# Copyright 2008 Nanorex, Inc. See LICENSE file for details. """ BackrubProteinSim_PropertyManager.py The BackrubProteinSim_PropertyManager class provides a Property Manager for the B{Backrub protein sequence design} command on the flyout toolbar in the Build > Protein > Simulate mode. @author: Urmi @version: $Id$ @copyright: 2008 Nanorex, Inc. See LICENSE file for details. """ import string import foundation.env as env from utilities.Log import redmsg from widgets.DebugMenuMixin import DebugMenuMixin from utilities.prefs_constants import rosetta_backrub_enabled_prefs_key from PyQt4.Qt import SIGNAL from PyQt4.Qt import Qt from PyQt4 import QtGui from PyQt4.Qt import QString from PM.PM_PushButton import PM_PushButton from PM.PM_Dialog import PM_Dialog from PM.PM_GroupBox import PM_GroupBox from PM.PM_TextEdit import PM_TextEdit from PM.PM_CheckBox import PM_CheckBox from PM.PM_Constants import PM_DONE_BUTTON from PM.PM_Constants import PM_WHATS_THIS_BUTTON from PM.PM_SpinBox import PM_SpinBox from PM.PM_DoubleSpinBox import PM_DoubleSpinBox from PM.PM_ComboBox import PM_ComboBox #debug flag to keep signals always connected from utilities.GlobalPreferences import KEEP_SIGNALS_ALWAYS_CONNECTED class BackrubProteinSim_PropertyManager( PM_Dialog, DebugMenuMixin ): """ The BackrubProteinSim_PropertyManager class provides a Property Manager for the B{Fixed backbone Protein Sequence Design} command on the flyout toolbar in the Build > Protein > Simulate 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 = "Protein Sequence Design with Backrub motion" pmName = title iconPath = "ui/actions/Simulation/Rosetta.png" def __init__( self, command ): """ Constructor for the property manager. """ self.command = command self.win = self.command.w self.pw = self.command.pw self.o = self.win.glpane PM_Dialog.__init__(self, self.pmName, self.iconPath, self.title) DebugMenuMixin._init1( self ) self.showTopRowButtons( PM_DONE_BUTTON | \ PM_WHATS_THIS_BUTTON) msg = "Choose various parameters from below to design an optimized" \ " protein sequence with Rosetta with backrub motion allowed." self.updateMessage(msg) if KEEP_SIGNALS_ALWAYS_CONNECTED: self.connect_or_disconnect_signals(True) def connect_or_disconnect_signals(self, isConnect = True): """ Connect or disconnect widget signals sent to their slot methods. This can be overridden in subclasses. By default it does nothing. @param isConnect: If True the widget will send the signals to the slot method. @type isConnect: boolean """ if isConnect: change_connect = self.win.connect else: change_connect = self.win.disconnect change_connect(self.ex1Checkbox, SIGNAL("stateChanged(int)"), self.update_ex1) change_connect(self.ex1aroCheckbox, SIGNAL("stateChanged(int)"), self.update_ex1aro) change_connect(self.ex2Checkbox, SIGNAL("stateChanged(int)"), self.update_ex2) change_connect(self.ex2aroOnlyCheckbox, SIGNAL("stateChanged(int)"), self.update_ex2aro_only) change_connect(self.ex3Checkbox, SIGNAL("stateChanged(int)"), self.update_ex3) change_connect(self.ex4Checkbox, SIGNAL("stateChanged(int)"), self.update_ex4) change_connect(self.rotOptCheckbox, SIGNAL("stateChanged(int)"), self.update_rot_opt) change_connect(self.tryBothHisTautomersCheckbox, SIGNAL("stateChanged(int)"), self.update_try_both_his_tautomers) change_connect(self.softRepDesignCheckbox, SIGNAL("stateChanged(int)"), self.update_soft_rep_design) change_connect(self.useElecRepCheckbox, SIGNAL("stateChanged(int)"), self.update_use_elec_rep) change_connect(self.norepackDisulfCheckbox, SIGNAL("stateChanged(int)"), self.update_norepack_disulf) #signal slot connections for the push buttons change_connect(self.okButton, SIGNAL("clicked()"), self.runRosettaBackrubSim) return #Protein Display methods def ok_btn_clicked(self): """ Slot for the OK button """ self.win.toolsDone() def cancel_btn_clicked(self): """ Slot for the Cancel button. """ self.win.toolsDone() def show(self): """ Shows the Property Manager. Overrides PM_Dialog.show. """ self.sequenceEditor = self.win.createProteinSequenceEditorIfNeeded() self.sequenceEditor.hide() #update the min and max residues spinbox max values based on the length #of the current protein numResidues = self._getNumResiduesForCurrentProtein() if numResidues == 0: self.minresSpinBox.setMaximum(numResidues + 2) self.maxresSpinBox.setMaximum(numResidues + 2) else: self.minresSpinBox.setMaximum(numResidues) self.maxresSpinBox.setMaximum(numResidues) PM_Dialog.show(self) if not KEEP_SIGNALS_ALWAYS_CONNECTED: self.connect_or_disconnect_signals(True) return def close(self): """ Closes the Property Manager. Overrides PM_Dialog.close. """ if not KEEP_SIGNALS_ALWAYS_CONNECTED: self.connect_or_disconnect_signals(False) PM_Dialog.close(self) return def _addGroupBoxes( self ): """ Add the Property Manager group boxes. """ self._pmGroupBox2 = PM_GroupBox( self, title = "Backrub specific parameters") self._loadGroupBox2( self._pmGroupBox2 ) self._pmGroupBox1 = PM_GroupBox( self, title = "Rosetta sequence design parameters") self._loadGroupBox1( self._pmGroupBox1 ) return def _loadGroupBox2(self, pmGroupBox): """ Load widgets in group box. """ self.bondAngleWeightSimSpinBox = PM_DoubleSpinBox( pmGroupBox, labelColumn = 0, label = "Bond angle weight:", minimum = 0.01, decimals = 2, maximum = 1.0, singleStep = 0.01, value = 1.0, setAsDefault = False, spanWidth = False) bond_angle_param_list = ['Amber', 'Charmm'] self.bondAngleParamComboBox = PM_ComboBox( pmGroupBox, label = "Bond angle parameters:", choices = bond_angle_param_list, setAsDefault = False) self.onlybbSpinBox = PM_DoubleSpinBox( pmGroupBox, labelColumn = 0, label = "Only backbone rotation:", minimum = 0.01, maximum = 1.0, value = 0.75, decimals = 2, singleStep = 0.01, setAsDefault = False, spanWidth = False) self.onlyrotSpinBox = PM_DoubleSpinBox( pmGroupBox, labelColumn = 0, label = "Only rotamer rotation:", minimum = 0.01, maximum = 1.0, decimals = 2, value = 0.25, singleStep = 0.01, setAsDefault = False, spanWidth = False) self.mctempSpinBox = PM_DoubleSpinBox( pmGroupBox, labelColumn = 0, label = "MC simulation temperature:", minimum = 0.1, value = 0.6, maximum = 1.0, decimals = 2, singleStep = 0.1, setAsDefault = False, spanWidth = False) numResidues = self._getNumResiduesForCurrentProtein() self.minresSpinBox = PM_SpinBox( pmGroupBox, labelColumn = 0, label = "Minimum number of residues:", minimum = 2, maximum = numResidues, singleStep = 1, setAsDefault = False, spanWidth = False) self.maxresSpinBox = PM_SpinBox( pmGroupBox, labelColumn = 0, label = "Maximum number of residues:", minimum = 2, maximum = numResidues, singleStep = 1, setAsDefault = False, spanWidth = False) if numResidues == 0: self.minresSpinBox.setMaximum(numResidues + 2) self.maxresSpinBox.setMaximum(numResidues + 2) return def _getNumResiduesForCurrentProtein(self): """ Get number of residues for the current protein """ previousCommand = self.command.find_parent_command_named('MODEL_AND_SIMULATE_PROTEIN') if previousCommand: #Urmi 20080728: get the protein currently selected in the combo box current_protein = previousCommand.propMgr.get_current_protein_chunk_name() for mol in self.win.assy.molecules: if mol.isProteinChunk() and current_protein == mol.name: return len(mol.protein.get_sequence_string()) else: return 0 return 0 def _loadGroupBox1(self, pmGroupBox): """ Load widgets in group box. """ self.numSimSpinBox = PM_SpinBox( pmGroupBox, labelColumn = 0, label = "Number of trials:", minimum = 1000, maximum = 1000000, singleStep = 1000, setAsDefault = False, spanWidth = False) self.ex1Checkbox = PM_CheckBox(pmGroupBox, text = "Expand rotamer library for chi1 angle", state = Qt.Unchecked, setAsDefault = False, widgetColumn = 0, spanWidth = True) self.ex1aroCheckbox = PM_CheckBox(pmGroupBox, text = "Use large chi1 library for aromatic residues", state = Qt.Unchecked, setAsDefault = False, widgetColumn = 0, spanWidth = True) self.ex2Checkbox = PM_CheckBox(pmGroupBox, text = "Expand rotamer library for chi2 angle", state = Qt.Unchecked, setAsDefault = False, widgetColumn = 0, spanWidth = True) self.ex2aroOnlyCheckbox = PM_CheckBox(pmGroupBox, text = "Use large chi2 library only for aromatic residues", state = Qt.Unchecked, setAsDefault = False, widgetColumn = 0, spanWidth = True) self.ex3Checkbox = PM_CheckBox(pmGroupBox, text = "Expand rotamer library for chi3 angle", state = Qt.Unchecked, setAsDefault = False, widgetColumn = 0, spanWidth = True) self.ex4Checkbox = PM_CheckBox(pmGroupBox, text ="Expand rotamer library for chi4 angle", state = Qt.Unchecked, setAsDefault = False, widgetColumn = 0, spanWidth = True) self.rotOptCheckbox = PM_CheckBox(pmGroupBox, text ="Optimize one-body energy", state = Qt.Unchecked, setAsDefault = False, widgetColumn = 0, spanWidth = True) self.tryBothHisTautomersCheckbox = PM_CheckBox(pmGroupBox, text ="Try both histidine tautomers", state = Qt.Unchecked, setAsDefault = False, widgetColumn = 0, spanWidth = True) self.softRepDesignCheckbox = PM_CheckBox(pmGroupBox, text ="Use softer Lennard-Jones repulsive term", state = Qt.Unchecked, setAsDefault = False, widgetColumn = 0, spanWidth = True) self.useElecRepCheckbox = PM_CheckBox(pmGroupBox, text ="Use electrostatic repulsion", state = Qt.Unchecked, setAsDefault = False, widgetColumn = 0, spanWidth = True) self.norepackDisulfCheckbox = PM_CheckBox(pmGroupBox, text ="Don't re-pack disulphide bonds", state = Qt.Unchecked, setAsDefault = False, widgetColumn = 0, spanWidth = True) self.otherCommandLineOptions = PM_TextEdit(pmGroupBox, label = "Command line options:", spanWidth = True) self.otherCommandLineOptions.setFixedHeight(80) self.okButton = PM_PushButton( pmGroupBox, text = "Run Rosetta", setAsDefault = True, spanWidth = True) return def update_ex1(self, state): """ Update the command text edit depending on the state of the update_ex1 checkbox @param state:state of the update_ex1 checkbox @type state: int """ otherOptionsText = str(self.otherCommandLineOptions.toPlainText()) if self.ex1Checkbox.isChecked() == True: otherOptionsText = otherOptionsText + ' -ex1 ' else: otherOptionsText = otherOptionsText.replace(' -ex1 ', '') self.otherCommandLineOptions.setText(otherOptionsText) return def update_ex1aro(self, state): """ Update the command text edit depending on the state of the update_ex1aro checkbox @param state:state of the update_ex1aro checkbox @type state: int """ otherOptionsText = str(self.otherCommandLineOptions.toPlainText()) if self.ex1aroCheckbox.isChecked() == True: otherOptionsText = otherOptionsText + ' -ex1aro ' else: otherOptionsText = otherOptionsText.replace(' -ex1aro ', '') self.otherCommandLineOptions.setText(otherOptionsText) return def update_ex2(self, state): """ Update the command text edit depending on the state of the update_ex2 checkbox @param state:state of the update_ex2 checkbox @type state: int """ otherOptionsText = str(self.otherCommandLineOptions.toPlainText()) if self.ex2Checkbox.isChecked() == True: otherOptionsText = otherOptionsText + ' -ex2 ' else: otherOptionsText = otherOptionsText.replace(' -ex2 ', '') self.otherCommandLineOptions.setText(otherOptionsText) return def update_ex2aro_only(self, state): """ Update the command text edit depending on the state of the update_ex2aro_only checkbox @param state:state of the update_ex2aro_only checkbox @type state: int """ otherOptionsText = str(self.otherCommandLineOptions.toPlainText()) if self.ex2aroOnlyCheckbox.isChecked() == True: otherOptionsText = otherOptionsText + ' -ex2aro_only ' else: otherOptionsText = otherOptionsText.replace(' -ex2aro_only ', '') self.otherCommandLineOptions.setText(otherOptionsText) return def update_ex3(self, state): """ Update the command text edit depending on the state of the update_ex3 checkbox @param state:state of the update_ex3 checkbox @type state: int """ otherOptionsText = str(self.otherCommandLineOptions.toPlainText()) if self.ex3Checkbox.isChecked() == True: otherOptionsText = otherOptionsText + ' -ex3 ' else: otherOptionsText = otherOptionsText.replace(' -ex3 ', '') self.otherCommandLineOptions.setText(otherOptionsText) return def update_ex4(self, state): """ Update the command text edit depending on the state of the update_ex4 checkbox @param state:state of the update_ex4 checkbox @type state: int """ otherOptionsText = str(self.otherCommandLineOptions.toPlainText()) if self.ex4Checkbox.isChecked() == True: otherOptionsText = otherOptionsText + ' -ex4 ' else: otherOptionsText = otherOptionsText.replace(' -ex4 ', '') self.otherCommandLineOptions.setText(otherOptionsText) return def update_rot_opt(self, state): """ Update the command text edit depending on the state of the update_rot_opt checkbox @param state:state of the update_rot_opt checkbox @type state: int """ otherOptionsText = str(self.otherCommandLineOptions.toPlainText()) if self.rotOptCheckbox.isChecked() == True: otherOptionsText = otherOptionsText + ' -rot_opt ' else: otherOptionsText = otherOptionsText.replace(' -rot_opt ', '') self.otherCommandLineOptions.setText(otherOptionsText) return def update_try_both_his_tautomers(self, state): """ Update the command text edit depending on the state of the update_try_both_his_tautomers checkbox @param state:state of the update_try_both_his_tautomers checkbox @type state: int """ otherOptionsText = str(self.otherCommandLineOptions.toPlainText()) if self.tryBothHisTautomersCheckbox.isChecked() == True: otherOptionsText = otherOptionsText + ' -try_both_his_tautomers ' else: otherOptionsText = otherOptionsText.replace(' -try_both_his_tautomers ', '') self.otherCommandLineOptions.setText(otherOptionsText) return def update_soft_rep_design(self, state): """ Update the command text edit depending on the state of the update_soft_rep_design checkbox @param state:state of the update_soft_rep_design checkbox @type state: int """ otherOptionsText = str(self.otherCommandLineOptions.toPlainText()) if self.softRepDesignCheckbox.isChecked() == True: otherOptionsText = otherOptionsText + ' -soft_rep_design ' else: otherOptionsText = otherOptionsText.replace(' -soft_rep_design ', '') self.otherCommandLineOptions.setText(otherOptionsText) return def update_use_elec_rep(self, state): """ Update the command text edit depending on the state of the update_use_elec_rep checkbox @param state:state of the update_use_elec_rep checkbox @type state: int """ otherOptionsText = str(self.otherCommandLineOptions.toPlainText()) if self.useElecRepCheckbox.isChecked() == True: otherOptionsText = otherOptionsText + ' -use_electrostatic_repulsion ' else: otherOptionsText = otherOptionsText.replace(' -use_electrostatic_repulsion ', '') self.otherCommandLineOptions.setText(otherOptionsText) return def update_norepack_disulf(self, state): """ Update the command text edit depending on the state of the update_no_repack checkbox @param state:state of the update_no_repack checkbox @type state: int """ otherOptionsText = str(self.otherCommandLineOptions.toPlainText()) if self.norepackDisulfCheckbox.isChecked() == True: otherOptionsText = otherOptionsText + ' -norepack_disulf ' else: otherOptionsText = otherOptionsText.replace(' -norepack_disulf ', '') self.otherCommandLineOptions.setText(otherOptionsText) return def runRosettaBackrubSim(self): """ Get all the parameters from the PM and run a rosetta simulation """ otherOptionsText = str(self.otherCommandLineOptions.toPlainText()) numSim = self.numSimSpinBox.value() previousCommand = self.command.find_parent_command_named('MODEL_AND_SIMULATE_PROTEIN') protein = previousCommand.propMgr.get_current_protein_chunk_name() argList = [numSim, otherOptionsText, protein] backrubSpecificArgList = self.getBackrubSpecificArgumentList() from simulation.ROSETTA.rosetta_commandruns import rosettaSetup_CommandRun if argList[0] > 0: env.prefs[rosetta_backrub_enabled_prefs_key] = True cmdrun = rosettaSetup_CommandRun(self.win, argList, "BACKRUB_PROTEIN_SEQUENCE_DESIGN", backrubSpecificArgList) cmdrun.run() return def getBackrubSpecificArgumentList(self): """ get list of backrub specific parameters from PM """ listOfArgs = [] bond_angle_weight = str(self.bondAngleWeightSimSpinBox.value()) listOfArgs.append('-bond_angle_weight') listOfArgs.append( bond_angle_weight) if self.bondAngleParamComboBox.currentIndex() == 0: bond_angle_params = 'bond_angle_amber_rosetta' else: bond_angle_params = 'bond_angle_charmm_rosetta' listOfArgs.append('-bond_angle_params') listOfArgs.append(bond_angle_params) only_bb = str(self.onlybbSpinBox.value()) listOfArgs.append('-only_bb') listOfArgs.append( only_bb) only_rot = str(self.onlyrotSpinBox.value()) listOfArgs.append('-only_rot') listOfArgs.append( only_rot) mc_temp = str(self.mctempSpinBox.value()) listOfArgs.append('-mc_temp') listOfArgs.append( mc_temp) min_res = self.minresSpinBox.value() max_res = self.maxresSpinBox.value() if max_res < min_res: msg = redmsg("Maximum number of residues for rosetta simulation with backrub" \ " motion cannot be less than minimum number of residues."\ " Neglecting this parameter for this simulation.") env.history.message("BACKRUB SIMULATION: " + msg) else: listOfArgs.append('-min_res') listOfArgs.append( str(min_res)) listOfArgs.append('-max_res') listOfArgs.append( str(max_res)) return listOfArgs