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 PlanePropertyManager(EditCommand_PM): """ The PlanePropertyManager class provides a Property Manager for a (reference) Plane. """ # The title that appears in the Property Manager header. title = "Plane" # The name of this Property Manager. This will be set to # the name of the PM_Dialog object via setObjectName(). pmName = title # The relative path to the PNG file that appears in the header iconPath = "ui/actions/Insert/Reference Geometry/Plane.png" def __init__(self, command): """ Construct the Plane Property Manager. @param plane: The plane. @type plane: L{Plane} """ #see self.connect_or_disconnect_signals for comment about this flag self.isAlreadyConnected = False self.isAlreadyDisconnected = False self.gridColor = black self.gridXSpacing = 4.0 self.gridYSpacing = 4.0 self.gridLineType = 3 self.displayLabels = False self.originLocation = PLANE_ORIGIN_LOWER_LEFT self.displayLabelStyle = LABELS_ALONG_ORIGIN EditCommand_PM.__init__(self, command) # Hide Preview and Restore defaults buttons self.hideTopRowButtons(PM_RESTORE_DEFAULTS_BUTTON) def _addGroupBoxes(self): """ Add the 1st group box to the Property Manager. """ # Placement Options radio button list to create radio button list. # Format: buttonId, buttonText, tooltip PLACEMENT_OPTIONS_BUTTON_LIST = [ \ ( 0, "Parallel to screen", "Parallel to screen" ), ( 1, "Through selected atoms", "Through selected atoms" ), ( 2, "Offset to a plane", "Offset to a plane" ), ( 3, "Custom", "Custom" ) ] self.pmPlacementOptions = \ PM_RadioButtonList( self, title = "Placement Options", buttonList = PLACEMENT_OPTIONS_BUTTON_LIST, checkedId = 3 ) self.pmGroupBox1 = PM_GroupBox(self, title="Parameters") self._loadGroupBox1(self.pmGroupBox1) #image groupbox self.pmGroupBox2 = PM_GroupBox(self, title="Image") self._loadGroupBox2(self.pmGroupBox2) #grid plane groupbox self.pmGroupBox3 = PM_GroupBox(self, title="Grid") self._loadGroupBox3(self.pmGroupBox3) def _loadGroupBox3(self, pmGroupBox): """ Load widgets in the grid plane group box. @param pmGroupBox: The grid group box in the PM. @type pmGroupBox: L{PM_GroupBox} """ self.gridPlaneCheckBox = \ PM_CheckBox( pmGroupBox, text = "Show grid", widgetColumn = 0, setAsDefault = True, spanWidth = True ) connect_checkbox_with_boolean_pref(self.gridPlaneCheckBox, PlanePM_showGrid_prefs_key) self.gpXSpacingDoubleSpinBox = \ PM_DoubleSpinBox( pmGroupBox, label = "X Spacing:", value = 4.000, setAsDefault = True, minimum = 1.00, maximum = 200.0, decimals = 3, singleStep = 1.0, spanWidth = False) self.gpYSpacingDoubleSpinBox = \ PM_DoubleSpinBox( pmGroupBox, label = "Y Spacing:", value = 4.000, setAsDefault = True, minimum = 1.00, maximum = 200.0, decimals = 3, singleStep = 1.0, spanWidth = False) lineTypeChoices = ['Dotted (default)', 'Dashed', 'Solid'] self.gpLineTypeComboBox = \ PM_ComboBox( pmGroupBox , label = "Line type:", choices = lineTypeChoices, setAsDefault = True) hhColorList = [ black, orange, red, magenta, cyan, blue, white, yellow, gray ] hhColorNames = [ "Black (default)", "Orange", "Red", "Magenta", "Cyan", "Blue", "White", "Yellow", "Other color..." ] self.gpColorTypeComboBox = \ PM_ColorComboBox( pmGroupBox, colorList = hhColorList, colorNames = hhColorNames, color = black ) self.pmGroupBox5 = PM_GroupBox(pmGroupBox) self.gpDisplayLabels =\ PM_CheckBox( self.pmGroupBox5, text = "Display labels", widgetColumn = 0, state = Qt.Unchecked, setAsDefault = True, spanWidth = True ) originChoices = [ 'Lower left (default)', 'Upper left', 'Lower right', 'Upper right' ] self.gpOriginComboBox = \ PM_ComboBox( self.pmGroupBox5 , label = "Origin:", choices = originChoices, setAsDefault = True ) positionChoices = ['Origin axes (default)', 'Plane perimeter'] self.gpPositionComboBox = \ PM_ComboBox( self.pmGroupBox5 , label = "Position:", choices = positionChoices, setAsDefault = True) self._showHideGPWidgets() if env.prefs[PlanePM_showGridLabels_prefs_key]: self.displayLabels = True self.gpOriginComboBox.setEnabled(True) self.gpPositionComboBox.setEnabled(True) else: self.displayLabels = False self.gpOriginComboBox.setEnabled(False) self.gpPositionComboBox.setEnabled(False) 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: Fix for 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 actually 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 #UPDATE: (comment copied and modifief from BuildNanotube_PropertyManager. #The general problem still remains -- Ninad 2008-06-25 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 change_connect(self.pmPlacementOptions.buttonGroup, SIGNAL("buttonClicked(int)"), self.changePlanePlacement) change_connect(self.widthDblSpinBox, SIGNAL("valueChanged(double)"), self.change_plane_width) change_connect(self.heightDblSpinBox, SIGNAL("valueChanged(double)"), self.change_plane_height) change_connect(self.aspectRatioCheckBox, SIGNAL("stateChanged(int)"), self._enableAspectRatioSpinBox) #signal slot connection for imageDisplayCheckBox change_connect(self.imageDisplayCheckBox, SIGNAL("stateChanged(int)"), self.toggleFileChooserBehavior) #signal slot connection for imageDisplayFileChooser change_connect(self.imageDisplayFileChooser.lineEdit, SIGNAL("editingFinished()"), self.update_imageFile) #signal slot connection for heightfieldDisplayCheckBox change_connect(self.heightfieldDisplayCheckBox, SIGNAL("stateChanged(int)"), self.toggleHeightfield) #signal slot connection for heightfieldHQDisplayCheckBox change_connect(self.heightfieldHQDisplayCheckBox, SIGNAL("stateChanged(int)"), self.toggleHeightfieldHQ) #signal slot connection for heightfieldTextureCheckBox change_connect(self.heightfieldTextureCheckBox, SIGNAL("stateChanged(int)"), self.toggleTexture) #signal slot connection for vScaleSpinBox change_connect(self.vScaleSpinBox, SIGNAL("valueChanged(double)"), self.change_vertical_scale) change_connect(self.plusNinetyButton, SIGNAL("clicked()"), self.rotate_90) change_connect(self.minusNinetyButton, SIGNAL("clicked()"), self.rotate_neg_90) change_connect(self.flipButton, SIGNAL("clicked()"), self.flip_image) change_connect(self.mirrorButton, SIGNAL("clicked()"), self.mirror_image) change_connect(self.gridPlaneCheckBox, SIGNAL("stateChanged(int)"), self.displayGridPlane) change_connect(self.gpXSpacingDoubleSpinBox, SIGNAL("valueChanged(double)"), self.changeXSpacingInGP) change_connect(self.gpYSpacingDoubleSpinBox, SIGNAL("valueChanged(double)"), self.changeYSpacingInGP) change_connect(self.gpLineTypeComboBox, SIGNAL("currentIndexChanged(int)"), self.changeLineTypeInGP) change_connect(self.gpColorTypeComboBox, SIGNAL("editingFinished()"), self.changeColorTypeInGP) change_connect(self.gpDisplayLabels, SIGNAL("stateChanged(int)"), self.displayLabelsInGP) change_connect(self.gpOriginComboBox, SIGNAL("currentIndexChanged(int)"), self.changeOriginInGP) change_connect(self.gpPositionComboBox, SIGNAL("currentIndexChanged(int)"), self.changePositionInGP) self._connect_checkboxes_to_global_prefs_keys() return def _connect_checkboxes_to_global_prefs_keys(self): """ """ connect_checkbox_with_boolean_pref(self.gridPlaneCheckBox, PlanePM_showGrid_prefs_key) connect_checkbox_with_boolean_pref(self.gpDisplayLabels, PlanePM_showGridLabels_prefs_key) def changePositionInGP(self, idx): """ Change Display of origin Labels (choices are along origin edges or along the plane perimeter. @param idx: Current index of the change grid label position combo box @type idx: int """ if idx == 0: self.displayLabelStyle = LABELS_ALONG_ORIGIN elif idx == 1: self.displayLabelStyle = LABELS_ALONG_PLANE_EDGES else: print "Invalid index", idx return def changeOriginInGP(self, idx): """ Change Display of origin Labels based on the location of the origin @param idx: Current index of the change origin position combo box @type idx: int """ if idx == 0: self.originLocation = PLANE_ORIGIN_LOWER_LEFT elif idx == 1: self.originLocation = PLANE_ORIGIN_UPPER_LEFT elif idx == 2: self.originLocation = PLANE_ORIGIN_LOWER_RIGHT elif idx == 3: self.originLocation = PLANE_ORIGIN_UPPER_RIGHT else: print "Invalid index", idx return def displayLabelsInGP(self, state): """ Choose to show or hide grid labels @param state: State of the Display Label Checkbox @type state: boolean """ if env.prefs[PlanePM_showGridLabels_prefs_key]: self.gpOriginComboBox.setEnabled(True) self.gpPositionComboBox.setEnabled(True) self.displayLabels = True self.originLocation = PLANE_ORIGIN_LOWER_LEFT self.displayLabelStyle = LABELS_ALONG_ORIGIN else: self.gpOriginComboBox.setEnabled(False) self.gpPositionComboBox.setEnabled(False) self.displayLabels = False return def changeColorTypeInGP(self): """ Change Color of grid """ self.gridColor = self.gpColorTypeComboBox.getColor() return def changeLineTypeInGP(self, idx): """ Change line type in grid @param idx: Current index of the Line type combo box @type idx: int """ #line_type for actually drawing the grid is: 0=None, 1=Solid, 2=Dashed" or 3=Dotted if idx == 0: self.gridLineType = 3 if idx == 1: self.gridLineType = 2 if idx == 2: self.gridLineType = 1 return def changeYSpacingInGP(self, val): """ Change Y spacing on the grid @param val:value of Y spacing @type val: double """ self.gridYSpacing = float(val) return def changeXSpacingInGP(self, val): """ Change X spacing on the grid @param val:value of X spacing @type val: double """ self.gridXSpacing = float(val) return def displayGridPlane(self, state): """ Display or hide grid based on the state of the checkbox @param state: State of the Display Label Checkbox @type state: boolean """ self._showHideGPWidgets() if self.gridPlaneCheckBox.isChecked(): env.prefs[PlanePM_showGrid_prefs_key] = True self._makeGridPlane() else: env.prefs[PlanePM_showGrid_prefs_key] = False return def _makeGridPlane(self): """ Show grid on the plane """ #get all the grid related values in here self.gridXSpacing = float(self.gpXSpacingDoubleSpinBox.value()) self.gridYSpacing = float(self.gpYSpacingDoubleSpinBox.value()) #line_type for actually drawing the grid is: 0=None, 1=Solid, 2=Dashed" or 3=Dotted idx = self.gpLineTypeComboBox.currentIndex() self.changeLineTypeInGP(idx) self.gridColor = self.gpColorTypeComboBox.getColor() return def _showHideGPWidgets(self): """ Enable Disable grid related widgets based on the state of the show grid checkbox. """ if self.gridPlaneCheckBox.isChecked(): self.gpXSpacingDoubleSpinBox.setEnabled(True) self.gpYSpacingDoubleSpinBox.setEnabled(True) self.gpLineTypeComboBox.setEnabled(True) self.gpColorTypeComboBox.setEnabled(True) self.gpDisplayLabels.setEnabled(True) else: self.gpXSpacingDoubleSpinBox.setEnabled(False) self.gpXSpacingDoubleSpinBox.setEnabled(False) self.gpYSpacingDoubleSpinBox.setEnabled(False) self.gpLineTypeComboBox.setEnabled(False) self.gpColorTypeComboBox.setEnabled(False) self.gpDisplayLabels.setEnabled(False) return def _loadGroupBox2(self, pmGroupBox): """ Load widgets in the image group box. @param pmGroupBox: The image group box in the PM. @type pmGroupBox: L{PM_GroupBox} """ self.imageDisplayCheckBox = \ PM_CheckBox( pmGroupBox, text = "Display image", widgetColumn = 0, state = Qt.Unchecked, setAsDefault = True, spanWidth = True ) self.imageDisplayFileChooser = \ PM_FileChooser(pmGroupBox, label = 'Image file:', text = '' , spanWidth = True, filter = "PNG (*.png);;"\ "All Files (*.*)" ) self.imageDisplayFileChooser.setEnabled(False) # add change image properties button BUTTON_LIST = [ ("QToolButton", 1, "+90", "ui/actions/Properties Manager/RotateImage+90.png", "+90", "", 0), ("QToolButton", 2, "-90", "ui/actions/Properties Manager/RotateImage-90.png", "-90", "", 1), ("QToolButton", 3, "FLIP", "ui/actions/Properties Manager/FlipImageVertical.png", "Flip", "", 2), ("QToolButton", 4, "MIRROR", "ui/actions/Properties Manager/FlipImageHorizontal.png", "Mirror", "", 3) ] #image change button groupbox self.pmGroupBox2 = PM_GroupBox(pmGroupBox, title="Modify Image") self.imageChangeButtonGroup = \ PM_ToolButtonRow( self.pmGroupBox2, title = "", buttonList = BUTTON_LIST, spanWidth = True, isAutoRaise = False, isCheckable = False, setAsDefault = True, ) self.imageChangeButtonGroup.buttonGroup.setExclusive(False) self.plusNinetyButton = self.imageChangeButtonGroup.getButtonById(1) self.minusNinetyButton = self.imageChangeButtonGroup.getButtonById(2) self.flipButton = self.imageChangeButtonGroup.getButtonById(3) self.mirrorButton = self.imageChangeButtonGroup.getButtonById(4) # buttons enabled when a valid image is loaded self.mirrorButton.setEnabled(False) self.plusNinetyButton.setEnabled(False) self.minusNinetyButton.setEnabled(False) self.flipButton.setEnabled(False) self.heightfieldDisplayCheckBox = \ PM_CheckBox( pmGroupBox, text = "Create 3D relief", widgetColumn = 0, state = Qt.Unchecked, setAsDefault = True, spanWidth = True ) self.heightfieldHQDisplayCheckBox = \ PM_CheckBox( pmGroupBox, text = "High quality", widgetColumn = 0, state = Qt.Unchecked, setAsDefault = True, spanWidth = True ) self.heightfieldTextureCheckBox = \ PM_CheckBox( pmGroupBox, text = "Use texture", widgetColumn = 0, state = Qt.Checked, setAsDefault = True, spanWidth = True ) self.vScaleSpinBox = \ PM_DoubleSpinBox(pmGroupBox, label = " Vertical scale:", value = 1.0, setAsDefault = True, minimum = -1000.0, # -1000 A maximum = 1000.0, # 1000 A singleStep = 0.1, decimals = 1, suffix = ' Angstroms') self.heightfieldDisplayCheckBox.setEnabled(False) self.heightfieldHQDisplayCheckBox.setEnabled(False) self.heightfieldTextureCheckBox.setEnabled(False) self.vScaleSpinBox.setEnabled(False) def _loadGroupBox1(self, pmGroupBox): """ Load widgets in 1st group box. @param pmGroupBox: The 1st group box in the PM. @type pmGroupBox: L{PM_GroupBox} """ self.widthDblSpinBox = \ PM_DoubleSpinBox(pmGroupBox, label = "Width:", value = 16.0, setAsDefault = True, minimum = 1.0, maximum = 10000.0, # 1000 nm singleStep = 1.0, decimals = 1, suffix = ' Angstroms') self.heightDblSpinBox = \ PM_DoubleSpinBox(pmGroupBox, label =" Height:", value = 16.0, setAsDefault = True, minimum = 1.0, maximum = 10000.0, # 1000 nm singleStep = 1.0, decimals = 1, suffix = ' Angstroms') self.aspectRatioCheckBox = \ PM_CheckBox(pmGroupBox, text = 'Maintain Aspect Ratio of:' , widgetColumn = 1, state = Qt.Unchecked ) self.aspectRatioSpinBox = \ PM_DoubleSpinBox( pmGroupBox, label = "", value = 1.0, setAsDefault = True, minimum = 0.1, maximum = 10.0, singleStep = 0.1, decimals = 2, suffix = " to 1.00") if self.aspectRatioCheckBox.isChecked(): self.aspectRatioSpinBox.setEnabled(True) else: self.aspectRatioSpinBox.setEnabled(False) def _addWhatsThisText(self): """ What's This text for some of the widgets in this Property Manager. @note: Many PM widgets are still missing their "What's This" text. """ from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_PlanePropertyManager whatsThis_PlanePropertyManager(self) def toggleFileChooserBehavior(self, checked): """ Enables FileChooser and displays image when checkbox is checked otherwise not """ self.imageDisplayFileChooser.lineEdit.emit(SIGNAL("editingFinished()")) if checked == Qt.Checked: self.imageDisplayFileChooser.setEnabled(True) elif checked == Qt.Unchecked: self.imageDisplayFileChooser.setEnabled(False) # if an image is already displayed, that's need to be hidden as well else: pass self.command.struct.glpane.gl_update() def toggleHeightfield(self, checked): """ Enables 3D relief drawing mode. """ if self.command and self.command.struct: plane = self.command.struct plane.display_heightfield = checked if checked: self.heightfieldHQDisplayCheckBox.setEnabled(True) self.heightfieldTextureCheckBox.setEnabled(True) self.vScaleSpinBox.setEnabled(True) plane.computeHeightfield() else: self.heightfieldHQDisplayCheckBox.setEnabled(False) self.heightfieldTextureCheckBox.setEnabled(False) self.vScaleSpinBox.setEnabled(False) plane.heightfield = None plane.glpane.gl_update() def toggleHeightfieldHQ(self, checked): """ Enables high quality rendering in 3D relief mode. """ if self.command and self.command.struct: plane = self.command.struct plane.heightfield_hq = checked plane.computeHeightfield() plane.glpane.gl_update() def toggleTexture(self, checked): """ Enables texturing in 3D relief mode. """ if self.command and self.command.struct: plane = self.command.struct plane.heightfield_use_texture = checked # It is not necessary to re-compute the heightfield coordinates # at this point, they are re-computed whenever the "3D relief image" # checkbox is set. plane.glpane.gl_update() def update_spinboxes(self): """ Update the width and height spinboxes. @see: Plane.resizeGeometry() This typically gets called when the plane is resized from the 3D workspace (which marks assy as modified) .So, update the spinboxes that represent the Plane's width and height, but do no emit 'valueChanged' signal when the spinbox value changes. @see: Plane.resizeGeometry() @see: self._update_UI_do_updates() @see: Plane_EditCommand.command_update_internal_state() """ # blockSignals = True make sure that spinbox.valueChanged() # signal is not emitted after calling spinbox.setValue(). This is done #because the spinbox valu changes as a result of resizing the plane #from the 3D workspace. if self.command.hasValidStructure(): self.heightDblSpinBox.setValue(self.command.struct.height, blockSignals=True) self.widthDblSpinBox.setValue(self.command.struct.width, blockSignals=True) def update_imageFile(self): """ Loads image file if path is valid """ # Update buttons and checkboxes. self.mirrorButton.setEnabled(False) self.plusNinetyButton.setEnabled(False) self.minusNinetyButton.setEnabled(False) self.flipButton.setEnabled(False) self.heightfieldDisplayCheckBox.setEnabled(False) self.heightfieldHQDisplayCheckBox.setEnabled(False) self.heightfieldTextureCheckBox.setEnabled(False) self.vScaleSpinBox.setEnabled(False) plane = self.command.struct # Delete current image and heightfield plane.deleteImage() plane.heightfield = None plane.display_image = self.imageDisplayCheckBox.isChecked() if plane.display_image: imageFile = str(self.imageDisplayFileChooser.lineEdit.text()) from model.Plane import checkIfValidImagePath validPath = checkIfValidImagePath(imageFile) if validPath: from PIL import Image # Load image from file plane.image = Image.open(imageFile) plane.loadImage(imageFile) # Compute the relief image plane.computeHeightfield() if plane.image: self.mirrorButton.setEnabled(True) self.plusNinetyButton.setEnabled(True) self.minusNinetyButton.setEnabled(True) self.flipButton.setEnabled(True) self.heightfieldDisplayCheckBox.setEnabled(True) if plane.display_heightfield: self.heightfieldHQDisplayCheckBox.setEnabled(True) self.heightfieldTextureCheckBox.setEnabled(True) self.vScaleSpinBox.setEnabled(True) def show(self): """ Show the Plane Property Manager. """ EditCommand_PM.show(self) #It turns out that if updateCosmeticProps is called before #EditCommand_PM.show, the 'preview' properties are not updated #when you are editing an existing plane. Don't know the cause at this #time, issue is trivial. So calling it in the end -- Ninad 2007-10-03 if self.command.struct: plane = self.command.struct plane.updateCosmeticProps(previewing=True) if plane.imagePath: self.imageDisplayFileChooser.setText(plane.imagePath) self.imageDisplayCheckBox.setChecked(plane.display_image) #Make sure that the plane placement option is always set to #'Custom' when the Plane PM is shown. This makes sure that bugs like #2949 won't occur. Let the user change the plane placement option #explicitely button = self.pmPlacementOptions.getButtonById(3) button.setChecked(True) def setParameters(self, params): """ """ width, height, gridColor, gridLineType, \ gridXSpacing, gridYSpacing, originLocation, \ displayLabelStyle = params # blockSignals = True flag makes sure that the # spinbox.valueChanged() # signal is not emitted after calling spinbox.setValue(). self.widthDblSpinBox.setValue(width, blockSignals=True) self.heightDblSpinBox.setValue(height, blockSignals=True) self.win.glpane.gl_update() self.gpColorTypeComboBox.setColor(gridColor) self.gridLineType = gridLineType self.gpXSpacingDoubleSpinBox.setValue(gridXSpacing) self.gpYSpacingDoubleSpinBox.setValue(gridYSpacing) self.gpOriginComboBox.setCurrentIndex(originLocation) self.gpPositionComboBox.setCurrentIndex(displayLabelStyle) def getCurrrentDisplayParams(self): """ Returns a tuple containing current display parameters such as current image path and grid display params. @see: Plane_EditCommand.command_update_internal_state() which uses this to decide whether to modify the structure (e.g. because of change in the image path or display parameters.) """ imagePath = self.imageDisplayFileChooser.text gridColor = self.gpColorTypeComboBox.getColor() return (imagePath, gridColor, self.gridLineType, self.gridXSpacing, self.gridYSpacing, self.originLocation, self.displayLabelStyle) def getParameters(self): """ """ width = self.widthDblSpinBox.value() height = self.heightDblSpinBox.value() gridColor = self.gpColorTypeComboBox.getColor() params = (width, height, gridColor, self.gridLineType, self.gridXSpacing, self.gridYSpacing, self.originLocation, self.displayLabelStyle) return params def change_plane_width(self, newWidth): """ Slot for width spinbox in the Property Manager. @param newWidth: width in Angstroms. @type newWidth: float """ if self.aspectRatioCheckBox.isChecked(): self.command.struct.width = newWidth self.command.struct.height = self.command.struct.width / \ self.aspectRatioSpinBox.value() self.update_spinboxes() else: self.change_plane_size() self._updateAspectRatio() def change_plane_height(self, newHeight): """ Slot for height spinbox in the Property Manager. @param newHeight: height in Angstroms. @type newHeight: float """ if self.aspectRatioCheckBox.isChecked(): self.command.struct.height = newHeight self.command.struct.width = self.command.struct.height * \ self.aspectRatioSpinBox.value() self.update_spinboxes() else: self.change_plane_size() self._updateAspectRatio() def change_plane_size(self, gl_update=True): """ Slot to change the Plane's width and height. @param gl_update: Forces an update of the glpane. @type gl_update: bool """ self.command.struct.width = self.widthDblSpinBox.value() self.command.struct.height = self.heightDblSpinBox.value() if gl_update: self.command.struct.glpane.gl_update() def change_vertical_scale(self, scale): """ Changes vertical scaling of the heightfield. """ if self.command and self.command.struct: plane = self.command.struct plane.heightfield_scale = scale plane.computeHeightfield() plane.glpane.gl_update() def changePlanePlacement(self, buttonId): """ Slot to change the placement of the plane depending upon the option checked in the "Placement Options" group box of the PM. @param buttonId: The button id of the selected radio button (option). @type buttonId: int """ if buttonId == 0: msg = "Create a Plane parallel to the screen. "\ "With <b>Parallel to Screen</b> plane placement option, the "\ "center of the plane is always (0,0,0)" self.updateMessage(msg) self.command.placePlaneParallelToScreen() elif buttonId == 1: msg = "Create a Plane with center coinciding with the common center "\ "of <b> 3 or more selected atoms </b>. If exactly 3 atoms are "\ "selected, the Plane will pass through those atoms." self.updateMessage(msg) self.command.placePlaneThroughAtoms() if self.command.logMessage: env.history.message(self.command.logMessage) elif buttonId == 2: msg = "Create a Plane at an <b>offset</b> to the selected plane "\ "indicated by the direction arrow. "\ "you can click on the direction arrow to reverse its direction." self.updateMessage(msg) self.command.placePlaneOffsetToAnother() if self.command.logMessage: env.history.message(self.command.logMessage) elif buttonId == 3: #'Custom' plane placement. Do nothing (only update message box) # Fixes bug 2439 msg = "Create a plane with a <b>Custom</b> plane placement. "\ "The plane is placed parallel to the screen, with "\ "center at (0, 0, 0). User can then modify the plane placement." self.updateMessage(msg) def _enableAspectRatioSpinBox(self, enable): """ Slot for "Maintain Aspect Ratio" checkbox which enables or disables the Aspect Ratio spin box. @param enable: True = enable, False = disable. @type enable: bool """ self.aspectRatioSpinBox.setEnabled(enable) def _updateAspectRatio(self): """ Updates the Aspect Ratio spin box based on the current width and height. """ aspectRatio = self.command.struct.width / self.command.struct.height self.aspectRatioSpinBox.setValue(aspectRatio) def _update_UI_do_updates(self): """ Overrides superclass method. @see: Command_PropertyManager._update_UI_do_updates() for documentation. @see: Plane.resizeGeometry() @see: self.update_spinboxes() @see: Plane_EditCommand.command_update_internal_state() """ #This typically gets called when the plane is resized from the #3D workspace (which marks assy as modified) . So, update the spinboxes #that represent the Plane's width and height. self.update_spinboxes() def update_props_if_needed_before_closing(self): """ This updates some cosmetic properties of the Plane (e.g. fill color, border color, etc.) before closing the Property Manager. """ # Example: The Plane Property Manager is open and the user is # 'previewing' the plane. Now the user clicks on "Build > Atoms" # to invoke the next command (without clicking "Done"). # This calls openPropertyManager() which replaces the current PM # with the Build Atoms PM. Thus, it creates and inserts the Plane # that was being previewed. Before the plane is permanently inserted # into the part, it needs to change some of its cosmetic properties # (e.g. fill color, border color, etc.) which distinguishes it as # a new plane in the part. This function changes those properties. # ninad 2007-06-13 #called in updatePropertyManager in MWsemeantics.py --(Partwindow class) EditCommand_PM.update_props_if_needed_before_closing(self) #Don't draw the direction arrow when the object is finalized. if self.command.struct and \ self.command.struct.offsetParentGeometry: dirArrow = self.command.struct.offsetParentGeometry.directionArrow dirArrow.setDrawRequested(False) def updateMessage(self, msg=''): """ Updates the message box with an informative message @param message: Message to be displayed in the Message groupbox of the property manager @type message: string """ self.MessageGroupBox.insertHtmlMessage(msg, setAsDefault=False, minLines=5) def rotate_90(self): """ Rotate the image clockwise. """ if self.command.hasValidStructure(): self.command.struct.rotateImage(0) return def rotate_neg_90(self): """ Rotate the image counterclockwise. """ if self.command.hasValidStructure(): self.command.struct.rotateImage(1) return def flip_image(self): """ Flip the image horizontally. """ if self.command.hasValidStructure(): self.command.struct.mirrorImage(1) return def mirror_image(self): """ Flip the image vertically. """ if self.command.hasValidStructure(): self.command.struct.mirrorImage(0) return
class InsertPeptide_PropertyManager(EditCommand_PM): """ The InsertPeptide_PropertyManager class provides a Property Manager for the "Insert > Peptide" command. """ # The title that appears in the property manager header. title = "Insert Peptide" # The name of this property manager. This will be set to # the name of the PropMgr (this) object via setObjectName(). pmName = title # The relative path to PNG file that appears in the header. iconPath = "ui/actions/Command Toolbar/BuildProtein/InsertPeptide.png" # phi psi angles will define the secondary structure of the peptide chain phi = -57.0 psi = -47.0 chirality = 1 secondary = SS_HELIX current_amino_acid = 7 # Glycine # DEPRECATED ATTRS #peptide_cache = [] #peptide_cache.append((0, 0, 0)) def __init__(self, command): """ Construct the Property Manager. """ _superclass.__init__(self, command) self.showTopRowButtons( PM_DONE_BUTTON | \ PM_CANCEL_BUTTON | \ PM_WHATS_THIS_BUTTON) return def show(self): """ Extends superclass method. """ _superclass.show(self) self.updateMessage("Choose the peptide parameters below, then click "\ "two endpoints in the graphics area to insert a "\ "peptide chain.") return def getParameters(self): """ Return the parameters from this property manager to be used to create the peptide. @return: A tuple containing the parameters @rtype: tuple @see: L{InsertPeptide_EditCommand._gatherParameters()} where this is used """ return (self.secondary, self.phi, self.psi, self.current_amino_acid) def _addGroupBoxes(self): """ Add the group boxe to the Peptide Property Manager dialog. """ self.pmGroupBox1 = \ PM_GroupBox( self, title = "Peptide Parameters" ) # Add group box widgets. self._loadGroupBox1(self.pmGroupBox1) return def _loadGroupBox1(self, inPmGroupBox): """ Load widgets in the group box. """ memberChoices = [ "Custom", "Alpha helix", "Beta strand", "Pi helix", "3_10 helix", "Polyproline-II helix", "Fully extended" ] self.aaTypeComboBox= \ PM_ComboBox( inPmGroupBox, label = "Conformation:", choices = memberChoices, index = 1, setAsDefault = True, spanWidth = False ) self.connect(self.aaTypeComboBox, SIGNAL("currentIndexChanged(int)"), self._aaTypeChanged) self.phiAngleField = \ PM_DoubleSpinBox( inPmGroupBox, label = "Phi angle:", value = self.phi, setAsDefault = True, minimum = -180.0, maximum = 180.0, singleStep = 1.0, decimals = 1, suffix = " degrees") self.connect(self.phiAngleField, SIGNAL("valueChanged(double)"), self._aaPhiAngleChanged) self.phiAngleField.setEnabled(False) self.psiAngleField = \ PM_DoubleSpinBox( inPmGroupBox, label = "Psi angle:", value = self.psi, setAsDefault = True, minimum = -180.0, maximum = 180.0, singleStep = 1.0, decimals = 1, suffix = " degrees" ) self.connect(self.psiAngleField, SIGNAL("valueChanged(double)"), self._aaPsiAngleChanged) self.psiAngleField.setEnabled(False) self.aaTypesButtonGroup = \ PM_ToolButtonGrid( inPmGroupBox, buttonList = AA_BUTTON_LIST, label = "Amino acids", checkedId = self.current_amino_acid, # Glycine setAsDefault = True ) self.connect(self.aaTypesButtonGroup.buttonGroup, SIGNAL("buttonClicked(int)"), self._setAminoAcidType) return def _addWhatsThisText(self): """ What's This text for widgets in this Property Manager. """ from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_InsertPeptide_PropertyManager whatsThis_InsertPeptide_PropertyManager(self) return def _addToolTipText(self): """ Tool Tip text for widgets in this Property Manager. """ from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_InsertPeptide_PropertyManager ToolTip_InsertPeptide_PropertyManager(self) return def _aaChiralityChanged(self): """ Set chirality of the peptide chain. """ # This feature is currently disable as it was confusing to the users # who expected control over chirality of amino acids (D/L conformers) # rather than over polypeptide chain (left/right-handed structure). self.psi *= -1 self.phi *= -1 self.phiAngleField.setValue(self.phi) self.psiAngleField.setValue(self.psi) return def _aaTypeChanged(self, idx): """ Slot for Peptide Structure Type combo box. Changes phi/psi angles for secondary structure. @param idx: index of secondary structure combo box @type idx: int """ self.ss_idx = idx if idx == 0: self.phiAngleField.setEnabled(True) self.psiAngleField.setEnabled(True) else: self.phiAngleField.setEnabled(False) self.psiAngleField.setEnabled(False) if idx == 1: # alpha helix self.phi = -57.0 self.psi = -47.0 self.secondary = SS_HELIX elif idx == 2: # beta strand self.phi = -135.0 self.psi = 135.0 self.secondary = SS_STRAND elif idx == 3: # 3-10 helix self.phi = -55.0 self.psi = -70.0 self.secondary = SS_HELIX elif idx == 4: # pi helix self.phi = -49.0 self.psi = -26.0 self.secondary = SS_HELIX elif idx == 5: # polyprolin-II self.phi = -75.0 self.psi = 150.0 self.secondary = SS_COIL elif idx == 6: # fully extended self.phi = -180.0 self.psi = 180.0 self.secondary = SS_STRAND else: self.phi = self.phiAngleField.value() self.psi = self.psiAngleField.value() self.secondary = SS_COIL self.phi *= self.chirality self.psi *= self.chirality self.command.secondary = self.secondary self.phiAngleField.setValue(self.phi) self.psiAngleField.setValue(self.psi) return def _aaPhiAngleChanged(self, phi): """ Called when phi angle spin box has changed. @param phi: phi angle value @type phi: float """ self.phi = self.phiAngleField.value() return def _aaPsiAngleChanged(self, psi): """ Called when psi angle spin box has changed. @param psi: psi angle value @type psi: float """ self.psi = self.psiAngleField.value() return def _setAminoAcidType(self, index): """ Sets the current amino acid type to I{index}. """ self.current_amino_acid = index return # -------------------------------------------------------------------- # Deprecated methods to keep until we're certain this is working. # --Mark 2008-12-12. def addAminoAcid_DEPRECATED(self, index): """ Adds a new amino acid to the peptide molecule. """ # This commened out code is obsolete in interactive peptide builder. # The interactive peptide builder creates homopeptides. # add a new amino acid and chain conformation to the peptide cache #self.peptide_cache.append((index,self.phi,self.psi)) #self.peptide_cache[0] = (index,self.phi,self.psi) self.current_amino_acid = index return def _setAminoAcidType_DEPRECATED(self, aaTypeIndex): """ Adds a new amino acid to the peptide molecule. """ # piotr 080911: this method is obsolete as of 080911. It was used in # the old Peptide Generator. button, idx, short_name, dum, name, symbol, x, y = AA_BUTTON_LIST[ aaTypeIndex] if self.ss_idx == 1: aa_txt = "<font color=red>" elif self.ss_idx == 2: aa_txt = "<font color=blue>" elif self.ss_idx == 3: aa_txt = "<font color=green>" elif self.ss_idx == 4: aa_txt = "<font color=orange>" elif self.ss_idx == 5: aa_txt = "<font color=magenta>" elif self.ss_idx == 6: aa_txt = "<font color=darkblue>" else: aa_txt = "<font color=black>" aa_txt += symbol + "</font>" #self.sequenceEditor.insertHtml(aa_txt, False, 4, 10, False) return
class PlanePropertyManager(EditCommand_PM): """ The PlanePropertyManager class provides a Property Manager for a (reference) Plane. """ # The title that appears in the Property Manager header. title = "Plane" # The name of this Property Manager. This will be set to # the name of the PM_Dialog object via setObjectName(). pmName = title # The relative path to the PNG file that appears in the header iconPath = "ui/actions/Insert/Reference Geometry/Plane.png" def __init__(self, command): """ Construct the Plane Property Manager. @param plane: The plane. @type plane: L{Plane} """ #see self.connect_or_disconnect_signals for comment about this flag self.isAlreadyConnected = False self.isAlreadyDisconnected = False self.gridColor = black self.gridXSpacing = 4.0 self.gridYSpacing = 4.0 self.gridLineType = 3 self.displayLabels = False self.originLocation = PLANE_ORIGIN_LOWER_LEFT self.displayLabelStyle = LABELS_ALONG_ORIGIN EditCommand_PM.__init__( self, command) # Hide Preview and Restore defaults buttons self.hideTopRowButtons(PM_RESTORE_DEFAULTS_BUTTON) def _addGroupBoxes(self): """ Add the 1st group box to the Property Manager. """ # Placement Options radio button list to create radio button list. # Format: buttonId, buttonText, tooltip PLACEMENT_OPTIONS_BUTTON_LIST = [ \ ( 0, "Parallel to screen", "Parallel to screen" ), ( 1, "Through selected atoms", "Through selected atoms" ), ( 2, "Offset to a plane", "Offset to a plane" ), ( 3, "Custom", "Custom" ) ] self.pmPlacementOptions = \ PM_RadioButtonList( self, title = "Placement Options", buttonList = PLACEMENT_OPTIONS_BUTTON_LIST, checkedId = 3 ) self.pmGroupBox1 = PM_GroupBox(self, title = "Parameters") self._loadGroupBox1(self.pmGroupBox1) #image groupbox self.pmGroupBox2 = PM_GroupBox(self, title = "Image") self._loadGroupBox2(self.pmGroupBox2) #grid plane groupbox self.pmGroupBox3 = PM_GroupBox(self, title = "Grid") self._loadGroupBox3(self.pmGroupBox3) def _loadGroupBox3(self, pmGroupBox): """ Load widgets in the grid plane group box. @param pmGroupBox: The grid group box in the PM. @type pmGroupBox: L{PM_GroupBox} """ self.gridPlaneCheckBox = \ PM_CheckBox( pmGroupBox, text = "Show grid", widgetColumn = 0, setAsDefault = True, spanWidth = True ) connect_checkbox_with_boolean_pref( self.gridPlaneCheckBox , PlanePM_showGrid_prefs_key) self.gpXSpacingDoubleSpinBox = \ PM_DoubleSpinBox( pmGroupBox, label = "X Spacing:", value = 4.000, setAsDefault = True, minimum = 1.00, maximum = 200.0, decimals = 3, singleStep = 1.0, spanWidth = False) self.gpYSpacingDoubleSpinBox = \ PM_DoubleSpinBox( pmGroupBox, label = "Y Spacing:", value = 4.000, setAsDefault = True, minimum = 1.00, maximum = 200.0, decimals = 3, singleStep = 1.0, spanWidth = False) lineTypeChoices = [ 'Dotted (default)', 'Dashed', 'Solid' ] self.gpLineTypeComboBox = \ PM_ComboBox( pmGroupBox , label = "Line type:", choices = lineTypeChoices, setAsDefault = True) hhColorList = [ black, orange, red, magenta, cyan, blue, white, yellow, gray ] hhColorNames = [ "Black (default)", "Orange", "Red", "Magenta", "Cyan", "Blue", "White", "Yellow", "Other color..." ] self.gpColorTypeComboBox = \ PM_ColorComboBox( pmGroupBox, colorList = hhColorList, colorNames = hhColorNames, color = black ) self.pmGroupBox5 = PM_GroupBox( pmGroupBox ) self.gpDisplayLabels =\ PM_CheckBox( self.pmGroupBox5, text = "Display labels", widgetColumn = 0, state = Qt.Unchecked, setAsDefault = True, spanWidth = True ) originChoices = [ 'Lower left (default)', 'Upper left', 'Lower right', 'Upper right' ] self.gpOriginComboBox = \ PM_ComboBox( self.pmGroupBox5 , label = "Origin:", choices = originChoices, setAsDefault = True ) positionChoices = [ 'Origin axes (default)', 'Plane perimeter' ] self.gpPositionComboBox = \ PM_ComboBox( self.pmGroupBox5 , label = "Position:", choices = positionChoices, setAsDefault = True) self._showHideGPWidgets() if env.prefs[PlanePM_showGridLabels_prefs_key]: self.displayLabels = True self.gpOriginComboBox.setEnabled( True ) self.gpPositionComboBox.setEnabled( True ) else: self.displayLabels = False self.gpOriginComboBox.setEnabled( False ) self.gpPositionComboBox.setEnabled( False ) 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: Fix for 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 actually 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 #UPDATE: (comment copied and modifief from BuildNanotube_PropertyManager. #The general problem still remains -- Ninad 2008-06-25 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 change_connect(self.pmPlacementOptions.buttonGroup, SIGNAL("buttonClicked(int)"), self.changePlanePlacement) change_connect(self.widthDblSpinBox, SIGNAL("valueChanged(double)"), self.change_plane_width) change_connect(self.heightDblSpinBox, SIGNAL("valueChanged(double)"), self.change_plane_height) change_connect(self.aspectRatioCheckBox, SIGNAL("stateChanged(int)"), self._enableAspectRatioSpinBox) #signal slot connection for imageDisplayCheckBox change_connect(self.imageDisplayCheckBox, SIGNAL("stateChanged(int)"), self.toggleFileChooserBehavior) #signal slot connection for imageDisplayFileChooser change_connect(self.imageDisplayFileChooser.lineEdit, SIGNAL("editingFinished()"), self.update_imageFile) #signal slot connection for heightfieldDisplayCheckBox change_connect(self.heightfieldDisplayCheckBox, SIGNAL("stateChanged(int)"), self.toggleHeightfield) #signal slot connection for heightfieldHQDisplayCheckBox change_connect(self.heightfieldHQDisplayCheckBox, SIGNAL("stateChanged(int)"), self.toggleHeightfieldHQ) #signal slot connection for heightfieldTextureCheckBox change_connect(self.heightfieldTextureCheckBox, SIGNAL("stateChanged(int)"), self.toggleTexture) #signal slot connection for vScaleSpinBox change_connect(self.vScaleSpinBox, SIGNAL("valueChanged(double)"), self.change_vertical_scale) change_connect(self.plusNinetyButton, SIGNAL("clicked()"), self.rotate_90) change_connect(self.minusNinetyButton, SIGNAL("clicked()"), self.rotate_neg_90) change_connect(self.flipButton, SIGNAL("clicked()"), self.flip_image) change_connect(self.mirrorButton, SIGNAL("clicked()"), self.mirror_image) change_connect(self.gridPlaneCheckBox, SIGNAL("stateChanged(int)"), self.displayGridPlane) change_connect(self.gpXSpacingDoubleSpinBox, SIGNAL("valueChanged(double)"), self.changeXSpacingInGP) change_connect(self.gpYSpacingDoubleSpinBox, SIGNAL("valueChanged(double)"), self.changeYSpacingInGP) change_connect( self.gpLineTypeComboBox, SIGNAL("currentIndexChanged(int)"), self.changeLineTypeInGP ) change_connect( self.gpColorTypeComboBox, SIGNAL("editingFinished()"), self.changeColorTypeInGP ) change_connect( self.gpDisplayLabels, SIGNAL("stateChanged(int)"), self.displayLabelsInGP ) change_connect( self.gpOriginComboBox, SIGNAL("currentIndexChanged(int)"), self.changeOriginInGP ) change_connect( self.gpPositionComboBox, SIGNAL("currentIndexChanged(int)"), self.changePositionInGP ) self._connect_checkboxes_to_global_prefs_keys() return def _connect_checkboxes_to_global_prefs_keys(self): """ """ connect_checkbox_with_boolean_pref( self.gridPlaneCheckBox , PlanePM_showGrid_prefs_key) connect_checkbox_with_boolean_pref( self.gpDisplayLabels, PlanePM_showGridLabels_prefs_key) def changePositionInGP(self, idx): """ Change Display of origin Labels (choices are along origin edges or along the plane perimeter. @param idx: Current index of the change grid label position combo box @type idx: int """ if idx == 0: self.displayLabelStyle = LABELS_ALONG_ORIGIN elif idx == 1: self.displayLabelStyle = LABELS_ALONG_PLANE_EDGES else: print "Invalid index", idx return def changeOriginInGP(self, idx): """ Change Display of origin Labels based on the location of the origin @param idx: Current index of the change origin position combo box @type idx: int """ if idx == 0: self.originLocation = PLANE_ORIGIN_LOWER_LEFT elif idx ==1: self.originLocation = PLANE_ORIGIN_UPPER_LEFT elif idx == 2: self.originLocation = PLANE_ORIGIN_LOWER_RIGHT elif idx == 3: self.originLocation = PLANE_ORIGIN_UPPER_RIGHT else: print "Invalid index", idx return def displayLabelsInGP(self, state): """ Choose to show or hide grid labels @param state: State of the Display Label Checkbox @type state: boolean """ if env.prefs[PlanePM_showGridLabels_prefs_key]: self.gpOriginComboBox.setEnabled(True) self.gpPositionComboBox.setEnabled(True) self.displayLabels = True self.originLocation = PLANE_ORIGIN_LOWER_LEFT self.displayLabelStyle = LABELS_ALONG_ORIGIN else: self.gpOriginComboBox.setEnabled(False) self.gpPositionComboBox.setEnabled(False) self.displayLabels = False return def changeColorTypeInGP(self): """ Change Color of grid """ self.gridColor = self.gpColorTypeComboBox.getColor() return def changeLineTypeInGP(self, idx): """ Change line type in grid @param idx: Current index of the Line type combo box @type idx: int """ #line_type for actually drawing the grid is: 0=None, 1=Solid, 2=Dashed" or 3=Dotted if idx == 0: self.gridLineType = 3 if idx == 1: self.gridLineType = 2 if idx == 2: self.gridLineType = 1 return def changeYSpacingInGP(self, val): """ Change Y spacing on the grid @param val:value of Y spacing @type val: double """ self.gridYSpacing = float(val) return def changeXSpacingInGP(self, val): """ Change X spacing on the grid @param val:value of X spacing @type val: double """ self.gridXSpacing = float(val) return def displayGridPlane(self, state): """ Display or hide grid based on the state of the checkbox @param state: State of the Display Label Checkbox @type state: boolean """ self._showHideGPWidgets() if self.gridPlaneCheckBox.isChecked(): env.prefs[PlanePM_showGrid_prefs_key] = True self._makeGridPlane() else: env.prefs[PlanePM_showGrid_prefs_key] = False return def _makeGridPlane(self): """ Show grid on the plane """ #get all the grid related values in here self.gridXSpacing = float(self.gpXSpacingDoubleSpinBox.value()) self.gridYSpacing = float(self.gpYSpacingDoubleSpinBox.value()) #line_type for actually drawing the grid is: 0=None, 1=Solid, 2=Dashed" or 3=Dotted idx = self.gpLineTypeComboBox.currentIndex() self.changeLineTypeInGP(idx) self.gridColor = self.gpColorTypeComboBox.getColor() return def _showHideGPWidgets(self): """ Enable Disable grid related widgets based on the state of the show grid checkbox. """ if self.gridPlaneCheckBox.isChecked(): self.gpXSpacingDoubleSpinBox.setEnabled(True) self.gpYSpacingDoubleSpinBox.setEnabled(True) self.gpLineTypeComboBox.setEnabled(True) self.gpColorTypeComboBox.setEnabled(True) self.gpDisplayLabels.setEnabled(True) else: self.gpXSpacingDoubleSpinBox.setEnabled(False) self.gpXSpacingDoubleSpinBox.setEnabled(False) self.gpYSpacingDoubleSpinBox.setEnabled(False) self.gpLineTypeComboBox.setEnabled(False) self.gpColorTypeComboBox.setEnabled(False) self.gpDisplayLabels.setEnabled(False) return def _loadGroupBox2(self, pmGroupBox): """ Load widgets in the image group box. @param pmGroupBox: The image group box in the PM. @type pmGroupBox: L{PM_GroupBox} """ self.imageDisplayCheckBox = \ PM_CheckBox( pmGroupBox, text = "Display image", widgetColumn = 0, state = Qt.Unchecked, setAsDefault = True, spanWidth = True ) self.imageDisplayFileChooser = \ PM_FileChooser(pmGroupBox, label = 'Image file:', text = '' , spanWidth = True, filter = "PNG (*.png);;"\ "All Files (*.*)" ) self.imageDisplayFileChooser.setEnabled(False) # add change image properties button BUTTON_LIST = [ ( "QToolButton", 1, "+90", "ui/actions/Properties Manager/RotateImage+90.png", "+90", "", 0), ( "QToolButton", 2, "-90", "ui/actions/Properties Manager/RotateImage-90.png", "-90", "", 1), ( "QToolButton", 3, "FLIP", "ui/actions/Properties Manager/FlipImageVertical.png", "Flip", "", 2), ( "QToolButton", 4, "MIRROR", "ui/actions/Properties Manager/FlipImageHorizontal.png", "Mirror", "", 3) ] #image change button groupbox self.pmGroupBox2 = PM_GroupBox(pmGroupBox, title = "Modify Image") self.imageChangeButtonGroup = \ PM_ToolButtonRow( self.pmGroupBox2, title = "", buttonList = BUTTON_LIST, spanWidth = True, isAutoRaise = False, isCheckable = False, setAsDefault = True, ) self.imageChangeButtonGroup.buttonGroup.setExclusive(False) self.plusNinetyButton = self.imageChangeButtonGroup.getButtonById(1) self.minusNinetyButton = self.imageChangeButtonGroup.getButtonById(2) self.flipButton = self.imageChangeButtonGroup.getButtonById(3) self.mirrorButton = self.imageChangeButtonGroup.getButtonById(4) # buttons enabled when a valid image is loaded self.mirrorButton.setEnabled(False) self.plusNinetyButton.setEnabled(False) self.minusNinetyButton.setEnabled(False) self.flipButton.setEnabled(False) self.heightfieldDisplayCheckBox = \ PM_CheckBox( pmGroupBox, text = "Create 3D relief", widgetColumn = 0, state = Qt.Unchecked, setAsDefault = True, spanWidth = True ) self.heightfieldHQDisplayCheckBox = \ PM_CheckBox( pmGroupBox, text = "High quality", widgetColumn = 0, state = Qt.Unchecked, setAsDefault = True, spanWidth = True ) self.heightfieldTextureCheckBox = \ PM_CheckBox( pmGroupBox, text = "Use texture", widgetColumn = 0, state = Qt.Checked, setAsDefault = True, spanWidth = True ) self.vScaleSpinBox = \ PM_DoubleSpinBox(pmGroupBox, label = " Vertical scale:", value = 1.0, setAsDefault = True, minimum = -1000.0, # -1000 A maximum = 1000.0, # 1000 A singleStep = 0.1, decimals = 1, suffix = ' Angstroms') self.heightfieldDisplayCheckBox.setEnabled(False) self.heightfieldHQDisplayCheckBox.setEnabled(False) self.heightfieldTextureCheckBox.setEnabled(False) self.vScaleSpinBox.setEnabled(False) def _loadGroupBox1(self, pmGroupBox): """ Load widgets in 1st group box. @param pmGroupBox: The 1st group box in the PM. @type pmGroupBox: L{PM_GroupBox} """ self.widthDblSpinBox = \ PM_DoubleSpinBox(pmGroupBox, label = "Width:", value = 16.0, setAsDefault = True, minimum = 1.0, maximum = 10000.0, # 1000 nm singleStep = 1.0, decimals = 1, suffix = ' Angstroms') self.heightDblSpinBox = \ PM_DoubleSpinBox(pmGroupBox, label =" Height:", value = 16.0, setAsDefault = True, minimum = 1.0, maximum = 10000.0, # 1000 nm singleStep = 1.0, decimals = 1, suffix = ' Angstroms') self.aspectRatioCheckBox = \ PM_CheckBox(pmGroupBox, text = 'Maintain Aspect Ratio of:' , widgetColumn = 1, state = Qt.Unchecked ) self.aspectRatioSpinBox = \ PM_DoubleSpinBox( pmGroupBox, label = "", value = 1.0, setAsDefault = True, minimum = 0.1, maximum = 10.0, singleStep = 0.1, decimals = 2, suffix = " to 1.00") if self.aspectRatioCheckBox.isChecked(): self.aspectRatioSpinBox.setEnabled(True) else: self.aspectRatioSpinBox.setEnabled(False) def _addWhatsThisText(self): """ What's This text for some of the widgets in this Property Manager. @note: Many PM widgets are still missing their "What's This" text. """ from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_PlanePropertyManager whatsThis_PlanePropertyManager(self) def toggleFileChooserBehavior(self, checked): """ Enables FileChooser and displays image when checkbox is checked otherwise not """ self.imageDisplayFileChooser.lineEdit.emit(SIGNAL("editingFinished()")) if checked == Qt.Checked: self.imageDisplayFileChooser.setEnabled(True) elif checked == Qt.Unchecked: self.imageDisplayFileChooser.setEnabled(False) # if an image is already displayed, that's need to be hidden as well else: pass self.command.struct.glpane.gl_update() def toggleHeightfield(self, checked): """ Enables 3D relief drawing mode. """ if self.command and self.command.struct: plane = self.command.struct plane.display_heightfield = checked if checked: self.heightfieldHQDisplayCheckBox.setEnabled(True) self.heightfieldTextureCheckBox.setEnabled(True) self.vScaleSpinBox.setEnabled(True) plane.computeHeightfield() else: self.heightfieldHQDisplayCheckBox.setEnabled(False) self.heightfieldTextureCheckBox.setEnabled(False) self.vScaleSpinBox.setEnabled(False) plane.heightfield = None plane.glpane.gl_update() def toggleHeightfieldHQ(self, checked): """ Enables high quality rendering in 3D relief mode. """ if self.command and self.command.struct: plane = self.command.struct plane.heightfield_hq = checked plane.computeHeightfield() plane.glpane.gl_update() def toggleTexture(self, checked): """ Enables texturing in 3D relief mode. """ if self.command and self.command.struct: plane = self.command.struct plane.heightfield_use_texture = checked # It is not necessary to re-compute the heightfield coordinates # at this point, they are re-computed whenever the "3D relief image" # checkbox is set. plane.glpane.gl_update() def update_spinboxes(self): """ Update the width and height spinboxes. @see: Plane.resizeGeometry() This typically gets called when the plane is resized from the 3D workspace (which marks assy as modified) .So, update the spinboxes that represent the Plane's width and height, but do no emit 'valueChanged' signal when the spinbox value changes. @see: Plane.resizeGeometry() @see: self._update_UI_do_updates() @see: Plane_EditCommand.command_update_internal_state() """ # blockSignals = True make sure that spinbox.valueChanged() # signal is not emitted after calling spinbox.setValue(). This is done #because the spinbox valu changes as a result of resizing the plane #from the 3D workspace. if self.command.hasValidStructure(): self.heightDblSpinBox.setValue(self.command.struct.height, blockSignals = True) self.widthDblSpinBox.setValue(self.command.struct.width, blockSignals = True) def update_imageFile(self): """ Loads image file if path is valid """ # Update buttons and checkboxes. self.mirrorButton.setEnabled(False) self.plusNinetyButton.setEnabled(False) self.minusNinetyButton.setEnabled(False) self.flipButton.setEnabled(False) self.heightfieldDisplayCheckBox.setEnabled(False) self.heightfieldHQDisplayCheckBox.setEnabled(False) self.heightfieldTextureCheckBox.setEnabled(False) self.vScaleSpinBox.setEnabled(False) plane = self.command.struct # Delete current image and heightfield plane.deleteImage() plane.heightfield = None plane.display_image = self.imageDisplayCheckBox.isChecked() if plane.display_image: imageFile = str(self.imageDisplayFileChooser.lineEdit.text()) from model.Plane import checkIfValidImagePath validPath = checkIfValidImagePath(imageFile) if validPath: from PIL import Image # Load image from file plane.image = Image.open(imageFile) plane.loadImage(imageFile) # Compute the relief image plane.computeHeightfield() if plane.image: self.mirrorButton.setEnabled(True) self.plusNinetyButton.setEnabled(True) self.minusNinetyButton.setEnabled(True) self.flipButton.setEnabled(True) self.heightfieldDisplayCheckBox.setEnabled(True) if plane.display_heightfield: self.heightfieldHQDisplayCheckBox.setEnabled(True) self.heightfieldTextureCheckBox.setEnabled(True) self.vScaleSpinBox.setEnabled(True) def show(self): """ Show the Plane Property Manager. """ EditCommand_PM.show(self) #It turns out that if updateCosmeticProps is called before #EditCommand_PM.show, the 'preview' properties are not updated #when you are editing an existing plane. Don't know the cause at this #time, issue is trivial. So calling it in the end -- Ninad 2007-10-03 if self.command.struct: plane = self.command.struct plane.updateCosmeticProps(previewing = True) if plane.imagePath: self.imageDisplayFileChooser.setText(plane.imagePath) self.imageDisplayCheckBox.setChecked(plane.display_image) #Make sure that the plane placement option is always set to #'Custom' when the Plane PM is shown. This makes sure that bugs like #2949 won't occur. Let the user change the plane placement option #explicitely button = self.pmPlacementOptions.getButtonById(3) button.setChecked(True) def setParameters(self, params): """ """ width, height, gridColor, gridLineType, \ gridXSpacing, gridYSpacing, originLocation, \ displayLabelStyle = params # blockSignals = True flag makes sure that the # spinbox.valueChanged() # signal is not emitted after calling spinbox.setValue(). self.widthDblSpinBox.setValue(width, blockSignals = True) self.heightDblSpinBox.setValue(height, blockSignals = True) self.win.glpane.gl_update() self.gpColorTypeComboBox.setColor(gridColor) self.gridLineType = gridLineType self.gpXSpacingDoubleSpinBox.setValue(gridXSpacing) self.gpYSpacingDoubleSpinBox.setValue(gridYSpacing) self.gpOriginComboBox.setCurrentIndex(originLocation) self.gpPositionComboBox.setCurrentIndex(displayLabelStyle) def getCurrrentDisplayParams(self): """ Returns a tuple containing current display parameters such as current image path and grid display params. @see: Plane_EditCommand.command_update_internal_state() which uses this to decide whether to modify the structure (e.g. because of change in the image path or display parameters.) """ imagePath = self.imageDisplayFileChooser.text gridColor = self.gpColorTypeComboBox.getColor() return (imagePath, gridColor, self.gridLineType, self.gridXSpacing, self.gridYSpacing, self.originLocation, self.displayLabelStyle) def getParameters(self): """ """ width = self.widthDblSpinBox.value() height = self.heightDblSpinBox.value() gridColor = self.gpColorTypeComboBox.getColor() params = (width, height, gridColor, self.gridLineType, self.gridXSpacing, self.gridYSpacing, self.originLocation, self.displayLabelStyle) return params def change_plane_width(self, newWidth): """ Slot for width spinbox in the Property Manager. @param newWidth: width in Angstroms. @type newWidth: float """ if self.aspectRatioCheckBox.isChecked(): self.command.struct.width = newWidth self.command.struct.height = self.command.struct.width / \ self.aspectRatioSpinBox.value() self.update_spinboxes() else: self.change_plane_size() self._updateAspectRatio() def change_plane_height(self, newHeight): """ Slot for height spinbox in the Property Manager. @param newHeight: height in Angstroms. @type newHeight: float """ if self.aspectRatioCheckBox.isChecked(): self.command.struct.height = newHeight self.command.struct.width = self.command.struct.height * \ self.aspectRatioSpinBox.value() self.update_spinboxes() else: self.change_plane_size() self._updateAspectRatio() def change_plane_size(self, gl_update = True): """ Slot to change the Plane's width and height. @param gl_update: Forces an update of the glpane. @type gl_update: bool """ self.command.struct.width = self.widthDblSpinBox.value() self.command.struct.height = self.heightDblSpinBox.value() if gl_update: self.command.struct.glpane.gl_update() def change_vertical_scale(self, scale): """ Changes vertical scaling of the heightfield. """ if self.command and self.command.struct: plane = self.command.struct plane.heightfield_scale = scale plane.computeHeightfield() plane.glpane.gl_update() def changePlanePlacement(self, buttonId): """ Slot to change the placement of the plane depending upon the option checked in the "Placement Options" group box of the PM. @param buttonId: The button id of the selected radio button (option). @type buttonId: int """ if buttonId == 0: msg = "Create a Plane parallel to the screen. "\ "With <b>Parallel to Screen</b> plane placement option, the "\ "center of the plane is always (0,0,0)" self.updateMessage(msg) self.command.placePlaneParallelToScreen() elif buttonId == 1: msg = "Create a Plane with center coinciding with the common center "\ "of <b> 3 or more selected atoms </b>. If exactly 3 atoms are "\ "selected, the Plane will pass through those atoms." self.updateMessage(msg) self.command.placePlaneThroughAtoms() if self.command.logMessage: env.history.message(self.command.logMessage) elif buttonId == 2: msg = "Create a Plane at an <b>offset</b> to the selected plane "\ "indicated by the direction arrow. "\ "you can click on the direction arrow to reverse its direction." self.updateMessage(msg) self.command.placePlaneOffsetToAnother() if self.command.logMessage: env.history.message(self.command.logMessage) elif buttonId == 3: #'Custom' plane placement. Do nothing (only update message box) # Fixes bug 2439 msg = "Create a plane with a <b>Custom</b> plane placement. "\ "The plane is placed parallel to the screen, with "\ "center at (0, 0, 0). User can then modify the plane placement." self.updateMessage(msg) def _enableAspectRatioSpinBox(self, enable): """ Slot for "Maintain Aspect Ratio" checkbox which enables or disables the Aspect Ratio spin box. @param enable: True = enable, False = disable. @type enable: bool """ self.aspectRatioSpinBox.setEnabled(enable) def _updateAspectRatio(self): """ Updates the Aspect Ratio spin box based on the current width and height. """ aspectRatio = self.command.struct.width / self.command.struct.height self.aspectRatioSpinBox.setValue(aspectRatio) def _update_UI_do_updates(self): """ Overrides superclass method. @see: Command_PropertyManager._update_UI_do_updates() for documentation. @see: Plane.resizeGeometry() @see: self.update_spinboxes() @see: Plane_EditCommand.command_update_internal_state() """ #This typically gets called when the plane is resized from the #3D workspace (which marks assy as modified) . So, update the spinboxes #that represent the Plane's width and height. self.update_spinboxes() def update_props_if_needed_before_closing(self): """ This updates some cosmetic properties of the Plane (e.g. fill color, border color, etc.) before closing the Property Manager. """ # Example: The Plane Property Manager is open and the user is # 'previewing' the plane. Now the user clicks on "Build > Atoms" # to invoke the next command (without clicking "Done"). # This calls openPropertyManager() which replaces the current PM # with the Build Atoms PM. Thus, it creates and inserts the Plane # that was being previewed. Before the plane is permanently inserted # into the part, it needs to change some of its cosmetic properties # (e.g. fill color, border color, etc.) which distinguishes it as # a new plane in the part. This function changes those properties. # ninad 2007-06-13 #called in updatePropertyManager in MWsemeantics.py --(Partwindow class) EditCommand_PM.update_props_if_needed_before_closing(self) #Don't draw the direction arrow when the object is finalized. if self.command.struct and \ self.command.struct.offsetParentGeometry: dirArrow = self.command.struct.offsetParentGeometry.directionArrow dirArrow.setDrawRequested(False) def updateMessage(self, msg = ''): """ Updates the message box with an informative message @param message: Message to be displayed in the Message groupbox of the property manager @type message: string """ self.MessageGroupBox.insertHtmlMessage(msg, setAsDefault = False, minLines = 5) def rotate_90(self): """ Rotate the image clockwise. """ if self.command.hasValidStructure(): self.command.struct.rotateImage(0) return def rotate_neg_90(self): """ Rotate the image counterclockwise. """ if self.command.hasValidStructure(): self.command.struct.rotateImage(1) return def flip_image(self): """ Flip the image horizontally. """ if self.command.hasValidStructure(): self.command.struct.mirrorImage(1) return def mirror_image(self): """ Flip the image vertically. """ if self.command.hasValidStructure(): self.command.struct.mirrorImage(0) return
class PeptideGeneratorPropertyManager(PM_Dialog): """ The PeptideGeneratorPropertyManager class provides a Property Manager for the "Build > Peptide" command. """ # The title that appears in the property manager header. title = "Peptide Generator" # The name of this property manager. This will be set to # the name of the PropMgr (this) object via setObjectName(). pmName = title # The relative path to PNG file that appears in the header. iconPath = "ui/actions/Tools/Build Structures/Peptide.png" def __init__(self): """Construct the Peptide Property Manager. """ PM_Dialog.__init__(self, self.pmName, self.iconPath, self.title) # phi psi angles will define the secondary structure of the peptide chain self.phi = -57.0 self.psi = -47.0 self.chirality = 1 self.ss_idx = 1 self.peptide_cache = [] self.updateMessageGroupBox() def updateMessageGroupBox(self): msg = "" msg = msg + "Click on the Amino Acid buttons to add a new residuum to\ the polypeptide chain. Click <b>Done</b> to insert it into the project." # This causes the "Message" box to be displayed as well. # setAsDefault=True causes this message to be reset whenever # this PropMgr is (re)displayed via show(). Mark 2007-06-01. self.MessageGroupBox.insertHtmlMessage(msg, setAsDefault=True) def _addGroupBoxes(self): """ Add the group boxe to the Peptide Property Manager dialog. """ self.pmGroupBox1 = \ PM_GroupBox( self, title = "Peptide Parameters" ) # Add group box widgets. self._loadGroupBox1(self.pmGroupBox1) def _loadGroupBox1(self, inPmGroupBox): """ Load widgets in the group box. """ memberChoices = ["Custom", "Alpha helix", "Beta strand", "Pi helix", "3_10 helix", "Polyproline-II helix", "Fully extended"] self.aaTypeComboBox= \ PM_ComboBox( inPmGroupBox, label = "Conformation :", choices = memberChoices, index = 1, setAsDefault = True, spanWidth = False ) self.connect( self.aaTypeComboBox, SIGNAL("currentIndexChanged(int)"), self._aaTypeChanged) self.phiAngleField = \ PM_DoubleSpinBox( inPmGroupBox, label = "Phi angle :", value = -57.0, setAsDefault = True, minimum = -180.0, maximum = 180.0, singleStep = 1.0, decimals = 1, suffix = " degrees") self.connect( self.phiAngleField, SIGNAL("valueChanged(double)"), self._aaPhiAngleChanged) self.phiAngleField.setEnabled(False) self.psiAngleField = \ PM_DoubleSpinBox( inPmGroupBox, label = "Psi angle :", value = -47.0, setAsDefault = True, minimum = -180.0, maximum = 180.0, singleStep = 1.0, decimals = 1, suffix = " degrees" ) self.connect( self.psiAngleField, SIGNAL("valueChanged(double)"), self._aaPsiAngleChanged) self.psiAngleField.setEnabled(False) self.invertChiralityPushButton = \ PM_PushButton( inPmGroupBox, text = 'Invert chirality' , spanWidth = False ) self.connect(self.invertChiralityPushButton, SIGNAL("clicked()"), self._aaChiralityChanged) self.aaTypesButtonGroup = \ PM_ToolButtonGrid( inPmGroupBox, buttonList = AA_BUTTON_LIST, label = "Amino acids :", checkedId = 0, setAsDefault = True ) self.connect( self.aaTypesButtonGroup.buttonGroup, SIGNAL("buttonClicked(int)"), self._setAminoAcidType) self.sequenceEditor = \ PM_TextEdit( inPmGroupBox, label = "Sequence", spanWidth = True ) self.sequenceEditor.insertHtml("", False, 4, 10, True) self.sequenceEditor.setReadOnly(True) self.startOverButton = \ PM_PushButton( inPmGroupBox, label = "", text = "Start Over", spanWidth = True, setAsDefault = True ) self.connect( self.startOverButton, SIGNAL("clicked()"), self._startOverClicked) def _addWhatsThisText(self): """ What's This text for widgets in this Property Manager. """ from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_PeptideGeneratorPropertyManager whatsThis_PeptideGeneratorPropertyManager(self) def _addToolTipText(self): """ Tool Tip text for widgets in this Property Manager. """ from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_PeptideGeneratorPropertyManager ToolTip_PeptideGeneratorPropertyManager(self) def _aaChiralityChanged(self): """ Set chirality of the peptide chain. """ self.psi *= -1 self.phi *= -1 self.phiAngleField.setValue(self.phi) self.psiAngleField.setValue(self.psi) def _aaTypeChanged(self, idx): """ Slot for Peptide Structure Type combobox. Changes phi/psi angles for secondary structure. """ self.ss_idx = idx if idx == 0: self.phiAngleField.setEnabled(True) self.psiAngleField.setEnabled(True) else: self.phiAngleField.setEnabled(False) self.psiAngleField.setEnabled(False) if idx == 1: # alpha helix self.phi = -57.0 self.psi = -47.0 elif idx == 2: # beta strand self.phi = -135.0 self.psi = 135.0 elif idx == 3: # 3-10 helix self.phi = -55.0 self.psi = -70.0 elif idx == 4: # pi helix self.phi = -49.0 self.psi = -26.0 elif idx == 5: # polyprolin-II self.phi = -75.0 self.psi = 150.0 elif idx == 6: # fully extended self.phi = -180.0 self.psi = 180.0 else: self.phi = self.phiAngleField.value() self.psi = self.psiAngleField.value() self.phi *= self.chirality self.psi *= self.chirality self.phiAngleField.setValue(self.phi) self.psiAngleField.setValue(self.psi) pass def _aaPhiAngleChanged(self, phi): self.phi = self.phiAngleField.value() pass def _aaPsiAngleChanged(self, psi): self.psi = self.psiAngleField.value() pass def _setAminoAcidType(self, aaTypeIndex): """ Adds a new amino acid to the peptide molecule. """ button, idx, short_name, dum, name, symbol, x, y = AA_BUTTON_LIST[aaTypeIndex] if self.ss_idx==1: aa_txt = "<font color=red>" elif self.ss_idx==2: aa_txt = "<font color=blue>" elif self.ss_idx==3: aa_txt = "<font color=green>" elif self.ss_idx==4: aa_txt = "<font color=orange>" elif self.ss_idx==5: aa_txt = "<font color=magenta>" elif self.ss_idx==6: aa_txt = "<font color=darkblue>" else: aa_txt = "<font color=black>" aa_txt += symbol+"</font>" self.sequenceEditor.insertHtml(aa_txt, False, 4, 10, False) self.addAminoAcid(aaTypeIndex) pass def _startOverClicked(self): """ Resets a sequence in the sequence editor window. """ self.sequenceEditor.clear() self.peptide_cache = [] pass
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 PeptideGeneratorPropertyManager(PM_Dialog): """ The PeptideGeneratorPropertyManager class provides a Property Manager for the "Build > Peptide" command. """ # The title that appears in the property manager header. title = "Peptide Generator" # The name of this property manager. This will be set to # the name of the PropMgr (this) object via setObjectName(). pmName = title # The relative path to PNG file that appears in the header. iconPath = "ui/actions/Tools/Build Structures/Peptide.png" def __init__(self): """Construct the Peptide Property Manager. """ PM_Dialog.__init__(self, self.pmName, self.iconPath, self.title) # phi psi angles will define the secondary structure of the peptide chain self.phi = -57.0 self.psi = -47.0 self.chirality = 1 self.ss_idx = 1 self.peptide_cache = [] self.updateMessageGroupBox() def updateMessageGroupBox(self): msg = "" msg = msg + "Click on the Amino Acid buttons to add a new residuum to\ the polypeptide chain. Click <b>Done</b> to insert it into the project." # This causes the "Message" box to be displayed as well. # setAsDefault=True causes this message to be reset whenever # this PropMgr is (re)displayed via show(). Mark 2007-06-01. self.MessageGroupBox.insertHtmlMessage(msg, setAsDefault=True) def _addGroupBoxes(self): """ Add the group boxe to the Peptide Property Manager dialog. """ self.pmGroupBox1 = \ PM_GroupBox( self, title = "Peptide Parameters" ) # Add group box widgets. self._loadGroupBox1(self.pmGroupBox1) def _loadGroupBox1(self, inPmGroupBox): """ Load widgets in the group box. """ memberChoices = [ "Custom", "Alpha helix", "Beta strand", "Pi helix", "3_10 helix", "Polyproline-II helix", "Fully extended" ] self.aaTypeComboBox= \ PM_ComboBox( inPmGroupBox, label = "Conformation :", choices = memberChoices, index = 1, setAsDefault = True, spanWidth = False ) self.connect(self.aaTypeComboBox, SIGNAL("currentIndexChanged(int)"), self._aaTypeChanged) self.phiAngleField = \ PM_DoubleSpinBox( inPmGroupBox, label = "Phi angle :", value = -57.0, setAsDefault = True, minimum = -180.0, maximum = 180.0, singleStep = 1.0, decimals = 1, suffix = " degrees") self.connect(self.phiAngleField, SIGNAL("valueChanged(double)"), self._aaPhiAngleChanged) self.phiAngleField.setEnabled(False) self.psiAngleField = \ PM_DoubleSpinBox( inPmGroupBox, label = "Psi angle :", value = -47.0, setAsDefault = True, minimum = -180.0, maximum = 180.0, singleStep = 1.0, decimals = 1, suffix = " degrees" ) self.connect(self.psiAngleField, SIGNAL("valueChanged(double)"), self._aaPsiAngleChanged) self.psiAngleField.setEnabled(False) self.invertChiralityPushButton = \ PM_PushButton( inPmGroupBox, text = 'Invert chirality' , spanWidth = False ) self.connect(self.invertChiralityPushButton, SIGNAL("clicked()"), self._aaChiralityChanged) self.aaTypesButtonGroup = \ PM_ToolButtonGrid( inPmGroupBox, buttonList = AA_BUTTON_LIST, label = "Amino acids :", checkedId = 0, setAsDefault = True ) self.connect(self.aaTypesButtonGroup.buttonGroup, SIGNAL("buttonClicked(int)"), self._setAminoAcidType) self.sequenceEditor = \ PM_TextEdit( inPmGroupBox, label = "Sequence", spanWidth = True ) self.sequenceEditor.insertHtml("", False, 4, 10, True) self.sequenceEditor.setReadOnly(True) self.startOverButton = \ PM_PushButton( inPmGroupBox, label = "", text = "Start Over", spanWidth = True, setAsDefault = True ) self.connect(self.startOverButton, SIGNAL("clicked()"), self._startOverClicked) def _addWhatsThisText(self): """ What's This text for widgets in this Property Manager. """ from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_PeptideGeneratorPropertyManager whatsThis_PeptideGeneratorPropertyManager(self) def _addToolTipText(self): """ Tool Tip text for widgets in this Property Manager. """ from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_PeptideGeneratorPropertyManager ToolTip_PeptideGeneratorPropertyManager(self) def _aaChiralityChanged(self): """ Set chirality of the peptide chain. """ self.psi *= -1 self.phi *= -1 self.phiAngleField.setValue(self.phi) self.psiAngleField.setValue(self.psi) def _aaTypeChanged(self, idx): """ Slot for Peptide Structure Type combobox. Changes phi/psi angles for secondary structure. """ self.ss_idx = idx if idx == 0: self.phiAngleField.setEnabled(True) self.psiAngleField.setEnabled(True) else: self.phiAngleField.setEnabled(False) self.psiAngleField.setEnabled(False) if idx == 1: # alpha helix self.phi = -57.0 self.psi = -47.0 elif idx == 2: # beta strand self.phi = -135.0 self.psi = 135.0 elif idx == 3: # 3-10 helix self.phi = -55.0 self.psi = -70.0 elif idx == 4: # pi helix self.phi = -49.0 self.psi = -26.0 elif idx == 5: # polyprolin-II self.phi = -75.0 self.psi = 150.0 elif idx == 6: # fully extended self.phi = -180.0 self.psi = 180.0 else: self.phi = self.phiAngleField.value() self.psi = self.psiAngleField.value() self.phi *= self.chirality self.psi *= self.chirality self.phiAngleField.setValue(self.phi) self.psiAngleField.setValue(self.psi) pass def _aaPhiAngleChanged(self, phi): self.phi = self.phiAngleField.value() pass def _aaPsiAngleChanged(self, psi): self.psi = self.psiAngleField.value() pass def _setAminoAcidType(self, aaTypeIndex): """ Adds a new amino acid to the peptide molecule. """ button, idx, short_name, dum, name, symbol, x, y = AA_BUTTON_LIST[ aaTypeIndex] if self.ss_idx == 1: aa_txt = "<font color=red>" elif self.ss_idx == 2: aa_txt = "<font color=blue>" elif self.ss_idx == 3: aa_txt = "<font color=green>" elif self.ss_idx == 4: aa_txt = "<font color=orange>" elif self.ss_idx == 5: aa_txt = "<font color=magenta>" elif self.ss_idx == 6: aa_txt = "<font color=darkblue>" else: aa_txt = "<font color=black>" aa_txt += symbol + "</font>" self.sequenceEditor.insertHtml(aa_txt, False, 4, 10, False) self.addAminoAcid(aaTypeIndex) pass def _startOverClicked(self): """ Resets a sequence in the sequence editor window. """ self.sequenceEditor.clear() self.peptide_cache = [] pass
class InsertPeptide_PropertyManager(EditCommand_PM): """ The InsertPeptide_PropertyManager class provides a Property Manager for the "Insert > Peptide" command. """ # The title that appears in the property manager header. title = "Insert Peptide" # The name of this property manager. This will be set to # the name of the PropMgr (this) object via setObjectName(). pmName = title # The relative path to PNG file that appears in the header. iconPath = "ui/actions/Command Toolbar/BuildProtein/InsertPeptide.png" # phi psi angles will define the secondary structure of the peptide chain phi = -57.0 psi = -47.0 chirality = 1 secondary = SS_HELIX current_amino_acid = 7 # Glycine # DEPRECATED ATTRS #peptide_cache = [] #peptide_cache.append((0, 0, 0)) def __init__( self, command ): """ Construct the Property Manager. """ _superclass.__init__( self, command ) self.showTopRowButtons( PM_DONE_BUTTON | \ PM_CANCEL_BUTTON | \ PM_WHATS_THIS_BUTTON) return def show(self): """ Extends superclass method. """ _superclass.show(self) self.updateMessage("Choose the peptide parameters below, then click "\ "two endpoints in the graphics area to insert a "\ "peptide chain.") return def getParameters(self): """ Return the parameters from this property manager to be used to create the peptide. @return: A tuple containing the parameters @rtype: tuple @see: L{InsertPeptide_EditCommand._gatherParameters()} where this is used """ return (self.secondary, self.phi, self.psi, self.current_amino_acid) def _addGroupBoxes(self): """ Add the group boxe to the Peptide Property Manager dialog. """ self.pmGroupBox1 = \ PM_GroupBox( self, title = "Peptide Parameters" ) # Add group box widgets. self._loadGroupBox1(self.pmGroupBox1) return def _loadGroupBox1(self, inPmGroupBox): """ Load widgets in the group box. """ memberChoices = ["Custom", "Alpha helix", "Beta strand", "Pi helix", "3_10 helix", "Polyproline-II helix", "Fully extended"] self.aaTypeComboBox= \ PM_ComboBox( inPmGroupBox, label = "Conformation:", choices = memberChoices, index = 1, setAsDefault = True, spanWidth = False ) self.connect( self.aaTypeComboBox, SIGNAL("currentIndexChanged(int)"), self._aaTypeChanged) self.phiAngleField = \ PM_DoubleSpinBox( inPmGroupBox, label = "Phi angle:", value = self.phi, setAsDefault = True, minimum = -180.0, maximum = 180.0, singleStep = 1.0, decimals = 1, suffix = " degrees") self.connect( self.phiAngleField, SIGNAL("valueChanged(double)"), self._aaPhiAngleChanged) self.phiAngleField.setEnabled(False) self.psiAngleField = \ PM_DoubleSpinBox( inPmGroupBox, label = "Psi angle:", value = self.psi, setAsDefault = True, minimum = -180.0, maximum = 180.0, singleStep = 1.0, decimals = 1, suffix = " degrees" ) self.connect( self.psiAngleField, SIGNAL("valueChanged(double)"), self._aaPsiAngleChanged) self.psiAngleField.setEnabled(False) self.aaTypesButtonGroup = \ PM_ToolButtonGrid( inPmGroupBox, buttonList = AA_BUTTON_LIST, label = "Amino acids", checkedId = self.current_amino_acid, # Glycine setAsDefault = True ) self.connect( self.aaTypesButtonGroup.buttonGroup, SIGNAL("buttonClicked(int)"), self._setAminoAcidType) return def _addWhatsThisText(self): """ What's This text for widgets in this Property Manager. """ from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_InsertPeptide_PropertyManager whatsThis_InsertPeptide_PropertyManager(self) return def _addToolTipText(self): """ Tool Tip text for widgets in this Property Manager. """ from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_InsertPeptide_PropertyManager ToolTip_InsertPeptide_PropertyManager(self) return def _aaChiralityChanged(self): """ Set chirality of the peptide chain. """ # This feature is currently disable as it was confusing to the users # who expected control over chirality of amino acids (D/L conformers) # rather than over polypeptide chain (left/right-handed structure). self.psi *= -1 self.phi *= -1 self.phiAngleField.setValue(self.phi) self.psiAngleField.setValue(self.psi) return def _aaTypeChanged(self, idx): """ Slot for Peptide Structure Type combo box. Changes phi/psi angles for secondary structure. @param idx: index of secondary structure combo box @type idx: int """ self.ss_idx = idx if idx == 0: self.phiAngleField.setEnabled(True) self.psiAngleField.setEnabled(True) else: self.phiAngleField.setEnabled(False) self.psiAngleField.setEnabled(False) if idx == 1: # alpha helix self.phi = -57.0 self.psi = -47.0 self.secondary = SS_HELIX elif idx == 2: # beta strand self.phi = -135.0 self.psi = 135.0 self.secondary = SS_STRAND elif idx == 3: # 3-10 helix self.phi = -55.0 self.psi = -70.0 self.secondary = SS_HELIX elif idx == 4: # pi helix self.phi = -49.0 self.psi = -26.0 self.secondary = SS_HELIX elif idx == 5: # polyprolin-II self.phi = -75.0 self.psi = 150.0 self.secondary = SS_COIL elif idx == 6: # fully extended self.phi = -180.0 self.psi = 180.0 self.secondary = SS_STRAND else: self.phi = self.phiAngleField.value() self.psi = self.psiAngleField.value() self.secondary = SS_COIL self.phi *= self.chirality self.psi *= self.chirality self.command.secondary = self.secondary self.phiAngleField.setValue(self.phi) self.psiAngleField.setValue(self.psi) return def _aaPhiAngleChanged(self, phi): """ Called when phi angle spin box has changed. @param phi: phi angle value @type phi: float """ self.phi = self.phiAngleField.value() return def _aaPsiAngleChanged(self, psi): """ Called when psi angle spin box has changed. @param psi: psi angle value @type psi: float """ self.psi = self.psiAngleField.value() return def _setAminoAcidType(self, index): """ Sets the current amino acid type to I{index}. """ self.current_amino_acid = index return # -------------------------------------------------------------------- # Deprecated methods to keep until we're certain this is working. # --Mark 2008-12-12. def addAminoAcid_DEPRECATED(self, index): """ Adds a new amino acid to the peptide molecule. """ # This commened out code is obsolete in interactive peptide builder. # The interactive peptide builder creates homopeptides. # add a new amino acid and chain conformation to the peptide cache #self.peptide_cache.append((index,self.phi,self.psi)) #self.peptide_cache[0] = (index,self.phi,self.psi) self.current_amino_acid = index return def _setAminoAcidType_DEPRECATED(self, aaTypeIndex): """ Adds a new amino acid to the peptide molecule. """ # piotr 080911: this method is obsolete as of 080911. It was used in # the old Peptide Generator. button, idx, short_name, dum, name, symbol, x, y = AA_BUTTON_LIST[aaTypeIndex] if self.ss_idx==1: aa_txt = "<font color=red>" elif self.ss_idx==2: aa_txt = "<font color=blue>" elif self.ss_idx==3: aa_txt = "<font color=green>" elif self.ss_idx==4: aa_txt = "<font color=orange>" elif self.ss_idx==5: aa_txt = "<font color=magenta>" elif self.ss_idx==6: aa_txt = "<font color=darkblue>" else: aa_txt = "<font color=black>" aa_txt += symbol+"</font>" #self.sequenceEditor.insertHtml(aa_txt, False, 4, 10, False) return