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 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 BuildNanotube_PropertyManager(EditCommand_PM):
"""
The BuildNanotube_PropertyManager class provides a Property Manager
for the B{Build > 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 = "Build Nanotube"
pmName = title
iconPath = "ui/actions/Command Toolbar/BuildNanotube/BuildNanotube.png"
def __init__(self, command):
"""
Constructor for the Build Nanotube property manager.
"""
#Attributes for self._update_UI_do_updates() to keep track of changes
#in these , since the last call of that method. These are used to
#determine whether certain UI updates are needed.
self._previousSelectionParams = None
self._previousStructureParams = None
self._previousCommandStackParams = None
#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_WHATS_THIS_BUTTON)
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 actually reconnects the signal!
#This gives rise to lots of bugs. This needs a more general fix in
#the Temporary mode API.
# -- Ninad 2008-01-09 (similar comment exists in MovePropertyManager.py
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
self.nanotubeListWidget.connect_or_disconnect_signals(isConnect)
change_connect(self.editNanotubePropertiesButton, SIGNAL("clicked()"),
self._editNanotube)
return
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.
"""
#For new command API, we will always show the exit button to check
#if Exit button really exits the subcommand and the parent command
#(earlier there were bugs) . Regaring 'whether this should be the
#default behavior', its a UI design issue and we will worry about it
#later -- Ninad 2008-08-27 (based on an email exchanged with Bruce)
pass
def _update_UI_do_updates(self):
"""
Overrides superclass method.
@see: Command_PropertyManager._update_UI_do_updates()
"""
newSelectionParams = self._currentSelectionParams()
current_struct_params = self._currentStructureParams()
selection_params_unchanged = same_vals(newSelectionParams,
self._previousSelectionParams)
#introducing self._previousStructureParams and
#adding structure_params_unchanged check to the 'if' condition below
#fixes bug 2910.
structure_params_unchanged = same_vals(self._previousStructureParams,
current_struct_params)
current_command_stack_params = self._currentCommandStackParams()
#Check if command stack params changed since last call of this
#PM update method. This is used to fix bugs like 2940
command_stack_params_unchanged = same_vals(
self._previousCommandStackParams, current_command_stack_params)
#No need to proceed if any of the selection/ structure and commandstack
#parameters remained unchanged since last call. --- [CONDITION A]
if selection_params_unchanged and \
structure_params_unchanged and \
command_stack_params_unchanged:
return
self._previousStructureParams = current_struct_params
self._previousSelectionParams = newSelectionParams
self._previousCommandStackParams = current_command_stack_params
if structure_params_unchanged:
#NOTE: We checked if either of the selection struct or command stack
#parameters or both changed. (this was referred as '[CONDITION A]'
#above). So, this condition (structure_params_unchanged)also means
#either selection or command stack or both parameters were changed.
if not command_stack_params_unchanged:
#update the nanotube list widget *before* updating the selection if
#the command stack changed. This ensures that the selection box
#appears around the list widget items that are selected.
self.updateNanotubesListWidget()
selectedNanotubeSegments = newSelectionParams
self.nanotubeListWidget.updateSelection(selectedNanotubeSegments)
self.updateNanotubePropertiesButton()
return
self.updateNanotubesListWidget()
return
def _currentCommandStackParams(self):
"""
The return value is supposed to be used by BUILD_NANOTUBE command PM ONLY
and NOT by any subclasses.
Returns a tuple containing current command stack change indicator and
the name of the command 'BUILD_NANOTUBE'. These
parameters are then used to decide whether updating widgets
in this property manager is needed, when self._update_UI_do_updates()
is called.
@NOTE:
- Command_PropertyManager.update_UI() already does a check to see if
any of the global change indicators in assembly (command_stack_change,
model_change, selection_change) changed since last call and then only
calls self._update_UI_do_updates().
- But this method is just used to keep track of the
local command stack change counter in order to update the list
widgets.
- This is used to fix bug 2940
@see: self._update_UI_do_updates()
"""
commandStackCounter = self.command.assy.command_stack_change_indicator(
)
#Append 'BUILD_NANOTUBE to the tuple to be returned. This is just to remind
#us that this method is meant for BUILD_NANOTUBE command PM only. (and not
#by any subclasses) Should we assert this? I think it will slow things
#down so this comment is enough -- Ninad 2008-09-30
return (commandStackCounter, 'BUILD_NANOTUBE')
def _currentSelectionParams(self):
"""
Returns a tuple containing current selection parameters. These
parameters are then used to decide whether updating widgets
in this property manager is needed when L{self.model_changed}
method is called.
@return: A tuple that contains total number of selected nanotubes.
@rtype: tuple
@NOTE: This method may be renamed in future.
It's possible that there are other groupboxes in the PM that need to be
updated when something changes in the glpane.
"""
selectedNanotubeSegments = []
if self.command is not None: # and self.command.hasValidStructure():
selectedNanotubeSegments = self.win.assy.getSelectedNanotubeSegments(
)
return (selectedNanotubeSegments)
def _currentStructureParams(self):
"""
Return current structure parameters of interest to self.model_changed.
Right now it only returns the number of nanotubes within the structure
(or None). This is a good enough check (and no need to compare
each and every nanotube within the structure with a previously stored
set of strands).
"""
params = None
if self.command: # and self.command.hasValidStructure():
nanotubeSegmentList = []
nanotubeSegmentList = getAllNanotubeSegmentsInPart(self.win.assy)
params = len(nanotubeSegmentList)
return params
def close(self):
"""
Closes the Property Manager. Overrides EditCommand_PM.close()
"""
#Clear tags, if any, due to the selection in the self.strandListWidget.
#self.nanotubeListWidget.clear()
env.history.statusbar_msg("")
EditCommand_PM.close(self)
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.
"""
env.history.statusbar_msg("")
EditCommand_PM.show(self)
# NOTE: Think about moving this msg to _update_UI_do_updates() where
# custom msgs can be created based on the current selection, etc.
# Mark 2008-12-14
msg = "Select <b>Insert Nanotube</b> to create a nanotube or "\
"select an existing nantube to modify it."
self.updateMessage(msg)
return
def _editNanotube(self):
"""
Slot for the "Edit Properties" button.
"""
#if not self.command.hasValidStructure():
# return
nanotubeSegment = self.win.assy.getSelectedNanotubeSegment()
if nanotubeSegment:
nanotubeSegment.edit()
return
def _addWhatsThisText(self):
"""
What's This text for widgets in the CNT Property Manager.
"""
pass
def _addToolTipText(self):
"""
Tool Tip text for widgets in the CNT Property Manager.
"""
pass
def _addGroupBoxes(self):
"""
Add the Nanotube Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox(self, title="Nanotubes")
self._loadGroupBox1(self._pmGroupBox1)
return
def _loadGroupBox1(self, pmGroupBox):
"""
load widgets in groupbox1
"""
self.nanotubeListWidget = PM_SelectionListWidget(pmGroupBox,
self.win,
label="",
heightByRows=12)
self.nanotubeListWidget.setObjectName('nanotubeListWidget')
self.nanotubeListWidget.setTagInstruction('PICK_ITEM_IN_GLPANE')
self.editNanotubePropertiesButton = PM_PushButton(
pmGroupBox, label="", text="Edit Properties...")
self.editNanotubePropertiesButton.setEnabled(False)
return
def updateNanotubesListWidget(self):
"""
Updates the nanotubes (selection) groupbox. This includes both the
nanotube selection list widget (showing all nanotubes in the part)
and the B{Edit Properties} button just below it (enabled if only
one of the nanotubes is selected).
"""
nanotubeSegmentList = getAllNanotubeSegmentsInPart(self.win.assy)
if nanotubeSegmentList:
self.nanotubeListWidget.insertItems(row=0,
items=nanotubeSegmentList)
else:
self.nanotubeListWidget.clear()
self.updateNanotubePropertiesButton()
return
def updateNanotubePropertiesButton(self):
"""
Enables the B{Edit Properties} button if a single nanotube is currently
selected. Otherwise, the button is disabled.
"""
self.editNanotubePropertiesButton.setEnabled(
bool(self.win.assy.getSelectedNanotubeSegment()))
return
class BuildDna_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 DNA"
pmName = title
iconPath = "ui/actions/Tools/Build Structures/DNA.png"
def __init__( self, win, editCommand ):
"""
Constructor for the Build DNA property manager.
"""
#For model changed signal
self._previousSelectionParams = None
self._previousStructureParams = None
#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 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
self.strandListWidget.connect_or_disconnect_signals(isConnect)
self.segmentListWidget.connect_or_disconnect_signals(isConnect)
change_connect(self.editStrandPropertiesButton,
SIGNAL("clicked()"),
self._editDnaStrand)
change_connect(self.editSegmentPropertiesButton,
SIGNAL("clicked()"),
self._editDnaSegment)
change_connect(self.searchForCrossoversButton,
SIGNAL("clicked()"),
self._enterMakeCrossoversCommand)
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.exitDnaAction.setEnabled(not bool_enable)
def model_changed(self):
"""
When the editCommand is treated as a 'command' by the
commandSequencer. this method will override basicCommand.model_changed.
@WARNING: Ideally this property manager should implement both
model_changed and selection_changed methods in the mode/command
API.
model_changed method will be used here when the selected atom is
dragged, transmuted etc. The selection_changed method will be
used when the selection (picking/ unpicking) changes.
At present, selection_changed and model_changed methods are
called too frequently that it doesn't matter which one you use.
Its better to use only a single method for preformance reasons
(at the moment). This should change when the original
methods in the API are revised to be called at appropiraite
time.
"""
newSelectionParams = self._currentSelectionParams()
selection_params_unchanged = same_vals(newSelectionParams,
self._previousSelectionParams)
#introduing self._previousStructureParams and adding structure_params_unchanged
#check to the if condition below fixes bug 2910.
structure_params_unchanged = same_vals(self._previousStructureParams,
self._currentStructureParams())
if selection_params_unchanged and \
structure_params_unchanged:
#This second condition above fixes bug 2888
return
self._previousStructureParams = self._currentStructureParams()
if not selection_params_unchanged and structure_params_unchanged:
self._previousSelectionParams = newSelectionParams
selectedStrands, selectedSegments = newSelectionParams
self.strandListWidget.updateSelection(selectedStrands)
self.segmentListWidget.updateSelection(selectedSegments)
if len(selectedStrands) == 1:
self.editStrandPropertiesButton.setEnabled(True)
else:
self.editStrandPropertiesButton.setEnabled(False)
if len(selectedSegments) == 1:
self.editSegmentPropertiesButton.setText("Edit Properties...")
self.editSegmentPropertiesButton.setEnabled(True)
elif len(selectedSegments) > 1:
resizeString = "Resize Selected Segments (%d)..."%len(selectedSegments)
self.editSegmentPropertiesButton.setText(resizeString)
self.editSegmentPropertiesButton.setEnabled(True)
self.searchForCrossoversButton.setEnabled(True)
else:
self.editSegmentPropertiesButton.setText("Edit Properties...")
self.editSegmentPropertiesButton.setEnabled(False)
self.searchForCrossoversButton.setEnabled(False)
#Update the strand and segmment list widgets.
#Ideally it should only update when the structure is modified
#example --when structure is deleted. But as of 2008-02-21
#this feature is not easily available in the API method.
#see Command class for some proposed methods such as 'something_changed'
#etc. The list widgets are updated even when selection changes.
#NOTE: If this is called before listwidget's 'updateSelection' call,
#done above, it 'may give' (as of 2008-02-25, it is unlikely to happen
#because of a better implementation) C/C++ object deleted errors.
#So better to do it in the end. Cause -- unknown.
#Guess : something to do with clearing the widget list and them readding
#items (done by self.updateListWidgets)
#..This probably interferes with the selection
#within that list. So better to do it after updating the selection.
if not structure_params_unchanged:
self.updateListWidgets()
def _currentSelectionParams(self):
"""
This needs commandSequencer to treat various
edit controllers as commands. Until then, the 'model_changed' method
(and thus this method) will never be called.
Returns a tuple containing current selection parameters. These
parameters are then used to decide whether updating widgets
in this property manager is needed when L{self.model_changed} or
L{self.selection_changed} methods are called.
@return: A tuple that contains following selection parameters
- Total number of selected atoms (int)
- Selected Atom if a single atom is selected, else None
- Position vector of the single selected atom or None
@rtype: tuple
@NOTE: The method name may be renamed in future.
Its possible that there are other groupboxes in the PM that need to be
updated when something changes in the glpane.
"""
selectedStrands = []
selectedSegments = []
if self.editCommand is not None and self.editCommand.hasValidStructure():
selectedStrands = self.editCommand.struct.getSelectedStrands()
selectedSegments = self.editCommand.struct.getSelectedSegments()
return (selectedStrands, selectedSegments)
def _currentStructureParams(self):
"""
Return current structure parameters of interest to self.model_changed.
Right now it only returns the number of strands within the structure
(or None) . This is a good enough check (and no need to compare
each and evry strand within the structure with a previously stored
set of strands)
"""
#Can it happen that the total number of strands remains the same even
#after some alterations to the strands? Unlikely. (Example: a single
#Break strands operation will increase the number of strands by one.
#Or Join strands decrease it by 1)
params = None
if self.editCommand and self.editCommand.hasValidStructure():
strandList = []
strandList = self.editCommand.struct.getStrands()
params = len(strandList)
return params
def ok_btn_clicked(self):
"""
Slot for the OK button
"""
if self.editCommand:
self.editCommand.preview_or_finalize_structure(previewing = False)
self.win.toolsDone()
def cancel_btn_clicked(self):
"""
Slot for the Cancel button.
"""
if self.editCommand:
self.editCommand.cancelStructure()
self.win.toolsCancel()
def close(self):
"""
Closes the Property Manager. Overrides EditCommand_PM.close()
"""
#Clear tags, if any, due to the selection in the self.strandListWidget.
if self.strandListWidget:
self.strandListWidget.clear()
if self.segmentListWidget:
self.segmentListWidget.clear()
EditCommand_PM.close(self)
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
"""
EditCommand_PM.show(self)
self.updateListWidgets()
def _editDnaStrand(self):
"""
Enter the DnaStrand_EditCommand to edit the selected strand.
"""
if not self.editCommand.hasValidStructure():
return
selectedStrandList = self.editCommand.struct.getSelectedStrands()
if len(selectedStrandList) == 1:
strand = selectedStrandList[0]
strand.edit()
def _editDnaSegment(self):
"""
"""
if self.editCommand is not None and self.editCommand.hasValidStructure():
selectedSegments = self.editCommand.struct.getSelectedSegments()
if len(selectedSegments) == 1:
selectedSegments[0].edit()
elif len(selectedSegments) > 1:
self.win.resizeSelectedDnaSegments()
def _enterMakeCrossoversCommand(self):
"""
If more than one segments in the segment list widget
are selected, enter make crossovers command
@BUG: This enters Make Crossover command which searches for *ALL*
of the selected DnaSegments in the model and not just the selected
segments of the DnaGroup you are editing in the BuildDna command
This is misleading.
"""
self.win.enterMakeCrossoversCommand()
def _update_widgets_in_PM_before_show(self):
"""
Update various widgets in this Property manager.
Overrides EditCommand_PM._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.editcCommand.struct)
@see: MotorPropertyManager._update_widgets_in_PM_before_show
@see: self.show
"""
self.updateListWidgets()
def updateListWidgets(self):
"""
Update List Widgets (strand list and segment list)
in this property manager
@see: self.updateSegmentListWidgets, self.updateStrandListWidget
"""
self.updateStrandListWidget()
self.updateSegmentListWidget()
def updateStrandListWidget(self):
"""
Update the list of items inside the strandlist widget
Example: Origianally it shows two srands. User now edits an
existing dna, and deletes some of the strands, hits done. User then
again invokes the Edit command for this dna object -- now the strand
list widget must be updated so that it shows only the existing strands.
@see: B{Chunk.isStrandChunk}
@see: self.updateListWidgets, self.updateSegmentListWidget
"""
#TODO:
#Filter out only the chunks inside the dna group. the DnaDuplex.make
#doesn't implement the dan data model yet. Until thats implemented ,we
#will do an isinstance(node, Chunk) check . Note that it includes both
#Strands and Axis chunks -- Ninad 2008-01-09
if self.editCommand and self.editCommand.hasValidStructure():
strandChunkList = self.editCommand.struct.getStrands()
self.strandListWidget.insertItems(
row = 0,
items = strandChunkList)
else:
self.strandListWidget.clear()
def updateSegmentListWidget(self):
"""
Update the list of segments shown in the segments list widget
@see: self.updateListWidgets, self.updateStrandListWidget
"""
segmentList = []
if self.editCommand and self.editCommand.hasValidStructure():
def func(node):
if isinstance(node, self.win.assy.DnaSegment):
segmentList.append(node)
self.editCommand.struct.apply2all(func)
self.segmentListWidget.insertItems(
row = 0,
items = segmentList)
else:
self.segmentListWidget.clear()
def _addGroupBoxes( self ):
"""
Add the DNA Property Manager group boxes.
"""
#Unused 'References List Box' to be revided. (just commented out for the
#time being.
##self._pmGroupBox1 = PM_GroupBox( self, title = "Reference Plane" )
##self._loadGroupBox1( self._pmGroupBox1 )
self._pmGroupBox2 = PM_GroupBox( self, title = "Strands" )
self._loadGroupBox2( self._pmGroupBox2 )
self._pmGroupBox3 = PM_GroupBox( self, title = "Segments" )
self._loadGroupBox3( self._pmGroupBox3 )
def _loadGroupBox1(self, pmGroupBox):
"""
load widgets in groupbox1
"""
self.referencePlaneListWidget = PM_SelectionListWidget(
pmGroupBox,
self.win,
label = "",
color = pmReferencesListWidgetColor,
heightByRows = 2)
def _loadGroupBox2(self, pmGroupBox):
"""
load widgets in groupbox2
"""
self.strandListWidget = PM_SelectionListWidget(pmGroupBox,
self.win,
label = "",
heightByRows = 9 )
self.strandListWidget.setTagInstruction('PICK_ITEM_IN_GLPANE')
self.editStrandPropertiesButton = PM_PushButton(
pmGroupBox,
label = "",
text = "Edit Properties..." )
self.editStrandPropertiesButton.setEnabled(False)
def _loadGroupBox3(self, pmGroupBox):
"""
load widgets in groupbox3
"""
self.segmentListWidget = PM_SelectionListWidget(pmGroupBox,
self.win,
label = "",
heightByRows = 4 )
self.segmentListWidget.setObjectName('Segment_list_widget')
self.segmentListWidget.setTagInstruction('PICK_ITEM_IN_GLPANE')
self.editSegmentPropertiesButton = PM_PushButton(
pmGroupBox,
label = "",
text = "Edit Properties..." )
self.editSegmentPropertiesButton.setEnabled(False)
self.searchForCrossoversButton = PM_PushButton(
pmGroupBox,
label = "",
text = "Search For Crossovers..." )
self.searchForCrossoversButton.setEnabled(False)
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
class BuildProtein_PropertyManager(EditCommand_PM):
"""
The BuildProtein_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
iconPath = "ui/actions/Command Toolbar/BuildProtein/BuildProtein.png"
current_protein = "" # name of the single selected peptide. To be deprecated soon. --Mark 2008-12-14
def __init__(self, command):
"""
Constructor for the Build Protein property manager.
"""
#Attributes for self._update_UI_do_updates() to keep track of changes
#in these , since the last call of that method. These are used to
#determine whether certain UI updates are needed.
self._previousSelectionParams = None
self._previousStructureParams = None
self._previousCommandStackParams = None
#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)
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
self.proteinListWidget.connect_or_disconnect_signals(isConnect)
change_connect(self.editPeptidePropertiesButton, SIGNAL("clicked()"),
self._editPeptide)
change_connect(self.compareProteinsButton, SIGNAL("clicked()"),
self._compareProteins)
return
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.
"""
#For new command API, we will always show the exit button to check
#if Exit button really exits the subcommand and the parent command
#(earlier there were bugs) . Regaring 'whether this should be the
#default behavior', its a UI design issue and we will worry about it
#later -- Ninad 2008-08-27 (based on an email exchanged with Bruce)
pass
def _update_UI_do_updates(self):
"""
Overrides superclass method.
@see: Command_PropertyManager._update_UI_do_updates()
"""
newSelectionParams = self._currentSelectionParams()
current_struct_params = self._currentStructureParams()
selection_params_unchanged = same_vals(newSelectionParams,
self._previousSelectionParams)
#introducing self._previousStructureParams and
#adding structure_params_unchanged check to the 'if' condition below
#fixes bug 2910.
structure_params_unchanged = same_vals(self._previousStructureParams,
current_struct_params)
current_command_stack_params = self._currentCommandStackParams()
#Check if command stack params changed since last call of this
#PM update method. This is used to fix bugs like 2940
command_stack_params_unchanged = same_vals(
self._previousCommandStackParams, current_command_stack_params)
#No need to proceed if any of the selection/ structure and commandstack
#parameters remained unchanged since last call. --- [CONDITION A]
if selection_params_unchanged and structure_params_unchanged and command_stack_params_unchanged:
#This second condition above fixes bug 2888
if 0:
print "Build Protein: _update_UI_do_updates() - DO NOTHING"
return
self._previousStructureParams = current_struct_params
self._previousSelectionParams = newSelectionParams
self._previousCommandStackParams = current_command_stack_params
##if not selection_params_unchanged or not command_stack_params_unchanged and structure_params_unchanged:
if structure_params_unchanged:
#NOTE: We checked if either of the selection struct or command stack
#parameters or both changed. (this was referred as '[CONDITION A]'
#above). So, this condition (structure_params_unchanged)also means
#either selection or command stack or both parameters were changed.
if not command_stack_params_unchanged:
#update the protein list widget *before* updating the selection if
#the command stack changed. This ensures that the selection box
#appears around the list widget items that are selected.
self.updateProteinListWidget()
selectedProteins = newSelectionParams
self.proteinListWidget.updateSelection(selectedProteins)
# Enable/disable "Edit Sequence" button.
if len(selectedProteins) == 1:
self.editPeptidePropertiesButton.setEnabled(True)
else:
self.editPeptidePropertiesButton.setEnabled(False)
# Enable/disable "Compare Proteins" button.
if len(selectedProteins) == 2:
self.compareProteinsButton.setEnabled(True)
else:
self.compareProteinsButton.setEnabled(False)
return
self.updateProteinListWidget()
return
def _currentCommandStackParams(self):
"""
The return value is supposed to be used by BUILD_PROTEIN command PM ONLY
and NOT by any subclasses.
Returns a tuple containing current command stack change indicator and
the name of the command 'BUILD_PROTEIN'. These
parameters are then used to decide whether updating widgets
in this property manager is needed, when self._update_UI_do_updates()
is called.
@NOTE:
- Command_PropertyManager.update_UI() already does a check to see if
any of the global change indicators in assembly (command_stack_change,
model_change, selection_change) changed since last call and then only
calls self._update_UI_do_updates().
- But this method is just used to keep track of the
local command stack change counter in order to update the list
widgets.
- This is used to fix bug 2940
@see: self._update_UI_do_updates()
"""
commandStackCounter = self.command.assy.command_stack_change_indicator(
)
#Append 'BUILD_PROTEIN to the tuple to be returned. This is just to remind
#us that this method is meant for BUILD_PROTEIN command PM only. (and not
#by any subclasses) Should we assert this? I think it will slow things
#down so this comment is enough -- Ninad 2008-09-30
return (commandStackCounter, 'BUILD_PROTEIN')
def _currentSelectionParams(self):
"""
Returns a tuple containing current selection parameters. These
parameters are then used to decide whether updating widgets
in this property manager is needed when L{self.model_changed}
method is called.
@return: A tuple that contains total number of selected peptides.
@rtype: tuple
@NOTE: This method may be renamed in future.
It's possible that there are other groupboxes in the PM that need to be
updated when something changes in the glpane.
"""
selectedProteins = []
if self.command is not None: # and self.command.hasValidStructure():
selectedProteins = self.win.assy.getSelectedProteinChunks()
return (selectedProteins)
def _currentStructureParams(self):
"""
Return current structure parameters of interest to self.model_changed.
Right now it only returns the number of peptides within the structure
(or None). This is a good enough check (and no need to compare
each and every peptide within the structure with a previously stored
set of strands).
"""
#Can it happen that the total number of peptides remains the same even
#after some alterations to the peptides? Unlikely. (Example: a single
#(future) Break peptide operation will increase the number of peptides
#by one. Or Join peptides decrease it by 1)
params = None
if self.command: # and self.command.hasValidStructure():
proteinList = []
proteinList = getAllProteinChunksInPart(self.win.assy)
params = len(proteinList)
return params
def close(self):
"""
Closes the Property Manager. Overrides EditCommand_PM.close()
"""
#Clear tags, if any, due to the selection in the self.strandListWidget.
#self.proteinListWidget.clear()
env.history.statusbar_msg("")
EditCommand_PM.close(self)
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.
"""
env.history.statusbar_msg("")
EditCommand_PM.show(self)
# NOTE: Think about moving this msg to _update_UI_do_updates() where
# custom msgs can be created based on the current selection, etc.
# Mark 2008-12-14
msg = "Select <b>Insert Peptide</b> to create a peptide chain or "\
"select another modeling tool to modify an existing protein."
self.updateMessage(msg)
return
def _editPeptide(self):
"""
Slot for the "Edit Properties" button.
"""
#if not self.command.hasValidStructure():
# return
proteinChunk = self.win.assy.getSelectedProteinChunk()
if proteinChunk:
proteinChunk.protein.edit(self.win)
return
def _compareProteins(self):
"""
Slot for the "Compare Proteins" button.
"""
self.win.commandSequencer.userEnterCommand('COMPARE_PROTEINS')
return
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 Build Protein Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox(self, title="Peptides")
self._loadGroupBox1(self._pmGroupBox1)
return
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in groupbox1.
"""
self.proteinListWidget = PM_SelectionListWidget(pmGroupBox,
self.win,
label="",
heightByRows=6)
self.proteinListWidget.setObjectName('Peptide_list_widget')
self.proteinListWidget.setTagInstruction('PICK_ITEM_IN_GLPANE')
self.editPeptidePropertiesButton = PM_PushButton(
pmGroupBox, label="", text="Edit Properties...")
self.editPeptidePropertiesButton.setEnabled(False)
self.compareProteinsButton = PM_PushButton(pmGroupBox,
label="",
text="Compare Proteins...")
self.compareProteinsButton.setEnabled(False)
return
def updateProteinListWidget(self):
"""
Update the peptide list widget. It shows all peptides in the part.
"""
proteinChunkList = getAllProteinChunksInPart(self.win.assy)
if proteinChunkList:
self.proteinListWidget.insertItems(row=0, items=proteinChunkList)
else:
self.proteinListWidget.clear()
return
class BuildNanotube_PropertyManager(EditCommand_PM):
"""
The BuildNanotube_PropertyManager class provides a Property Manager
for the B{Build > 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 = "Build Nanotube"
pmName = title
iconPath = "ui/actions/Command Toolbar/BuildNanotube/BuildNanotube.png"
def __init__( self, command ):
"""
Constructor for the Build Nanotube property manager.
"""
#Attributes for self._update_UI_do_updates() to keep track of changes
#in these , since the last call of that method. These are used to
#determine whether certain UI updates are needed.
self._previousSelectionParams = None
self._previousStructureParams = None
self._previousCommandStackParams = None
#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_WHATS_THIS_BUTTON)
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 actually reconnects the signal!
#This gives rise to lots of bugs. This needs a more general fix in
#the Temporary mode API.
# -- Ninad 2008-01-09 (similar comment exists in MovePropertyManager.py
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
self.nanotubeListWidget.connect_or_disconnect_signals(isConnect)
change_connect(self.editNanotubePropertiesButton,
SIGNAL("clicked()"),
self._editNanotube)
return
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.
"""
#For new command API, we will always show the exit button to check
#if Exit button really exits the subcommand and the parent command
#(earlier there were bugs) . Regaring 'whether this should be the
#default behavior', its a UI design issue and we will worry about it
#later -- Ninad 2008-08-27 (based on an email exchanged with Bruce)
pass
def _update_UI_do_updates(self):
"""
Overrides superclass method.
@see: Command_PropertyManager._update_UI_do_updates()
"""
newSelectionParams = self._currentSelectionParams()
current_struct_params = self._currentStructureParams()
selection_params_unchanged = same_vals(newSelectionParams,
self._previousSelectionParams)
#introducing self._previousStructureParams and
#adding structure_params_unchanged check to the 'if' condition below
#fixes bug 2910.
structure_params_unchanged = same_vals(self._previousStructureParams,
current_struct_params)
current_command_stack_params = self._currentCommandStackParams()
#Check if command stack params changed since last call of this
#PM update method. This is used to fix bugs like 2940
command_stack_params_unchanged = same_vals(
self._previousCommandStackParams, current_command_stack_params)
#No need to proceed if any of the selection/ structure and commandstack
#parameters remained unchanged since last call. --- [CONDITION A]
if selection_params_unchanged and \
structure_params_unchanged and \
command_stack_params_unchanged:
return
self._previousStructureParams = current_struct_params
self._previousSelectionParams = newSelectionParams
self._previousCommandStackParams = current_command_stack_params
if structure_params_unchanged:
#NOTE: We checked if either of the selection struct or command stack
#parameters or both changed. (this was referred as '[CONDITION A]'
#above). So, this condition (structure_params_unchanged)also means
#either selection or command stack or both parameters were changed.
if not command_stack_params_unchanged:
#update the nanotube list widget *before* updating the selection if
#the command stack changed. This ensures that the selection box
#appears around the list widget items that are selected.
self.updateNanotubesListWidget()
selectedNanotubeSegments = newSelectionParams
self.nanotubeListWidget.updateSelection(selectedNanotubeSegments)
self.updateNanotubePropertiesButton()
return
self.updateNanotubesListWidget()
return
def _currentCommandStackParams(self):
"""
The return value is supposed to be used by BUILD_NANOTUBE command PM ONLY
and NOT by any subclasses.
Returns a tuple containing current command stack change indicator and
the name of the command 'BUILD_NANOTUBE'. These
parameters are then used to decide whether updating widgets
in this property manager is needed, when self._update_UI_do_updates()
is called.
@NOTE:
- Command_PropertyManager.update_UI() already does a check to see if
any of the global change indicators in assembly (command_stack_change,
model_change, selection_change) changed since last call and then only
calls self._update_UI_do_updates().
- But this method is just used to keep track of the
local command stack change counter in order to update the list
widgets.
- This is used to fix bug 2940
@see: self._update_UI_do_updates()
"""
commandStackCounter = self.command.assy.command_stack_change_indicator()
#Append 'BUILD_NANOTUBE to the tuple to be returned. This is just to remind
#us that this method is meant for BUILD_NANOTUBE command PM only. (and not
#by any subclasses) Should we assert this? I think it will slow things
#down so this comment is enough -- Ninad 2008-09-30
return (commandStackCounter, 'BUILD_NANOTUBE')
def _currentSelectionParams(self):
"""
Returns a tuple containing current selection parameters. These
parameters are then used to decide whether updating widgets
in this property manager is needed when L{self.model_changed}
method is called.
@return: A tuple that contains total number of selected nanotubes.
@rtype: tuple
@NOTE: This method may be renamed in future.
It's possible that there are other groupboxes in the PM that need to be
updated when something changes in the glpane.
"""
selectedNanotubeSegments = []
if self.command is not None: # and self.command.hasValidStructure():
selectedNanotubeSegments = self.win.assy.getSelectedNanotubeSegments()
return (selectedNanotubeSegments)
def _currentStructureParams(self):
"""
Return current structure parameters of interest to self.model_changed.
Right now it only returns the number of nanotubes within the structure
(or None). This is a good enough check (and no need to compare
each and every nanotube within the structure with a previously stored
set of strands).
"""
params = None
if self.command: # and self.command.hasValidStructure():
nanotubeSegmentList = []
nanotubeSegmentList = getAllNanotubeSegmentsInPart(self.win.assy)
params = len(nanotubeSegmentList)
return params
def close(self):
"""
Closes the Property Manager. Overrides EditCommand_PM.close()
"""
#Clear tags, if any, due to the selection in the self.strandListWidget.
#self.nanotubeListWidget.clear()
env.history.statusbar_msg("")
EditCommand_PM.close(self)
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.
"""
env.history.statusbar_msg("")
EditCommand_PM.show(self)
# NOTE: Think about moving this msg to _update_UI_do_updates() where
# custom msgs can be created based on the current selection, etc.
# Mark 2008-12-14
msg = "Select <b>Insert Nanotube</b> to create a nanotube or "\
"select an existing nantube to modify it."
self.updateMessage(msg)
return
def _editNanotube(self):
"""
Slot for the "Edit Properties" button.
"""
#if not self.command.hasValidStructure():
# return
nanotubeSegment = self.win.assy.getSelectedNanotubeSegment()
if nanotubeSegment:
nanotubeSegment.edit()
return
def _addWhatsThisText( self ):
"""
What's This text for widgets in the CNT Property Manager.
"""
pass
def _addToolTipText(self):
"""
Tool Tip text for widgets in the CNT Property Manager.
"""
pass
def _addGroupBoxes( self ):
"""
Add the Nanotube Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox( self, title = "Nanotubes" )
self._loadGroupBox1( self._pmGroupBox1 )
return
def _loadGroupBox1(self, pmGroupBox):
"""
load widgets in groupbox1
"""
self.nanotubeListWidget = PM_SelectionListWidget(pmGroupBox,
self.win,
label = "",
heightByRows = 12)
self.nanotubeListWidget.setObjectName('nanotubeListWidget')
self.nanotubeListWidget.setTagInstruction('PICK_ITEM_IN_GLPANE')
self.editNanotubePropertiesButton = PM_PushButton(pmGroupBox,
label = "",
text = "Edit Properties..." )
self.editNanotubePropertiesButton.setEnabled(False)
return
def updateNanotubesListWidget(self):
"""
Updates the nanotubes (selection) groupbox. This includes both the
nanotube selection list widget (showing all nanotubes in the part)
and the B{Edit Properties} button just below it (enabled if only
one of the nanotubes is selected).
"""
nanotubeSegmentList = getAllNanotubeSegmentsInPart(self.win.assy)
if nanotubeSegmentList:
self.nanotubeListWidget.insertItems(
row = 0,
items = nanotubeSegmentList)
else:
self.nanotubeListWidget.clear()
self.updateNanotubePropertiesButton()
return
def updateNanotubePropertiesButton(self):
"""
Enables the B{Edit Properties} button if a single nanotube is currently
selected. Otherwise, the button is disabled.
"""
self.editNanotubePropertiesButton.setEnabled(
bool(self.win.assy.getSelectedNanotubeSegment()))
return
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 BuildDna_PropertyManager(EditCommand_PM):
"""
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 DNA"
pmName = title
iconPath = "ui/actions/Tools/Build Structures/DNA.png"
sponsor_keyword = None # Nanorex is the sponsor. Change to 'DNA' to the
# the NUPACK logo.
def __init__(self, command):
"""
Constructor for the Build DNA property manager.
"""
#Attributes for self._update_UI_do_updates() to keep track of changes
#in these , since the last call of that method. These are used to
#determine whether certain UI updates are needed.
self._previousSelectionParams = None
self._previousStructureParams = None
self._previousCommandStackParams = None
#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 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
self.strandListWidget.connect_or_disconnect_signals(isConnect)
self.segmentListWidget.connect_or_disconnect_signals(isConnect)
change_connect(self.editStrandPropertiesButton, SIGNAL("clicked()"),
self._editDnaStrand)
change_connect(self.editSegmentPropertiesButton, SIGNAL("clicked()"),
self._editDnaSegment)
change_connect(self.searchForCrossoversButton, SIGNAL("clicked()"),
self._enterMakeCrossoversCommand)
self._baseNumberLabelGroupBox.connect_or_disconnect_signals(isConnect)
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.
"""
#For new command API, we will always show the exit button to check
#if Exit button really exits the subcommand and the parent command
#(earlier there were bugs) . Regaring 'whether this should be the
#default behavior', its a UI design issue and we will worry about it
#later -- Ninad 2008-08-27 (based on an email exchanged with Bruce)
pass
def _update_UI_do_updates(self):
"""
Overrides superclass method.
@see: Command_PropertyManager._update_UI_do_updates()
"""
newSelectionParams = self._currentSelectionParams()
current_struct_params = self._currentStructureParams()
selection_params_unchanged = same_vals(newSelectionParams,
self._previousSelectionParams)
#introducing self._previousStructureParams and
#adding structure_params_unchanged check to the 'if' condition below
#fixes bug 2910.
structure_params_unchanged = same_vals(self._previousStructureParams,
current_struct_params)
current_command_stack_params = self._currentCommandStackParams()
#Check if command stack params changed since last call of this
#PM update method. This is used to fix bugs like 2940
command_stack_params_unchanged = same_vals(
self._previousCommandStackParams, current_command_stack_params)
#No need to proceed if any of the selection/ structure and commandstack
#parameters remained unchanged since last call. --- [CONDITION A]
if selection_params_unchanged and structure_params_unchanged and command_stack_params_unchanged:
#This second condition above fixes bug 2888
return
self._previousStructureParams = current_struct_params
self._previousSelectionParams = newSelectionParams
self._previousCommandStackParams = current_command_stack_params
##if not selection_params_unchanged or not command_stack_params_unchanged and structure_params_unchanged:
if structure_params_unchanged:
#NOTE: We checked if either of the selection struct or command stack
#parameters or both changed. (this was referred as '[CONDITION A]'
#above). So, this condition (structure_params_unchanged)also means
#either selection or command stack or both parameters were changed.
if not command_stack_params_unchanged:
#update the list widgets *before* updating the selection if
#the command stack changed. This ensures that the selection box
#appears around the list widget items that are selected.
self.updateListWidgets()
selectedStrands, selectedSegments = newSelectionParams
self.strandListWidget.updateSelection(selectedStrands)
self.segmentListWidget.updateSelection(selectedSegments)
if len(selectedStrands) == 1:
self.editStrandPropertiesButton.setEnabled(True)
else:
self.editStrandPropertiesButton.setEnabled(False)
if len(selectedSegments) == 1:
self.editSegmentPropertiesButton.setText("Edit Properties...")
self.editSegmentPropertiesButton.setEnabled(True)
elif len(selectedSegments) > 1:
resizeString = "Resize Selected Segments (%d)..." % len(
selectedSegments)
self.editSegmentPropertiesButton.setText(resizeString)
self.editSegmentPropertiesButton.setEnabled(True)
self.searchForCrossoversButton.setEnabled(True)
else:
self.editSegmentPropertiesButton.setText("Edit Properties...")
self.editSegmentPropertiesButton.setEnabled(False)
self.searchForCrossoversButton.setEnabled(False)
return
# Calling updateListWidgets() here fixes bug 2950 without undoing the
# fix to bug 2940. --Mark 2008-12-13.
self.updateListWidgets()
return
def _currentCommandStackParams(self):
"""
The return value is supposed to be used by BUILD_DNA command PM ONLY
and NOT by any subclasses.
Returns a tuple containing current scommand stack change indicator and
the name of the command 'BUILD_DNA'. These
parameters are then used to decide whether updating widgets
in this property manager is needed, when self._update_UI_do_updates()
is called.
@NOTE:
- Command_PropertyManager.update_UI() already does a check to see if
any of the global change indicators in assembly (command_stack_change,
model_change, selection_change) changed since last call and then only
calls self._update_UI_do_updates().
- But this method is just used to keep track of the
local command stack change counter in order to update the list
widgets.
- This is used to fix bug 2940
@see: self._update_UI_do_updates()
"""
commandStackCounter = self.command.assy.command_stack_change_indicator(
)
#Append 'BUILD_DNA to the tuple to be returned. This is just to remind
#us that this method is meant for BUIL_DNA command PM only. (and not
#by any subclasses) Should we assert this? I think it will slow things
#down so this comment is enough -- Ninad 2008-09-30
return (commandStackCounter, 'BUILD_DNA')
def _currentSelectionParams(self):
"""
Returns a tuple containing current selection parameters. These
parameters are then used to decide whether updating widgets
in this property manager is needed when L{self.model_changed}
method is called.
@return: A tuple that contains following selection parameters
- Total number of selected atoms (int)
- Selected Atom if a single atom is selected, else None
- Position vector of the single selected atom or None
@rtype: tuple
@NOTE: This method may be renamed in future.
It's possible that there are other groupboxes in the PM that need to be
updated when something changes in the glpane.
"""
selectedStrands = []
selectedSegments = []
if self.command is not None and self.command.hasValidStructure():
selectedStrands = self.command.struct.getSelectedStrands()
selectedSegments = self.command.struct.getSelectedSegments()
return (selectedStrands, selectedSegments)
def _currentStructureParams(self):
"""
Return current structure parameters of interest to self.model_changed.
Right now it only returns the number of strands within the structure
(or None). This is a good enough check (and no need to compare
each and every strand within the structure with a previously stored
set of strands).
"""
#Can it happen that the total number of strands remains the same even
#after some alterations to the strands? Unlikely. (Example: a single
#Break strands operation will increase the number of strands by one.
#Or Join strands decrease it by 1)
params = None
if self.command and self.command.hasValidStructure():
strandList = []
strandList = self.command.struct.getStrands()
params = len(strandList)
return params
def close(self):
"""
Closes the Property Manager. Overrides EditCommand_PM.close()
"""
#Clear tags, if any, due to the selection in the self.strandListWidget.
if self.strandListWidget:
self.strandListWidget.clear()
if self.segmentListWidget:
self.segmentListWidget.clear()
EditCommand_PM.close(self)
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
"""
EditCommand_PM.show(self)
self.updateMessage("Use appropriate command in the command "\
"toolbar to create or modify a DNA Object"\
"<br>" )
def _editDnaStrand(self):
"""
Enter the DnaStrand_EditCommand to edit the selected strand.
"""
if not self.command.hasValidStructure():
return
selectedStrandList = self.command.struct.getSelectedStrands()
if len(selectedStrandList) == 1:
strand = selectedStrandList[0]
strand.edit()
def _editDnaSegment(self):
"""
"""
if self.command is not None and self.command.hasValidStructure():
selectedSegments = self.command.struct.getSelectedSegments()
if len(selectedSegments) == 1:
selectedSegments[0].edit()
elif len(selectedSegments) > 1:
self.win.resizeSelectedDnaSegments()
def _enterMakeCrossoversCommand(self):
"""
If more than one segments in the segment list widget
are selected, enter make crossovers command
@BUG: This enters Make Crossover command which searches for *ALL*
of the selected DnaSegments in the model and not just the selected
segments of the DnaGroup you are editing in the BuildDna command
This is misleading.
"""
self.win.enterMakeCrossoversCommand()
def updateListWidgets(self):
"""
Update List Widgets (strand list and segment list)
in this property manager
@see: self.updateSegmentListWidgets, self.updateStrandListWidget
"""
self.updateStrandListWidget()
self.updateSegmentListWidget()
def updateStrandListWidget(self):
"""
Update the list of items inside the strandlist widget
Example: Origianally it shows two srands. User now edits an
existing dna, and deletes some of the strands, hits done. User then
again invokes the Edit command for this dna object -- now the strand
list widget must be updated so that it shows only the existing strands.
@see: B{Chunk.isStrandChunk}
@see: self.updateListWidgets, self.updateSegmentListWidget
"""
#TODO:
#Filter out only the chunks inside the dna group. the DnaDuplex.make
#doesn't implement the dna data model yet. Until that's implemented, we
#will do an isinstance(node, Chunk) check. Note that it includes both
#Strands and Axis chunks -- Ninad 2008-01-09
if self.command.hasValidStructure():
strandChunkList = self.command.struct.getStrands()
self.strandListWidget.insertItems(row=0, items=strandChunkList)
else:
self.strandListWidget.clear()
def updateSegmentListWidget(self):
"""
Update the list of segments shown in the segments list widget
@see: self.updateListWidgets, self.updateStrandListWidget
"""
segmentList = []
if self.command.isCurrentCommand():
if self.command.hasValidStructure():
def func(node):
if isinstance(node, self.win.assy.DnaSegment):
segmentList.append(node)
self.command.struct.apply2all(func)
self.segmentListWidget.insertItems(row=0, items=segmentList)
else:
self.segmentListWidget.clear()
def _addGroupBoxes(self):
"""
Add the DNA Property Manager group boxes.
"""
#Unused 'References List Box' to be revided. (just commented out for the
#time being.
##self._pmGroupBox1 = PM_GroupBox( self, title = "Reference Plane" )
##self._loadGroupBox1( self._pmGroupBox1 )
self._pmGroupBox2 = PM_GroupBox(self, title="Strands")
self._loadGroupBox2(self._pmGroupBox2)
self._pmGroupBox3 = PM_GroupBox(self, title="Segments")
self._loadGroupBox3(self._pmGroupBox3)
self._loadBaseNumberLabelGroupBox(self)
def _loadGroupBox1(self, pmGroupBox):
"""
load widgets in groupbox1
"""
self.referencePlaneListWidget = PM_SelectionListWidget(
pmGroupBox,
self.win,
label="",
color=pmReferencesListWidgetColor,
heightByRows=2)
def _loadGroupBox2(self, pmGroupBox):
"""
load widgets in groupbox2
"""
self.strandListWidget = PM_SelectionListWidget(pmGroupBox,
self.win,
label="",
heightByRows=9)
self.strandListWidget.setTagInstruction('PICK_ITEM_IN_GLPANE')
self.editStrandPropertiesButton = PM_PushButton(
pmGroupBox, label="", text="Edit Properties...")
self.editStrandPropertiesButton.setEnabled(False)
def _loadGroupBox3(self, pmGroupBox):
"""
load widgets in groupbox3
"""
self.segmentListWidget = PM_SelectionListWidget(pmGroupBox,
self.win,
label="",
heightByRows=4)
self.segmentListWidget.setObjectName('Segment_list_widget')
self.segmentListWidget.setTagInstruction('PICK_ITEM_IN_GLPANE')
self.editSegmentPropertiesButton = PM_PushButton(
pmGroupBox, label="", text="Edit Properties...")
self.editSegmentPropertiesButton.setEnabled(False)
self.searchForCrossoversButton = PM_PushButton(
pmGroupBox, label="", text="Search For Crossovers...")
self.searchForCrossoversButton.setEnabled(False)
def _loadBaseNumberLabelGroupBox(self, pmGroupBox):
"""
"""
self._baseNumberLabelGroupBox = PM_DnaBaseNumberLabelsGroupBox(
pmGroupBox, self.command)
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
class BuildProtein_PropertyManager(EditCommand_PM):
"""
The BuildProtein_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
iconPath = "ui/actions/Command Toolbar/BuildProtein/BuildProtein.png"
current_protein = "" # name of the single selected peptide. To be deprecated soon. --Mark 2008-12-14
def __init__( self, command):
"""
Constructor for the Build Protein property manager.
"""
#Attributes for self._update_UI_do_updates() to keep track of changes
#in these , since the last call of that method. These are used to
#determine whether certain UI updates are needed.
self._previousSelectionParams = None
self._previousStructureParams = None
self._previousCommandStackParams = None
#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)
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
self.proteinListWidget.connect_or_disconnect_signals(isConnect)
change_connect(self.editPeptidePropertiesButton,
SIGNAL("clicked()"),
self._editPeptide)
change_connect(self.compareProteinsButton,
SIGNAL("clicked()"),
self._compareProteins)
return
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.
"""
#For new command API, we will always show the exit button to check
#if Exit button really exits the subcommand and the parent command
#(earlier there were bugs) . Regaring 'whether this should be the
#default behavior', its a UI design issue and we will worry about it
#later -- Ninad 2008-08-27 (based on an email exchanged with Bruce)
pass
def _update_UI_do_updates(self):
"""
Overrides superclass method.
@see: Command_PropertyManager._update_UI_do_updates()
"""
newSelectionParams = self._currentSelectionParams()
current_struct_params = self._currentStructureParams()
selection_params_unchanged = same_vals(newSelectionParams,
self._previousSelectionParams)
#introducing self._previousStructureParams and
#adding structure_params_unchanged check to the 'if' condition below
#fixes bug 2910.
structure_params_unchanged = same_vals(self._previousStructureParams,
current_struct_params)
current_command_stack_params = self._currentCommandStackParams()
#Check if command stack params changed since last call of this
#PM update method. This is used to fix bugs like 2940
command_stack_params_unchanged = same_vals(
self._previousCommandStackParams, current_command_stack_params)
#No need to proceed if any of the selection/ structure and commandstack
#parameters remained unchanged since last call. --- [CONDITION A]
if selection_params_unchanged and structure_params_unchanged and command_stack_params_unchanged:
#This second condition above fixes bug 2888
if 0:
print "Build Protein: _update_UI_do_updates() - DO NOTHING"
return
self._previousStructureParams = current_struct_params
self._previousSelectionParams = newSelectionParams
self._previousCommandStackParams = current_command_stack_params
##if not selection_params_unchanged or not command_stack_params_unchanged and structure_params_unchanged:
if structure_params_unchanged:
#NOTE: We checked if either of the selection struct or command stack
#parameters or both changed. (this was referred as '[CONDITION A]'
#above). So, this condition (structure_params_unchanged)also means
#either selection or command stack or both parameters were changed.
if not command_stack_params_unchanged:
#update the protein list widget *before* updating the selection if
#the command stack changed. This ensures that the selection box
#appears around the list widget items that are selected.
self.updateProteinListWidget()
selectedProteins = newSelectionParams
self.proteinListWidget.updateSelection(selectedProteins)
# Enable/disable "Edit Sequence" button.
if len(selectedProteins) == 1:
self.editPeptidePropertiesButton.setEnabled(True)
else:
self.editPeptidePropertiesButton.setEnabled(False)
# Enable/disable "Compare Proteins" button.
if len(selectedProteins) == 2:
self.compareProteinsButton.setEnabled(True)
else:
self.compareProteinsButton.setEnabled(False)
return
self.updateProteinListWidget()
return
def _currentCommandStackParams(self):
"""
The return value is supposed to be used by BUILD_PROTEIN command PM ONLY
and NOT by any subclasses.
Returns a tuple containing current command stack change indicator and
the name of the command 'BUILD_PROTEIN'. These
parameters are then used to decide whether updating widgets
in this property manager is needed, when self._update_UI_do_updates()
is called.
@NOTE:
- Command_PropertyManager.update_UI() already does a check to see if
any of the global change indicators in assembly (command_stack_change,
model_change, selection_change) changed since last call and then only
calls self._update_UI_do_updates().
- But this method is just used to keep track of the
local command stack change counter in order to update the list
widgets.
- This is used to fix bug 2940
@see: self._update_UI_do_updates()
"""
commandStackCounter = self.command.assy.command_stack_change_indicator()
#Append 'BUILD_PROTEIN to the tuple to be returned. This is just to remind
#us that this method is meant for BUILD_PROTEIN command PM only. (and not
#by any subclasses) Should we assert this? I think it will slow things
#down so this comment is enough -- Ninad 2008-09-30
return (commandStackCounter, 'BUILD_PROTEIN')
def _currentSelectionParams(self):
"""
Returns a tuple containing current selection parameters. These
parameters are then used to decide whether updating widgets
in this property manager is needed when L{self.model_changed}
method is called.
@return: A tuple that contains total number of selected peptides.
@rtype: tuple
@NOTE: This method may be renamed in future.
It's possible that there are other groupboxes in the PM that need to be
updated when something changes in the glpane.
"""
selectedProteins = []
if self.command is not None: # and self.command.hasValidStructure():
selectedProteins = self.win.assy.getSelectedProteinChunks()
return (selectedProteins)
def _currentStructureParams(self):
"""
Return current structure parameters of interest to self.model_changed.
Right now it only returns the number of peptides within the structure
(or None). This is a good enough check (and no need to compare
each and every peptide within the structure with a previously stored
set of strands).
"""
#Can it happen that the total number of peptides remains the same even
#after some alterations to the peptides? Unlikely. (Example: a single
#(future) Break peptide operation will increase the number of peptides
#by one. Or Join peptides decrease it by 1)
params = None
if self.command: # and self.command.hasValidStructure():
proteinList = []
proteinList = getAllProteinChunksInPart(self.win.assy)
params = len(proteinList)
return params
def close(self):
"""
Closes the Property Manager. Overrides EditCommand_PM.close()
"""
#Clear tags, if any, due to the selection in the self.strandListWidget.
#self.proteinListWidget.clear()
env.history.statusbar_msg("")
EditCommand_PM.close(self)
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.
"""
env.history.statusbar_msg("")
EditCommand_PM.show(self)
# NOTE: Think about moving this msg to _update_UI_do_updates() where
# custom msgs can be created based on the current selection, etc.
# Mark 2008-12-14
msg = "Select <b>Insert Peptide</b> to create a peptide chain or "\
"select another modeling tool to modify an existing protein."
self.updateMessage(msg)
return
def _editPeptide(self):
"""
Slot for the "Edit Properties" button.
"""
#if not self.command.hasValidStructure():
# return
proteinChunk = self.win.assy.getSelectedProteinChunk()
if proteinChunk:
proteinChunk.protein.edit(self.win)
return
def _compareProteins(self):
"""
Slot for the "Compare Proteins" button.
"""
self.win.commandSequencer.userEnterCommand('COMPARE_PROTEINS')
return
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 Build Protein Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox(self, title = "Peptides")
self._loadGroupBox1(self._pmGroupBox1)
return
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in groupbox1.
"""
self.proteinListWidget = PM_SelectionListWidget(pmGroupBox,
self.win,
label = "",
heightByRows = 6 )
self.proteinListWidget.setObjectName('Peptide_list_widget')
self.proteinListWidget.setTagInstruction('PICK_ITEM_IN_GLPANE')
self.editPeptidePropertiesButton = PM_PushButton(pmGroupBox,
label = "",
text = "Edit Properties..." )
self.editPeptidePropertiesButton.setEnabled(False)
self.compareProteinsButton = PM_PushButton(pmGroupBox,
label = "",
text = "Compare Proteins..." )
self.compareProteinsButton.setEnabled(False)
return
def updateProteinListWidget(self):
"""
Update the peptide list widget. It shows all peptides in the part.
"""
proteinChunkList = getAllProteinChunksInPart(self.win.assy)
if proteinChunkList:
self.proteinListWidget.insertItems(
row = 0,
items = proteinChunkList)
else:
self.proteinListWidget.clear()
return
class BuildDna_PropertyManager(EditCommand_PM):
"""
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 DNA"
pmName = title
iconPath = "ui/actions/Tools/Build Structures/DNA.png"
sponsor_keyword = None # Nanorex is the sponsor. Change to 'DNA' to the
# the NUPACK logo.
def __init__( self, command ):
"""
Constructor for the Build DNA property manager.
"""
#Attributes for self._update_UI_do_updates() to keep track of changes
#in these , since the last call of that method. These are used to
#determine whether certain UI updates are needed.
self._previousSelectionParams = None
self._previousStructureParams = None
self._previousCommandStackParams = None
#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 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
self.strandListWidget.connect_or_disconnect_signals(isConnect)
self.segmentListWidget.connect_or_disconnect_signals(isConnect)
change_connect(self.editStrandPropertiesButton,
SIGNAL("clicked()"),
self._editDnaStrand)
change_connect(self.editSegmentPropertiesButton,
SIGNAL("clicked()"),
self._editDnaSegment)
change_connect(self.searchForCrossoversButton,
SIGNAL("clicked()"),
self._enterMakeCrossoversCommand)
self._baseNumberLabelGroupBox.connect_or_disconnect_signals(isConnect)
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.
"""
#For new command API, we will always show the exit button to check
#if Exit button really exits the subcommand and the parent command
#(earlier there were bugs) . Regaring 'whether this should be the
#default behavior', its a UI design issue and we will worry about it
#later -- Ninad 2008-08-27 (based on an email exchanged with Bruce)
pass
def _update_UI_do_updates(self):
"""
Overrides superclass method.
@see: Command_PropertyManager._update_UI_do_updates()
"""
newSelectionParams = self._currentSelectionParams()
current_struct_params = self._currentStructureParams()
selection_params_unchanged = same_vals(newSelectionParams,
self._previousSelectionParams)
#introducing self._previousStructureParams and
#adding structure_params_unchanged check to the 'if' condition below
#fixes bug 2910.
structure_params_unchanged = same_vals(self._previousStructureParams,
current_struct_params)
current_command_stack_params = self._currentCommandStackParams()
#Check if command stack params changed since last call of this
#PM update method. This is used to fix bugs like 2940
command_stack_params_unchanged = same_vals(
self._previousCommandStackParams, current_command_stack_params)
#No need to proceed if any of the selection/ structure and commandstack
#parameters remained unchanged since last call. --- [CONDITION A]
if selection_params_unchanged and structure_params_unchanged and command_stack_params_unchanged:
#This second condition above fixes bug 2888
return
self._previousStructureParams = current_struct_params
self._previousSelectionParams = newSelectionParams
self._previousCommandStackParams = current_command_stack_params
##if not selection_params_unchanged or not command_stack_params_unchanged and structure_params_unchanged:
if structure_params_unchanged:
#NOTE: We checked if either of the selection struct or command stack
#parameters or both changed. (this was referred as '[CONDITION A]'
#above). So, this condition (structure_params_unchanged)also means
#either selection or command stack or both parameters were changed.
if not command_stack_params_unchanged:
#update the list widgets *before* updating the selection if
#the command stack changed. This ensures that the selection box
#appears around the list widget items that are selected.
self.updateListWidgets()
selectedStrands, selectedSegments = newSelectionParams
self.strandListWidget.updateSelection(selectedStrands)
self.segmentListWidget.updateSelection(selectedSegments)
if len(selectedStrands) == 1:
self.editStrandPropertiesButton.setEnabled(True)
else:
self.editStrandPropertiesButton.setEnabled(False)
if len(selectedSegments) == 1:
self.editSegmentPropertiesButton.setText("Edit Properties...")
self.editSegmentPropertiesButton.setEnabled(True)
elif len(selectedSegments) > 1:
resizeString = "Resize Selected Segments (%d)..." % len(selectedSegments)
self.editSegmentPropertiesButton.setText(resizeString)
self.editSegmentPropertiesButton.setEnabled(True)
self.searchForCrossoversButton.setEnabled(True)
else:
self.editSegmentPropertiesButton.setText("Edit Properties...")
self.editSegmentPropertiesButton.setEnabled(False)
self.searchForCrossoversButton.setEnabled(False)
return
# Calling updateListWidgets() here fixes bug 2950 without undoing the
# fix to bug 2940. --Mark 2008-12-13.
self.updateListWidgets()
return
def _currentCommandStackParams(self):
"""
The return value is supposed to be used by BUILD_DNA command PM ONLY
and NOT by any subclasses.
Returns a tuple containing current scommand stack change indicator and
the name of the command 'BUILD_DNA'. These
parameters are then used to decide whether updating widgets
in this property manager is needed, when self._update_UI_do_updates()
is called.
@NOTE:
- Command_PropertyManager.update_UI() already does a check to see if
any of the global change indicators in assembly (command_stack_change,
model_change, selection_change) changed since last call and then only
calls self._update_UI_do_updates().
- But this method is just used to keep track of the
local command stack change counter in order to update the list
widgets.
- This is used to fix bug 2940
@see: self._update_UI_do_updates()
"""
commandStackCounter = self.command.assy.command_stack_change_indicator()
#Append 'BUILD_DNA to the tuple to be returned. This is just to remind
#us that this method is meant for BUIL_DNA command PM only. (and not
#by any subclasses) Should we assert this? I think it will slow things
#down so this comment is enough -- Ninad 2008-09-30
return (commandStackCounter, 'BUILD_DNA')
def _currentSelectionParams(self):
"""
Returns a tuple containing current selection parameters. These
parameters are then used to decide whether updating widgets
in this property manager is needed when L{self.model_changed}
method is called.
@return: A tuple that contains following selection parameters
- Total number of selected atoms (int)
- Selected Atom if a single atom is selected, else None
- Position vector of the single selected atom or None
@rtype: tuple
@NOTE: This method may be renamed in future.
It's possible that there are other groupboxes in the PM that need to be
updated when something changes in the glpane.
"""
selectedStrands = []
selectedSegments = []
if self.command is not None and self.command.hasValidStructure():
selectedStrands = self.command.struct.getSelectedStrands()
selectedSegments = self.command.struct.getSelectedSegments()
return (selectedStrands, selectedSegments)
def _currentStructureParams(self):
"""
Return current structure parameters of interest to self.model_changed.
Right now it only returns the number of strands within the structure
(or None). This is a good enough check (and no need to compare
each and every strand within the structure with a previously stored
set of strands).
"""
#Can it happen that the total number of strands remains the same even
#after some alterations to the strands? Unlikely. (Example: a single
#Break strands operation will increase the number of strands by one.
#Or Join strands decrease it by 1)
params = None
if self.command and self.command.hasValidStructure():
strandList = []
strandList = self.command.struct.getStrands()
params = len(strandList)
return params
def close(self):
"""
Closes the Property Manager. Overrides EditCommand_PM.close()
"""
#Clear tags, if any, due to the selection in the self.strandListWidget.
if self.strandListWidget:
self.strandListWidget.clear()
if self.segmentListWidget:
self.segmentListWidget.clear()
EditCommand_PM.close(self)
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
"""
EditCommand_PM.show(self)
self.updateMessage("Use appropriate command in the command "\
"toolbar to create or modify a DNA Object"\
"<br>" )
def _editDnaStrand(self):
"""
Enter the DnaStrand_EditCommand to edit the selected strand.
"""
if not self.command.hasValidStructure():
return
selectedStrandList = self.command.struct.getSelectedStrands()
if len(selectedStrandList) == 1:
strand = selectedStrandList[0]
strand.edit()
def _editDnaSegment(self):
"""
"""
if self.command is not None and self.command.hasValidStructure():
selectedSegments = self.command.struct.getSelectedSegments()
if len(selectedSegments) == 1:
selectedSegments[0].edit()
elif len(selectedSegments) > 1:
self.win.resizeSelectedDnaSegments()
def _enterMakeCrossoversCommand(self):
"""
If more than one segments in the segment list widget
are selected, enter make crossovers command
@BUG: This enters Make Crossover command which searches for *ALL*
of the selected DnaSegments in the model and not just the selected
segments of the DnaGroup you are editing in the BuildDna command
This is misleading.
"""
self.win.enterMakeCrossoversCommand()
def updateListWidgets(self):
"""
Update List Widgets (strand list and segment list)
in this property manager
@see: self.updateSegmentListWidgets, self.updateStrandListWidget
"""
self.updateStrandListWidget()
self.updateSegmentListWidget()
def updateStrandListWidget(self):
"""
Update the list of items inside the strandlist widget
Example: Origianally it shows two srands. User now edits an
existing dna, and deletes some of the strands, hits done. User then
again invokes the Edit command for this dna object -- now the strand
list widget must be updated so that it shows only the existing strands.
@see: B{Chunk.isStrandChunk}
@see: self.updateListWidgets, self.updateSegmentListWidget
"""
#TODO:
#Filter out only the chunks inside the dna group. the DnaDuplex.make
#doesn't implement the dna data model yet. Until that's implemented, we
#will do an isinstance(node, Chunk) check. Note that it includes both
#Strands and Axis chunks -- Ninad 2008-01-09
if self.command.hasValidStructure():
strandChunkList = self.command.struct.getStrands()
self.strandListWidget.insertItems(
row = 0,
items = strandChunkList)
else:
self.strandListWidget.clear()
def updateSegmentListWidget(self):
"""
Update the list of segments shown in the segments list widget
@see: self.updateListWidgets, self.updateStrandListWidget
"""
segmentList = []
if self.command.isCurrentCommand():
if self.command.hasValidStructure():
def func(node):
if isinstance(node, self.win.assy.DnaSegment):
segmentList.append(node)
self.command.struct.apply2all(func)
self.segmentListWidget.insertItems(
row = 0,
items = segmentList)
else:
self.segmentListWidget.clear()
def _addGroupBoxes( self ):
"""
Add the DNA Property Manager group boxes.
"""
#Unused 'References List Box' to be revided. (just commented out for the
#time being.
##self._pmGroupBox1 = PM_GroupBox( self, title = "Reference Plane" )
##self._loadGroupBox1( self._pmGroupBox1 )
self._pmGroupBox2 = PM_GroupBox( self, title = "Strands" )
self._loadGroupBox2( self._pmGroupBox2 )
self._pmGroupBox3 = PM_GroupBox( self, title = "Segments" )
self._loadGroupBox3( self._pmGroupBox3 )
self._loadBaseNumberLabelGroupBox(self)
def _loadGroupBox1(self, pmGroupBox):
"""
load widgets in groupbox1
"""
self.referencePlaneListWidget = PM_SelectionListWidget(
pmGroupBox,
self.win,
label = "",
color = pmReferencesListWidgetColor,
heightByRows = 2)
def _loadGroupBox2(self, pmGroupBox):
"""
load widgets in groupbox2
"""
self.strandListWidget = PM_SelectionListWidget(pmGroupBox,
self.win,
label = "",
heightByRows = 9 )
self.strandListWidget.setTagInstruction('PICK_ITEM_IN_GLPANE')
self.editStrandPropertiesButton = PM_PushButton(
pmGroupBox,
label = "",
text = "Edit Properties..." )
self.editStrandPropertiesButton.setEnabled(False)
def _loadGroupBox3(self, pmGroupBox):
"""
load widgets in groupbox3
"""
self.segmentListWidget = PM_SelectionListWidget(pmGroupBox,
self.win,
label = "",
heightByRows = 4 )
self.segmentListWidget.setObjectName('Segment_list_widget')
self.segmentListWidget.setTagInstruction('PICK_ITEM_IN_GLPANE')
self.editSegmentPropertiesButton = PM_PushButton(
pmGroupBox,
label = "",
text = "Edit Properties..." )
self.editSegmentPropertiesButton.setEnabled(False)
self.searchForCrossoversButton = PM_PushButton(
pmGroupBox,
label = "",
text = "Search For Crossovers..." )
self.searchForCrossoversButton.setEnabled(False)
def _loadBaseNumberLabelGroupBox(self, pmGroupBox):
"""
"""
self._baseNumberLabelGroupBox = PM_DnaBaseNumberLabelsGroupBox(pmGroupBox,
self.command)
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
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