path: root/cad/src/protein/commands/EditResidues/EditResidues_PropertyManager.py

# Copyright 2008 Nanorex, Inc.  See LICENSE file for details.
"""
EditResidues_PropertyManager.py

B{Edit Residues} is a front-end for

The EditResidues_PropertyManager class provides a Property Manager
for the B{Edit Residues} command on the flyout toolbar in the
Build > Protein mode.

@author: Piotr
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.

To do:
- Auto-adjust width of PM to accomodate all widgets when entering cmd or
  after selecting a new structure.
"""
import os, sys, time, fnmatch, string, re
import foundation.env as env

from widgets.prefs_widgets import connect_checkbox_with_boolean_pref

from utilities.prefs_constants import getDefaultWorkingDirectory
from utilities.prefs_constants import workingDirectory_prefs_key
from utilities.prefs_constants import proteinCustomDescriptors_prefs_key

from utilities.Log import greenmsg
from utilities.constants import yellow, orange, red, magenta
from utilities.constants import cyan, blue, white, black, gray

from PyQt4.Qt import SIGNAL
from PyQt4.Qt import Qt
from PyQt4.Qt import QCheckBox
from PyQt4.Qt import QLabel
from PyQt4.Qt import QFont
from PyQt4.Qt import QComboBox
from PyQt4.Qt import QTableWidgetItem
from PyQt4.Qt import QSize


from PyQt4 import QtGui

from PyQt4.Qt import QFileDialog, QString, QMessageBox, QSlider
from PM.PM_PushButton   import PM_PushButton
from command_support.Command_PropertyManager import Command_PropertyManager
from PM.PM_GroupBox import PM_GroupBox
from PM.PM_ComboBox import PM_ComboBox
from PM.PM_LineEdit import PM_LineEdit
from PM.PM_StackedWidget import PM_StackedWidget
from PM.PM_CheckBox import PM_CheckBox
from PM.PM_DoubleSpinBox import PM_DoubleSpinBox
from PM.PM_ToolButtonRow import PM_ToolButtonRow
from PM.PM_Slider import PM_Slider
from PM.PM_Constants import PM_DONE_BUTTON
from PM.PM_Constants import PM_WHATS_THIS_BUTTON
from PM.PM_ColorComboBox import PM_ColorComboBox
from PM.PM_TableWidget import PM_TableWidget
from PM.PM_WidgetGrid import PM_WidgetGrid

_superclass = Command_PropertyManager
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