ("Number of bases", dnaStrandEditCommand_cursorTextCheckBox_numberOfBases_prefs_key), ("Number of bases to be changed", dnaStrandEditCommand_cursorTextCheckBox_changedBases_prefs_key) ] return params def getParameters(self): numberOfBases = self.numberOfBasesSpinBox.value() dnaForm = self._conformation dnaModel = self.dnaModel basesPerTurn = self.basesPerTurn duplexRise = self.duplexRise color = self._colorChooser.getColor() return (numberOfBases, dnaForm, dnaModel, basesPerTurn, duplexRise, color) def setParameters(self, params): """ This is usually called when you are editing an existing structure. Some property manager ui elements then display the information obtained from the object being edited. TODO: - Make this a EditCommand_PM API method? - See also the routines GraphicsMode.setParams or object.setProps ..better to name them all in one style? """ #Set the duplex rise and bases per turn spinbox values. numberOfBases, \ dnaForm, \ dnaModel, \ basesPerTurn, \ duplexRise, \ color = params if numberOfBases is not None: self.numberOfBasesSpinBox.setValue(numberOfBases) if dnaForm is not None: self._conformation = dnaForm if dnaModel is not None: self.dnaModel = dnaModel if duplexRise is not None: self.duplexRiseDoubleSpinBox.setValue(duplexRise) if basesPerTurn is not None: self.basesPerTurnDoubleSpinBox.setValue(basesPerTurn) if color is not None: self._colorChooser.setColor(color) def connect_or_disconnect_signals(self, isConnect): """ Connect or disconnect widget signals sent to their slot methods. This can be overridden in subclasses. By default it does nothing. @param isConnect: If True the widget will send the signals to the slot method. @type isConnect: boolean """ #TODO: This is a temporary fix for a bug. When you invoke a temporary # mode Entering such a temporary mode keeps the signals of #PM from the previous mode connected ( #but while exiting that temporary mode and reentering the #previous mode, it atucally reconnects the signal! This gives rise to #lots of bugs. This needs more general fix in Temporary mode API. # -- Ninad 2008-01-09 (similar comment exists in MovePropertyManager.py if isConnect and self.isAlreadyConnected: if debug_flags.atom_debug: print_compact_stack("warning: attempt to connect widgets"\ "in this PM that are already connected." ) return if not isConnect and self.isAlreadyDisconnected: if debug_flags.atom_debug: print_compact_stack("warning: attempt to disconnect widgets"\ "in this PM that are already disconnected.") return self.isAlreadyConnected = isConnect self.isAlreadyDisconnected = not isConnect if isConnect: change_connect = self.win.connect else: change_connect = self.win.disconnect if self.sequenceEditor: self.sequenceEditor.connect_or_disconnect_signals(isConnect) _superclass.connect_or_disconnect_signals(self, isConnect) change_connect(self.disableStructHighlightingCheckbox, SIGNAL('stateChanged(int)'), self.change_struct_highlightPolicy) change_connect(self.showCursorTextCheckBox, SIGNAL('stateChanged(int)'), self._update_state_of_cursorTextGroupBox) def model_changed(self): """ @see: DnaStrand_EditCommand.model_changed() @see: DnaStrand_EditCommand.hasResizableStructure() """ isStructResizable, why_not = self.editCommand.hasResizableStructure() if not isStructResizable: #disable all widgets if self._pmGroupBox1.isEnabled(): self._pmGroupBox1.setEnabled(False) msg1 = ("Viewing properties of %s <br>") % ( self.editCommand.struct.name) msg2 = redmsg("DnaStrand is not resizable. Reason: %s" % (why_not)) self.updateMessage(msg1 + msg2) else: if not self._pmGroupBox1.isEnabled(): self._pmGroupBox1.setEnabled(True) msg1 = ("Viewing properties of %s <br>") % ( self.editCommand.struct.name) msg2 = "Use resize handles to resize the strand. Use sequence editor"\ "to assign a new sequence or the current one to a file." self.updateMessage(msg1 + msg2) def show(self): """ Show this PM As of 2007-11-20, it also shows the Sequence Editor widget and hides the history widget. This implementation may change in the near future This method also retrives the name information from the editCommand's structure for its name line edit field. @see: DnaStrand_EditCommand.getStructureName() @see: self.close() """ _superclass.show(self) self._showSequenceEditor() if self.editCommand is not None: name = self.editCommand.getStructureName() if name is not None: self.nameLineEdit.setText(name) def close(self): """ Close this property manager. Also sets the name of the self.editCommand's structure to the one displayed in the line edit field. @see self.show() @see: DnaSegment_EditCommand.setStructureName """ if self.editCommand is not None: name = str(self.nameLineEdit.text()) self.editCommand.setStructureName(name) if self.sequenceEditor: self.sequenceEditor.close() _superclass.close(self) def _showSequenceEditor(self): if self.sequenceEditor: if not self.sequenceEditor.isVisible(): #Show the sequence editor #ATTENTION: the sequence editor also closes (temporarily) the #reports dockwidget (if visible) Its state is later restored when #the sequuence Editor is closed. self.sequenceEditor.show() self.updateSequence() def updateSequence(self): """ Update the sequence string in the sequence editor @see: DnaSequenceEditor.setSequence() @see DnaSequenceEditor._determine_complementSequence() @see: DnaSequenceEditor.setComplementSequence() @see: DnaStrand.getStrandSequenceAndItsComplement() """ #Read in the strand sequence of the selected strand and #show it in the text edit in the sequence editor. ##strand = self.strandListWidget.getPickedItem() if not self.editCommand.hasValidStructure(): return strand = self.editCommand.struct titleString = 'Sequence Editor for ' + strand.name self.sequenceEditor.setWindowTitle(titleString) sequenceString, complementSequenceString = strand.getStrandSequenceAndItsComplement( ) if sequenceString: sequenceString = QString(sequenceString) sequenceString = sequenceString.toUpper() #Set the initial sequence (read in from the file) self.sequenceEditor.setSequence(sequenceString) #Set the initial complement sequence for DnaSequence editor. #do this independently because 'complementSequenceString' may have #some characters (such as * ) that denote a missing base on the #complementary strand. this information is used by the sequence #editor. See DnaSequenceEditor._determine_complementSequence() #for more details. See also bug 2787 self.sequenceEditor.setComplementSequence(complementSequenceString) def change_struct_highlightPolicy(self, checkedState=False): """ Change the 'highlight policy' of the structure being edited (i.e. self.editCommand.struct) . @param checkedState: The checked state of the checkbox that says 'Don't highlight while editing DNA'. So, it its True, the structure being edited won't get highlighted. @see: DnaStrand.setHighlightPolicy for more comments """ if self.editCommand and self.editCommand.hasValidStructure(): highlight = not checkedState self.editCommand.struct.setHighlightPolicy(highlight=highlight) def _addWhatsThisText(self): """ Add what's this text. Abstract method. """ pass
class CompareProteins_PropertyManager(Command_PropertyManager): """ The CompareProteins_PropertyManager class provides a Property Manager for the B{Compare Proteins} command on the Build Protein flyout toolbar. @ivar title: The title that appears in the property manager header. @type title: str @ivar pmName: The name of this property manager. This is used to set the name of the PM_Dialog object via setObjectName(). @type name: str @ivar iconPath: The relative path to the PNG file that contains a 22 x 22 icon image that appears in the PM header. @type iconPath: str @ivar proteinChunk1: The first currently selected protein to be compared. @type proteinChunk1: protein chunk @ivar proteinChunk2: The second currently selected protein to be compared. @type proteinChunk2: protein chunk """ title = "Compare Proteins" pmName = title iconPath = "ui/actions/Command Toolbar/BuildProtein/Compare.png" proteinChunk1 = None proteinChunk2 = None def __init__(self, command): """ Constructor for the property manager. """ self.threshold = 10.0 _superclass.__init__(self, command) self.showTopRowButtons( PM_DONE_BUTTON | \ PM_WHATS_THIS_BUTTON) return def connect_or_disconnect_signals(self, isConnect=True): if isConnect: change_connect = self.win.connect else: change_connect = self.win.disconnect change_connect(self.comparePushButton, SIGNAL("clicked()"), self._compareProteins) change_connect(self.thresholdDoubleSpinBox, SIGNAL("valueChanged(double)"), self._thresholdChanged) change_connect(self.hidePushButton, SIGNAL("clicked()"), self._hideDifferences) return def close(self): """ Closes the Property Manager. Overrides EditCommand_PM.close() """ env.history.statusbar_msg("") self._resetAminoAcids() _superclass.close(self) # Restore the original global display style. self.o.setGlobalDisplayStyle(self.originalDisplayStyle) return def show(self): """ Show the PM. Extends superclass method. @note: _update_UI_do_updates() gets called immediately after this and updates PM widgets with their correct values/settings. """ _superclass.show(self) env.history.statusbar_msg("") # Force the Global Display Style to "Protein" since this is the only way # to see comparisons. The global display style will be restored when leaving # this command (via self.close()). self.originalDisplayStyle = self.o.displayMode self.o.setGlobalDisplayStyle(diPROTEIN) return def _addGroupBoxes(self): """ Add the Property Manager group boxes. """ self._pmGroupBox1 = PM_GroupBox(self, title="Compare") self._loadGroupBox1(self._pmGroupBox1) return def _addWhatsThisText(self): """ What's This text for widgets in this Property Manager. """ pass def _addToolTipText(self): """ Tool Tip text for widgets in this Property Manager. """ pass def _loadGroupBox1(self, pmGroupBox): """ Load widgets in group box. """ self.structure1LineEdit = \ PM_LineEdit( pmGroupBox, label = "First structure:", setAsDefault = False) self.structure1LineEdit.setEnabled(False) self.structure2LineEdit = \ PM_LineEdit( pmGroupBox, label = "Second structure:", setAsDefault = False) self.structure2LineEdit.setEnabled(False) self.thresholdDoubleSpinBox = \ PM_DoubleSpinBox( pmGroupBox, label = "Threshold:", value = self.threshold, setAsDefault = True, minimum = 0.0, maximum = 360.0, decimals = 1, singleStep = 30.0, suffix = " deg", spanWidth = False) self.comparePushButton = \ PM_PushButton( pmGroupBox, text = "Compare", setAsDefault = True) self.hidePushButton = \ PM_PushButton( pmGroupBox, text = "Hide differences", setAsDefault = True) return def _compareProteins(self): """ Slot for Compare button. Compares two selected proteins of the same length. Amino acids that differ greater than the "threshold" value are displayed in two colors (red for the first protein and yellow for the second protein) and are only visible when the two proteins are displayed in the reduced display style. """ from utilities.constants import red, orange, green, cyan if not self.proteinChunk1 or \ not self.proteinChunk2: return protein_1 = self.proteinChunk1.protein protein_2 = self.proteinChunk2.protein if protein_1 and \ protein_2: aa_list_1 = protein_1.get_amino_acids() aa_list_2 = protein_2.get_amino_acids() protein_1.collapse_all_rotamers() protein_2.collapse_all_rotamers() if len(aa_list_1) == len(aa_list_2): for aa1, aa2 in zip(aa_list_1, aa_list_2): aa1.color = None aa2.color = None #aa1.collapse() #aa2.collapse() if aa1.get_one_letter_code() != aa2.get_one_letter_code(): aa1.set_color(red) aa1.expand() aa2.set_color(yellow) aa2.expand() else: max = 0.0 for chi in range(0, 3): angle1 = aa1.get_chi_angle(chi) angle2 = aa2.get_chi_angle(chi) if angle1 and \ angle2: if angle1 < 0.0: angle1 += 360.0 if angle2 < 0.0: angle2 += 360.0 diff = abs(angle1 - angle2) if diff > max: max = diff if max >= self.threshold: # This be a parameter. aa1.set_color(green) aa1.expand() aa2.set_color(cyan) aa2.expand() self.win.glpane.gl_update() else: msg = "The lengths of compared proteins are not equal." self.updateMessage(msg) env.history.redmsg(msg) return def _hideDifferences(self): """ Slot for the "Hide differences" button. Hides amino acids that differ greater than the "threshold" value. @warning: Untested. Code looks suspicious. """ if not self.proteinChunk1 or \ not self.proteinChunk2: return protein_1 = self.proteinChunk1.protein protein_2 = self.proteinChunk2.protein if protein_1 and \ protein_2: aa_list_1 = protein_1.get_amino_acids() aa_list_2 = protein_2.get_amino_acids() if len(aa_list_1) == len(aa_list_2): protein_1.collapse_all_rotamers() #@@@ protein_2.collapse_all_rotamers() #@@@ for aa1, aa2 in zip(aa_list_1, aa_list_2): aa1.color = None aa2.color = None aa1.collapse() aa2.collapse() self.win.glpane.gl_update() return def _thresholdChanged(self, value): """ Slot for Threshold spinbox. """ self.threshold = value self._compareProteins() return def _resetAminoAcids(self): """ Resets the color and collapse all amino acids of all proteins. """ proteinChunkList = getAllProteinChunksInPart(self.win.assy) for proteinChunk in proteinChunkList: proteinChunk.protein.collapse_all_rotamers() aa_list = proteinChunk.protein.get_amino_acids() for aa in aa_list: aa.color = None aa.collapse() self.win.glpane.gl_update() return def _update_UI_do_updates(self): """ Overrides superclass method. @see: Command_PropertyManager._update_UI_do_updates() """ self.proteinChunk1 = None self.proteinChunk2 = None self.comparePushButton.setEnabled(False) self.hidePushButton.setEnabled(False) selectedProteinList = self.win.assy.getSelectedProteinChunks() if len(selectedProteinList) == 0: self.structure1LineEdit.setText("") self.structure2LineEdit.setText("") msg = "Select two structures of the same length in the graphics area, "\ "then click the <b>Compare</b> button to compare them." elif len(selectedProteinList) == 1: self.proteinChunk1 = selectedProteinList[0] aa1_count = " (%d)" % self.proteinChunk1.protein.count_amino_acids( ) self.structure1LineEdit.setText(self.proteinChunk1.name + aa1_count) self.structure2LineEdit.setText("") msg = "Select one more structure in the graphics area that is the same "\ "length as <b>" + self.proteinChunk1.name + "</b>. "\ "Then click the <b>Compare</b> button to compare them." elif len(selectedProteinList) == 2: self.proteinChunk1 = selectedProteinList[0] aa1_count = " (%d)" % self.proteinChunk1.protein.count_amino_acids( ) self.structure1LineEdit.setText(self.proteinChunk1.name + aa1_count) self.proteinChunk2 = selectedProteinList[1] aa2_count = " (%d)" % self.proteinChunk2.protein.count_amino_acids( ) self.structure2LineEdit.setText(self.proteinChunk2.name + aa2_count) if aa1_count == aa2_count: self.comparePushButton.setEnabled(True) self.hidePushButton.setEnabled(True) msg = "Click the <b>Compare</b> button to compare the two selected structures." else: msg = "<b>%s</b> and <b>%s</b> are not the same length." % \ (self.proteinChunk1.name, self.proteinChunk2.name) msg = redmsg(msg) else: self.structure1LineEdit.setText("") self.structure2LineEdit.setText("") msg = redmsg("Too many proteins selected.") self.updateMessage(msg) env.history.redmsg(msg) return
class EditNanotube_PropertyManager(DnaOrCnt_PropertyManager): """ The NanotubeSegmenta_PropertyManager class provides a Property Manager for the EditNanotube_EditCommand. @ivar title: The title that appears in the property manager header. @type title: str @ivar pmName: The name of this property manager. This is used to set the name of the PM_Dialog object via setObjectName(). @type name: str @ivar iconPath: The relative path to the PNG file that contains a 22 x 22 icon image that appears in the PM header. @type iconPath: str """ title = "Nanotube Properties" pmName = title iconPath = "ui/actions/Command Toolbar/BuildNanotube/EditNanotube.png" def __init__(self, command): """ Constructor for the Cnt Segment Properties property manager. """ #For model changed signal self.previousSelectionParams = None #see self.connect_or_disconnect_signals for comment about this flag self.isAlreadyConnected = False self.isAlreadyDisconnected = False # Initialized here. Their values will be set in # _update_widgets_in_PM_before_show() self.endPoint1 = V(0, 0, 0) self.endPoint2 = V(0, 0, 0) _superclass.__init__(self, command) self.showTopRowButtons( PM_DONE_BUTTON | \ PM_CANCEL_BUTTON | \ PM_WHATS_THIS_BUTTON) def connect_or_disconnect_signals(self, isConnect): """ Connect or disconnect widget signals sent to their slot methods. This can be overridden in subclasses. By default it does nothing. @param isConnect: If True the widget will send the signals to the slot method. @type isConnect: boolean """ if isConnect: change_connect = self.win.connect else: change_connect = self.win.disconnect change_connect(self.nameLineEdit, SIGNAL("editingFinished()"), self._nameChanged) change_connect(self.showCursorTextCheckBox, SIGNAL('stateChanged(int)'), self._update_state_of_cursorTextGroupBox) return def show(self): """ Show this property manager. Overrides EditCommand_PM.show() This method also retrives the name information from the command's structure for its name line edit field. @see: EditNanotube_EditCommand.getStructureName() @see: self.close() """ _superclass.show(self) #if self.command is not None: #name = self.command.getStructureName() #if name is not None: #self.nameLineEdit.setText(name) def close(self): """ Close this property manager. Also sets the name of the self.command's structure to the one displayed in the line edit field. @see self.show() @see: EditNanotube_EditCommand.setStructureName """ if self.command is not None: name = str(self.nameLineEdit.text()) self.command.setStructureName(name) _superclass.close(self) def _connect_showCursorTextCheckBox(self): """ Connect the show cursor text checkbox with user prefs_key. Overrides DnaOrCnt_PropertyManager._connect_showCursorTextCheckBox """ connect_checkbox_with_boolean_pref( self.showCursorTextCheckBox, editNanotubeEditCommand_showCursorTextCheckBox_prefs_key) def _params_for_creating_cursorTextCheckBoxes(self): """ Returns params needed to create various cursor text checkboxes connected to prefs_keys that allow custom cursor texts. @return: A list containing tuples in the following format: ('checkBoxTextString' , preference_key). PM_PrefsCheckBoxes uses this data to create checkboxes with the the given names and connects them to the provided preference keys. (Note that PM_PrefsCheckBoxes puts thes within a GroupBox) @rtype: list @see: PM_PrefsCheckBoxes @see: self._loadDisplayOptionsGroupBox where this list is used. @see: Superclass method which is overridden here -- DnaOrCnt_PropertyManager._params_for_creating_cursorTextCheckBoxes() """ params = \ [ #Format: (" checkbox text", prefs_key) ("Nanotube length", editNanotubeEditCommand_cursorTextCheckBox_length_prefs_key) ] return params def setParameters(self, params): """ This is called when entering "Nanotube Segment Properties (i.e. "Edit properties...") to retrieve and set parameters of the nanotube segment that might be modified during this command and are needed to regenerate the nanotube segment. @param params: The parameters of the nanotube segment. These parameters are retreived via L{NanotubeSegment.getProps()}, called from L{EditNanotube_EditCommand.editStructure()}. Parameters: - n, m (chirality) - type (i.e. carbon or boron nitride) - endings (none, hydrogen, nitrogen) - endpoints (endPoint1, endPoint2) @type params: list (n, m), type, endings, (endPoint1, endPoint2) @note: Any widgets in the property manager that display these parameters should be updated here. @see: L{NanotubeSegment.getProps()} TODO: - Make this a EditCommand_PM API method? - See also the routines GraphicsMode.setParams or object.setProps ..better to name them all in one style? """ (self.n, self.m), self.type, self.endings,\ (self.endPoint1, self.endPoint2) = params # This is needed to update the endpoints since the Nanotube segment # may have been moved (i.e. translated or rotated). In that case, # the endpoints are not updated, so we recompute them here. nanotubeChunk = self.command.struct.members[0] self.endPoint1, self.endPoint2, radius = \ self.command.struct.nanotube.computeEndPointsFromChunk(nanotubeChunk) if 0: print "\n--------------" print "setParameters():" print "Struct=", self.command.struct print "N, M:", self.n, self.m print "type:", self.type print "endings:", self.endings print "pt1, pt2:", self.endPoint1, self.endPoint2 def getParameters(self): """ Get the parameters that the edit command will use to determine if any have changed. If any have, then the nanotube will be modified. """ if 0: print "\n--------------" print "getParameters():" print "Struct=", self.command.struct print "N, M:", self.n, self.m print "type:", self.type print "endings:", self.endings print "pt1, pt2:", self.endPoint1, self.endPoint2 return (self.n, self.m, self.type, self.endings, self.endPoint1, self.endPoint2) def _update_widgets_in_PM_before_show(self): """ This is called only when user is editing an existing structure. Its different than self.update_widgets_in_pm_before_show. (that method is called just before showing the property manager) @see: EditNanotube_EditCommand.editStructure() """ if self.command and self.command.hasValidStructure(): self.nanotube = self.command.struct.nanotube self.n, self.m = self.nanotube.getChirality() self.type = self.nanotube.getType() self.endings = self.nanotube.getEndings() self.endPoint1, self.endPoint2 = self.nanotube.getEndPoints() pass # Note that _update_widgets_in_PM_before_show() is called in # self.show, before you connect the signals. So, for the # 'first show' we will need to manually set the value of any # widgets that need updated. But later, when a different # NanotubeSegment is clicked, (while still in # EditNanotube_EditCommand, the propMgr will already be connected # so any calls in that case is redundant. self.updateNameField() self.updateLength() self.updateNanotubeDiameter() self.updateChirality() return def _update_UI_do_updates(self): """ Overrides superclass method. @see: Command_PropertyManager._update_UI_do_updates() """ self._update_widgets_in_PM_before_show() if self.command.struct: msg = "Editing structure <b>%s</b>." % \ self.command.getStructureName() else: msg = "Select a nanotube to edit." self.updateMessage(msg) return def _addGroupBoxes(self): """ Add the Property Manager group boxes. """ self._pmGroupBox1 = PM_GroupBox(self, title="Parameters") self._loadGroupBox1(self._pmGroupBox1) self._displayOptionsGroupBox = PM_GroupBox(self, title="Display Options") self._loadDisplayOptionsGroupBox(self._displayOptionsGroupBox) def _loadGroupBox1(self, pmGroupBox): """ Load widgets in group box 4. """ self.nameLineEdit = PM_LineEdit(pmGroupBox, label="Name:", text="", setAsDefault=False) # Nanotube Length self.ntLengthLineEdit = \ PM_LineEdit( pmGroupBox, label = "Length: ", text = "0.0 Angstroms", setAsDefault = False) self.ntLengthLineEdit.setDisabled(True) # Nanotube Radius self.ntDiameterLineEdit = \ PM_LineEdit( pmGroupBox, label = "Nanotube Diameter: ", setAsDefault = False) self.ntDiameterLineEdit.setDisabled(True) # Nanotube chirality. These are disabled (read-only) for now. --Mark self.chiralityNSpinBox = \ PM_SpinBox( pmGroupBox, label = "Chirality (n) :", minimum = 2, maximum = 100, setAsDefault = True ) self.chiralityNSpinBox.setDisabled(True) self.chiralityMSpinBox = \ PM_SpinBox( pmGroupBox, label = "Chirality (m) :", minimum = 0, maximum = 100, setAsDefault = True ) self.chiralityMSpinBox.setDisabled(True) def _addWhatsThisText(self): """ Add what's this text. """ pass def _addToolTipText(self): """ Add Tooltip text """ pass def _nameChanged(self): """ Slot for "Name" field. @TODO: Include a validator for the name field. """ _name = str(self.nameLineEdit.text()) if not _name: # Minimal test. Need to implement a validator. self.updateNameField() return self.command.setStructureName(_name) msg = "Editing structure <b>%s</b>." % _name self.updateMessage(msg) return def updateNameField(self): """ Update the name field showing the name of the currently selected protein. clear the combobox list. """ if self.command.hasValidStructure(): self.nameLineEdit.setEnabled(True) self.nameLineEdit.setText(self.command.getStructureName()) else: self.nameLineEdit.setDisabled(True) self.nameLineEdit.setText("") return def updateLength(self): """ Update the nanotube Length lineEdit widget. """ if self.command.hasValidStructure(): _nanotubeLength = vlen(self.endPoint1 - self.endPoint2) _lengthText = "%-7.4f Angstroms" % (_nanotubeLength) else: _lengthText = "" self.ntLengthLineEdit.setText(_lengthText) return def updateNanotubeDiameter(self): """ Update the nanotube Diameter lineEdit widget. """ if self.command.hasValidStructure(): _diameterText = "%-7.4f Angstroms" % (self.nanotube.getDiameter()) else: _diameterText = "" self.ntDiameterLineEdit.setText(_diameterText) return def updateChirality(self): """ Update the nanotube chirality spinboxes (read-only). """ if self.command.hasValidStructure(): n, m = self.nanotube.getChirality() else: n = 0 m = 0 self.chiralityNSpinBox.setValue(n) self.chiralityMSpinBox.setValue(m) return pass # End of EditNanotube_PropertyManager class
class DnaDuplexPropertyManager( DnaOrCnt_PropertyManager ): """ The DnaDuplexPropertyManager class provides a Property Manager for the B{Build > DNA > Duplex} command. @ivar title: The title that appears in the property manager header. @type title: str @ivar pmName: The name of this property manager. This is used to set the name of the PM_Dialog object via setObjectName(). @type name: str @ivar iconPath: The relative path to the PNG file that contains a 22 x 22 icon image that appears in the PM header. @type iconPath: str """ title = "Insert DNA" pmName = title iconPath = "ui/actions/Tools/Build Structures/InsertDsDna.png" def __init__( self, win, editCommand ): """ Constructor for the DNA Duplex property manager. """ self.endPoint1 = None self.endPoint2 = None self._conformation = "B-DNA" self._numberOfBases = 0 self._basesPerTurn = getDuplexBasesPerTurn(self._conformation) self._duplexRise = getDuplexRise(self._conformation) self._duplexLength = getDuplexLength(self._conformation, self._numberOfBases) _superclass.__init__( self, win, editCommand) self.showTopRowButtons( PM_DONE_BUTTON | \ PM_CANCEL_BUTTON | \ PM_WHATS_THIS_BUTTON) def connect_or_disconnect_signals(self, isConnect): """ Connect or disconnect widget signals sent to their slot methods. This can be overridden in subclasses. By default it does nothing. @param isConnect: If True the widget will send the signals to the slot method. @type isConnect: boolean """ if isConnect: change_connect = self.win.connect else: change_connect = self.win.disconnect change_connect(self._placementOptions.buttonGroup, SIGNAL("buttonClicked(int)"), self.activateSpecifyReferencePlaneTool) change_connect( self.conformationComboBox, SIGNAL("currentIndexChanged(int)"), self.conformationComboBoxChanged ) change_connect( self.numberOfBasePairsSpinBox, SIGNAL("valueChanged(int)"), self.numberOfBasesChanged ) change_connect( self.basesPerTurnDoubleSpinBox, SIGNAL("valueChanged(double)"), self.basesPerTurnChanged ) change_connect( self.duplexRiseDoubleSpinBox, SIGNAL("valueChanged(double)"), self.duplexRiseChanged ) change_connect(self.showCursorTextCheckBox, SIGNAL('stateChanged(int)'), self._update_state_of_cursorTextGroupBox) self.duplexRiseDoubleSpinBox.connectWithState( Preferences_StateRef_double( bdnaRise_prefs_key, env.prefs[bdnaRise_prefs_key] ) ) self.basesPerTurnDoubleSpinBox.connectWithState( Preferences_StateRef_double( bdnaBasesPerTurn_prefs_key, env.prefs[bdnaBasesPerTurn_prefs_key] ) ) def ok_btn_clicked(self): """ Slot for the OK button """ if self.editCommand: self.editCommand.preview_or_finalize_structure(previewing = False) ##env.history.message(self.editCommand.logMessage) self.win.toolsDone() def cancel_btn_clicked(self): """ Slot for the Cancel button. """ if self.editCommand: self.editCommand.cancelStructure() self.win.toolsCancel() def _update_widgets_in_PM_before_show(self): """ Update various widgets in this Property manager. Overrides superclass method @see: MotorPropertyManager._update_widgets_in_PM_before_show @see: self.show where it is called. """ pass def getFlyoutActionList(self): """ returns custom actionlist that will be used in a specific mode or editing a feature etc Example: while in movie mode, the _createFlyoutToolBar method calls this """ #'allActionsList' returns all actions in the flyout toolbar #including the subcontrolArea actions allActionsList = [] #Action List for subcontrol Area buttons. #In this mode there is really no subcontrol area. #We will treat subcontrol area same as 'command area' #(subcontrol area buttons will have an empty list as their command area #list). We will set the Comamnd Area palette background color to the #subcontrol area. subControlAreaActionList =[] self.exitEditCommandAction.setChecked(True) subControlAreaActionList.append(self.exitEditCommandAction) separator = QAction(self.w) separator.setSeparator(True) subControlAreaActionList.append(separator) allActionsList.extend(subControlAreaActionList) #Empty actionlist for the 'Command Area' commandActionLists = [] #Append empty 'lists' in 'commandActionLists equal to the #number of actions in subControlArea for i in range(len(subControlAreaActionList)): lst = [] commandActionLists.append(lst) params = (subControlAreaActionList, commandActionLists, allActionsList) return params def _addGroupBoxes( self ): """ Add the DNA Property Manager group boxes. """ self._pmReferencePlaneGroupBox = PM_GroupBox( self, title = "Placement Options" ) self._loadReferencePlaneGroupBox( self._pmReferencePlaneGroupBox ) self._pmGroupBox1 = PM_GroupBox( self, title = "Endpoints" ) self._loadGroupBox1( self._pmGroupBox1 ) self._pmGroupBox1.hide() self._pmGroupBox2 = PM_GroupBox( self, title = "Parameters" ) self._loadGroupBox2( self._pmGroupBox2 ) self._displayOptionsGroupBox = PM_GroupBox( self, title = "Display Options" ) self._loadDisplayOptionsGroupBox( self._displayOptionsGroupBox ) def _loadGroupBox1(self, pmGroupBox): """ Load widgets in group box 3. """ #Folllowing toolbutton facilitates entering a temporary DnaLineMode #to create a DNA using endpoints of the specified line. self.specifyDnaLineButton = PM_ToolButton( pmGroupBox, text = "Specify Endpoints", iconPath = "ui/actions/Properties Manager/Pencil.png", spanWidth = True ) self.specifyDnaLineButton.setCheckable(True) self.specifyDnaLineButton.setAutoRaise(True) self.specifyDnaLineButton.setToolButtonStyle( Qt.ToolButtonTextBesideIcon) #EndPoint1 and endPoint2 coordinates. These widgets are hidden # as of 2007- 12 - 05 self._endPoint1SpinBoxes = PM_CoordinateSpinBoxes(pmGroupBox, label = "End Point 1") self.x1SpinBox = self._endPoint1SpinBoxes.xSpinBox self.y1SpinBox = self._endPoint1SpinBoxes.ySpinBox self.z1SpinBox = self._endPoint1SpinBoxes.zSpinBox self._endPoint2SpinBoxes = PM_CoordinateSpinBoxes(pmGroupBox, label = "End Point 2") self.x2SpinBox = self._endPoint2SpinBoxes.xSpinBox self.y2SpinBox = self._endPoint2SpinBoxes.ySpinBox self.z2SpinBox = self._endPoint2SpinBoxes.zSpinBox self._endPoint1SpinBoxes.hide() self._endPoint2SpinBoxes.hide() def _loadGroupBox2(self, pmGroupBox): """ Load widgets in group box 4. """ self.conformationComboBox = \ PM_ComboBox( pmGroupBox, label = "Conformation:", choices = ["B-DNA"], setAsDefault = True) dnaModelChoices = ['PAM3', 'PAM5'] self.dnaModelComboBox = \ PM_ComboBox( pmGroupBox, label = "Model:", choices = dnaModelChoices, setAsDefault = True) self.basesPerTurnDoubleSpinBox = \ PM_DoubleSpinBox( pmGroupBox, label = "Bases per turn:", value = env.prefs[bdnaBasesPerTurn_prefs_key], setAsDefault = True, minimum = 8.0, maximum = 20.0, decimals = 2, singleStep = 0.1 ) self.duplexRiseDoubleSpinBox = \ PM_DoubleSpinBox( pmGroupBox, label = "Rise:", value = env.prefs[bdnaRise_prefs_key], setAsDefault = True, minimum = 2.0, maximum = 4.0, decimals = 3, singleStep = 0.01 ) # Strand Length (i.e. the number of bases) self.numberOfBasePairsSpinBox = \ PM_SpinBox( pmGroupBox, label = "Base pairs:", value = self._numberOfBases, setAsDefault = False, minimum = 0, maximum = 10000 ) self.numberOfBasePairsSpinBox.setDisabled(True) # Duplex Length self.duplexLengthLineEdit = \ PM_LineEdit( pmGroupBox, label = "Duplex length: ", text = "0.0 Angstroms", setAsDefault = False) self.duplexLengthLineEdit.setDisabled(True) def _loadDisplayOptionsGroupBox(self, pmGroupBox): """ Load widgets in the Display Options GroupBox @see: DnaOrCnt_PropertyManager. _loadDisplayOptionsGroupBox """ #Call the superclass method that loads the cursor text checkboxes. #Note, as of 2008-05-19, the superclass, DnaOrCnt_PropertyManager #only loads the cursor text groupboxes. Subclasses like this can #call custom methods like self._loadCursorTextCheckBoxes etc if they #don't need all groupboxes that the superclass loads. _superclass._loadDisplayOptionsGroupBox(self, pmGroupBox) self._rubberbandLineGroupBox = PM_GroupBox( pmGroupBox, title = 'Rubber band line:') dnaLineChoices = ['Ribbons', 'Ladder'] self.dnaRubberBandLineDisplayComboBox = \ PM_ComboBox( self._rubberbandLineGroupBox , label = " Display as:", choices = dnaLineChoices, setAsDefault = True) self.lineSnapCheckBox = \ PM_CheckBox(self._rubberbandLineGroupBox , text = 'Enable line snap' , widgetColumn = 1, state = Qt.Checked ) def _connect_showCursorTextCheckBox(self): """ Connect the show cursor text checkbox with user prefs_key. Overrides DnaOrCnt_PropertyManager._connect_showCursorTextCheckBox """ connect_checkbox_with_boolean_pref( self.showCursorTextCheckBox , dnaDuplexEditCommand_showCursorTextCheckBox_prefs_key) def _params_for_creating_cursorTextCheckBoxes(self): """ Returns params needed to create various cursor text checkboxes connected to prefs_keys that allow custom cursor texts. @return: A list containing tuples in the following format: ('checkBoxTextString' , preference_key). PM_PrefsCheckBoxes uses this data to create checkboxes with the the given names and connects them to the provided preference keys. (Note that PM_PrefsCheckBoxes puts thes within a GroupBox) @rtype: list @see: PM_PrefsCheckBoxes @see: self._loadDisplayOptionsGroupBox where this list is used. @see: Superclass method which is overridden here -- DnaOrCnt_PropertyManager._params_for_creating_cursorTextCheckBoxes() """ params = \ [ #Format: (" checkbox text", prefs_key) ("Number of base pairs", dnaDuplexEditCommand_cursorTextCheckBox_numberOfBasePairs_prefs_key), ("Number of turns", dnaDuplexEditCommand_cursorTextCheckBox_numberOfTurns_prefs_key), ("Duplex length", dnaDuplexEditCommand_cursorTextCheckBox_length_prefs_key), ("Angle", dnaDuplexEditCommand_cursorTextCheckBox_angle_prefs_key) ] return params def _addToolTipText(self): """ Tool Tip text for widgets in the DNA Property Manager. """ pass def conformationComboBoxChanged( self, inIndex ): """ Slot for the Conformation combobox. It is called whenever the Conformation choice is changed. @param inIndex: The new index. @type inIndex: int """ conformation = self.conformationComboBox.currentText() if conformation == "B-DNA": self.basesPerTurnDoubleSpinBox.setValue("10.0") elif conformation == "Z-DNA": self.basesPerTurnDoubleSpinBox.setValue("12.0") else: msg = redmsg("conformationComboBoxChanged(): \ Error - unknown DNA conformation. Index = "+ inIndex) env.history.message(msg) self.duplexLengthSpinBox.setSingleStep(getDuplexRise(conformation)) def numberOfBasesChanged( self, numberOfBases ): """ Slot for the B{Number of Bases} spinbox. """ # Update the Duplex Length lineEdit widget. text = str(getDuplexLength(self._conformation, numberOfBases, self._duplexRise)) \ + " Angstroms" self.duplexLengthLineEdit.setText(text) return def basesPerTurnChanged( self, basesPerTurn ): """ Slot for the B{Bases per turn} spinbox. """ self.editCommand.basesPerTurn = basesPerTurn self._basesPerTurn = basesPerTurn return def duplexRiseChanged( self, rise ): """ Slot for the B{Rise} spinbox. """ self.editCommand.duplexRise = rise self._duplexRise = rise return def getParameters(self): """ Return the parameters from this property manager to be used to create the DNA duplex. @return: A tuple containing the parameters @rtype: tuple @see: L{DnaDuplex_EditCommand._gatherParameters} where this is used """ numberOfBases = self.numberOfBasePairsSpinBox.value() dnaForm = str(self.conformationComboBox.currentText()) basesPerTurn = self.basesPerTurnDoubleSpinBox.value() duplexRise = self.duplexRiseDoubleSpinBox.value() dnaModel = str(self.dnaModelComboBox.currentText()) # First endpoint (origin) of DNA duplex x1 = self.x1SpinBox.value() y1 = self.y1SpinBox.value() z1 = self.z1SpinBox.value() # Second endpoint (direction vector/axis) of DNA duplex. x2 = self.x2SpinBox.value() y2 = self.y2SpinBox.value() z2 = self.z2SpinBox.value() if not self.endPoint1: self.endPoint1 = V(x1, y1, z1) if not self.endPoint2: self.endPoint2 = V(x2, y2, z2) return (numberOfBases, dnaForm, dnaModel, basesPerTurn, duplexRise, self.endPoint1, self.endPoint2) def _addWhatsThisText(self): """ What's This text for widgets in this Property Manager. """ whatsThis_DnaDuplexPropertyManager(self)
class OrderDna_PropertyManager(Command_PropertyManager): """ The OrderDna_PropertyManager class provides a Property Manager for the B{Order Dna} command on the flyout toolbar in the Build > Dna mode. @ivar title: The title that appears in the property manager header. @type title: str @ivar pmName: The name of this property manager. This is used to set the name of the PM_Dialog object via setObjectName(). @type name: str @ivar iconPath: The relative path to the PNG file that contains a 22 x 22 icon image that appears in the PM header. @type iconPath: str """ title = "Order DNA" pmName = title iconPath = "ui/actions/Command Toolbar/BuildDna/OrderDna.png" def __init__( self, command ): """ Constructor for the property manager. """ _superclass.__init__(self, command) self.assy = self.win.assy self.showTopRowButtons( PM_DONE_BUTTON | \ PM_WHATS_THIS_BUTTON) self.update_includeStrands() # Updates the message box. return def connect_or_disconnect_signals(self, isConnect): """ Connect or disconnect widget signals sent to their slot methods. This can be overridden in subclasses. By default it does nothing. @param isConnect: If True the widget will send the signals to the slot method. @type isConnect: boolean """ if isConnect: change_connect = self.win.connect else: change_connect = self.win.disconnect change_connect( self.viewDnaOrderFileButton, SIGNAL("clicked()"), self.viewDnaOrderFile) change_connect( self.includeStrandsComboBox, SIGNAL("activated(int)"), self.update_includeStrands ) return def _addGroupBoxes( self ): """ Add the Property Manager group boxes. """ self._pmGroupBox1 = PM_GroupBox( self, title = "Options" ) self._loadGroupBox1( self._pmGroupBox1 ) def _loadGroupBox1(self, pmGroupBox): """ Load widgets in group box. """ includeStrandsChoices = ["All strands in model", "Selected strands only"] self.includeStrandsComboBox = \ PM_ComboBox( pmGroupBox, label = "Include strands:", choices = includeStrandsChoices, setAsDefault = True) self.numberOfBasesLineEdit = \ PM_LineEdit( pmGroupBox, label = "Total nucleotides:", text = str(self.getNumberOfBases())) self.numberOfBasesLineEdit.setEnabled(False) self.numberOfXBasesLineEdit = \ PM_LineEdit( pmGroupBox, label = "Unassigned:", text = str(self.getNumberOfBases(unassignedOnly = True))) self.numberOfXBasesLineEdit.setEnabled(False) self.viewDnaOrderFileButton = \ PM_PushButton( pmGroupBox, label = "", text = "View DNA Order File...", spanWidth = True) return def _addWhatsThisText(self): """ What's This text for widgets in this Property Manager. """ whatsThis_OrderDna_PropertyManager(self) return def _addToolTipText(self): """ Tool Tip text for widgets in the DNA Property Manager. """ pass # Ask Bruce where this should live (i.e. class Part?) --Mark def getAllDnaStrands(self, selectedOnly = False): """ Returns a list of all the DNA strands in the current part, or only the selected strands if I{selectedOnly} is True. @param selectedOnly: If True, return only the selected DNA strands. @type selectedOnly: bool """ dnaStrandList = [] def func(node): if isinstance(node, DnaStrand): if selectedOnly: if node.picked: dnaStrandList.append(node) else: dnaStrandList.append(node) self.win.assy.part.topnode.apply2all(func) return dnaStrandList def getNumberOfBases(self, selectedOnly = False, unassignedOnly = False): """ Returns the number of bases count for all the DNA strands in the current part, or only the selected strand if I{selectedOnly} is True. @param selectedOnly: If True, return only the number of bases in the selected DNA strands. @type selectedOnly: bool @param unassignedOnly: If True, return only the number of unassigned bases (i.e. base letters = X). @type unassignedOnly: bool """ dnaSequenceString = '' selectedOnly = self.includeStrandsComboBox.currentIndex() strandList = self.getAllDnaStrands(selectedOnly) for strand in strandList: strandSequenceString = str(strand.getStrandSequence()) dnaSequenceString += strandSequenceString if unassignedOnly: return dnaSequenceString.count("X") return len(dnaSequenceString) def _update_UI_do_updates(self): """ Overrides superclass method. """ self.update_includeStrands() return def getDnaSequence(self, format = 'CSV'): """ Return the complete Dna sequence information string (i.e. all strand sequences) in the specified format. @return: The Dna sequence string @rtype: string """ if format == 'CSV': #comma separated values. separator = ',' dnaSequenceString = '' selectedOnly = self.includeStrandsComboBox.currentIndex() strandList = self.getAllDnaStrands(selectedOnly) for strand in strandList: dnaSequenceString = dnaSequenceString + strand.name + separator strandSequenceString = str(strand.getStrandSequence()) if strandSequenceString: strandSequenceString = strandSequenceString.upper() strandLength = str(len(strandSequenceString)) + separator dnaSequenceString = dnaSequenceString + strandLength + strandSequenceString dnaSequenceString = dnaSequenceString + "\n" return dnaSequenceString def viewDnaOrderFile(self, openFileInEditor = True): """ Writes a DNA Order file in comma-separated values (CSV) format and opens it in a text editor. The user must save the file to a permanent location using the text editor. @see: Ui_DnaFlyout.orderDnaCommand @see: writeDnaOrderFile() @TODO: assy.getAllDnaObjects(). """ dnaSequence = self.getDnaSequence(format = 'CSV') if dnaSequence: tmpdir = find_or_make_Nanorex_subdir('temp') fileBaseName = 'DnaOrder' temporaryFile = os.path.join(tmpdir, "%s.csv" % fileBaseName) writeDnaOrderFile(temporaryFile, self.assy, self.getNumberOfBases(), self.getNumberOfBases(unassignedOnly = True), dnaSequence) if openFileInEditor: open_file_in_editor(temporaryFile) return def update_includeStrands(self, ignoreVal = 0): """ Slot method for "Include (strands)" combobox. """ idx = self.includeStrandsComboBox.currentIndex() includeType = ["model", "selection"] _numberOfBases = self.getNumberOfBases() self.numberOfBasesLineEdit.setText(str(_numberOfBases) + " bases") _numberOfXBases = self.getNumberOfBases(unassignedOnly = True) self.numberOfXBasesLineEdit.setText(str(_numberOfXBases) + " bases") # Make the background color red if there are any unassigned bases. if _numberOfXBases: self.numberOfXBasesLineEdit.setStyleSheet(\ "QLineEdit {"\ "background-color: rgb(255, 0, 0)"\ "}") else: self.numberOfXBasesLineEdit.setStyleSheet(\ "QLineEdit {"\ "background-color: rgb(255, 255, 255)"\ "}") if _numberOfBases > 0: self.viewDnaOrderFileButton.setEnabled(True) msg = "Click on <b>View DNA Order File...</b> to preview a " \ "DNA order for all DNA strands in the current %s." \ % includeType[idx] else: self.viewDnaOrderFileButton.setEnabled(False) msg = "<font color=red>" \ "There are no DNA strands in the current %s." \ % includeType[idx] self.updateMessage(msg) return