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