class BuildProtein_PropertyManager(EditCommand_PM):
"""
The BuildDna_PropertyManager class provides a Property Manager
for the B{Build > Protein } 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 = "Build Protein"
pmName = title
#change this icon path later
iconPath = "ui/actions/Tools/Build Structures/Protein.png"
def __init__( self, command ):
"""
Constructor for the Build DNA property manager.
"""
self.current_protein = ""
self.sequenceEditor = command.win.createProteinSequenceEditorIfNeeded()
#see self.connect_or_disconnect_signals for comment about this flag
self.isAlreadyConnected = False
self.isAlreadyDisconnected = False
EditCommand_PM.__init__( self, command)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_CANCEL_BUTTON | \
PM_WHATS_THIS_BUTTON)
def _updateProteinListForShow(self):
"""
Update the list of proteins in the combo box in the PM.
"""
#first remove from combo box all the proteins that do not exist in NE-1
#part anymore
currentProteinNameList = []
for mol in self.win.assy.molecules:
currentProteinNameList.append(mol.name)
for name in self.protein_name_list:
try:
index = currentProteinNameList.index(name)
except ValueError:
#protein does not exist any more, need to remove it
i = self.protein_name_list.index(name)
self.protein_chunk_list.pop(i)
self.protein_name_list.pop(i)
j = self.structureComboBox.findText(name)
self.structureComboBox.removeItem(j)
for mol in self.win.assy.molecules:
#if molecules does not already exist in combo box list, need to add
#them
if mol.isProteinChunk():
try:
self.protein_name_list.index(mol.name)
except ValueError:
self.protein_chunk_list.append(mol)
self.protein_name_list.append(mol.name)
self.structureComboBox.addItem(mol.name)
return
def show(self):
"""
Overrides superclass show method
"""
env.history.statusbar_msg("")
self._updateProteinListForShow()
self._showProteinParametersAndSequenceEditor()
EditCommand_PM.show(self)
self.updateMessage()
return
def close(self):
"""
Overrides superclass close method
"""
self.sequenceEditor.hide()
env.history.statusbar_msg("")
EditCommand_PM.close(self)
return
def _updateProteinList(self):
"""
Update the list of proteins so that the protein name combo box in this
PM can be populated.
"""
self.protein_chunk_list = []
self.protein_name_list = []
for mol in self.win.assy.molecules:
if mol.isProteinChunk():
self.protein_chunk_list.append(mol)
self.protein_name_list.append(mol.name)
return
def _showProteinParametersAndSequenceEditor(self):
"""
Show/ Hide protein parameters and sequence editor based on if there's
any protein in NE-1 part.
"""
part = self.win.assy.part
proteinExists, proteinChunk = checkIfProteinChunkInPart(part)
if proteinExists:
#check to see if current_protein is still in part, otherwise set
# this to first available protein
try:
index = self.structureComboBox.findText(self.current_protein)
index1 = self.protein_name_list.index(self.current_protein)
except ValueError:
index = 0
index1 = 0
self.set_current_protein_chunk_name(self.protein_name_list[index1])
self.structureComboBox.setCurrentIndex(index)
proteinChunk = self.protein_chunk_list[index1]
self._numberOfAA = len(proteinChunk.protein.get_sequence_string())
else:
#remove all items from the combo box
count = self.structureComboBox.count()
for i in range(count):
self.structureComboBox.removeItem(0)
self._numberOfAA = 0
self.set_current_protein_chunk_name("")
self.numberOfAASpinBox.setValue(self._numberOfAA)
#get the sequence for this protein chunk
if proteinExists:
sequence = proteinChunk.protein.get_sequence_string()
self.sequenceEditor.setSequence(sequence)
secStructure = proteinChunk.protein.get_secondary_structure_string()
self.sequenceEditor.setSecondaryStructure(secStructure)
self.sequenceEditor.setRuler(len(secStructure))
self.editPropertiesPushButton.setEnabled(True)
else:
self.editPropertiesPushButton.setEnabled(False)
self.sequenceEditor.hide()
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 and self.isAlreadyConnected:
return
if not isConnect and self.isAlreadyDisconnected:
return
self.isAlreadyConnected = isConnect
self.isAlreadyDisconnected = not isConnect
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
change_connect(self.structureComboBox,
SIGNAL("currentIndexChanged(int)"),
self._updateProteinParameters)
change_connect(self.editPropertiesPushButton,
SIGNAL("clicked()"),
self._showSeqEditor)
def _showSeqEditor(self):
"""
Show sequence editor
"""
if self.editPropertiesPushButton.isEnabled():
self.sequenceEditor.show()
return
def _updateProteinParameters(self, index):
"""
Update number of amino acids and sequence editor, as well as set the
current protein pdb id which will be used in the child commands and for
rosetta simulation from inside the build protein mode.
@param index: index of the protein combo box
@type index: int
"""
for mol in self.protein_chunk_list:
if mol.name == self.structureComboBox.currentText():
self._numberOfAA = len(mol.protein.get_sequence_string())
self.numberOfAASpinBox.setValue(self._numberOfAA)
sequence = mol.protein.get_sequence_string()
self.sequenceEditor.setSequence(sequence)
secStructure = mol.protein.get_secondary_structure_string()
self.sequenceEditor.setSecondaryStructure(secStructure)
self.sequenceEditor.setRuler(len(secStructure))
break
self.set_current_protein_chunk_name(mol.name)
env.history.statusbar_msg("")
return
def set_current_protein_chunk_name(self, name):
"""
Sets the current protein name
@param name: pdb id of the protein currently selected in the combo box
@type name: str
"""
self.current_protein = name
return
def get_current_protein_chunk_name(self):
"""
gets the current protein name
@return: pdb id of the protein currently selected in the combo box
"""
return self.current_protein
def enable_or_disable_gui_actions(self, bool_enable = False):
"""
Enable or disable some gui actions when this property manager is
opened or closed, depending on the bool_enable.
@param bool_enable: enables/disables some gui action
@type bool_enable: bool
"""
if hasattr(self.command, 'flyoutToolbar') and \
self.command.flyoutToolbar:
self.command.flyoutToolbar.exitProteinAction.setEnabled(not bool_enable)
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
def _addGroupBoxes(self):
"""
Add the DNA Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox(self, title = "Parameters")
self._loadGroupBox1(self._pmGroupBox1)
return
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box 1.
@param pmGroupBox: group box that contains protein name combo box and
number of amino acids spin box
@see: L{PM_GroupBox}
"""
self._updateProteinList()
if len(self.protein_name_list) >= 1:
self.set_current_protein_chunk_name(self.protein_name_list[0])
self.structureComboBox = PM_ComboBox( pmGroupBox,
label = "Name:",
choices = self.protein_name_list,
setAsDefault = False)
#Urmi 20080713: May be useful to set the minimum value to not zero
#Now it does not matter, since its disabled. But zero as the minimum
#value in a spinbox does not work otherwise.
self.numberOfAASpinBox = \
PM_SpinBox( pmGroupBox,
label = "Amino Acids:",
value = 0,
setAsDefault = False,
minimum = 0,
maximum = 10000 )
#for now we do not allow changing number of residues
self.numberOfAASpinBox.setEnabled(False)
self.editPropertiesPushButton = PM_PushButton( pmGroupBox,
text = "Edit Sequence",
setAsDefault = True
)
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 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 BuildProtein_PropertyManager( EditCommand_PM, DebugMenuMixin ):
"""
The BuildDna_PropertyManager class provides a Property Manager
for the B{Build > 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 = "Build Protein"
pmName = title
#change this ico path later
iconPath = "ui/actions/Tools/Build Structures/Peptide.png"
def __init__( self, win, editCommand ):
"""
Constructor for the Build DNA property manager.
"""
#For model changed signal
self.previousSelectionParams = None
#Urmi 20080713: set the protein chunk name and its length
#for the first available chunk and not the selected one, that's
#not implemented as yet
#self.showProteinParametersAndSequenceEditorForInit(win)
#see self.connect_or_disconnect_signals for comment about this flag
self.isAlreadyConnected = False
self.isAlreadyDisconnected = False
EditCommand_PM.__init__( self,
win,
editCommand)
DebugMenuMixin._init1( self )
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_CANCEL_BUTTON | \
PM_WHATS_THIS_BUTTON)
def show(self):
self.showProteinParametersAndSequenceEditor(self.win)
EditCommand_PM.show(self)
return
def close(self):
self.sequenceEditor.hide()
env.history.statusbar_msg("")
EditCommand_PM.close(self)
return
def showProteinParametersAndSequenceEditor(self, win):
"""
Show/ Hide protein parameters and sequence editor based
"""
part = win.assy.part
from simulation.ROSETTA.rosetta_commandruns import checkIfProteinChunkInPart
proteinExists, proteinChunk = checkIfProteinChunkInPart(part)
if proteinExists:
self._proteinChunkName = proteinChunk.protein.get_pdb_id() + proteinChunk.protein.get_chain_id()
self._numberOfAA = len(proteinChunk.protein.get_sequence_string())
else:
self._proteinChunkName = ''
self._numberOfAA = 0
self.nameLineEdit.setText(self._proteinChunkName)
self.numberOfAASpinBox.setValue(self._numberOfAA)
if proteinExists:
self.nameLineEdit.setEnabled(True)
else:
self.nameLineEdit.setEnabled(False)
self.sequenceEditor = win.createProteinSequenceEditorIfNeeded()
#get the sequence for this protein chunk
if proteinExists:
sequence = proteinChunk.protein.get_sequence_string()
self.sequenceEditor.setSequence(sequence)
secStructure = proteinChunk.protein.get_secondary_structure_string()
self.sequenceEditor.setSecondaryStructure(secStructure)
self.sequenceEditor.setRuler(len(secStructure))
self.sequenceEditor.show()
else:
self.sequenceEditor.hide()
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 and self.isAlreadyConnected:
return
if not isConnect and self.isAlreadyDisconnected:
return
self.isAlreadyConnected = isConnect
self.isAlreadyDisconnected = not isConnect
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
def enable_or_disable_gui_actions(self, bool_enable = False):
"""
Enable or disable some gui actions when this property manager is
opened or closed, depending on the bool_enable.
"""
#TODO: This is bad. It would have been much better to enable/disable
#gui actions using a API method in command/commandSequencer which gets
#called when you enter another command exiting or suspending the
#previous one. . At present. it doesn't exist (first needs cleanup in
#command/command sequencer (Done and other methods._)-- Ninad 2008-01-09
if hasattr(self.editCommand, 'flyoutToolbar') and \
self.editCommand.flyoutToolbar:
self.editCommand.flyoutToolbar.exitProteinAction.setEnabled(not bool_enable)
def ok_btn_clicked(self):
"""
Slot for the OK button
"""
self.win.toolsDone()
def cancel_btn_clicked(self):
"""
Slot for the Cancel button.
"""
self.win.toolsCancel()
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
def _addGroupBoxes( self ):
"""
Add the DNA Property Manager group boxes.
"""
"""
Add the DNA Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox( self, title = "Parameters" )
self._loadGroupBox1( self._pmGroupBox1 )
pass
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box 4.
"""
self.nameLineEdit = PM_LineEdit( pmGroupBox,
label = "Protein chunk name:",
text = "",
setAsDefault = False)
#Urmi 20080713: May be useful to set the minimum value to not zero
self.numberOfAASpinBox = \
PM_SpinBox( pmGroupBox,
label = "Number of amino acids:",
value = 0,
setAsDefault = False,
minimum = 0,
maximum = 10000 )
self.numberOfAASpinBox.setEnabled(False)
class BuildProtein_PropertyManager(EditCommand_PM):
"""
The BuildDna_PropertyManager class provides a Property Manager
for the B{Build > Protein } 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 = "Build Protein"
pmName = title
#change this icon path later
iconPath = "ui/actions/Tools/Build Structures/Protein.png"
def __init__(self, command):
"""
Constructor for the Build DNA property manager.
"""
self.current_protein = ""
self.sequenceEditor = command.win.createProteinSequenceEditorIfNeeded()
#see self.connect_or_disconnect_signals for comment about this flag
self.isAlreadyConnected = False
self.isAlreadyDisconnected = False
EditCommand_PM.__init__(self, command)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_CANCEL_BUTTON | \
PM_WHATS_THIS_BUTTON)
def _updateProteinListForShow(self):
"""
Update the list of proteins in the combo box in the PM.
"""
#first remove from combo box all the proteins that do not exist in NE-1
#part anymore
currentProteinNameList = []
for mol in self.win.assy.molecules:
currentProteinNameList.append(mol.name)
for name in self.protein_name_list:
try:
index = currentProteinNameList.index(name)
except ValueError:
#protein does not exist any more, need to remove it
i = self.protein_name_list.index(name)
self.protein_chunk_list.pop(i)
self.protein_name_list.pop(i)
j = self.structureComboBox.findText(name)
self.structureComboBox.removeItem(j)
for mol in self.win.assy.molecules:
#if molecules does not already exist in combo box list, need to add
#them
if mol.isProteinChunk():
try:
self.protein_name_list.index(mol.name)
except ValueError:
self.protein_chunk_list.append(mol)
self.protein_name_list.append(mol.name)
self.structureComboBox.addItem(mol.name)
return
def show(self):
"""
Overrides superclass show method
"""
env.history.statusbar_msg("")
self._updateProteinListForShow()
self._showProteinParametersAndSequenceEditor()
EditCommand_PM.show(self)
self.updateMessage()
return
def close(self):
"""
Overrides superclass close method
"""
self.sequenceEditor.hide()
env.history.statusbar_msg("")
EditCommand_PM.close(self)
return
def _updateProteinList(self):
"""
Update the list of proteins so that the protein name combo box in this
PM can be populated.
"""
self.protein_chunk_list = []
self.protein_name_list = []
for mol in self.win.assy.molecules:
if mol.isProteinChunk():
self.protein_chunk_list.append(mol)
self.protein_name_list.append(mol.name)
return
def _showProteinParametersAndSequenceEditor(self):
"""
Show/ Hide protein parameters and sequence editor based on if there's
any protein in NE-1 part.
"""
part = self.win.assy.part
proteinExists, proteinChunk = checkIfProteinChunkInPart(part)
if proteinExists:
#check to see if current_protein is still in part, otherwise set
# this to first available protein
try:
index = self.structureComboBox.findText(self.current_protein)
index1 = self.protein_name_list.index(self.current_protein)
except ValueError:
index = 0
index1 = 0
self.set_current_protein_chunk_name(
self.protein_name_list[index1])
self.structureComboBox.setCurrentIndex(index)
proteinChunk = self.protein_chunk_list[index1]
self._numberOfAA = len(proteinChunk.protein.get_sequence_string())
else:
#remove all items from the combo box
count = self.structureComboBox.count()
for i in range(count):
self.structureComboBox.removeItem(0)
self._numberOfAA = 0
self.set_current_protein_chunk_name("")
self.numberOfAASpinBox.setValue(self._numberOfAA)
#get the sequence for this protein chunk
if proteinExists:
sequence = proteinChunk.protein.get_sequence_string()
self.sequenceEditor.setSequence(sequence)
secStructure = proteinChunk.protein.get_secondary_structure_string(
)
self.sequenceEditor.setSecondaryStructure(secStructure)
self.sequenceEditor.setRuler(len(secStructure))
self.editPropertiesPushButton.setEnabled(True)
else:
self.editPropertiesPushButton.setEnabled(False)
self.sequenceEditor.hide()
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 and self.isAlreadyConnected:
return
if not isConnect and self.isAlreadyDisconnected:
return
self.isAlreadyConnected = isConnect
self.isAlreadyDisconnected = not isConnect
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
change_connect(self.structureComboBox,
SIGNAL("currentIndexChanged(int)"),
self._updateProteinParameters)
change_connect(self.editPropertiesPushButton, SIGNAL("clicked()"),
self._showSeqEditor)
def _showSeqEditor(self):
"""
Show sequence editor
"""
if self.editPropertiesPushButton.isEnabled():
self.sequenceEditor.show()
return
def _updateProteinParameters(self, index):
"""
Update number of amino acids and sequence editor, as well as set the
current protein pdb id which will be used in the child commands and for
rosetta simulation from inside the build protein mode.
@param index: index of the protein combo box
@type index: int
"""
for mol in self.protein_chunk_list:
if mol.name == self.structureComboBox.currentText():
self._numberOfAA = len(mol.protein.get_sequence_string())
self.numberOfAASpinBox.setValue(self._numberOfAA)
sequence = mol.protein.get_sequence_string()
self.sequenceEditor.setSequence(sequence)
secStructure = mol.protein.get_secondary_structure_string()
self.sequenceEditor.setSecondaryStructure(secStructure)
self.sequenceEditor.setRuler(len(secStructure))
break
self.set_current_protein_chunk_name(mol.name)
env.history.statusbar_msg("")
return
def set_current_protein_chunk_name(self, name):
"""
Sets the current protein name
@param name: pdb id of the protein currently selected in the combo box
@type name: str
"""
self.current_protein = name
return
def get_current_protein_chunk_name(self):
"""
gets the current protein name
@return: pdb id of the protein currently selected in the combo box
"""
return self.current_protein
def enable_or_disable_gui_actions(self, bool_enable=False):
"""
Enable or disable some gui actions when this property manager is
opened or closed, depending on the bool_enable.
@param bool_enable: enables/disables some gui action
@type bool_enable: bool
"""
if hasattr(self.command, 'flyoutToolbar') and \
self.command.flyoutToolbar:
self.command.flyoutToolbar.exitProteinAction.setEnabled(
not bool_enable)
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
def _addGroupBoxes(self):
"""
Add the DNA Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox(self, title="Parameters")
self._loadGroupBox1(self._pmGroupBox1)
return
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box 1.
@param pmGroupBox: group box that contains protein name combo box and
number of amino acids spin box
@see: L{PM_GroupBox}
"""
self._updateProteinList()
if len(self.protein_name_list) >= 1:
self.set_current_protein_chunk_name(self.protein_name_list[0])
self.structureComboBox = PM_ComboBox(pmGroupBox,
label="Name:",
choices=self.protein_name_list,
setAsDefault=False)
#Urmi 20080713: May be useful to set the minimum value to not zero
#Now it does not matter, since its disabled. But zero as the minimum
#value in a spinbox does not work otherwise.
self.numberOfAASpinBox = \
PM_SpinBox( pmGroupBox,
label = "Amino Acids:",
value = 0,
setAsDefault = False,
minimum = 0,
maximum = 10000 )
#for now we do not allow changing number of residues
self.numberOfAASpinBox.setEnabled(False)
self.editPropertiesPushButton = PM_PushButton(pmGroupBox,
text="Edit Sequence",
setAsDefault=True)
class BuildProtein_PropertyManager(EditCommand_PM, DebugMenuMixin):
"""
The BuildDna_PropertyManager class provides a Property Manager
for the B{Build > 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 = "Build Protein"
pmName = title
#change this ico path later
iconPath = "ui/actions/Tools/Build Structures/Peptide.png"
def __init__(self, win, editCommand):
"""
Constructor for the Build DNA property manager.
"""
#For model changed signal
self.previousSelectionParams = None
#Urmi 20080713: set the protein chunk name and its length
#for the first available chunk and not the selected one, that's
#not implemented as yet
#self.showProteinParametersAndSequenceEditorForInit(win)
#see self.connect_or_disconnect_signals for comment about this flag
self.isAlreadyConnected = False
self.isAlreadyDisconnected = False
EditCommand_PM.__init__(self, win, editCommand)
DebugMenuMixin._init1(self)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_CANCEL_BUTTON | \
PM_WHATS_THIS_BUTTON)
def show(self):
self.showProteinParametersAndSequenceEditor(self.win)
EditCommand_PM.show(self)
return
def close(self):
self.sequenceEditor.hide()
env.history.statusbar_msg("")
EditCommand_PM.close(self)
return
def showProteinParametersAndSequenceEditor(self, win):
"""
Show/ Hide protein parameters and sequence editor based
"""
part = win.assy.part
from simulation.ROSETTA.rosetta_commandruns import checkIfProteinChunkInPart
proteinExists, proteinChunk = checkIfProteinChunkInPart(part)
if proteinExists:
self._proteinChunkName = proteinChunk.protein.get_pdb_id(
) + proteinChunk.protein.get_chain_id()
self._numberOfAA = len(proteinChunk.protein.get_sequence_string())
else:
self._proteinChunkName = ''
self._numberOfAA = 0
self.nameLineEdit.setText(self._proteinChunkName)
self.numberOfAASpinBox.setValue(self._numberOfAA)
if proteinExists:
self.nameLineEdit.setEnabled(True)
else:
self.nameLineEdit.setEnabled(False)
self.sequenceEditor = win.createProteinSequenceEditorIfNeeded()
#get the sequence for this protein chunk
if proteinExists:
sequence = proteinChunk.protein.get_sequence_string()
self.sequenceEditor.setSequence(sequence)
secStructure = proteinChunk.protein.get_secondary_structure_string(
)
self.sequenceEditor.setSecondaryStructure(secStructure)
self.sequenceEditor.setRuler(len(secStructure))
self.sequenceEditor.show()
else:
self.sequenceEditor.hide()
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 and self.isAlreadyConnected:
return
if not isConnect and self.isAlreadyDisconnected:
return
self.isAlreadyConnected = isConnect
self.isAlreadyDisconnected = not isConnect
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
def enable_or_disable_gui_actions(self, bool_enable=False):
"""
Enable or disable some gui actions when this property manager is
opened or closed, depending on the bool_enable.
"""
#TODO: This is bad. It would have been much better to enable/disable
#gui actions using a API method in command/commandSequencer which gets
#called when you enter another command exiting or suspending the
#previous one. . At present. it doesn't exist (first needs cleanup in
#command/command sequencer (Done and other methods._)-- Ninad 2008-01-09
if hasattr(self.editCommand, 'flyoutToolbar') and \
self.editCommand.flyoutToolbar:
self.editCommand.flyoutToolbar.exitProteinAction.setEnabled(
not bool_enable)
def ok_btn_clicked(self):
"""
Slot for the OK button
"""
self.win.toolsDone()
def cancel_btn_clicked(self):
"""
Slot for the Cancel button.
"""
self.win.toolsCancel()
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
def _addGroupBoxes(self):
"""
Add the DNA Property Manager group boxes.
"""
"""
Add the DNA Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox(self, title="Parameters")
self._loadGroupBox1(self._pmGroupBox1)
pass
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box 4.
"""
self.nameLineEdit = PM_LineEdit(pmGroupBox,
label="Protein chunk name:",
text="",
setAsDefault=False)
#Urmi 20080713: May be useful to set the minimum value to not zero
self.numberOfAASpinBox = \
PM_SpinBox( pmGroupBox,
label = "Number of amino acids:",
value = 0,
setAsDefault = False,
minimum = 0,
maximum = 10000 )
self.numberOfAASpinBox.setEnabled(False)
