class EditProtein_PropertyManager(Command_PropertyManager):
"""
The ProteinDisplayStyle_PropertyManager class provides a Property Manager
for the B{Edit Protein} command on the Build Protein command toolbar.
The selected peptide/protein is displayed in the protein reduced display
style. The user can select individual rotamers and edit their chi angles.
This is useful for certain types of protein design protocols using a
3rd party program like Rosetta.
@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 = "Protein Properties"
pmName = title
iconPath = "ui/actions/Command Toolbar/BuildProtein/EditProtein.png"
current_protein = None # The currently selected peptide.
previous_protein = None # The last peptide selected.
current_aa = None # The current amino acid.
def __init__( self, command ):
"""
Constructor for the property manager.
"""
self.currentWorkingDirectory = env.prefs[workingDirectory_prefs_key]
_superclass.__init__(self, command)
self.sequenceEditor = self.win.createProteinSequenceEditorIfNeeded()
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.nameLineEdit,
SIGNAL("editingFinished()"),
self._nameChanged)
change_connect(self.currentResidueComboBox,
SIGNAL("activated(int)"),
self.setCurrentAminoAcid)
change_connect(self.prevButton,
SIGNAL("clicked()"),
self._expandPreviousRotamer)
change_connect(self.nextButton,
SIGNAL("clicked()"),
self._expandNextRotamer)
change_connect(self.recenterViewCheckBox,
SIGNAL("toggled(bool)"),
self._centerViewToggled)
change_connect(self.showAllResiduesCheckBox,
SIGNAL("toggled(bool)"),
self._showAllResidues)
# Rotamer control widgets.
change_connect(self.chi1Dial,
SIGNAL("valueChanged(int)"),
self._rotateChi1)
change_connect(self.chi2Dial,
SIGNAL("valueChanged(int)"),
self._rotateChi2)
change_connect(self.chi3Dial,
SIGNAL("valueChanged(int)"),
self._rotateChi3)
# Chi4 dial is hidden.
change_connect(self.chi4Dial,
SIGNAL("valueChanged(double)"),
self._rotateChi4)
return
#==
def _nameChanged(self):
"""
Slot for "Name" field.
@TODO: Include a validator for the name field.
"""
if not self.current_protein:
return
_name = str(self.nameLineEdit.text())
if not _name: # Minimal test. Need to implement a validator.
if self.current_protein:
self.nameLineEdit.setText(self.current_protein.name)
return
self.current_protein.name = _name
msg = "Editing structure <b>%s</b>." % _name
self.updateMessage(msg)
return
def update_name_field(self):
"""
Update the name field showing the name of the currently selected protein.
clear the combobox list.
"""
if not self.current_protein:
self.nameLineEdit.setText("")
else:
self.nameLineEdit.setText(self.current_protein.name)
return
def update_length_field(self):
"""
Update the name field showing the name of the currently selected protein.
clear the combobox list.
"""
if not self.current_protein:
self.lengthLineEdit.setText("")
else:
length_str = "%d residues" % self.current_protein.protein.count_amino_acids()
self.lengthLineEdit.setText(length_str)
return
def update_residue_combobox(self):
"""
Update the residue combobox with the amino acid sequence of the
currently selected protein. If there is no currently selected protein,
clear the combobox list.
"""
self.currentResidueComboBox.clear()
if not self.current_protein:
return
aa_list = self.current_protein.protein.get_amino_acid_id_list()
for j in range(len(aa_list)):
aa_id, residue_id = aa_list[j].strip().split(":")
self.currentResidueComboBox.addItem(residue_id)
pass
self.setCurrentAminoAcid()
return
def close(self):
"""
Closes the Property Manager. Overrides EditCommand_PM.close()
"""
self.sequenceEditor.hide()
env.history.statusbar_msg("")
if self.current_protein:
self.current_protein.setDisplayStyle(self.previous_protein_display_style)
self.previous_protein = None
# Update name in case the it was changed by the user.
self.current_protein.name = str(self.nameLineEdit.text())
_superclass.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.
"""
_superclass.show(self)
env.history.statusbar_msg("")
return
def _addGroupBoxes( self ):
"""
Add the Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox( self,
title = "Parameters")
self._loadGroupBox1( self._pmGroupBox1 )
self._pmGroupBox2 = PM_GroupBox( self,
title = "Rotamer Controls")
self._loadGroupBox2( self._pmGroupBox2 )
return
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
self.nameLineEdit = PM_LineEdit( pmGroupBox,
label = "Name:")
self.lengthLineEdit = PM_LineEdit( pmGroupBox,
label = "Length:")
self.lengthLineEdit.setEnabled(False)
self.currentResidueComboBox = PM_ComboBox( pmGroupBox,
label = "Current residue:",
setAsDefault = False)
BUTTON_LIST = [
("QToolButton", 1, "Previous residue",
"ui/actions/Properties Manager/Previous.png",
"", "Previous residue", 0 ),
( "QToolButton", 2, "Next residue",
"ui/actions/Properties Manager/Next.png",
"", "Next residue", 1 )
]
self.prevNextButtonRow = \
PM_ToolButtonRow( pmGroupBox,
title = "",
buttonList = BUTTON_LIST,
label = 'Previous / Next:',
isAutoRaise = True,
isCheckable = False
)
self.prevButton = self.prevNextButtonRow.getButtonById(1)
self.nextButton = self.prevNextButtonRow.getButtonById(2)
self.recenterViewCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Center view on current residue",
setAsDefault = True,
state = Qt.Unchecked,
widgetColumn = 0,
spanWidth = True)
self.lockEditedCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Lock edited rotamers",
setAsDefault = True,
state = Qt.Checked,
widgetColumn = 0,
spanWidth = True)
self.showAllResiduesCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Show all residues",
setAsDefault = False,
state = Qt.Unchecked,
widgetColumn = 0,
spanWidth = True)
return
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in group box.
"""
self.discreteStepsCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Use discrete steps",
setAsDefault = True,
state = Qt.Unchecked)
self.chi1Dial = \
PM_Dial( pmGroupBox,
label = "Chi1:",
value = 0.000,
setAsDefault = True,
minimum = -180.0,
maximum = 180.0,
wrapping = True,
suffix = "deg",
spanWidth = False)
self.chi1Dial.setEnabled(False)
self.chi2Dial = \
PM_Dial( pmGroupBox,
label = "Chi2:",
value = 0.000,
setAsDefault = True,
minimum = -180.0,
maximum = 180.0,
suffix = "deg",
spanWidth = False)
self.chi2Dial.setEnabled(False)
self.chi3Dial = \
PM_Dial( pmGroupBox,
label = "Chi3:",
value = 0.000,
setAsDefault = True,
minimum = -180.0,
maximum = 180.0,
suffix = "deg",
spanWidth = False)
self.chi3Dial.setEnabled(False)
self.chi4Dial = \
PM_Dial( pmGroupBox,
label = "Chi4:",
value = 0.000,
setAsDefault = True,
minimum = -180.0,
maximum = 180.0,
suffix = "deg",
spanWidth = False)
self.chi4Dial.setEnabled(False)
self.chi4Dial.hide()
return
def _addWhatsThisText( self ):
pass
def _addToolTipText(self):
pass
def _expandNextRotamer(self):
"""
Displays the next rotamer in the chain.
@attention: this only works when the GDS is a reduced display style.
"""
if not self.current_protein:
return
self.current_protein.protein.traverse_forward()
self.setCurrentAminoAcid()
return
def _expandPreviousRotamer(self):
"""
Displays the previous rotamer in the chain.
@attention: this only works when the GDS is a reduced display style.
"""
if not self.current_protein:
return
self.current_protein.protein.traverse_backward()
self.setCurrentAminoAcid()
return
def _centerViewToggled(self, checked):
"""
Slot for "Center view on current residue" checkbox.
"""
if checked:
self.display_and_recenter()
return
def _showAllResidues(self, show):
"""
Slot for "Show all residues" checkbox.
"""
if not self.current_protein:
return
print "Show =",show
if show:
self._expandAllRotamers()
else:
self._collapseAllRotamers()
return
def _collapseAllRotamers(self):
"""
Hides all the rotamers (except the current rotamer).
"""
self.display_and_recenter()
return
def _expandAllRotamers(self):
"""
Displays all the rotamers.
"""
if not self.current_protein:
return
self.current_protein.protein.expand_all_rotamers()
self.win.glpane.gl_update()
return
def display_and_recenter(self):
"""
Recenter the view on the current amino acid selected in the
residue combobox (or the sequence editor). All rotamers
except the current rotamer are collapsed (hidden).
"""
if not self.current_protein:
return
# Uncheck the "Show all residues" checkbox since they are being collapsed.
# Disconnect signals so that showAllResiduesCheckBox won't general a signal.
self.connect_or_disconnect_signals(isConnect = False)
self.showAllResiduesCheckBox.setChecked(False)
self.connect_or_disconnect_signals(isConnect = True)
self.current_protein.protein.collapse_all_rotamers()
# Display the current amino acid and center it in the view if the
# "Center view on current residue" is checked.
if self.current_aa:
self.current_protein.protein.expand_rotamer(self.current_aa)
self._update_chi_angles(self.current_aa)
if self.recenterViewCheckBox.isChecked():
ca_atom = self.current_aa.get_c_alpha_atom()
if ca_atom:
self.win.glpane.pov = -ca_atom.posn()
self.win.glpane.gl_update()
return
def _update_chi_angles(self, aa):
"""
"""
angle = aa.get_chi_angle(0)
if angle:
self.chi1Dial.setEnabled(True)
self.chi1Dial.setValue(angle)
else:
self.chi1Dial.setEnabled(False)
self.chi1Dial.setValue(0.0)
angle = aa.get_chi_angle(1)
if angle:
self.chi2Dial.setEnabled(True)
self.chi2Dial.setValue(angle)
else:
self.chi2Dial.setEnabled(False)
self.chi2Dial.setValue(0.0)
angle = aa.get_chi_angle(2)
if angle:
self.chi3Dial.setEnabled(True)
self.chi3Dial.setValue(angle)
else:
self.chi3Dial.setEnabled(False)
self.chi3Dial.setValue(0.0)
angle = aa.get_chi_angle(3)
if angle:
self.chi4Dial.setEnabled(True)
self.chi4Dial.setValue(angle)
else:
self.chi4Dial.setEnabled(False)
self.chi4Dial.setValue(0.0)
return
def setCurrentAminoAcid(self, aa_index = -1):
"""
Set the current amino acid to I{aa_index} and update the
"Current residue" combobox and the sequence editor.
@param aa_index: the amino acid index. If negative, update the PM and
sequence editor based on the current aa_index.
@type aa_index: int
@note: This is the slot for the "Current residue" combobox.
"""
if not self.current_protein:
return
if aa_index < 0:
aa_index = self.current_protein.protein.get_current_amino_acid_index()
if 0: # Debugging statement
print"setCurrentAminoAcid(): aa_index=", aa_index
self.currentResidueComboBox.setCurrentIndex(aa_index)
self.current_protein.protein.set_current_amino_acid_index(aa_index)
self.current_aa = self.current_protein.protein.get_current_amino_acid()
self.display_and_recenter()
self.sequenceEditor.setCursorPosition(aa_index)
return
def _rotateChiAngle(self, chi, angle):
"""
Rotate around chi1 angle.
"""
if not self.current_protein:
return
if self.current_aa:
self.current_protein.protein.expand_rotamer(self.current_aa)
self.current_aa.set_chi_angle(chi, angle)
self.win.glpane.gl_update()
return
def _rotateChi1(self, angle):
"""
Slot for Chi1 dial.
"""
self._rotateChiAngle(0, angle)
self.chi1Dial.updateValueLabel()
return
def _rotateChi2(self, angle):
"""
Slot for Chi2 dial.
"""
self._rotateChiAngle(1, angle)
self.chi2Dial.updateValueLabel()
return
def _rotateChi3(self, angle):
"""
Slot for Chi3 dial.
"""
self._rotateChiAngle(2, angle)
self.chi3Dial.updateValueLabel()
return
def _rotateChi4(self, angle):
"""
Slot for Chi4 dial.
@note: this dial is currently hidden and unused.
"""
self._rotateChiAngle(3, angle)
return
def _update_UI_do_updates(self):
"""
Overrides superclass method.
@see: Command_PropertyManager._update_UI_do_updates()
"""
self.current_protein = self.win.assy.getSelectedProteinChunk()
if self.current_protein is self.previous_protein:
if 0:
print "Edit Protein: _update_UI_do_updates() - DO NOTHING."
return
# It is common that the user will unselect the current protein.
# If so, set current_protein to previous_protein so that it
# (the previously selected protein) remains the current protein
# in the PM and sequence editor.
if not self.current_protein:
self.current_protein = self.previous_protein
return
# Update all PM widgets that need to be since something has changed.
if 0:
print "Edit Protein: _update_UI_do_updates() - UPDATING THE PMGR."
self.update_name_field()
self.update_length_field()
self.sequenceEditor.updateSequence(proteinChunk = self.current_protein)
self.update_residue_combobox()
# NOTE: Changing the display style of the protein chunks can take some
# time. We should put up the wait (hourglass) cursor and restore
# before returning.
if self.previous_protein:
self.previous_protein.setDisplayStyle(self.previous_protein_display_style)
self.previous_protein = self.current_protein
if self.current_protein:
self.previous_protein_display_style = self.current_protein.getDisplayStyle()
self.current_protein.setDisplayStyle(diPROTEIN)
if self.current_protein:
msg = "Editing structure <b>%s</b>." % self.current_protein.name
else:
msg = "Select a single structure to edit."
self.updateMessage(msg)
return
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in group box.
"""
self.discreteStepsCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Use discrete steps",
setAsDefault = True,
state = Qt.Unchecked)
self.chi1Dial = \
PM_Dial( pmGroupBox,
label = "Chi1:",
value = 0.000,
setAsDefault = True,
minimum = -180.0,
maximum = 180.0,
wrapping = True,
suffix = "deg",
spanWidth = False)
self.chi1Dial.setEnabled(False)
self.chi2Dial = \
PM_Dial( pmGroupBox,
label = "Chi2:",
value = 0.000,
setAsDefault = True,
minimum = -180.0,
maximum = 180.0,
suffix = "deg",
spanWidth = False)
self.chi2Dial.setEnabled(False)
self.chi3Dial = \
PM_Dial( pmGroupBox,
label = "Chi3:",
value = 0.000,
setAsDefault = True,
minimum = -180.0,
maximum = 180.0,
suffix = "deg",
spanWidth = False)
self.chi3Dial.setEnabled(False)
self.chi4Dial = \
PM_Dial( pmGroupBox,
label = "Chi4:",
value = 0.000,
setAsDefault = True,
minimum = -180.0,
maximum = 180.0,
suffix = "deg",
spanWidth = False)
self.chi4Dial.setEnabled(False)
self.chi4Dial.hide()
return