def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in the second group box.
"""
self.headerdata_seq = ['', 'ID', 'Set', 'BR', 'Descriptor']
self.recenterViewCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Re-center view on selected residue",
setAsDefault = True,
widgetColumn = 0,
state = Qt.Unchecked)
self.selectAllPushButton = PM_PushButton(pmGroupBox,
text="All",
setAsDefault=True)
self.selectAllPushButton.setFixedHeight(25)
self.selectNonePushButton = PM_PushButton(pmGroupBox,
text="None",
setAsDefault=True)
self.selectNonePushButton.setFixedHeight(25)
self.selectInvertPushButton = PM_PushButton(pmGroupBox,
text="Invert",
setAsDefault=True)
self.selectInvertPushButton.setFixedHeight(25)
buttonList = [('PM_PushButton', self.selectAllPushButton, 0, 0),
('PM_PushButton', self.selectNonePushButton, 1, 0),
('PM_PushButton', self.selectInvertPushButton, 2, 0)]
self.buttonGrid = PM_WidgetGrid(pmGroupBox, widgetList=buttonList)
self.sequenceTable = PM_TableWidget(pmGroupBox)
#self.sequenceTable.setModel(self.tableModel)
self.sequenceTable.resizeColumnsToContents()
self.sequenceTable.verticalHeader().setVisible(False)
#self.sequenceTable.setRowCount(0)
self.sequenceTable.setColumnCount(5)
self.checkbox = QCheckBox()
self.sequenceTable.setFixedHeight(345)
self.sequenceTable.setGridStyle(Qt.NoPen)
self.sequenceTable.setHorizontalHeaderLabels(self.headerdata_seq)
###self._fillSequenceTable()
self.showSequencePushButton = PM_PushButton(pmGroupBox,
text="Show Sequence",
setAsDefault=True,
spanWidth=True)
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in the second group box.
"""
self.headerdata_seq = ['', 'ID', 'Set', 'BR', 'Descriptor']
self.recenterViewCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Re-center view on selected residue",
setAsDefault = True,
widgetColumn = 0,
state = Qt.Unchecked)
self.selectAllPushButton = PM_PushButton( pmGroupBox,
text = "All",
setAsDefault = True)
self.selectAllPushButton.setFixedHeight(25)
self.selectNonePushButton = PM_PushButton( pmGroupBox,
text = "None",
setAsDefault = True)
self.selectNonePushButton.setFixedHeight(25)
self.selectInvertPushButton = PM_PushButton( pmGroupBox,
text = "Invert",
setAsDefault = True)
self.selectInvertPushButton.setFixedHeight(25)
buttonList = [ ('PM_PushButton', self.selectAllPushButton, 0, 0),
('PM_PushButton', self.selectNonePushButton, 1, 0),
('PM_PushButton', self.selectInvertPushButton, 2, 0)]
self.buttonGrid = PM_WidgetGrid( pmGroupBox,
widgetList = buttonList)
self.sequenceTable = PM_TableWidget( pmGroupBox)
#self.sequenceTable.setModel(self.tableModel)
self.sequenceTable.resizeColumnsToContents()
self.sequenceTable.verticalHeader().setVisible(False)
#self.sequenceTable.setRowCount(0)
self.sequenceTable.setColumnCount(5)
self.checkbox = QCheckBox()
self.sequenceTable.setFixedHeight(345)
self.sequenceTable.setGridStyle(Qt.NoPen)
self.sequenceTable.setHorizontalHeaderLabels(self.headerdata_seq)
###self._fillSequenceTable()
self.showSequencePushButton = PM_PushButton( pmGroupBox,
text = "Show Sequence",
setAsDefault = True,
spanWidth = True)
class EditResidues_PropertyManager(Command_PropertyManager):
"""
The ProteinDisplayStyle_PropertyManager class provides a Property Manager
for the B{Display Style} command on the flyout toolbar in the
Build > Protein 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 = "Edit Residues"
pmName = title
iconPath = "ui/actions/Command Toolbar/BuildProtein/Residues.png"
rosetta_all_set = "PGAVILMFWYCSTNQDEHKR"
rosetta_polar_set = "___________STNQDEHKR"
rosetta_apolar_set = "PGAVILMFWYC_________"
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)
self.editingItem = False
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.applyAnyPushButton,
SIGNAL("clicked()"),
self._applyAny)
change_connect(self.applySamePushButton,
SIGNAL("clicked()"),
self._applySame)
change_connect(self.applyLockedPushButton,
SIGNAL("clicked()"),
self._applyLocked)
change_connect(self.applyPolarPushButton,
SIGNAL("clicked()"),
self._applyPolar)
change_connect(self.applyApolarPushButton,
SIGNAL("clicked()"),
self._applyApolar)
change_connect(self.selectAllPushButton,
SIGNAL("clicked()"),
self._selectAll)
change_connect(self.selectNonePushButton,
SIGNAL("clicked()"),
self._selectNone)
change_connect(self.selectInvertPushButton,
SIGNAL("clicked()"),
self._invertSelection)
change_connect(self.applyDescriptorPushButton,
SIGNAL("clicked()"),
self._applyDescriptor)
change_connect(self.removeDescriptorPushButton,
SIGNAL("clicked()"),
self._removeDescriptor)
change_connect(self.sequenceTable,
SIGNAL("cellClicked(int, int)"),
self._sequenceTableCellChanged)
change_connect(self.sequenceTable,
SIGNAL("itemChanged(QTableWidgetItem*)"),
self._sequenceTableItemChanged)
change_connect(self.descriptorsTable,
SIGNAL("itemChanged(QTableWidgetItem*)"),
self._descriptorsTableItemChanged)
change_connect(self.newDescriptorPushButton,
SIGNAL("clicked()"),
self._addNewDescriptor)
change_connect(self.showSequencePushButton,
SIGNAL("clicked()"),
self._showSeqEditor)
return
def _showSeqEditor(self):
"""
Shows sequence editor
"""
if self.showSequencePushButton.isEnabled():
self.sequenceEditor.show()
return
def show(self):
"""
Shows the Property Manager. Extends superclass method.
"""
env.history.statusbar_msg("")
#Urmi 20080728: Set the current protein and this will be used for accessing
#various properties of this protein
self.set_current_protein()
if self.current_protein:
msg = "Editing structure <b>%s</b>." % self.current_protein.name
self.showSequencePushButton.setEnabled(True)
else:
msg = "Select a single structure to edit."
self.showSequencePushButton.setEnabled(False)
self.sequenceEditor.hide()
_superclass.show(self)
self._fillSequenceTable()
self.updateMessage(msg)
return
def set_current_protein(self):
"""
Set the current protein for which all the properties are displayed to the
one chosen in the build protein combo box
"""
self.current_protein = self.win.assy.getSelectedProteinChunk()
return
def _addGroupBoxes( self ):
"""
Add the Property Manager group boxes.
"""
if sys.platform == "darwin":
# Workaround for table font size difference between Mac/Win
self.labelfont = QFont("Helvetica", 12)
self.descriptorfont = QFont("Courier New", 12)
else:
self.labelfont = QFont("Helvetica", 9)
self.descriptorfont = QFont("Courier New", 9)
self._pmGroupBox1 = PM_GroupBox( self,
title = "Descriptors")
self._loadGroupBox1( self._pmGroupBox1 )
self._pmGroupBox2 = PM_GroupBox( self,
title = "Sequence")
self._loadGroupBox2( self._pmGroupBox2 )
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in the first group box.
"""
self.headerdata_desc = ['Name', 'Descriptor']
self.set_names = ["Any", "Same", "Locked", "Apolar", "Polar"]
self.rosetta_set_names = ["ALLAA", "NATAA", "NATRO", "APOLA", "POLAR"]
self.descriptor_list = ["PGAVILMFWYCSTNQDEHKR",
"____________________",
"____________________",
"PGAVILMFWYC_________",
"___________STNQDEHKR"]
self.applyAnyPushButton = PM_PushButton( pmGroupBox,
text = "ALLAA",
setAsDefault = True)
self.applySamePushButton = PM_PushButton( pmGroupBox,
text = "NATAA",
setAsDefault = True)
self.applyLockedPushButton = PM_PushButton( pmGroupBox,
text = "NATRO",
setAsDefault = True)
self.applyPolarPushButton = PM_PushButton( pmGroupBox,
text = "APOLA",
setAsDefault = True)
self.applyApolarPushButton = PM_PushButton( pmGroupBox,
text = "POLAR",
setAsDefault = True)
#self.applyBackrubPushButton = PM_PushButton( pmGroupBox,
# text = "BACKRUB",
# setAsDefault = True)
self.applyAnyPushButton.setFixedHeight(25)
self.applyAnyPushButton.setFixedWidth(60)
self.applySamePushButton.setFixedHeight(25)
self.applySamePushButton.setFixedWidth(60)
self.applyLockedPushButton.setFixedHeight(25)
self.applyLockedPushButton.setFixedWidth(60)
self.applyPolarPushButton.setFixedHeight(25)
self.applyPolarPushButton.setFixedWidth(60)
self.applyApolarPushButton.setFixedHeight(25)
self.applyApolarPushButton.setFixedWidth(60)
applyButtonList = [
('PM_PushButton', self.applyAnyPushButton, 0, 0),
('PM_PushButton', self.applySamePushButton, 1, 0),
('PM_PushButton', self.applyLockedPushButton, 2, 0),
('PM_PushButton', self.applyPolarPushButton, 3, 0),
('PM_PushButton', self.applyApolarPushButton, 4, 0) ]
self.applyButtonGrid = PM_WidgetGrid( pmGroupBox,
label = "Apply standard set",
widgetList = applyButtonList)
self.descriptorsTable = PM_TableWidget( pmGroupBox,
label = "Custom descriptors")
self.descriptorsTable.setFixedHeight(100)
self.descriptorsTable.setRowCount(0)
self.descriptorsTable.setColumnCount(2)
self.descriptorsTable.verticalHeader().setVisible(False)
self.descriptorsTable.horizontalHeader().setVisible(True)
self.descriptorsTable.setGridStyle(Qt.NoPen)
self.descriptorsTable.setHorizontalHeaderLabels(self.headerdata_desc)
self._updateSetLists()
self._fillDescriptorsTable()
self.descriptorsTable.resizeColumnsToContents()
self.newDescriptorPushButton = PM_PushButton( pmGroupBox,
text = "New",
setAsDefault = True)
self.newDescriptorPushButton.setFixedHeight(25)
self.removeDescriptorPushButton = PM_PushButton( pmGroupBox,
text = "Remove",
setAsDefault = True)
self.removeDescriptorPushButton.setFixedHeight(25)
self.applyDescriptorPushButton = PM_PushButton( pmGroupBox,
text = "Apply",
setAsDefault = True)
self.applyDescriptorPushButton.setFixedHeight(25)
addDescriptorButtonList = [('PM_PushButton', self.newDescriptorPushButton, 0, 0),
('PM_PushButton', self.removeDescriptorPushButton, 1, 0),
('PM_PushButton', self.applyDescriptorPushButton, 2, 0) ]
self.addDescriptorGrid = PM_WidgetGrid( pmGroupBox,
alignment = "Center",
widgetList = addDescriptorButtonList)
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in the second group box.
"""
self.headerdata_seq = ['', 'ID', 'Set', 'BR', 'Descriptor']
self.recenterViewCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Re-center view on selected residue",
setAsDefault = True,
widgetColumn = 0,
state = Qt.Unchecked)
self.selectAllPushButton = PM_PushButton( pmGroupBox,
text = "All",
setAsDefault = True)
self.selectAllPushButton.setFixedHeight(25)
self.selectNonePushButton = PM_PushButton( pmGroupBox,
text = "None",
setAsDefault = True)
self.selectNonePushButton.setFixedHeight(25)
self.selectInvertPushButton = PM_PushButton( pmGroupBox,
text = "Invert",
setAsDefault = True)
self.selectInvertPushButton.setFixedHeight(25)
buttonList = [ ('PM_PushButton', self.selectAllPushButton, 0, 0),
('PM_PushButton', self.selectNonePushButton, 1, 0),
('PM_PushButton', self.selectInvertPushButton, 2, 0)]
self.buttonGrid = PM_WidgetGrid( pmGroupBox,
widgetList = buttonList)
self.sequenceTable = PM_TableWidget( pmGroupBox)
#self.sequenceTable.setModel(self.tableModel)
self.sequenceTable.resizeColumnsToContents()
self.sequenceTable.verticalHeader().setVisible(False)
#self.sequenceTable.setRowCount(0)
self.sequenceTable.setColumnCount(5)
self.checkbox = QCheckBox()
self.sequenceTable.setFixedHeight(345)
self.sequenceTable.setGridStyle(Qt.NoPen)
self.sequenceTable.setHorizontalHeaderLabels(self.headerdata_seq)
###self._fillSequenceTable()
self.showSequencePushButton = PM_PushButton( pmGroupBox,
text = "Show Sequence",
setAsDefault = True,
spanWidth = True)
def _addWhatsThisText( self ):
#from ne1_ui.WhatsThisText_for_PropertyManagers import WhatsThis_EditResidues_PropertyManager
#WhatsThis_EditResidues_PropertyManager(self)
pass
def _addToolTipText(self):
#from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_EditProteinDisplayStyle_PropertyManager
#ToolTip_EditProteinDisplayStyle_PropertyManager(self)
pass
def _fillSequenceTable(self):
"""
Fills in the sequence table.
"""
if not self.current_protein:
return
else:
currentProteinChunk = self.current_protein
self.editingItem = True
aa_list = currentProteinChunk.protein.get_amino_acids()
aa_list_len = len(aa_list)
self.sequenceTable.setRowCount(aa_list_len)
for index in range(aa_list_len):
# Selection checkbox column
item_widget = QTableWidgetItem("")
item_widget.setFont(self.labelfont)
item_widget.setCheckState(Qt.Checked)
item_widget.setTextAlignment(Qt.AlignLeft)
item_widget.setSizeHint(QSize(20,12))
item_widget.setFlags(Qt.ItemIsSelectable |
Qt.ItemIsEnabled |
Qt.ItemIsUserCheckable)
self.sequenceTable.setItem(index, 0, item_widget)
# Amino acid index column
item_widget = QTableWidgetItem(str(index+1))
item_widget.setFont(self.labelfont)
item_widget.setFlags(
Qt.ItemIsSelectable |
Qt.ItemIsEnabled)
item_widget.setTextAlignment(Qt.AlignCenter)
self.sequenceTable.setItem(index, 1, item_widget)
# Mutation descriptor name column
aa = self._get_aa_for_index(index)
item_widget = QTableWidgetItem(self._get_descriptor_name(aa))
item_widget.setFont(self.labelfont)
item_widget.setFlags(Qt.ItemIsSelectable |
Qt.ItemIsEnabled)
item_widget.setTextAlignment(Qt.AlignCenter)
self.sequenceTable.setItem(index, 2, item_widget)
# Backrub checkbox column
item_widget = QTableWidgetItem("")
item_widget.setFont(self.labelfont)
if aa.get_backrub_mode():
item_widget.setCheckState(Qt.Checked)
else:
item_widget.setCheckState(Qt.Unchecked)
item_widget.setTextAlignment(Qt.AlignLeft)
item_widget.setSizeHint(QSize(20,12))
item_widget.setFlags(Qt.ItemIsSelectable |
Qt.ItemIsEnabled |
Qt.ItemIsUserCheckable)
self.sequenceTable.setItem(index, 3, item_widget)
# Mutation descriptor column
aa_string = self._get_mutation_descriptor(aa)
item_widget = QTableWidgetItem(aa_string)
item_widget.setFont(self.descriptorfont)
self.sequenceTable.setItem(index, 4, item_widget)
self.sequenceTable.setRowHeight(index, 16)
self.editingItem = False
self.sequenceTable.resizeColumnsToContents()
self.sequenceTable.setColumnWidth(0, 35)
self.sequenceTable.setColumnWidth(2, 80)
self.sequenceTable.setColumnWidth(3, 35)
return
def _fillDescriptorsTable(self):
"""
Fills in the descriptors table from descriptors user pref.
"""
dstr = env.prefs[proteinCustomDescriptors_prefs_key].split(":")
for i in range(len(dstr) / 2):
self._addNewDescriptorTableRow(dstr[2*i], dstr[2*i+1])
def _selectAll(self):
"""
Select all rows in the sequence table.
"""
for row in range(self.sequenceTable.rowCount()):
self.sequenceTable.item(row, 0).setCheckState(Qt.Checked)
def _selectNone(self):
"""
Unselect all rows in the sequence table.
"""
for row in range(self.sequenceTable.rowCount()):
self.sequenceTable.item(row, 0).setCheckState(Qt.Unchecked)
def _invertSelection(self):
"""
Inverto row selection range in the sequence table.
"""
for row in range(self.sequenceTable.rowCount()):
item_widget = self.sequenceTable.item(row, 0)
if item_widget.checkState() == Qt.Checked:
item_widget.setCheckState(Qt.Unchecked)
else:
item_widget.setCheckState(Qt.Checked)
def _get_mutation_descriptor(self, aa):
"""
Get mutation descriptor string for a given amino acid.
"""
aa_string = self.rosetta_all_set
range = aa.get_mutation_range()
aa_string = self.rosetta_all_set
if range == "NATRO" or \
range == "NATAA":
code = aa.get_one_letter_code()
aa_string = re.sub("[^"+code+"]",'_', aa_string)
elif range == "POLAR":
aa_string = self.rosetta_polar_set
elif range == "APOLA":
aa_string = self.rosetta_apolar_set
elif range == "PIKAA":
aa_string = aa.get_mutation_descriptor()
return aa_string
def _get_descriptor_name(self, aa):
"""
Returns a mutation descriptor name for an amino acid.
"""
range_name = aa.get_mutation_range()
for i in range(len(self.rosetta_set_names)):
if range_name == self.rosetta_set_names[i]:
if range_name == "PIKAA":
# Find a descriptor with a list of
# custom descriptors.
dstr = self._makeProperAAString(aa.get_mutation_descriptor())
for i in range(5, len(self.descriptor_list)):
if dstr == self.descriptor_list[i]:
return self.set_names[i]
else:
return self.set_names[i]
return "Custom"
def _get_aa_for_index(self, index, expand = False):
"""
Get amino acid by index.
@return: amino acid (Residue)
"""
if not self.current_protein:
return None
else:
currentProteinChunk = self.current_protein
currentProteinChunk.protein.set_current_amino_acid_index(index)
current_aa = currentProteinChunk.protein.get_current_amino_acid()
if expand:
currentProteinChunk.protein.collapse_all_rotamers()
currentProteinChunk.protein.expand_rotamer(current_aa)
return current_aa
def _sequenceTableCellChanged(self, crow, ccol):
"""
Slot for sequence table CellChanged event.
"""
item = self.sequenceTable.item(crow, ccol)
for row in range(self.sequenceTable.rowCount()):
self.sequenceTable.removeCellWidget(row, 2)
self.sequenceTable.setRowHeight(row, 16)
if ccol == 2:
# Make the row a little bit wider.
self.sequenceTable.setRowHeight(crow, 22)
# Create and insert a Combo Box into a current cell.
self.setComboBox = QComboBox()
self.setComboBox.addItems(self.set_names)
self.win.connect(self.setComboBox,
SIGNAL("activated(int)"),
self._setComboBoxIndexChanged)
self.sequenceTable.setCellWidget(crow, 2, self.setComboBox)
current_aa = self._get_aa_for_index(crow, expand=True)
if current_aa:
# Center on the selected amino acid.
if self.recenterViewCheckBox.isChecked():
ca_atom = current_aa.get_c_alpha_atom()
if ca_atom:
self.win.glpane.pov = -ca_atom.posn()
self.win.glpane.gl_update()
# Update backrub status for selected amino acid.
if ccol == 3:
cbox = self.sequenceTable.item(crow, 3)
if cbox.checkState() == Qt.Checked:
current_aa.set_backrub_mode(True)
else:
current_aa.set_backrub_mode(False)
from PyQt4.Qt import QTextCursor
cursor = self.sequenceEditor.sequenceTextEdit.textCursor()
#boundary condition
if crow == -1:
crow = 0
cursor.setPosition(crow, QTextCursor.MoveAnchor)
cursor.setPosition(crow + 1, QTextCursor.KeepAnchor)
self.sequenceEditor.sequenceTextEdit.setTextCursor( cursor )
def _applyDescriptor(self):
"""
Apply mutation descriptor to the selected amino acids.
"""
cdes = self.descriptorsTable.currentRow()
for row in range(self.sequenceTable.rowCount()):
self._setComboBoxIndexChanged(cdes + 5, tablerow = row, selectedOnly = True)
def _setComboBoxIndexChanged( self, index, tablerow = None, selectedOnly = False):
"""
Slot for mutation descriptor combo box (in third column of the sequence
table.)
"""
if tablerow is None:
crow = self.sequenceTable.currentRow()
else:
crow = tablerow
item = self.sequenceTable.item(crow, 2)
if item:
self.editingItem = True
cbox = self.sequenceTable.item(crow, 0)
if not selectedOnly or \
cbox.checkState() == Qt.Checked:
item.setText(self.set_names[index])
item = self.sequenceTable.item(crow, 4)
aa = self._get_aa_for_index(crow)
set_name = self.rosetta_set_names[index]
aa.set_mutation_range(set_name)
if set_name == "PIKAA":
aa.set_mutation_descriptor(self.descriptor_list[index])
item.setText(self._get_mutation_descriptor(aa))
for row in range(self.sequenceTable.rowCount()):
self.sequenceTable.removeCellWidget(row, 2)
self.sequenceTable.setRowHeight(row, 16)
self.editingItem = False
def scrollToPosition(self, index):
"""
Scrolls the Sequence Table to a given sequence position.
"""
item = self.sequenceTable.item(index, 0)
if item:
self.sequenceTable.scrollToItem(item)
def _applyAny(self):
"""
Apply "ALLAA" descriptor.
"""
for row in range(self.sequenceTable.rowCount()):
self._setComboBoxIndexChanged(0, tablerow = row, selectedOnly = True)
def _applySame(self):
"""
Apply "NATAA" descriptor.
"""
for row in range(self.sequenceTable.rowCount()):
self._setComboBoxIndexChanged(1, tablerow = row, selectedOnly = True)
def _applyLocked(self):
"""
Apply "NATRO" descriptor.
"""
for row in range(self.sequenceTable.rowCount()):
self._setComboBoxIndexChanged(2, tablerow = row, selectedOnly = True)
def _applyPolar(self):
"""
Apply "POLAR" descriptor.
"""
for row in range(self.sequenceTable.rowCount()):
self._setComboBoxIndexChanged(3, tablerow = row, selectedOnly = True)
def _applyApolar(self):
"""
Apply "APOLA" descriptor.
"""
for row in range(self.sequenceTable.rowCount()):
self._setComboBoxIndexChanged(4, tablerow = row, selectedOnly = True)
def resizeEvent(self, event):
"""
Called whenever PM width has changed. Sets correct width of the
rows in descriptor and sequence tables.
"""
self.descriptorsTable.setColumnWidth(1,
self.descriptorsTable.width()-self.descriptorsTable.columnWidth(0)-20)
self.sequenceTable.setColumnWidth(4,
self.sequenceTable.width()-
(self.sequenceTable.columnWidth(0) +
self.sequenceTable.columnWidth(1) +
self.sequenceTable.columnWidth(2) +
self.sequenceTable.columnWidth(3))-20)
def _addNewDescriptorTableRow(self, name, descriptor):
"""
Adds a new row to the descriptor table.
"""
row = self.descriptorsTable.rowCount()
self.descriptorsTable.insertRow(row)
item_widget = QTableWidgetItem(name)
item_widget.setFont(self.labelfont)
item_widget.setFlags(Qt.ItemIsSelectable |
Qt.ItemIsEnabled |
Qt.ItemIsEditable)
item_widget.setTextAlignment(Qt.AlignLeft)
self.descriptorsTable.setItem(row, 0, item_widget)
self.descriptorsTable.resizeColumnToContents(0)
s = self._makeProperAAString(descriptor)
item_widget = QTableWidgetItem(s)
item_widget.setFont(self.descriptorfont)
item_widget.setFlags(Qt.ItemIsSelectable |
Qt.ItemIsEnabled |
Qt.ItemIsEditable)
item_widget.setTextAlignment(Qt.AlignLeft)
self.descriptorsTable.setItem(row, 1, item_widget)
self.descriptorsTable.setColumnWidth(1,
self.descriptorsTable.width()-self.descriptorsTable.columnWidth(0)-20)
self.descriptorsTable.setRowHeight(row, 16)
def _addNewDescriptor(self):
"""
Adds a new descriptor to the descriptor table.
"""
self._addNewDescriptorTableRow("New Set", "PGAVILMFWYCSTNQDEHKR")
self._makeDescriptorUserPref()
self._updateSetLists()
def _removeDescriptor(self):
"""
Removes a highlighted descriptor from the descriptors table.
"""
crow = self.descriptorsTable.currentRow()
if crow >= 0:
self.descriptorsTable.removeRow(crow)
self._makeDescriptorUserPref()
self._updateSetLists()
def _makeDescriptorUserPref(self):
"""
Constructs a custom descriptors string.
"""
dstr = ""
for row in range(self.descriptorsTable.rowCount()):
item0 = self.descriptorsTable.item(row, 0)
item1 = self.descriptorsTable.item(row, 1)
if item0 and \
item1:
dstr += item0.text() + \
":" + \
item1.text() + \
":"
env.prefs[proteinCustomDescriptors_prefs_key] = dstr
def _makeProperAAString(self, string):
"""
Creates a proper amino acid string from an arbitrary string.
"""
aa_string = str(string).upper()
new_aa_string = ""
for i in range(len(self.rosetta_all_set)):
if aa_string.find(self.rosetta_all_set[i]) == -1:
new_aa_string += "_"
else:
new_aa_string += self.rosetta_all_set[i]
return new_aa_string
def _sequenceTableItemChanged(self, item):
"""
Called when an item in the sequence table has changed.
"""
if self.editingItem:
return
if self.sequenceTable.column(item) == 4:
self.editingItem = True
crow = self.sequenceTable.currentRow()
dstr = self._makeProperAAString(str(item.text()).upper())
item.setText(dstr)
aa = self._get_aa_for_index(crow)
if aa:
aa.set_mutation_range("PIKAA")
aa.set_mutation_descriptor(dstr.replace("_",""))
item = self.sequenceTable.item(crow, 2)
if item:
item.setText("Custom")
self.editingItem = False
def _descriptorsTableItemChanged(self, item):
"""
Called when an item in the descriptors table has changed.
"""
if self.editingItem:
return
if self.descriptorsTable.column(item) == 1:
self.editingItem = True
item.setText(self._makeProperAAString(str(item.text()).upper()))
self.editingItem = False
self._makeDescriptorUserPref()
self._updateSetLists()
def _updateSetLists(self):
"""
Updates lists of descriptor sets and descriptor set names.
"""
self.set_names = self.set_names[:5]
self.descriptor_list = self.descriptor_list[:5]
self.rosetta_set_names = self.rosetta_set_names[:5]
dstr = env.prefs[proteinCustomDescriptors_prefs_key].split(":")
for i in range(len(dstr) / 2):
self.set_names.append(dstr[2*i])
self.descriptor_list.append(dstr[2*i+1])
self.rosetta_set_names.append("PIKAA")
#self._addNewDescriptorTableRow(dstr[2*i], dstr[2*i+1])
return
def _update_UI_do_updates_TEMP(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:
print "_update_UI_do_updates(): DO NOTHING."
return
# NOTE: Changing the display styles of the protein chunks can take some
# time. We should put up the wait (hourglass) cursor here and restore
# before returning.
# Update all PM widgets that need to be since something has changed.
print "_update_UI_do_updates(): UPDATING the PMGR."
self.update_name_field()
self.sequenceEditor.update()
self.update_residue_combobox()
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)
return
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in the first group box.
"""
self.headerdata_desc = ['Name', 'Descriptor']
self.set_names = ["Any", "Same", "Locked", "Apolar", "Polar"]
self.rosetta_set_names = ["ALLAA", "NATAA", "NATRO", "APOLA", "POLAR"]
self.descriptor_list = ["PGAVILMFWYCSTNQDEHKR",
"____________________",
"____________________",
"PGAVILMFWYC_________",
"___________STNQDEHKR"]
self.applyAnyPushButton = PM_PushButton( pmGroupBox,
text = "ALLAA",
setAsDefault = True)
self.applySamePushButton = PM_PushButton( pmGroupBox,
text = "NATAA",
setAsDefault = True)
self.applyLockedPushButton = PM_PushButton( pmGroupBox,
text = "NATRO",
setAsDefault = True)
self.applyPolarPushButton = PM_PushButton( pmGroupBox,
text = "APOLA",
setAsDefault = True)
self.applyApolarPushButton = PM_PushButton( pmGroupBox,
text = "POLAR",
setAsDefault = True)
#self.applyBackrubPushButton = PM_PushButton( pmGroupBox,
# text = "BACKRUB",
# setAsDefault = True)
self.applyAnyPushButton.setFixedHeight(25)
self.applyAnyPushButton.setFixedWidth(60)
self.applySamePushButton.setFixedHeight(25)
self.applySamePushButton.setFixedWidth(60)
self.applyLockedPushButton.setFixedHeight(25)
self.applyLockedPushButton.setFixedWidth(60)
self.applyPolarPushButton.setFixedHeight(25)
self.applyPolarPushButton.setFixedWidth(60)
self.applyApolarPushButton.setFixedHeight(25)
self.applyApolarPushButton.setFixedWidth(60)
applyButtonList = [
('PM_PushButton', self.applyAnyPushButton, 0, 0),
('PM_PushButton', self.applySamePushButton, 1, 0),
('PM_PushButton', self.applyLockedPushButton, 2, 0),
('PM_PushButton', self.applyPolarPushButton, 3, 0),
('PM_PushButton', self.applyApolarPushButton, 4, 0) ]
self.applyButtonGrid = PM_WidgetGrid( pmGroupBox,
label = "Apply standard set",
widgetList = applyButtonList)
self.descriptorsTable = PM_TableWidget( pmGroupBox,
label = "Custom descriptors")
self.descriptorsTable.setFixedHeight(100)
self.descriptorsTable.setRowCount(0)
self.descriptorsTable.setColumnCount(2)
self.descriptorsTable.verticalHeader().setVisible(False)
self.descriptorsTable.horizontalHeader().setVisible(True)
self.descriptorsTable.setGridStyle(Qt.NoPen)
self.descriptorsTable.setHorizontalHeaderLabels(self.headerdata_desc)
self._updateSetLists()
self._fillDescriptorsTable()
self.descriptorsTable.resizeColumnsToContents()
self.newDescriptorPushButton = PM_PushButton( pmGroupBox,
text = "New",
setAsDefault = True)
self.newDescriptorPushButton.setFixedHeight(25)
self.removeDescriptorPushButton = PM_PushButton( pmGroupBox,
text = "Remove",
setAsDefault = True)
self.removeDescriptorPushButton.setFixedHeight(25)
self.applyDescriptorPushButton = PM_PushButton( pmGroupBox,
text = "Apply",
setAsDefault = True)
self.applyDescriptorPushButton.setFixedHeight(25)
addDescriptorButtonList = [('PM_PushButton', self.newDescriptorPushButton, 0, 0),
('PM_PushButton', self.removeDescriptorPushButton, 1, 0),
('PM_PushButton', self.applyDescriptorPushButton, 2, 0) ]
self.addDescriptorGrid = PM_WidgetGrid( pmGroupBox,
alignment = "Center",
widgetList = addDescriptorButtonList)
class EditResidues_PropertyManager(Command_PropertyManager):
"""
The ProteinDisplayStyle_PropertyManager class provides a Property Manager
for the B{Display Style} command on the flyout toolbar in the
Build > Protein 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 = "Edit Residues"
pmName = title
iconPath = "ui/actions/Command Toolbar/BuildProtein/Residues.png"
rosetta_all_set = "PGAVILMFWYCSTNQDEHKR"
rosetta_polar_set = "___________STNQDEHKR"
rosetta_apolar_set = "PGAVILMFWYC_________"
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)
self.editingItem = False
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.applyAnyPushButton, SIGNAL("clicked()"),
self._applyAny)
change_connect(self.applySamePushButton, SIGNAL("clicked()"),
self._applySame)
change_connect(self.applyLockedPushButton, SIGNAL("clicked()"),
self._applyLocked)
change_connect(self.applyPolarPushButton, SIGNAL("clicked()"),
self._applyPolar)
change_connect(self.applyApolarPushButton, SIGNAL("clicked()"),
self._applyApolar)
change_connect(self.selectAllPushButton, SIGNAL("clicked()"),
self._selectAll)
change_connect(self.selectNonePushButton, SIGNAL("clicked()"),
self._selectNone)
change_connect(self.selectInvertPushButton, SIGNAL("clicked()"),
self._invertSelection)
change_connect(self.applyDescriptorPushButton, SIGNAL("clicked()"),
self._applyDescriptor)
change_connect(self.removeDescriptorPushButton, SIGNAL("clicked()"),
self._removeDescriptor)
change_connect(self.sequenceTable, SIGNAL("cellClicked(int, int)"),
self._sequenceTableCellChanged)
change_connect(self.sequenceTable,
SIGNAL("itemChanged(QTableWidgetItem*)"),
self._sequenceTableItemChanged)
change_connect(self.descriptorsTable,
SIGNAL("itemChanged(QTableWidgetItem*)"),
self._descriptorsTableItemChanged)
change_connect(self.newDescriptorPushButton, SIGNAL("clicked()"),
self._addNewDescriptor)
change_connect(self.showSequencePushButton, SIGNAL("clicked()"),
self._showSeqEditor)
return
def _showSeqEditor(self):
"""
Shows sequence editor
"""
if self.showSequencePushButton.isEnabled():
self.sequenceEditor.show()
return
def show(self):
"""
Shows the Property Manager. Extends superclass method.
"""
env.history.statusbar_msg("")
#Urmi 20080728: Set the current protein and this will be used for accessing
#various properties of this protein
self.set_current_protein()
if self.current_protein:
msg = "Editing structure <b>%s</b>." % self.current_protein.name
self.showSequencePushButton.setEnabled(True)
else:
msg = "Select a single structure to edit."
self.showSequencePushButton.setEnabled(False)
self.sequenceEditor.hide()
_superclass.show(self)
self._fillSequenceTable()
self.updateMessage(msg)
return
def set_current_protein(self):
"""
Set the current protein for which all the properties are displayed to the
one chosen in the build protein combo box
"""
self.current_protein = self.win.assy.getSelectedProteinChunk()
return
def _addGroupBoxes(self):
"""
Add the Property Manager group boxes.
"""
if sys.platform == "darwin":
# Workaround for table font size difference between Mac/Win
self.labelfont = QFont("Helvetica", 12)
self.descriptorfont = QFont("Courier New", 12)
else:
self.labelfont = QFont("Helvetica", 9)
self.descriptorfont = QFont("Courier New", 9)
self._pmGroupBox1 = PM_GroupBox(self, title="Descriptors")
self._loadGroupBox1(self._pmGroupBox1)
self._pmGroupBox2 = PM_GroupBox(self, title="Sequence")
self._loadGroupBox2(self._pmGroupBox2)
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in the first group box.
"""
self.headerdata_desc = ['Name', 'Descriptor']
self.set_names = ["Any", "Same", "Locked", "Apolar", "Polar"]
self.rosetta_set_names = ["ALLAA", "NATAA", "NATRO", "APOLA", "POLAR"]
self.descriptor_list = [
"PGAVILMFWYCSTNQDEHKR", "____________________",
"____________________", "PGAVILMFWYC_________",
"___________STNQDEHKR"
]
self.applyAnyPushButton = PM_PushButton(pmGroupBox,
text="ALLAA",
setAsDefault=True)
self.applySamePushButton = PM_PushButton(pmGroupBox,
text="NATAA",
setAsDefault=True)
self.applyLockedPushButton = PM_PushButton(pmGroupBox,
text="NATRO",
setAsDefault=True)
self.applyPolarPushButton = PM_PushButton(pmGroupBox,
text="APOLA",
setAsDefault=True)
self.applyApolarPushButton = PM_PushButton(pmGroupBox,
text="POLAR",
setAsDefault=True)
#self.applyBackrubPushButton = PM_PushButton( pmGroupBox,
# text = "BACKRUB",
# setAsDefault = True)
self.applyAnyPushButton.setFixedHeight(25)
self.applyAnyPushButton.setFixedWidth(60)
self.applySamePushButton.setFixedHeight(25)
self.applySamePushButton.setFixedWidth(60)
self.applyLockedPushButton.setFixedHeight(25)
self.applyLockedPushButton.setFixedWidth(60)
self.applyPolarPushButton.setFixedHeight(25)
self.applyPolarPushButton.setFixedWidth(60)
self.applyApolarPushButton.setFixedHeight(25)
self.applyApolarPushButton.setFixedWidth(60)
applyButtonList = [('PM_PushButton', self.applyAnyPushButton, 0, 0),
('PM_PushButton', self.applySamePushButton, 1, 0),
('PM_PushButton', self.applyLockedPushButton, 2, 0),
('PM_PushButton', self.applyPolarPushButton, 3, 0),
('PM_PushButton', self.applyApolarPushButton, 4, 0)]
self.applyButtonGrid = PM_WidgetGrid(pmGroupBox,
label="Apply standard set",
widgetList=applyButtonList)
self.descriptorsTable = PM_TableWidget(pmGroupBox,
label="Custom descriptors")
self.descriptorsTable.setFixedHeight(100)
self.descriptorsTable.setRowCount(0)
self.descriptorsTable.setColumnCount(2)
self.descriptorsTable.verticalHeader().setVisible(False)
self.descriptorsTable.horizontalHeader().setVisible(True)
self.descriptorsTable.setGridStyle(Qt.NoPen)
self.descriptorsTable.setHorizontalHeaderLabels(self.headerdata_desc)
self._updateSetLists()
self._fillDescriptorsTable()
self.descriptorsTable.resizeColumnsToContents()
self.newDescriptorPushButton = PM_PushButton(pmGroupBox,
text="New",
setAsDefault=True)
self.newDescriptorPushButton.setFixedHeight(25)
self.removeDescriptorPushButton = PM_PushButton(pmGroupBox,
text="Remove",
setAsDefault=True)
self.removeDescriptorPushButton.setFixedHeight(25)
self.applyDescriptorPushButton = PM_PushButton(pmGroupBox,
text="Apply",
setAsDefault=True)
self.applyDescriptorPushButton.setFixedHeight(25)
addDescriptorButtonList = [
('PM_PushButton', self.newDescriptorPushButton, 0, 0),
('PM_PushButton', self.removeDescriptorPushButton, 1, 0),
('PM_PushButton', self.applyDescriptorPushButton, 2, 0)
]
self.addDescriptorGrid = PM_WidgetGrid(
pmGroupBox, alignment="Center", widgetList=addDescriptorButtonList)
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in the second group box.
"""
self.headerdata_seq = ['', 'ID', 'Set', 'BR', 'Descriptor']
self.recenterViewCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Re-center view on selected residue",
setAsDefault = True,
widgetColumn = 0,
state = Qt.Unchecked)
self.selectAllPushButton = PM_PushButton(pmGroupBox,
text="All",
setAsDefault=True)
self.selectAllPushButton.setFixedHeight(25)
self.selectNonePushButton = PM_PushButton(pmGroupBox,
text="None",
setAsDefault=True)
self.selectNonePushButton.setFixedHeight(25)
self.selectInvertPushButton = PM_PushButton(pmGroupBox,
text="Invert",
setAsDefault=True)
self.selectInvertPushButton.setFixedHeight(25)
buttonList = [('PM_PushButton', self.selectAllPushButton, 0, 0),
('PM_PushButton', self.selectNonePushButton, 1, 0),
('PM_PushButton', self.selectInvertPushButton, 2, 0)]
self.buttonGrid = PM_WidgetGrid(pmGroupBox, widgetList=buttonList)
self.sequenceTable = PM_TableWidget(pmGroupBox)
#self.sequenceTable.setModel(self.tableModel)
self.sequenceTable.resizeColumnsToContents()
self.sequenceTable.verticalHeader().setVisible(False)
#self.sequenceTable.setRowCount(0)
self.sequenceTable.setColumnCount(5)
self.checkbox = QCheckBox()
self.sequenceTable.setFixedHeight(345)
self.sequenceTable.setGridStyle(Qt.NoPen)
self.sequenceTable.setHorizontalHeaderLabels(self.headerdata_seq)
###self._fillSequenceTable()
self.showSequencePushButton = PM_PushButton(pmGroupBox,
text="Show Sequence",
setAsDefault=True,
spanWidth=True)
def _addWhatsThisText(self):
#from ne1_ui.WhatsThisText_for_PropertyManagers import WhatsThis_EditResidues_PropertyManager
#WhatsThis_EditResidues_PropertyManager(self)
pass
def _addToolTipText(self):
#from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_EditProteinDisplayStyle_PropertyManager
#ToolTip_EditProteinDisplayStyle_PropertyManager(self)
pass
def _fillSequenceTable(self):
"""
Fills in the sequence table.
"""
if not self.current_protein:
return
else:
currentProteinChunk = self.current_protein
self.editingItem = True
aa_list = currentProteinChunk.protein.get_amino_acids()
aa_list_len = len(aa_list)
self.sequenceTable.setRowCount(aa_list_len)
for index in range(aa_list_len):
# Selection checkbox column
item_widget = QTableWidgetItem("")
item_widget.setFont(self.labelfont)
item_widget.setCheckState(Qt.Checked)
item_widget.setTextAlignment(Qt.AlignLeft)
item_widget.setSizeHint(QSize(20, 12))
item_widget.setFlags(Qt.ItemIsSelectable | Qt.ItemIsEnabled
| Qt.ItemIsUserCheckable)
self.sequenceTable.setItem(index, 0, item_widget)
# Amino acid index column
item_widget = QTableWidgetItem(str(index + 1))
item_widget.setFont(self.labelfont)
item_widget.setFlags(Qt.ItemIsSelectable | Qt.ItemIsEnabled)
item_widget.setTextAlignment(Qt.AlignCenter)
self.sequenceTable.setItem(index, 1, item_widget)
# Mutation descriptor name column
aa = self._get_aa_for_index(index)
item_widget = QTableWidgetItem(self._get_descriptor_name(aa))
item_widget.setFont(self.labelfont)
item_widget.setFlags(Qt.ItemIsSelectable | Qt.ItemIsEnabled)
item_widget.setTextAlignment(Qt.AlignCenter)
self.sequenceTable.setItem(index, 2, item_widget)
# Backrub checkbox column
item_widget = QTableWidgetItem("")
item_widget.setFont(self.labelfont)
if aa.get_backrub_mode():
item_widget.setCheckState(Qt.Checked)
else:
item_widget.setCheckState(Qt.Unchecked)
item_widget.setTextAlignment(Qt.AlignLeft)
item_widget.setSizeHint(QSize(20, 12))
item_widget.setFlags(Qt.ItemIsSelectable | Qt.ItemIsEnabled
| Qt.ItemIsUserCheckable)
self.sequenceTable.setItem(index, 3, item_widget)
# Mutation descriptor column
aa_string = self._get_mutation_descriptor(aa)
item_widget = QTableWidgetItem(aa_string)
item_widget.setFont(self.descriptorfont)
self.sequenceTable.setItem(index, 4, item_widget)
self.sequenceTable.setRowHeight(index, 16)
self.editingItem = False
self.sequenceTable.resizeColumnsToContents()
self.sequenceTable.setColumnWidth(0, 35)
self.sequenceTable.setColumnWidth(2, 80)
self.sequenceTable.setColumnWidth(3, 35)
return
def _fillDescriptorsTable(self):
"""
Fills in the descriptors table from descriptors user pref.
"""
dstr = env.prefs[proteinCustomDescriptors_prefs_key].split(":")
for i in range(len(dstr) / 2):
self._addNewDescriptorTableRow(dstr[2 * i], dstr[2 * i + 1])
def _selectAll(self):
"""
Select all rows in the sequence table.
"""
for row in range(self.sequenceTable.rowCount()):
self.sequenceTable.item(row, 0).setCheckState(Qt.Checked)
def _selectNone(self):
"""
Unselect all rows in the sequence table.
"""
for row in range(self.sequenceTable.rowCount()):
self.sequenceTable.item(row, 0).setCheckState(Qt.Unchecked)
def _invertSelection(self):
"""
Inverto row selection range in the sequence table.
"""
for row in range(self.sequenceTable.rowCount()):
item_widget = self.sequenceTable.item(row, 0)
if item_widget.checkState() == Qt.Checked:
item_widget.setCheckState(Qt.Unchecked)
else:
item_widget.setCheckState(Qt.Checked)
def _get_mutation_descriptor(self, aa):
"""
Get mutation descriptor string for a given amino acid.
"""
aa_string = self.rosetta_all_set
range = aa.get_mutation_range()
aa_string = self.rosetta_all_set
if range == "NATRO" or \
range == "NATAA":
code = aa.get_one_letter_code()
aa_string = re.sub("[^" + code + "]", '_', aa_string)
elif range == "POLAR":
aa_string = self.rosetta_polar_set
elif range == "APOLA":
aa_string = self.rosetta_apolar_set
elif range == "PIKAA":
aa_string = aa.get_mutation_descriptor()
return aa_string
def _get_descriptor_name(self, aa):
"""
Returns a mutation descriptor name for an amino acid.
"""
range_name = aa.get_mutation_range()
for i in range(len(self.rosetta_set_names)):
if range_name == self.rosetta_set_names[i]:
if range_name == "PIKAA":
# Find a descriptor with a list of
# custom descriptors.
dstr = self._makeProperAAString(
aa.get_mutation_descriptor())
for i in range(5, len(self.descriptor_list)):
if dstr == self.descriptor_list[i]:
return self.set_names[i]
else:
return self.set_names[i]
return "Custom"
def _get_aa_for_index(self, index, expand=False):
"""
Get amino acid by index.
@return: amino acid (Residue)
"""
if not self.current_protein:
return None
else:
currentProteinChunk = self.current_protein
currentProteinChunk.protein.set_current_amino_acid_index(index)
current_aa = currentProteinChunk.protein.get_current_amino_acid()
if expand:
currentProteinChunk.protein.collapse_all_rotamers()
currentProteinChunk.protein.expand_rotamer(current_aa)
return current_aa
def _sequenceTableCellChanged(self, crow, ccol):
"""
Slot for sequence table CellChanged event.
"""
item = self.sequenceTable.item(crow, ccol)
for row in range(self.sequenceTable.rowCount()):
self.sequenceTable.removeCellWidget(row, 2)
self.sequenceTable.setRowHeight(row, 16)
if ccol == 2:
# Make the row a little bit wider.
self.sequenceTable.setRowHeight(crow, 22)
# Create and insert a Combo Box into a current cell.
self.setComboBox = QComboBox()
self.setComboBox.addItems(self.set_names)
self.win.connect(self.setComboBox, SIGNAL("activated(int)"),
self._setComboBoxIndexChanged)
self.sequenceTable.setCellWidget(crow, 2, self.setComboBox)
current_aa = self._get_aa_for_index(crow, expand=True)
if current_aa:
# Center on the selected amino acid.
if self.recenterViewCheckBox.isChecked():
ca_atom = current_aa.get_c_alpha_atom()
if ca_atom:
self.win.glpane.pov = -ca_atom.posn()
self.win.glpane.gl_update()
# Update backrub status for selected amino acid.
if ccol == 3:
cbox = self.sequenceTable.item(crow, 3)
if cbox.checkState() == Qt.Checked:
current_aa.set_backrub_mode(True)
else:
current_aa.set_backrub_mode(False)
from PyQt4.Qt import QTextCursor
cursor = self.sequenceEditor.sequenceTextEdit.textCursor()
#boundary condition
if crow == -1:
crow = 0
cursor.setPosition(crow, QTextCursor.MoveAnchor)
cursor.setPosition(crow + 1, QTextCursor.KeepAnchor)
self.sequenceEditor.sequenceTextEdit.setTextCursor(cursor)
def _applyDescriptor(self):
"""
Apply mutation descriptor to the selected amino acids.
"""
cdes = self.descriptorsTable.currentRow()
for row in range(self.sequenceTable.rowCount()):
self._setComboBoxIndexChanged(cdes + 5,
tablerow=row,
selectedOnly=True)
def _setComboBoxIndexChanged(self,
index,
tablerow=None,
selectedOnly=False):
"""
Slot for mutation descriptor combo box (in third column of the sequence
table.)
"""
if tablerow is None:
crow = self.sequenceTable.currentRow()
else:
crow = tablerow
item = self.sequenceTable.item(crow, 2)
if item:
self.editingItem = True
cbox = self.sequenceTable.item(crow, 0)
if not selectedOnly or \
cbox.checkState() == Qt.Checked:
item.setText(self.set_names[index])
item = self.sequenceTable.item(crow, 4)
aa = self._get_aa_for_index(crow)
set_name = self.rosetta_set_names[index]
aa.set_mutation_range(set_name)
if set_name == "PIKAA":
aa.set_mutation_descriptor(self.descriptor_list[index])
item.setText(self._get_mutation_descriptor(aa))
for row in range(self.sequenceTable.rowCount()):
self.sequenceTable.removeCellWidget(row, 2)
self.sequenceTable.setRowHeight(row, 16)
self.editingItem = False
def scrollToPosition(self, index):
"""
Scrolls the Sequence Table to a given sequence position.
"""
item = self.sequenceTable.item(index, 0)
if item:
self.sequenceTable.scrollToItem(item)
def _applyAny(self):
"""
Apply "ALLAA" descriptor.
"""
for row in range(self.sequenceTable.rowCount()):
self._setComboBoxIndexChanged(0, tablerow=row, selectedOnly=True)
def _applySame(self):
"""
Apply "NATAA" descriptor.
"""
for row in range(self.sequenceTable.rowCount()):
self._setComboBoxIndexChanged(1, tablerow=row, selectedOnly=True)
def _applyLocked(self):
"""
Apply "NATRO" descriptor.
"""
for row in range(self.sequenceTable.rowCount()):
self._setComboBoxIndexChanged(2, tablerow=row, selectedOnly=True)
def _applyPolar(self):
"""
Apply "POLAR" descriptor.
"""
for row in range(self.sequenceTable.rowCount()):
self._setComboBoxIndexChanged(3, tablerow=row, selectedOnly=True)
def _applyApolar(self):
"""
Apply "APOLA" descriptor.
"""
for row in range(self.sequenceTable.rowCount()):
self._setComboBoxIndexChanged(4, tablerow=row, selectedOnly=True)
def resizeEvent(self, event):
"""
Called whenever PM width has changed. Sets correct width of the
rows in descriptor and sequence tables.
"""
self.descriptorsTable.setColumnWidth(
1,
self.descriptorsTable.width() -
self.descriptorsTable.columnWidth(0) - 20)
self.sequenceTable.setColumnWidth(
4,
self.sequenceTable.width() - (self.sequenceTable.columnWidth(0) +
self.sequenceTable.columnWidth(1) +
self.sequenceTable.columnWidth(2) +
self.sequenceTable.columnWidth(3)) -
20)
def _addNewDescriptorTableRow(self, name, descriptor):
"""
Adds a new row to the descriptor table.
"""
row = self.descriptorsTable.rowCount()
self.descriptorsTable.insertRow(row)
item_widget = QTableWidgetItem(name)
item_widget.setFont(self.labelfont)
item_widget.setFlags(Qt.ItemIsSelectable | Qt.ItemIsEnabled
| Qt.ItemIsEditable)
item_widget.setTextAlignment(Qt.AlignLeft)
self.descriptorsTable.setItem(row, 0, item_widget)
self.descriptorsTable.resizeColumnToContents(0)
s = self._makeProperAAString(descriptor)
item_widget = QTableWidgetItem(s)
item_widget.setFont(self.descriptorfont)
item_widget.setFlags(Qt.ItemIsSelectable | Qt.ItemIsEnabled
| Qt.ItemIsEditable)
item_widget.setTextAlignment(Qt.AlignLeft)
self.descriptorsTable.setItem(row, 1, item_widget)
self.descriptorsTable.setColumnWidth(
1,
self.descriptorsTable.width() -
self.descriptorsTable.columnWidth(0) - 20)
self.descriptorsTable.setRowHeight(row, 16)
def _addNewDescriptor(self):
"""
Adds a new descriptor to the descriptor table.
"""
self._addNewDescriptorTableRow("New Set", "PGAVILMFWYCSTNQDEHKR")
self._makeDescriptorUserPref()
self._updateSetLists()
def _removeDescriptor(self):
"""
Removes a highlighted descriptor from the descriptors table.
"""
crow = self.descriptorsTable.currentRow()
if crow >= 0:
self.descriptorsTable.removeRow(crow)
self._makeDescriptorUserPref()
self._updateSetLists()
def _makeDescriptorUserPref(self):
"""
Constructs a custom descriptors string.
"""
dstr = ""
for row in range(self.descriptorsTable.rowCount()):
item0 = self.descriptorsTable.item(row, 0)
item1 = self.descriptorsTable.item(row, 1)
if item0 and \
item1:
dstr += item0.text() + \
":" + \
item1.text() + \
":"
env.prefs[proteinCustomDescriptors_prefs_key] = dstr
def _makeProperAAString(self, string):
"""
Creates a proper amino acid string from an arbitrary string.
"""
aa_string = str(string).upper()
new_aa_string = ""
for i in range(len(self.rosetta_all_set)):
if aa_string.find(self.rosetta_all_set[i]) == -1:
new_aa_string += "_"
else:
new_aa_string += self.rosetta_all_set[i]
return new_aa_string
def _sequenceTableItemChanged(self, item):
"""
Called when an item in the sequence table has changed.
"""
if self.editingItem:
return
if self.sequenceTable.column(item) == 4:
self.editingItem = True
crow = self.sequenceTable.currentRow()
dstr = self._makeProperAAString(str(item.text()).upper())
item.setText(dstr)
aa = self._get_aa_for_index(crow)
if aa:
aa.set_mutation_range("PIKAA")
aa.set_mutation_descriptor(dstr.replace("_", ""))
item = self.sequenceTable.item(crow, 2)
if item:
item.setText("Custom")
self.editingItem = False
def _descriptorsTableItemChanged(self, item):
"""
Called when an item in the descriptors table has changed.
"""
if self.editingItem:
return
if self.descriptorsTable.column(item) == 1:
self.editingItem = True
item.setText(self._makeProperAAString(str(item.text()).upper()))
self.editingItem = False
self._makeDescriptorUserPref()
self._updateSetLists()
def _updateSetLists(self):
"""
Updates lists of descriptor sets and descriptor set names.
"""
self.set_names = self.set_names[:5]
self.descriptor_list = self.descriptor_list[:5]
self.rosetta_set_names = self.rosetta_set_names[:5]
dstr = env.prefs[proteinCustomDescriptors_prefs_key].split(":")
for i in range(len(dstr) / 2):
self.set_names.append(dstr[2 * i])
self.descriptor_list.append(dstr[2 * i + 1])
self.rosetta_set_names.append("PIKAA")
#self._addNewDescriptorTableRow(dstr[2*i], dstr[2*i+1])
return
def _update_UI_do_updates_TEMP(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:
print "_update_UI_do_updates(): DO NOTHING."
return
# NOTE: Changing the display styles of the protein chunks can take some
# time. We should put up the wait (hourglass) cursor here and restore
# before returning.
# Update all PM widgets that need to be since something has changed.
print "_update_UI_do_updates(): UPDATING the PMGR."
self.update_name_field()
self.sequenceEditor.update()
self.update_residue_combobox()
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)
return
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in the first group box.
"""
self.headerdata_desc = ['Name', 'Descriptor']
self.set_names = ["Any", "Same", "Locked", "Apolar", "Polar"]
self.rosetta_set_names = ["ALLAA", "NATAA", "NATRO", "APOLA", "POLAR"]
self.descriptor_list = [
"PGAVILMFWYCSTNQDEHKR", "____________________",
"____________________", "PGAVILMFWYC_________",
"___________STNQDEHKR"
]
self.applyAnyPushButton = PM_PushButton(pmGroupBox,
text="ALLAA",
setAsDefault=True)
self.applySamePushButton = PM_PushButton(pmGroupBox,
text="NATAA",
setAsDefault=True)
self.applyLockedPushButton = PM_PushButton(pmGroupBox,
text="NATRO",
setAsDefault=True)
self.applyPolarPushButton = PM_PushButton(pmGroupBox,
text="APOLA",
setAsDefault=True)
self.applyApolarPushButton = PM_PushButton(pmGroupBox,
text="POLAR",
setAsDefault=True)
#self.applyBackrubPushButton = PM_PushButton( pmGroupBox,
# text = "BACKRUB",
# setAsDefault = True)
self.applyAnyPushButton.setFixedHeight(25)
self.applyAnyPushButton.setFixedWidth(60)
self.applySamePushButton.setFixedHeight(25)
self.applySamePushButton.setFixedWidth(60)
self.applyLockedPushButton.setFixedHeight(25)
self.applyLockedPushButton.setFixedWidth(60)
self.applyPolarPushButton.setFixedHeight(25)
self.applyPolarPushButton.setFixedWidth(60)
self.applyApolarPushButton.setFixedHeight(25)
self.applyApolarPushButton.setFixedWidth(60)
applyButtonList = [('PM_PushButton', self.applyAnyPushButton, 0, 0),
('PM_PushButton', self.applySamePushButton, 1, 0),
('PM_PushButton', self.applyLockedPushButton, 2, 0),
('PM_PushButton', self.applyPolarPushButton, 3, 0),
('PM_PushButton', self.applyApolarPushButton, 4, 0)]
self.applyButtonGrid = PM_WidgetGrid(pmGroupBox,
label="Apply standard set",
widgetList=applyButtonList)
self.descriptorsTable = PM_TableWidget(pmGroupBox,
label="Custom descriptors")
self.descriptorsTable.setFixedHeight(100)
self.descriptorsTable.setRowCount(0)
self.descriptorsTable.setColumnCount(2)
self.descriptorsTable.verticalHeader().setVisible(False)
self.descriptorsTable.horizontalHeader().setVisible(True)
self.descriptorsTable.setGridStyle(Qt.NoPen)
self.descriptorsTable.setHorizontalHeaderLabels(self.headerdata_desc)
self._updateSetLists()
self._fillDescriptorsTable()
self.descriptorsTable.resizeColumnsToContents()
self.newDescriptorPushButton = PM_PushButton(pmGroupBox,
text="New",
setAsDefault=True)
self.newDescriptorPushButton.setFixedHeight(25)
self.removeDescriptorPushButton = PM_PushButton(pmGroupBox,
text="Remove",
setAsDefault=True)
self.removeDescriptorPushButton.setFixedHeight(25)
self.applyDescriptorPushButton = PM_PushButton(pmGroupBox,
text="Apply",
setAsDefault=True)
self.applyDescriptorPushButton.setFixedHeight(25)
addDescriptorButtonList = [
('PM_PushButton', self.newDescriptorPushButton, 0, 0),
('PM_PushButton', self.removeDescriptorPushButton, 1, 0),
('PM_PushButton', self.applyDescriptorPushButton, 2, 0)
]
self.addDescriptorGrid = PM_WidgetGrid(
pmGroupBox, alignment="Center", widgetList=addDescriptorButtonList)
class EditResidues_PropertyManager(PM_Dialog, DebugMenuMixin):
"""
The ProteinDisplayStyle_PropertyManager class provides a Property Manager
for the B{Display Style} command on the flyout toolbar in the
Build > Protein 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 = "Edit Residues"
pmName = title
iconPath = "ui/actions/Edit/EditProteinDisplayStyle.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.currentWorkingDirectory = env.prefs[workingDirectory_prefs_key]
PM_Dialog.__init__(self, self.pmName, self.iconPath, self.title)
DebugMenuMixin._init1(self)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
msg = "Edit residues."
self.updateMessage(msg)
def connect_or_disconnect_signals(self, isConnect=True):
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
#change_connect(self.nextAAPushButton,
# SIGNAL("clicked()"),
# self._expandNextRotamer)
def ok_btn_clicked(self):
"""
Slot for the OK button
"""
self.win.toolsDone()
def cancel_btn_clicked(self):
"""
Slot for the Cancel button.
"""
#TODO: Cancel button needs to be removed. See comment at the top
self.win.toolsDone()
def show(self):
"""
Shows the Property Manager. Overrides PM_Dialog.show.
"""
self.sequenceEditor = self.win.createProteinSequenceEditorIfNeeded()
self.sequenceEditor.hide()
PM_Dialog.show(self)
# Update all PM widgets, then establish their signal-slot connections.
# note: It is important to update the widgets *first* since doing
# it in the reverse order will generate signals when updating
# the PM widgets (via updateDnaDisplayStyleWidgets()), causing
# unneccessary repaints of the model view.
self._fillSequenceTable()
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="Sequence")
self._loadGroupBox1(self._pmGroupBox1)
#self._pmGroupBox2 = PM_GroupBox( self,
# title = "Rotamer")
#self._loadGroupBox2( self._pmGroupBox2 )
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
self.labelfont = QFont("Helvetica", 12)
self.descriptorfont = QFont("Courier New", 12)
self.headerdata = ['', 'ID', 'Set', 'Descriptor']
self.set_names = ["Any", "Same", "Locked", "Polar", "Apolar"]
self.rosetta_set_names = ["ALLAA", "NATRO", "NATAA", "POLAR", "APOLA"]
self.descriptor_list = [
"GAVILMFWCSTYNQDEHKRP", "____________________",
"____________________", "________CSTYNQDEHKR_",
"GAVILMFW___________P"
]
self.descriptorsTable = PM_TableWidget(pmGroupBox)
self.descriptorsTable.setFixedHeight(100)
self.descriptorsTable.setRowCount(len(self.set_names))
self.descriptorsTable.setColumnCount(2)
self.descriptorsTable.verticalHeader().setVisible(False)
self.descriptorsTable.horizontalHeader().setVisible(False)
for index in range(len(self.set_names)):
item_widget = QTableWidgetItem(self.set_names[index])
item_widget.setFont(self.labelfont)
item_widget.setFlags(Qt.ItemIsSelectable | Qt.ItemIsEnabled
| Qt.ItemIsEditable)
item_widget.setTextAlignment(Qt.AlignCenter)
self.descriptorsTable.setItem(index, 0, item_widget)
item_widget = QTableWidgetItem(self.descriptor_list[index])
item_widget.setFont(self.descriptorfont)
item_widget.setFlags(Qt.ItemIsSelectable | Qt.ItemIsEnabled
| Qt.ItemIsEditable)
item_widget.setTextAlignment(Qt.AlignCenter)
self.descriptorsTable.setItem(index, 1, item_widget)
self.descriptorsTable.setRowHeight(index, 16)
pass
self.descriptorsTable.resizeColumnsToContents()
self.applyDescriptorPushButton = PM_PushButton(pmGroupBox,
text="Apply",
setAsDefault=True)
self.selectAllPushButton = PM_PushButton(pmGroupBox,
text="All",
setAsDefault=True)
self.selectNonePushButton = PM_PushButton(pmGroupBox,
text="None",
setAsDefault=True)
self.selectInvertPushButton = PM_PushButton(pmGroupBox,
text="Invert",
setAsDefault=True)
self.win.connect(self.applyDescriptorPushButton, SIGNAL("clicked()"),
self._applyDescriptor)
self.win.connect(self.selectAllPushButton, SIGNAL("clicked()"),
self._selectAll)
self.win.connect(self.selectNonePushButton, SIGNAL("clicked()"),
self._selectNone)
self.win.connect(self.selectInvertPushButton, SIGNAL("clicked()"),
self._invertSelection)
buttonList = [('PM_PushButton', self.applyDescriptorPushButton, 0, 0),
('QSpacerItem', 5, 5, 1, 0),
('PM_PushButton', self.selectAllPushButton, 2, 0),
('PM_PushButton', self.selectNonePushButton, 3, 0),
('PM_PushButton', self.selectInvertPushButton, 4, 0)]
self.buttonGrid = PM_WidgetGrid(pmGroupBox, widgetList=buttonList)
self.recenterViewCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Re-center view",
setAsDefault = True,
state = Qt.Checked)
self.sequenceTable = PM_TableWidget(pmGroupBox)
#self.sequenceTable.setModel(self.tableModel)
self.sequenceTable.resizeColumnsToContents()
self.sequenceTable.verticalHeader().setVisible(False)
#self.sequenceTable.setRowCount(0)
self.sequenceTable.setColumnCount(4)
self.checkbox = QCheckBox()
self.sequenceTable.setFixedHeight(345)
self.sequenceTable.setHorizontalHeaderLabels(self.headerdata)
###self._fillSequenceTable()
def _fillSequenceTable(self):
"""
"""
self.setComboBox = QComboBox()
for chunk in self.win.assy.molecules:
if chunk.isProteinChunk():
aa_list = chunk.protein.get_amino_acids()
aa_list_len = len(aa_list)
self.sequenceTable.setRowCount(aa_list_len)
for index in range(aa_list_len):
item_widget = QTableWidgetItem("")
item_widget.setFont(self.labelfont)
item_widget.setCheckState(Qt.Checked)
item_widget.setTextAlignment(Qt.AlignLeft)
item_widget.setSizeHint(QSize(20, 12))
item_widget.setFlags(Qt.ItemIsSelectable | Qt.ItemIsEnabled
| Qt.ItemIsUserCheckable)
self.sequenceTable.setItem(index, 0, item_widget)
item_widget = QTableWidgetItem(str(index + 1))
item_widget.setFont(self.labelfont)
item_widget.setFlags(Qt.ItemIsSelectable
| Qt.ItemIsEnabled)
item_widget.setTextAlignment(Qt.AlignCenter)
self.sequenceTable.setItem(index, 1, item_widget)
item_widget = QTableWidgetItem("Any")
item_widget.setFont(self.labelfont)
item_widget.setFlags(Qt.ItemIsSelectable
| Qt.ItemIsEnabled)
item_widget.setTextAlignment(Qt.AlignCenter)
self.sequenceTable.setItem(index, 2, item_widget)
aa_string = self._get_mutation_descriptor(
self._get_aa_for_index(index))
item_widget = QTableWidgetItem(aa_string)
item_widget.setFont(self.descriptorfont)
self.sequenceTable.setItem(index, 3, item_widget)
self.sequenceTable.setRowHeight(index, 16)
self.win.connect(self.sequenceTable, SIGNAL("cellClicked(int, int)"),
self._sequenceTableCellChanged)
self.sequenceTable.resizeColumnsToContents()
self.sequenceTable.setColumnWidth(0, 35)
self.sequenceTable.setColumnWidth(2, 80)
def _selectAll(self):
for row in range(self.sequenceTable.rowCount()):
self.sequenceTable.item(row, 0).setCheckState(Qt.Checked)
def _selectNone(self):
for row in range(self.sequenceTable.rowCount()):
self.sequenceTable.item(row, 0).setCheckState(Qt.Unchecked)
def _invertSelection(self):
for row in range(self.sequenceTable.rowCount()):
item_widget = self.sequenceTable.item(row, 0)
if item_widget.checkState() == Qt.Checked:
item_widget.setCheckState(Qt.Unchecked)
else:
item_widget.setCheckState(Qt.Checked)
def _get_mutation_descriptor(self, aa):
"""
"""
aa_string = "GAVILMFWCSTYNQDEHKRP"
range = aa.get_mutation_range()
if range == "NATRO" or \
range == "NATAA":
code = aa.get_one_letter_code()
aa_string = re.sub("[^" + code + "]", '_', aa_string)
elif range == "POLAR":
aa_string = "________CSTYNQDEHKR_"
elif range == "APOLA":
aa_string = "GAVILMFW___________P"
return aa_string
def _get_aa_for_index(self, index, expand=False):
"""
"""
# Center on a selected amino acid.
for chunk in self.win.assy.molecules:
if chunk.isProteinChunk():
chunk.protein.set_current_amino_acid_index(index)
current_aa = chunk.protein.get_current_amino_acid()
if expand:
chunk.protein.collapse_all_rotamers()
chunk.protein.expand_rotamer(current_aa)
return current_aa
return None
def _sequenceTableCellChanged(self, crow, ccol):
#print "CELL CHANGED: ", (crow, ccol)
item = self.sequenceTable.item(crow, ccol)
#print "ITEM = ", item
for row in range(self.sequenceTable.rowCount()):
self.sequenceTable.removeCellWidget(row, 2)
self.sequenceTable.setRowHeight(row, 16)
if ccol == 2:
# Make the row a little bit wider.
self.sequenceTable.setRowHeight(crow, 22)
# Create and insert a Combo Box into a current cell.
self.setComboBox = QComboBox()
self.setComboBox.addItems(self.set_names)
self.win.connect(self.setComboBox,
SIGNAL("currentIndexChanged(int)"),
self._setComboBoxIndexChanged)
self.sequenceTable.setCellWidget(crow, 2, self.setComboBox)
current_aa = self._get_aa_for_index(crow, expand=True)
if current_aa:
# Center on the selected amino acid.
if self.recenterViewCheckBox.isChecked():
ca_atom = current_aa.get_c_alpha_atom()
if ca_atom:
self.win.glpane.pov = -ca_atom.posn()
self.win.glpane.gl_update()
def _applyDescriptor(self):
"""
"""
cdes = self.descriptorsTable.currentRow()
for row in range(self.sequenceTable.rowCount()):
#print "row = ", row
self._setComboBoxIndexChanged(cdes,
tablerow=row,
selectedOnly=True)
def _setComboBoxIndexChanged(self,
index,
tablerow=None,
selectedOnly=False):
"""
"""
#print "INDEX = ", index
if tablerow is None:
crow = self.sequenceTable.currentRow()
else:
crow = tablerow
#print "current row: ", crow
item = self.sequenceTable.item(crow, 2)
if item:
cbox = self.sequenceTable.item(crow, 0)
if not selectedOnly or \
cbox.checkState() == Qt.Checked:
item.setText(self.set_names[index])
item = self.sequenceTable.item(crow, 3)
aa = self._get_aa_for_index(crow)
aa.set_mutation_range(self.rosetta_set_names[index])
item.setText(self._get_mutation_descriptor(aa))
###self._write_resfile()
def _write_resfile(self):
from protein.model.Protein import write_rosetta_resfile
for chunk in self.win.assy.molecules:
if chunk.isProteinChunk():
write_rosetta_resfile("/Users/piotr/test.resfile", chunk)
return
def _addWhatsThisText(self):
#from ne1_ui.WhatsThisText_for_PropertyManagers import WhatsThis_EditResidues_PropertyManager
#WhatsThis_EditResidues_PropertyManager(self)
pass
def _addToolTipText(self):
#from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_EditProteinDisplayStyle_PropertyManager
#ToolTip_EditProteinDisplayStyle_PropertyManager(self)
pass
def scrollToPosition(self, index):
"""
Scrolls the Sequence Table to a given sequence position.
"""
item = self.sequenceTable.item(index, 0)
if item:
self.sequenceTable.scrollToItem(item)
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
self.labelfont = QFont("Helvetica", 12)
self.descriptorfont = QFont("Courier New", 12)
self.headerdata = ['', 'ID', 'Set', 'Descriptor']
self.set_names = ["Any", "Same", "Locked", "Polar", "Apolar"]
self.rosetta_set_names = ["ALLAA", "NATRO", "NATAA", "POLAR", "APOLA"]
self.descriptor_list = [
"GAVILMFWCSTYNQDEHKRP", "____________________",
"____________________", "________CSTYNQDEHKR_",
"GAVILMFW___________P"
]
self.descriptorsTable = PM_TableWidget(pmGroupBox)
self.descriptorsTable.setFixedHeight(100)
self.descriptorsTable.setRowCount(len(self.set_names))
self.descriptorsTable.setColumnCount(2)
self.descriptorsTable.verticalHeader().setVisible(False)
self.descriptorsTable.horizontalHeader().setVisible(False)
for index in range(len(self.set_names)):
item_widget = QTableWidgetItem(self.set_names[index])
item_widget.setFont(self.labelfont)
item_widget.setFlags(Qt.ItemIsSelectable | Qt.ItemIsEnabled
| Qt.ItemIsEditable)
item_widget.setTextAlignment(Qt.AlignCenter)
self.descriptorsTable.setItem(index, 0, item_widget)
item_widget = QTableWidgetItem(self.descriptor_list[index])
item_widget.setFont(self.descriptorfont)
item_widget.setFlags(Qt.ItemIsSelectable | Qt.ItemIsEnabled
| Qt.ItemIsEditable)
item_widget.setTextAlignment(Qt.AlignCenter)
self.descriptorsTable.setItem(index, 1, item_widget)
self.descriptorsTable.setRowHeight(index, 16)
pass
self.descriptorsTable.resizeColumnsToContents()
self.applyDescriptorPushButton = PM_PushButton(pmGroupBox,
text="Apply",
setAsDefault=True)
self.selectAllPushButton = PM_PushButton(pmGroupBox,
text="All",
setAsDefault=True)
self.selectNonePushButton = PM_PushButton(pmGroupBox,
text="None",
setAsDefault=True)
self.selectInvertPushButton = PM_PushButton(pmGroupBox,
text="Invert",
setAsDefault=True)
self.win.connect(self.applyDescriptorPushButton, SIGNAL("clicked()"),
self._applyDescriptor)
self.win.connect(self.selectAllPushButton, SIGNAL("clicked()"),
self._selectAll)
self.win.connect(self.selectNonePushButton, SIGNAL("clicked()"),
self._selectNone)
self.win.connect(self.selectInvertPushButton, SIGNAL("clicked()"),
self._invertSelection)
buttonList = [('PM_PushButton', self.applyDescriptorPushButton, 0, 0),
('QSpacerItem', 5, 5, 1, 0),
('PM_PushButton', self.selectAllPushButton, 2, 0),
('PM_PushButton', self.selectNonePushButton, 3, 0),
('PM_PushButton', self.selectInvertPushButton, 4, 0)]
self.buttonGrid = PM_WidgetGrid(pmGroupBox, widgetList=buttonList)
self.recenterViewCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Re-center view",
setAsDefault = True,
state = Qt.Checked)
self.sequenceTable = PM_TableWidget(pmGroupBox)
#self.sequenceTable.setModel(self.tableModel)
self.sequenceTable.resizeColumnsToContents()
self.sequenceTable.verticalHeader().setVisible(False)
#self.sequenceTable.setRowCount(0)
self.sequenceTable.setColumnCount(4)
self.checkbox = QCheckBox()
self.sequenceTable.setFixedHeight(345)
self.sequenceTable.setHorizontalHeaderLabels(self.headerdata)
class EditResidues_PropertyManager( PM_Dialog, DebugMenuMixin ):
"""
The ProteinDisplayStyle_PropertyManager class provides a Property Manager
for the B{Display Style} command on the flyout toolbar in the
Build > Protein 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 = "Edit Residues"
pmName = title
iconPath = "ui/actions/Edit/EditProteinDisplayStyle.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.currentWorkingDirectory = env.prefs[workingDirectory_prefs_key]
PM_Dialog.__init__(self, self.pmName, self.iconPath, self.title)
DebugMenuMixin._init1( self )
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
msg = "Edit residues."
self.updateMessage(msg)
def connect_or_disconnect_signals(self, isConnect = True):
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
#change_connect(self.nextAAPushButton,
# SIGNAL("clicked()"),
# self._expandNextRotamer)
def ok_btn_clicked(self):
"""
Slot for the OK button
"""
self.win.toolsDone()
def cancel_btn_clicked(self):
"""
Slot for the Cancel button.
"""
#TODO: Cancel button needs to be removed. See comment at the top
self.win.toolsDone()
def show(self):
"""
Shows the Property Manager. Overrides PM_Dialog.show.
"""
self.sequenceEditor = self.win.createProteinSequenceEditorIfNeeded()
self.sequenceEditor.hide()
PM_Dialog.show(self)
# Update all PM widgets, then establish their signal-slot connections.
# note: It is important to update the widgets *first* since doing
# it in the reverse order will generate signals when updating
# the PM widgets (via updateDnaDisplayStyleWidgets()), causing
# unneccessary repaints of the model view.
self._fillSequenceTable()
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 = "Sequence")
self._loadGroupBox1( self._pmGroupBox1 )
#self._pmGroupBox2 = PM_GroupBox( self,
# title = "Rotamer")
#self._loadGroupBox2( self._pmGroupBox2 )
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
self.labelfont = QFont("Helvetica", 12)
self.descriptorfont = QFont("Courier New", 12)
self.headerdata = ['', 'ID', 'Set', 'Descriptor']
self.set_names = ["Any", "Same", "Locked", "Polar", "Apolar"]
self.rosetta_set_names = ["ALLAA", "NATRO", "NATAA", "POLAR", "APOLA"]
self.descriptor_list = ["GAVILMFWCSTYNQDEHKRP",
"____________________",
"____________________",
"________CSTYNQDEHKR_",
"GAVILMFW___________P"]
self.descriptorsTable = PM_TableWidget( pmGroupBox)
self.descriptorsTable.setFixedHeight(100)
self.descriptorsTable.setRowCount(len(self.set_names))
self.descriptorsTable.setColumnCount(2)
self.descriptorsTable.verticalHeader().setVisible(False)
self.descriptorsTable.horizontalHeader().setVisible(False)
for index in range(len(self.set_names)):
item_widget = QTableWidgetItem(self.set_names[index])
item_widget.setFont(self.labelfont)
item_widget.setFlags(Qt.ItemIsSelectable | Qt.ItemIsEnabled | Qt.ItemIsEditable)
item_widget.setTextAlignment(Qt.AlignCenter)
self.descriptorsTable.setItem(index, 0, item_widget)
item_widget = QTableWidgetItem(self.descriptor_list[index])
item_widget.setFont(self.descriptorfont)
item_widget.setFlags(Qt.ItemIsSelectable | Qt.ItemIsEnabled | Qt.ItemIsEditable)
item_widget.setTextAlignment(Qt.AlignCenter)
self.descriptorsTable.setItem(index, 1, item_widget)
self.descriptorsTable.setRowHeight(index, 16)
pass
self.descriptorsTable.resizeColumnsToContents()
self.applyDescriptorPushButton = PM_PushButton( pmGroupBox,
text = "Apply",
setAsDefault = True)
self.selectAllPushButton = PM_PushButton( pmGroupBox,
text = "All",
setAsDefault = True)
self.selectNonePushButton = PM_PushButton( pmGroupBox,
text = "None",
setAsDefault = True)
self.selectInvertPushButton = PM_PushButton( pmGroupBox,
text = "Invert",
setAsDefault = True)
self.win.connect(self.applyDescriptorPushButton,
SIGNAL("clicked()"),
self._applyDescriptor)
self.win.connect(self.selectAllPushButton,
SIGNAL("clicked()"),
self._selectAll)
self.win.connect(self.selectNonePushButton,
SIGNAL("clicked()"),
self._selectNone)
self.win.connect(self.selectInvertPushButton,
SIGNAL("clicked()"),
self._invertSelection)
buttonList = [('PM_PushButton', self.applyDescriptorPushButton, 0, 0),
('QSpacerItem', 5, 5, 1, 0),
('PM_PushButton', self.selectAllPushButton, 2, 0),
('PM_PushButton', self.selectNonePushButton, 3, 0),
('PM_PushButton', self.selectInvertPushButton, 4, 0)]
self.buttonGrid = PM_WidgetGrid( pmGroupBox,
widgetList = buttonList)
self.recenterViewCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Re-center view",
setAsDefault = True,
state = Qt.Checked)
self.sequenceTable = PM_TableWidget( pmGroupBox)
#self.sequenceTable.setModel(self.tableModel)
self.sequenceTable.resizeColumnsToContents()
self.sequenceTable.verticalHeader().setVisible(False)
#self.sequenceTable.setRowCount(0)
self.sequenceTable.setColumnCount(4)
self.checkbox = QCheckBox()
self.sequenceTable.setFixedHeight(345)
self.sequenceTable.setHorizontalHeaderLabels(self.headerdata)
###self._fillSequenceTable()
def _fillSequenceTable(self):
"""
"""
self.setComboBox = QComboBox()
for chunk in self.win.assy.molecules:
if chunk.isProteinChunk():
aa_list = chunk.protein.get_amino_acids()
aa_list_len = len(aa_list)
self.sequenceTable.setRowCount(aa_list_len)
for index in range(aa_list_len):
item_widget = QTableWidgetItem("")
item_widget.setFont(self.labelfont)
item_widget.setCheckState(Qt.Checked)
item_widget.setTextAlignment(Qt.AlignLeft)
item_widget.setSizeHint(QSize(20,12))
item_widget.setFlags(Qt.ItemIsSelectable | Qt.ItemIsEnabled | Qt.ItemIsUserCheckable)
self.sequenceTable.setItem(index, 0, item_widget)
item_widget = QTableWidgetItem(str(index+1))
item_widget.setFont(self.labelfont)
item_widget.setFlags(Qt.ItemIsSelectable | Qt.ItemIsEnabled)
item_widget.setTextAlignment(Qt.AlignCenter)
self.sequenceTable.setItem(index, 1, item_widget)
item_widget = QTableWidgetItem("Any")
item_widget.setFont(self.labelfont)
item_widget.setFlags(Qt.ItemIsSelectable | Qt.ItemIsEnabled)
item_widget.setTextAlignment(Qt.AlignCenter)
self.sequenceTable.setItem(index, 2, item_widget)
aa_string = self._get_mutation_descriptor(
self._get_aa_for_index(index))
item_widget = QTableWidgetItem(aa_string)
item_widget.setFont(self.descriptorfont)
self.sequenceTable.setItem(index, 3, item_widget)
self.sequenceTable.setRowHeight(index, 16)
self.win.connect(self.sequenceTable,
SIGNAL("cellClicked(int, int)"),
self._sequenceTableCellChanged)
self.sequenceTable.resizeColumnsToContents()
self.sequenceTable.setColumnWidth(0, 35)
self.sequenceTable.setColumnWidth(2, 80)
def _selectAll(self):
for row in range(self.sequenceTable.rowCount()):
self.sequenceTable.item(row, 0).setCheckState(Qt.Checked)
def _selectNone(self):
for row in range(self.sequenceTable.rowCount()):
self.sequenceTable.item(row, 0).setCheckState(Qt.Unchecked)
def _invertSelection(self):
for row in range(self.sequenceTable.rowCount()):
item_widget = self.sequenceTable.item(row, 0)
if item_widget.checkState() == Qt.Checked:
item_widget.setCheckState(Qt.Unchecked)
else:
item_widget.setCheckState(Qt.Checked)
def _get_mutation_descriptor(self, aa):
"""
"""
aa_string = "GAVILMFWCSTYNQDEHKRP"
range = aa.get_mutation_range()
if range == "NATRO" or \
range == "NATAA":
code = aa.get_one_letter_code()
aa_string = re.sub("[^"+code+"]",'_', aa_string)
elif range == "POLAR":
aa_string = "________CSTYNQDEHKR_"
elif range == "APOLA":
aa_string = "GAVILMFW___________P"
return aa_string
def _get_aa_for_index(self, index, expand=False):
"""
"""
# Center on a selected amino acid.
for chunk in self.win.assy.molecules:
if chunk.isProteinChunk():
chunk.protein.set_current_amino_acid_index(index)
current_aa = chunk.protein.get_current_amino_acid()
if expand:
chunk.protein.collapse_all_rotamers()
chunk.protein.expand_rotamer(current_aa)
return current_aa
return None
def _sequenceTableCellChanged(self, crow, ccol):
#print "CELL CHANGED: ", (crow, ccol)
item = self.sequenceTable.item(crow, ccol)
#print "ITEM = ", item
for row in range(self.sequenceTable.rowCount()):
self.sequenceTable.removeCellWidget(row, 2)
self.sequenceTable.setRowHeight(row, 16)
if ccol == 2:
# Make the row a little bit wider.
self.sequenceTable.setRowHeight(crow, 22)
# Create and insert a Combo Box into a current cell.
self.setComboBox = QComboBox()
self.setComboBox.addItems(self.set_names)
self.win.connect(self.setComboBox,
SIGNAL("currentIndexChanged(int)"),
self._setComboBoxIndexChanged)
self.sequenceTable.setCellWidget(crow, 2, self.setComboBox)
current_aa = self._get_aa_for_index(crow, expand=True)
if current_aa:
# Center on the selected amino acid.
if self.recenterViewCheckBox.isChecked():
ca_atom = current_aa.get_c_alpha_atom()
if ca_atom:
self.win.glpane.pov = -ca_atom.posn()
self.win.glpane.gl_update()
def _applyDescriptor(self):
"""
"""
cdes = self.descriptorsTable.currentRow()
for row in range(self.sequenceTable.rowCount()):
#print "row = ", row
self._setComboBoxIndexChanged(cdes, tablerow = row, selectedOnly = True)
def _setComboBoxIndexChanged( self, index, tablerow = None, selectedOnly = False):
"""
"""
#print "INDEX = ", index
if tablerow is None:
crow = self.sequenceTable.currentRow()
else:
crow = tablerow
#print "current row: ", crow
item = self.sequenceTable.item(crow, 2)
if item:
cbox = self.sequenceTable.item(crow, 0)
if not selectedOnly or \
cbox.checkState() == Qt.Checked:
item.setText(self.set_names[index])
item = self.sequenceTable.item(crow, 3)
aa = self._get_aa_for_index(crow)
aa.set_mutation_range(self.rosetta_set_names[index])
item.setText(self._get_mutation_descriptor(aa))
###self._write_resfile()
def _write_resfile(self):
from protein.model.Protein import write_rosetta_resfile
for chunk in self.win.assy.molecules:
if chunk.isProteinChunk():
write_rosetta_resfile("/Users/piotr/test.resfile", chunk)
return
def _addWhatsThisText( self ):
#from ne1_ui.WhatsThisText_for_PropertyManagers import WhatsThis_EditResidues_PropertyManager
#WhatsThis_EditResidues_PropertyManager(self)
pass
def _addToolTipText(self):
#from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_EditProteinDisplayStyle_PropertyManager
#ToolTip_EditProteinDisplayStyle_PropertyManager(self)
pass
def scrollToPosition(self, index):
"""
Scrolls the Sequence Table to a given sequence position.
"""
item = self.sequenceTable.item(index, 0)
if item:
self.sequenceTable.scrollToItem(item)
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
self.labelfont = QFont("Helvetica", 12)
self.descriptorfont = QFont("Courier New", 12)
self.headerdata = ['', 'ID', 'Set', 'Descriptor']
self.set_names = ["Any", "Same", "Locked", "Polar", "Apolar"]
self.rosetta_set_names = ["ALLAA", "NATRO", "NATAA", "POLAR", "APOLA"]
self.descriptor_list = ["GAVILMFWCSTYNQDEHKRP",
"____________________",
"____________________",
"________CSTYNQDEHKR_",
"GAVILMFW___________P"]
self.descriptorsTable = PM_TableWidget( pmGroupBox)
self.descriptorsTable.setFixedHeight(100)
self.descriptorsTable.setRowCount(len(self.set_names))
self.descriptorsTable.setColumnCount(2)
self.descriptorsTable.verticalHeader().setVisible(False)
self.descriptorsTable.horizontalHeader().setVisible(False)
for index in range(len(self.set_names)):
item_widget = QTableWidgetItem(self.set_names[index])
item_widget.setFont(self.labelfont)
item_widget.setFlags(Qt.ItemIsSelectable | Qt.ItemIsEnabled | Qt.ItemIsEditable)
item_widget.setTextAlignment(Qt.AlignCenter)
self.descriptorsTable.setItem(index, 0, item_widget)
item_widget = QTableWidgetItem(self.descriptor_list[index])
item_widget.setFont(self.descriptorfont)
item_widget.setFlags(Qt.ItemIsSelectable | Qt.ItemIsEnabled | Qt.ItemIsEditable)
item_widget.setTextAlignment(Qt.AlignCenter)
self.descriptorsTable.setItem(index, 1, item_widget)
self.descriptorsTable.setRowHeight(index, 16)
pass
self.descriptorsTable.resizeColumnsToContents()
self.applyDescriptorPushButton = PM_PushButton( pmGroupBox,
text = "Apply",
setAsDefault = True)
self.selectAllPushButton = PM_PushButton( pmGroupBox,
text = "All",
setAsDefault = True)
self.selectNonePushButton = PM_PushButton( pmGroupBox,
text = "None",
setAsDefault = True)
self.selectInvertPushButton = PM_PushButton( pmGroupBox,
text = "Invert",
setAsDefault = True)
self.win.connect(self.applyDescriptorPushButton,
SIGNAL("clicked()"),
self._applyDescriptor)
self.win.connect(self.selectAllPushButton,
SIGNAL("clicked()"),
self._selectAll)
self.win.connect(self.selectNonePushButton,
SIGNAL("clicked()"),
self._selectNone)
self.win.connect(self.selectInvertPushButton,
SIGNAL("clicked()"),
self._invertSelection)
buttonList = [('PM_PushButton', self.applyDescriptorPushButton, 0, 0),
('QSpacerItem', 5, 5, 1, 0),
('PM_PushButton', self.selectAllPushButton, 2, 0),
('PM_PushButton', self.selectNonePushButton, 3, 0),
('PM_PushButton', self.selectInvertPushButton, 4, 0)]
self.buttonGrid = PM_WidgetGrid( pmGroupBox,
widgetList = buttonList)
self.recenterViewCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Re-center view",
setAsDefault = True,
state = Qt.Checked)
self.sequenceTable = PM_TableWidget( pmGroupBox)
#self.sequenceTable.setModel(self.tableModel)
self.sequenceTable.resizeColumnsToContents()
self.sequenceTable.verticalHeader().setVisible(False)
#self.sequenceTable.setRowCount(0)
self.sequenceTable.setColumnCount(4)
self.checkbox = QCheckBox()
self.sequenceTable.setFixedHeight(345)
self.sequenceTable.setHorizontalHeaderLabels(self.headerdata)
