class BackrubProteinSim_PropertyManager(Command_PropertyManager):
"""
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 = "Backrub Motion"
pmName = title
iconPath = "ui/actions/Command Toolbar/BuildProtein/Backrub.png"
def __init__(self, command):
"""
Constructor for the property manager.
"""
_superclass.__init__(self, command)
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)
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 show(self):
"""
Shows the Property Manager. Exends superclass method.
"""
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)
_superclass.show(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 _addWhatsThisText(self):
"""
What's This text for widgets in this Property Manager.
"""
pass
def _addToolTipText(self):
"""
Tool Tip text for widgets in this Property Manager.
"""
pass
def _getNumResiduesForCurrentProtein(self):
"""
Get number of residues for the current protein
"""
_current_protein = self.win.assy.getSelectedProteinChunk()
if _current_protein:
return len(_current_protein.protein.get_sequence_string())
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
"""
proteinChunk = self.win.assy.getSelectedProteinChunk()
if not proteinChunk:
msg = "You must select a single protein to run a Rosetta <i>Backrub</i> simulation."
self.updateMessage(msg)
return
otherOptionsText = str(self.otherCommandLineOptions.toPlainText())
numSim = self.numSimSpinBox.value()
argList = [numSim, otherOptionsText, proteinChunk.name]
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
class BackrubProteinSim_PropertyManager(Command_PropertyManager):
"""
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 = "Backrub Motion"
pmName = title
iconPath = "ui/actions/Command Toolbar/BuildProtein/Backrub.png"
def __init__( self, command ):
"""
Constructor for the property manager.
"""
_superclass.__init__(self, command)
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)
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 show(self):
"""
Shows the Property Manager. Exends superclass method.
"""
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)
_superclass.show(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 _addWhatsThisText( self ):
"""
What's This text for widgets in this Property Manager.
"""
pass
def _addToolTipText(self):
"""
Tool Tip text for widgets in this Property Manager.
"""
pass
def _getNumResiduesForCurrentProtein(self):
"""
Get number of residues for the current protein
"""
_current_protein = self.win.assy.getSelectedProteinChunk()
if _current_protein:
return len(_current_protein.protein.get_sequence_string())
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
"""
proteinChunk = self.win.assy.getSelectedProteinChunk()
if not proteinChunk:
msg = "You must select a single protein to run a Rosetta <i>Backrub</i> simulation."
self.updateMessage(msg)
return
otherOptionsText = str(self.otherCommandLineOptions.toPlainText())
numSim = self.numSimSpinBox.value()
argList = [numSim, otherOptionsText, proteinChunk.name]
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
