# Copyright 2004-2008 Nanorex, Inc. See LICENSE file for details. """ InsertDna_PropertyManager.py @author: Mark Sims @version: $Id$ @copyright: 2004-2008 Nanorex, Inc. See LICENSE file for details. Mark 2007-10-18: - Created. Major rewrite of DnaGeneratorPropertyManager.py. Ninad 2007-10-24: - Another major rewrite to a) use EditCommand_PM superclass and b) Implement feature to generate Dna using endpoints of a line. """ import foundation.env as env from dna.model.Dna_Constants import getDuplexBasesPerTurn, getDuplexRise, getDuplexLength from utilities.Log import redmsg ##, greenmsg, orangemsg from PyQt4.Qt import SIGNAL from PyQt4.Qt import Qt from PyQt4.Qt import QAction from PM.PM_ComboBox import PM_ComboBox from PM.PM_DoubleSpinBox import PM_DoubleSpinBox from PM.PM_GroupBox import PM_GroupBox from PM.PM_SpinBox import PM_SpinBox from PM.PM_LineEdit import PM_LineEdit from PM.PM_ToolButton import PM_ToolButton from PM.PM_CoordinateSpinBoxes import PM_CoordinateSpinBoxes from PM.PM_CheckBox import PM_CheckBox from command_support.DnaOrCnt_PropertyManager import DnaOrCnt_PropertyManager from geometry.VQT import V from PM.PM_Constants import PM_DONE_BUTTON from PM.PM_Constants import PM_WHATS_THIS_BUTTON from PM.PM_Constants import PM_CANCEL_BUTTON from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_InsertDna_PropertyManager from utilities.prefs_constants import dnaDuplexEditCommand_cursorTextCheckBox_angle_prefs_key from utilities.prefs_constants import dnaDuplexEditCommand_cursorTextCheckBox_length_prefs_key from utilities.prefs_constants import dnaDuplexEditCommand_cursorTextCheckBox_numberOfBasePairs_prefs_key from utilities.prefs_constants import dnaDuplexEditCommand_cursorTextCheckBox_numberOfTurns_prefs_key from utilities.prefs_constants import dnaDuplexEditCommand_showCursorTextCheckBox_prefs_key from widgets.prefs_widgets import connect_checkbox_with_boolean_pref from utilities.prefs_constants import bdnaBasesPerTurn_prefs_key from utilities.prefs_constants import bdnaRise_prefs_key from widgets.prefs_widgets import Preferences_StateRef_double _superclass = DnaOrCnt_PropertyManager class InsertDna_PropertyManager( DnaOrCnt_PropertyManager ): """ The InsertDna_PropertyManager class provides a Property Manager for the B{Insert Dna} command. @ivar title: The title that appears in the property manager header. @type title: str @ivar pmName: The name of this property manager. This is used to set the name of the PM_Dialog object via setObjectName(). @type name: str @ivar iconPath: The relative path to the PNG file that contains a 22 x 22 icon image that appears in the PM header. @type iconPath: str """ title = "Insert DNA" pmName = title iconPath = "ui/actions/Command Toolbar/BuildDna/InsertDna.png" def __init__( self, command ): """ Constructor for the DNA Duplex property manager. """ self.endPoint1 = None self.endPoint2 = None self._conformation = "B-DNA" self._numberOfBases = 0 self._basesPerTurn = getDuplexBasesPerTurn(self._conformation) self._duplexRise = getDuplexRise(self._conformation) self._duplexLength = getDuplexLength(self._conformation, self._numberOfBases) _superclass.__init__( self, command) self.showTopRowButtons( PM_DONE_BUTTON | \ PM_CANCEL_BUTTON | \ PM_WHATS_THIS_BUTTON) def connect_or_disconnect_signals(self, isConnect): """ Connect or disconnect widget signals sent to their slot methods. This can be overridden in subclasses. By default it does nothing. @param isConnect: If True the widget will send the signals to the slot method. @type isConnect: boolean """ if isConnect: change_connect = self.win.connect else: change_connect = self.win.disconnect change_connect(self._placementOptions.buttonGroup, SIGNAL("buttonClicked(int)"), self.activateSpecifyReferencePlaneTool) change_connect( self.conformationComboBox, SIGNAL("currentIndexChanged(int)"), self.conformationComboBoxChanged ) change_connect( self.numberOfBasePairsSpinBox, SIGNAL("valueChanged(int)"), self.numberOfBasesChanged ) change_connect( self.basesPerTurnDoubleSpinBox, SIGNAL("valueChanged(double)"), self.basesPerTurnChanged ) change_connect( self.duplexRiseDoubleSpinBox, SIGNAL("valueChanged(double)"), self.duplexRiseChanged ) change_connect(self.showCursorTextCheckBox, SIGNAL('stateChanged(int)'), self._update_state_of_cursorTextGroupBox) self.duplexRiseDoubleSpinBox.connectWithState( Preferences_StateRef_double( bdnaRise_prefs_key, env.prefs[bdnaRise_prefs_key] ) ) self.basesPerTurnDoubleSpinBox.connectWithState( Preferences_StateRef_double( bdnaBasesPerTurn_prefs_key, env.prefs[bdnaBasesPerTurn_prefs_key] ) ) def show(self): _superclass.show(self) self.updateMessage("Specify the DNA parameters below, then click "\ "two endpoints in the graphics area to insert a DNA duplex.") def _addGroupBoxes( self ): """ Add the DNA Property Manager group boxes. """ self._pmReferencePlaneGroupBox = PM_GroupBox( self, title = "Placement Options" ) self._loadReferencePlaneGroupBox( self._pmReferencePlaneGroupBox ) self._pmGroupBox1 = PM_GroupBox( self, title = "Endpoints" ) self._loadGroupBox1( self._pmGroupBox1 ) self._pmGroupBox1.hide() self._pmGroupBox2 = PM_GroupBox( self, title = "Parameters" ) self._loadGroupBox2( self._pmGroupBox2 ) self._displayOptionsGroupBox = PM_GroupBox( self, title = "Display Options" ) self._loadDisplayOptionsGroupBox( self._displayOptionsGroupBox ) def _loadGroupBox1(self, pmGroupBox): """ Load widgets in group box 3. """ #Folllowing toolbutton facilitates entering a temporary DnaLineMode #to create a DNA using endpoints of the specified line. self.specifyDnaLineButton = PM_ToolButton( pmGroupBox, text = "Specify Endpoints", iconPath = "ui/actions/Properties Manager/Pencil.png", spanWidth = True ) self.specifyDnaLineButton.setCheckable(True) self.specifyDnaLineButton.setAutoRaise(True) self.specifyDnaLineButton.setToolButtonStyle( Qt.ToolButtonTextBesideIcon) #EndPoint1 and endPoint2 coordinates. These widgets are hidden # as of 2007- 12 - 05 self._endPoint1SpinBoxes = PM_CoordinateSpinBoxes(pmGroupBox, label = "End Point 1") self.x1SpinBox = self._endPoint1SpinBoxes.xSpinBox self.y1SpinBox = self._endPoint1SpinBoxes.ySpinBox self.z1SpinBox = self._endPoint1SpinBoxes.zSpinBox self._endPoint2SpinBoxes = PM_CoordinateSpinBoxes(pmGroupBox, label = "End Point 2") self.x2SpinBox = self._endPoint2SpinBoxes.xSpinBox self.y2SpinBox = self._endPoint2SpinBoxes.ySpinBox self.z2SpinBox = self._endPoint2SpinBoxes.zSpinBox self._endPoint1SpinBoxes.hide() self._endPoint2SpinBoxes.hide() def _loadGroupBox2(self, pmGroupBox): """ Load widgets in group box 4. """ self.conformationComboBox = \ PM_ComboBox( pmGroupBox, label = "Conformation:", choices = ["B-DNA"], setAsDefault = True) dnaModelChoices = ['PAM3', 'PAM5'] self.dnaModelComboBox = \ PM_ComboBox( pmGroupBox, label = "Model:", choices = dnaModelChoices, setAsDefault = True) self.basesPerTurnDoubleSpinBox = \ PM_DoubleSpinBox( pmGroupBox, label = "Bases per turn:", value = env.prefs[bdnaBasesPerTurn_prefs_key], setAsDefault = True, minimum = 8.0, maximum = 20.0, decimals = 2, singleStep = 0.1 ) self.duplexRiseDoubleSpinBox = \ PM_DoubleSpinBox( pmGroupBox, label = "Rise:", value = env.prefs[bdnaRise_prefs_key], setAsDefault = True, minimum = 2.0, maximum = 4.0, decimals = 3, singleStep = 0.01 ) # Strand Length (i.e. the number of bases) self.numberOfBasePairsSpinBox = \ PM_SpinBox( pmGroupBox, label = "Base pairs:", value = self._numberOfBases, setAsDefault = False, minimum = 0, maximum = 10000 ) self.numberOfBasePairsSpinBox.setDisabled(True) # Duplex Length self.duplexLengthLineEdit = \ PM_LineEdit( pmGroupBox, label = "Duplex length: ", text = "0.0 Angstroms", setAsDefault = False) self.duplexLengthLineEdit.setDisabled(True) def _loadDisplayOptionsGroupBox(self, pmGroupBox): """ Load widgets in the Display Options GroupBox @see: DnaOrCnt_PropertyManager. _loadDisplayOptionsGroupBox """ #Call the superclass method that loads the cursor text checkboxes. #Note, as of 2008-05-19, the superclass, DnaOrCnt_PropertyManager #only loads the cursor text groupboxes. Subclasses like this can #call custom methods like self._loadCursorTextCheckBoxes etc if they #don't need all groupboxes that the superclass loads. _superclass._loadDisplayOptionsGroupBox(self, pmGroupBox) self._rubberbandLineGroupBox = PM_GroupBox( pmGroupBox, title = 'Rubber band line:') dnaLineChoices = ['Ribbons', 'Ladder'] self.dnaRubberBandLineDisplayComboBox = \ PM_ComboBox( self._rubberbandLineGroupBox , label = " Display as:", choices = dnaLineChoices, setAsDefault = True) self.lineSnapCheckBox = \ PM_CheckBox(self._rubberbandLineGroupBox , text = 'Enable line snap' , widgetColumn = 1, state = Qt.Checked ) def _connect_showCursorTextCheckBox(self): """ Connect the show cursor text checkbox with user prefs_key. Overrides DnaOrCnt_PropertyManager._connect_showCursorTextCheckBox """ connect_checkbox_with_boolean_pref( self.showCursorTextCheckBox , dnaDuplexEditCommand_showCursorTextCheckBox_prefs_key) def _params_for_creating_cursorTextCheckBoxes(self): """ Returns params needed to create various cursor text checkboxes connected to prefs_keys that allow custom cursor texts. @return: A list containing tuples in the following format: ('checkBoxTextString' , preference_key). PM_PrefsCheckBoxes uses this data to create checkboxes with the the given names and connects them to the provided preference keys. (Note that PM_PrefsCheckBoxes puts thes within a GroupBox) @rtype: list @see: PM_PrefsCheckBoxes @see: self._loadDisplayOptionsGroupBox where this list is used. @see: Superclass method which is overridden here -- DnaOrCnt_PropertyManager._params_for_creating_cursorTextCheckBoxes() """ params = \ [ #Format: (" checkbox text", prefs_key) ("Number of base pairs", dnaDuplexEditCommand_cursorTextCheckBox_numberOfBasePairs_prefs_key), ("Number of turns", dnaDuplexEditCommand_cursorTextCheckBox_numberOfTurns_prefs_key), ("Duplex length", dnaDuplexEditCommand_cursorTextCheckBox_length_prefs_key), ("Angle", dnaDuplexEditCommand_cursorTextCheckBox_angle_prefs_key) ] return params def _addToolTipText(self): """ Tool Tip text for widgets in the DNA Property Manager. """ pass def conformationComboBoxChanged( self, inIndex ): """ Slot for the Conformation combobox. It is called whenever the Conformation choice is changed. @param inIndex: The new index. @type inIndex: int """ conformation = self.conformationComboBox.currentText() if conformation == "B-DNA": self.basesPerTurnDoubleSpinBox.setValue("10.0") elif conformation == "Z-DNA": self.basesPerTurnDoubleSpinBox.setValue("12.0") else: msg = redmsg("conformationComboBoxChanged(): \ Error - unknown DNA conformation. Index = "+ inIndex) env.history.message(msg) self.duplexLengthSpinBox.setSingleStep(getDuplexRise(conformation)) def numberOfBasesChanged( self, numberOfBases ): """ Slot for the B{Number of Bases} spinbox. """ # Update the Duplex Length lineEdit widget. text = str(getDuplexLength(self._conformation, numberOfBases, self._duplexRise)) \ + " Angstroms" self.duplexLengthLineEdit.setText(text) return def basesPerTurnChanged( self, basesPerTurn ): """ Slot for the B{Bases per turn} spinbox. """ self.command.basesPerTurn = basesPerTurn self._basesPerTurn = basesPerTurn return def duplexRiseChanged( self, rise ): """ Slot for the B{Rise} spinbox. """ self.command.duplexRise = rise self._duplexRise = rise return def getParameters(self): """ Return the parameters from this property manager to be used to create the DNA duplex. @return: A tuple containing the parameters @rtype: tuple @see: L{InsertDna_EditCommand._gatherParameters} where this is used """ numberOfBases = self.numberOfBasePairsSpinBox.value() dnaForm = str(self.conformationComboBox.currentText()) basesPerTurn = self.basesPerTurnDoubleSpinBox.value() duplexRise = self.duplexRiseDoubleSpinBox.value() dnaModel = str(self.dnaModelComboBox.currentText()) # First endpoint (origin) of DNA duplex x1 = self.x1SpinBox.value() y1 = self.y1SpinBox.value() z1 = self.z1SpinBox.value() # Second endpoint (direction vector/axis) of DNA duplex. x2 = self.x2SpinBox.value() y2 = self.y2SpinBox.value() z2 = self.z2SpinBox.value() if not self.endPoint1: self.endPoint1 = V(x1, y1, z1) if not self.endPoint2: self.endPoint2 = V(x2, y2, z2) return (numberOfBases, dnaForm, dnaModel, basesPerTurn, duplexRise, self.endPoint1, self.endPoint2) def _addWhatsThisText(self): """ What's This text for widgets in this Property Manager. """ whatsThis_InsertDna_PropertyManager(self)