/
__init__.py
530 lines (486 loc) · 25.6 KB
/
__init__.py
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"""
PyMOL simple membrane builder
The plugin is constructed to facilitate SAXS analysis/modeling of membrane protein systems
(D.Molodenskiy & H.D.T.Mertens 2019-2022 for BioSAXS team)
"""
from __future__ import absolute_import
from __future__ import print_function
# Avoid importing "expensive" modules here (e.g. scipy), since this code is
# executed on PyMOL's startup. Only import such modules inside functions.
import time
from .util import *
from pymol import cmd
# pymol.Qt provides the PyQt5 interface, but may support PyQt4 and/or PySide as well
from pymol.Qt import QtWidgets
from pymol.Qt.utils import loadUi
from sys import platform
viewer = 'primus'
if platform == 'win32' or platform == 'win64':
viewer = 'primusqt'
def __init_plugin__(app=None):
"""
Add an entry to the PyMOL "Plugin" menu
"""
from pymol.plugins import addmenuitemqt
addmenuitemqt('Membrane Builder Plugin', run_plugin_gui)
# global reference to avoid garbage collection of our dialog
mpb = None
def run_plugin_gui():
"""
Open plugin dialog
"""
global mpb
if mpb is None:
mpb = mpbuilder()
mpb.dialog.show()
class mpbuilder:
def changeForm(self, assembly):
isProtein = not self.form.checkBox_emptyAssembly.isChecked()
if assembly == "detergent":
self.form.label_6.setEnabled(isProtein)
self.form.input_filename_prot.setEnabled(isProtein)
self.form.btn_browse_prot.setEnabled(isProtein)
self.form.first_angle_label.setEnabled(True)
self.form.input_rotAng_min.setEnabled(True)
self.form.input_rotAng_max.setEnabled(True)
self.form.input_rotAng_step.setEnabled(True)
self.form.first_angle_label.setText(
r'<html><head/><body><p><span style=" font-size:10pt;">Max Polar Angle </span><span style=" '
r'font-size:10pt; font-weight:600;">ω</span><span style=" font-size:10pt;"> ('
r'deg.)</span></p></body></html>')
self.form.second_angle_label.setText(
r'<html><head/><body><p><span style=" font-size:10pt;">Density Angle </span><span style=" '
r'font-size:10pt; font-weight:600;">Δφ</span><span style=" font-size:10pt;"> ('
r'deg.)</span></p></body></html>')
self.form.label_7.setText("Detergent")
self.form.btn_browse_scaffold.setEnabled(False)
self.form.number_scaffold_label.setEnabled(False)
self.form.filename_scaffold_label.setEnabled(False)
self.form.copies_scaffold_label.setEnabled(False)
self.form.input_copies.setEnabled(False)
self.form.input_filename_scaffold.setEnabled(False)
self.form.btn_browse_scaffold.setEnabled(False)
self.form.number_scaffold_label.setEnabled(False)
self.form.input_scaffold_number_min.setEnabled(False)
self.form.input_scaffold_number_max.setEnabled(False)
self.form.input_scaffold_number_step.setEnabled(False)
self.form.second_angle_label.setEnabled(True)
self.form.input_rotAng_min_2.setEnabled(True)
self.form.input_rotAng_max_2.setEnabled(True)
self.form.input_rotAng_step_2.setEnabled(True)
self.form.label_2.setEnabled(False)
self.form.input_rotAng.setEnabled(False)
self.form.checkBox_prebuild_bilayer.setEnabled(False)
self.form.checkBox_emptyAssembly.setEnabled(True)
self.form.checkBox_expHyd.setEnabled(True)
self.form.checkBox_const.setEnabled(True)
elif assembly == "salipro":
self.form.label_6.setEnabled(isProtein)
self.form.input_filename_prot.setEnabled(isProtein)
self.form.btn_browse_prot.setEnabled(isProtein)
self.form.first_angle_label.setEnabled(True)
self.form.input_rotAng_min.setEnabled(True)
self.form.input_rotAng_max.setEnabled(True)
self.form.input_rotAng_step.setEnabled(True)
self.form.first_angle_label.setText("Scaffold Rotation Angle (deg.)")
self.form.label_7.setText("Lipid Bilayer")
self.form.btn_browse_scaffold.setEnabled(True)
self.form.input_copies.setEnabled(True)
self.form.number_scaffold_label.setEnabled(True)
self.form.filename_scaffold_label.setEnabled(True)
self.form.copies_scaffold_label.setEnabled(True)
self.form.filename_scaffold_label.setText("Scaffold")
self.form.input_filename_scaffold.setEnabled(True)
self.form.btn_browse_scaffold.setEnabled(True)
self.form.number_scaffold_label.setEnabled(True)
self.form.input_scaffold_number_min.setEnabled(True)
self.form.input_scaffold_number_max.setEnabled(True)
self.form.input_scaffold_number_step.setEnabled(True)
self.form.second_angle_label.setEnabled(False)
self.form.input_rotAng_step_2.setEnabled(False)
self.form.input_rotAng_min_2.setEnabled(False)
self.form.input_rotAng_max_2.setEnabled(False)
self.form.label_2.setEnabled(True)
self.form.input_rotAng.setEnabled(True)
self.form.checkBox_prebuild_bilayer.setEnabled(True)
self.form.checkBox_emptyAssembly.setEnabled(True)
elif assembly == "nanodisc":
self.form.label_6.setEnabled(isProtein)
self.form.input_filename_prot.setEnabled(isProtein)
self.form.btn_browse_prot.setEnabled(isProtein)
self.form.first_angle_label.setEnabled(True)
self.form.first_angle_label.setText("Offset along X-axis (A)")
self.form.input_rotAng_min.setEnabled(True)
self.form.input_rotAng_max.setEnabled(True)
self.form.input_rotAng_step.setEnabled(True)
self.form.label_7.setText("Lipid Bilayer")
self.form.btn_browse_scaffold.setEnabled(True)
self.form.input_copies.setEnabled(False)
self.form.number_scaffold_label.setEnabled(False)
self.form.filename_scaffold_label.setEnabled(True)
self.form.copies_scaffold_label.setEnabled(False)
self.form.filename_scaffold_label.setText("Scaffold")
self.form.input_filename_scaffold.setEnabled(True)
self.form.btn_browse_scaffold.setEnabled(True)
self.form.number_scaffold_label.setEnabled(False)
self.form.input_scaffold_number_min.setEnabled(False)
self.form.input_scaffold_number_max.setEnabled(False)
self.form.input_scaffold_number_step.setEnabled(False)
self.form.second_angle_label.setText("Offset along Y-axis (A)")
self.form.second_angle_label.setEnabled(True)
self.form.input_rotAng_step_2.setEnabled(True)
self.form.input_rotAng_min_2.setEnabled(True)
self.form.input_rotAng_max_2.setEnabled(True)
self.form.input_rotAng.setEnabled(False)
self.form.checkBox_prebuild_bilayer.setEnabled(True)
self.form.checkBox_emptyAssembly.setEnabled(True)
elif assembly == "bilayer":
self.form.label_6.setEnabled(False)
self.form.input_filename_prot.setEnabled(False)
self.form.btn_browse_prot.setEnabled(False)
self.form.first_angle_label.setEnabled(False)
self.form.input_rotAng_min.setEnabled(False)
self.form.input_rotAng_max.setEnabled(False)
self.form.input_rotAng_step.setEnabled(False)
self.form.label_7.setText("A single molecule")
self.form.btn_browse_scaffold.setEnabled(False)
self.form.input_copies.setEnabled(False)
self.form.number_scaffold_label.setEnabled(False)
self.form.filename_scaffold_label.setEnabled(False)
self.form.copies_scaffold_label.setEnabled(False)
self.form.input_filename_scaffold.setEnabled(False)
self.form.btn_browse_scaffold.setEnabled(False)
self.form.number_scaffold_label.setEnabled(False)
self.form.input_scaffold_number_min.setEnabled(False)
self.form.input_scaffold_number_max.setEnabled(False)
self.form.input_scaffold_number_step.setEnabled(False)
self.form.second_angle_label.setEnabled(False)
self.form.input_rotAng_step_2.setEnabled(False)
self.form.input_rotAng_min_2.setEnabled(False)
self.form.input_rotAng_max_2.setEnabled(False)
self.form.label_2.setEnabled(False)
self.form.input_rotAng.setEnabled(False)
self.form.checkBox_prebuild_bilayer.setEnabled(False)
self.form.checkBox_emptyAssembly.setEnabled(False)
elif assembly == "bicelle":
self.form.label_6.setEnabled(isProtein)
self.form.input_filename_prot.setEnabled(isProtein)
self.form.btn_browse_prot.setEnabled(isProtein)
self.form.first_angle_label.setEnabled(False)
self.form.input_rotAng_min.setEnabled(False)
self.form.input_rotAng_max.setEnabled(False)
self.form.input_rotAng_step.setEnabled(False)
self.form.label_7.setText("Lipid Bilayer")
self.form.input_copies.setEnabled(False)
self.form.number_scaffold_label.setEnabled(True)
self.form.filename_scaffold_label.setText("Detergent")
self.form.filename_scaffold_label.setEnabled(True)
self.form.btn_browse_scaffold.setEnabled(True)
self.form.copies_scaffold_label.setEnabled(False)
self.form.input_filename_scaffold.setEnabled(True)
self.form.btn_browse_scaffold.setEnabled(True)
self.form.number_scaffold_label.setEnabled(False)
self.form.input_scaffold_number_min.setEnabled(False)
self.form.input_scaffold_number_max.setEnabled(False)
self.form.input_scaffold_number_step.setEnabled(False)
self.form.second_angle_label.setEnabled(False)
self.form.input_rotAng_step_2.setEnabled(False)
self.form.input_rotAng_min_2.setEnabled(False)
self.form.input_rotAng_max_2.setEnabled(False)
self.form.label_2.setEnabled(False)
self.form.input_rotAng.setEnabled(False)
self.form.checkBox_prebuild_bilayer.setEnabled(True)
self.form.checkBox_emptyAssembly.setEnabled(True)
def change_assembly(self):
# Change active buttons
# type of protein-membrane assembly
assemblyType = self.form.input_type.currentText()
print('Assembly type is changed to: {}'.format(assemblyType))
self.changeForm(assemblyType)
def preOriProt(self):
"""
User defined orientation of protein true/false
"""
if self.form.checkBox_3.isChecked():
# print(f"Using pre-oriented membrane protein {self.protName} for model building ...")
print("Using pre-oriented membrane protein {} for model building ...".format(self.protName))
elif self.protName is None:
print("No protein to pre-align")
else:
# print(f"Centering and aligning membrane protein {self.protName} for model building ...")
print("Centering and aligning membrane protein {} for model building ...".format(self.protName))
center(self.protName)
def explicitHydrogens(self):
"""
Use explicit hydrogen flag for CRYSOL
"""
if self.form.checkBox_expHyd.isChecked():
# print(f"Using explicit hydrogens for fit ...")
print("Using explicit hydrogens for intensities calculation of {} ...".format(self.modelName))
self.explicitHydrogens = True
else:
print("Using implicit hydrogens for intensities calculation of {} ...".format(self.modelName))
self.explicitHydrogens = False
def constantSubtraction(self):
"""
Use constant flag for CRYSOL
"""
if self.form.checkBox_const.isChecked():
# print(f"Using constant for fit ...")
print("Using constant for fit of {} ...".format(self.modelName))
self.constantSubtraction = True
else:
print("Not using constant for fit of {} ...".format(self.modelName))
self.constantSubtraction = False
def emptyAssembly(self):
assemblyType = self.form.input_type.currentText()
if self.form.checkBox_emptyAssembly.isChecked():
print("No transmembrane protein, empty assembly will be generated ...")
self.changeForm(assemblyType)
self.protName = None
if assemblyType == "detergent":
self.form.first_angle_label.setText("Radius-vector (A)")
self.form.second_angle_label.setText("Number of detergent molecules")
else:
print("Transmembrane protein {} will be used for for model building ...".format(self.protName))
self.changeForm(assemblyType)
if assemblyType == "detergent":
self.form.first_angle_label.setText("Maximum Polar Angle Theta (deg.)")
self.form.second_angle_label.setText("Density Angle Phi (deg.)")
def preBuildBilayer(self):
"""
activate the button and store the variable
"""
if self.form.checkBox_prebuild_bilayer.isChecked():
print("Using pre-built membrane {}".format(self.membName))
self.buildMemb = False
else:
print("Using a single molecule to build a membrane")
self.buildMemb = True
# CRYSOL predict scattering on single assembly
def run_crysol_predict(self):
"""Prediction of model scattering"""
# def predcrysol(crycalc, models, prefix="tmp", param=" "):
if self.modelName:
#df = predcrysol(self.modelName, "yes")
df = predcrysol(self.modelName, self.explicitHydrogens, self.constantSubtraction, "yes")
if os.path.exists(df):
print('Theoretical SAXS profile generated')
systemCommand([viewer, df])
self.prediction = df
else:
print("pdb file is missing. Model Name: {}".format(self.modelName))
# CRYSOL fit run on single assembly
def run_crysol_fit(self):
"""Calculation of model fit"""
if (self.modelName != "" and self.dataName != ""):
#fitcrysol(self.modelName, self.dataName, "yes", True)
fitcrysol(self.modelName, self.dataName, self.explicitHydrogens, self.constantSubtraction, "yes", True)
else:
print('pdb or SAXS data file is missing!')
print('model file: {} data file: {}'.format(self.modelName, self.dataName))
def run_refinement(self):
"""Finds the model that fits SAXS data"""
if self.membName == None:
print("Please provide a PDB file!")
return
if self.dataName is None:
print("Please provide SAXS dat file!")
return
cmd.cache("clear")
cmd.reset()
self.runNumber += 1
seconds_init = time.time()
assemblyType = self.form.input_type.currentText()
print('Assembly is: {}'.format(assemblyType))
prefixName = self.form.output_filename_prefix.text()
# center protein
self.preOriProt()
rot_min_ang = self.form.input_rotAng_min.value()
rot_max_ang = self.form.input_rotAng_max.value() + 1
rot_step_ang = self.form.input_rotAng_step.value()
cmd.delete(self.modelName)
self.bestModel = ""
self.fit = ""
# type of protein-membrane assembly
if assemblyType == "detergent":
dens_min_ang = self.form.input_rotAng_min_2.value()
dens_max_ang = self.form.input_rotAng_max_2.value() + 1
dens_step_ang = self.form.input_rotAng_step_2.value()
bestModel, fit, run = crysolRefinementDetergent(rot_min_ang, rot_max_ang, rot_step_ang,
dens_min_ang, dens_max_ang, dens_step_ang,
self.protName, self.membName, self.dataName,
self.explicitHydrogens, self.constantSubtraction,
prefixName, self.runNumber)
elif assemblyType == "salipro":
cmd.reset()
scaffold_min = self.form.input_scaffold_number_min.value()
scaffold_max = self.form.input_scaffold_number_max.value() + 1
scaffold_step = self.form.input_scaffold_number_step.value()
if self.buildMemb:
self.membName = builderMembrane(self.membName)
self.form.input_filename_lip.setText(self.membName)
refresh()
bestModel, fit, run = crysolRefinementSalipro(rot_min_ang, rot_max_ang, rot_step_ang,
scaffold_min, scaffold_max, scaffold_step,
self.protName, self.membName, self.scafName, self.dataName,
self.explicitHydrogens, self.constantSubtraction,
prefixName, self.runNumber)
elif assemblyType == "nanodisc":
cmd.reset()
y_min = self.form.input_rotAng_min.value()
y_max = self.form.input_rotAng_max.value() + 1
y_step = self.form.input_rotAng_step.value()
if self.buildMemb:
self.membName = builderMembrane(self.membName)
self.form.input_filename_lip.setText(self.membName)
refresh()
bestModel, fit, run = crysolRefinementNanodisc(rot_min_ang, rot_max_ang, rot_step_ang,
y_min, y_max, y_step,
self.protName, self.membName, self.scafName, self.dataName,
self.explicitHydrogens, self.constantSubtraction,
prefixName, self.runNumber)
else:
print("Refinement is not supported for assembly type {}".format(assemblyType))
return
self.modelName = bestModel
self.fit = fit
self.runNumber += run
seconds_tmp = time.time()
refresh()
t = int((seconds_tmp - seconds_init))
print("{:d} seconds consumed.".format(t))
systemCommand([viewer, self.fit])
def run_build(self):
# callback for the "Build" button
cmd.cache("clear")
cmd.reset()
seconds_init = time.time()
self.runNumber += 1
# get form data
prefixName = self.form.output_filename_prefix.text()
assemblyType = self.form.input_type.currentText()
print('Assembly is: {}'.format(assemblyType))
print('Building model...')
# center protein if needed
self.preOriProt()
# delete old model
cmd.delete(self.modelName)
# executions depends on the assembly type
if assemblyType == "detergent":
# execute detergent builder
self.modelName = builderDetergent(self.protName, self.membName, prefixName, self.runNumber)
elif assemblyType == "salipro":
# execute salipro builder
rotAng = self.form.input_rotAng.value()
numScaffoldCopies = self.form.input_copies.value()
print('Number of scaffold copies: {}'.format(numScaffoldCopies))
if self.buildMemb:
self.membName = builderMembrane(self.membName)
self.form.input_filename_lip.setText(self.membName)
self.modelName = builderSalipro(self.protName, self.scafName, self.membName, prefixName,
self.runNumber, numScaffoldCopies, rotAng)
elif assemblyType == "nanodisc":
# execute nanodisc builder
# build bilayer if check box is activated
if self.buildMemb:
self.membName = builderMembrane(self.membName)
self.form.input_filename_lip.setText(self.membName)
# execute builder
self.modelName = builderNanodisc(self.protName, self.membName, self.scafName, prefixName, self.runNumber)
elif assemblyType == "bilayer":
# execute detergent builder
self.membName = builderMembrane(self.membName, self.runNumber)
self.form.input_filename_lip.setText(self.membName)
elif assemblyType == "bicelle":
# execute bicelle builder
# build bilayer if check box is activated
if self.buildMemb:
self.membName = builderMembrane(self.membName, self.runNumber)
self.form.input_filename_lip.setText(self.membName)
# execute builder
self.modelName = builderBicelle(self.protName, self.membName, self.scafName, prefixName, self.runNumber)
refresh()
print("Model name is {}".format(self.modelName))
seconds_tmp = time.time()
t = int((seconds_tmp - seconds_init))
print("{:d} seconds consumed.".format(t))
def browse_filename_data(self, _str):
filename = QtWidgets.QFileDialog.getOpenFileName(None, 'Open file', '', "dat files (*.dat);;")[0]
if filename:
f = os.path.relpath(filename)
self.form.input_filename_data.setText(f)
self.dataName = f
def browse_filename_prot(self):
filename = QtWidgets.QFileDialog.getOpenFileName(None, 'Open protein file', '',
"PDB files (*.pdb *.cif *.ent);;")[0]
filename = filename[:-4] # remove .pdb
loadModel(filename, self.protName)
f = os.path.basename(filename)
self.form.input_filename_prot.setText(f)
self.protName = f
refresh()
def browse_filename_lip(self):
filename = QtWidgets.QFileDialog.getOpenFileName(None, 'Open lipid/detergent file', '',
"PDB files (*.pdb *.cif *.ent);;")[0]
filename = filename[:-4] # remove .pdb
loadModel(filename, self.membName)
f = os.path.basename(filename)
self.form.input_filename_lip.setText(f)
self.membName = f
refresh()
def browse_filename_scaffold(self):
filename = QtWidgets.QFileDialog.getOpenFileName(None, 'Open scaffold file', '',
"PDB files (*.pdb *.cif *.ent);;")[0]
filename = filename[:-4] # remove .pdb
loadModel(filename, self.scafName)
f = os.path.basename(filename)
self.form.input_filename_scaffold.setText(f)
self.scafName = f
refresh()
def __init__(self):
# create a new Window
self.dialog = QtWidgets.QDialog()
# populate the Window from our *.ui file which was created with the Qt Designer
uifile = os.path.join(os.path.dirname(__file__), 'widgetMPbuilder.ui')
self.form = loadUi(uifile, self.dialog)
# open always on detergents
self.changeForm("detergent")
self.protName = None
self.membName = None
self.scafName = None
self.dataName = None
self.runNumber = 0
# name of the model
self.modelName = ""
# prefix
self.prefixName = ""
# crysol int prediction
self.prediction = ""
# crysol fit
self.fit = ""
# result of the fit
self.fitResult = {'chi2': -9999, 'Rg': -9999, 'eDens': -9999}
# whether to build a membrane or use prebuilt one
self.buildMemb = False
# hook up button callbacks
self.form.button_build.clicked.connect(self.run_build)
self.form.button_refinement.clicked.connect(self.run_refinement)
self.form.button_crysol_fit.clicked.connect(self.run_crysol_fit) # single fit of assembly to data
self.form.button_crysol_predict.clicked.connect(self.run_crysol_predict) # predict theory
# self.form.button_crysol_predict.clicked.connect(lambda: self.run_crysol_predict(modelName))
self.form.btn_browse_prot.clicked.connect(self.browse_filename_prot)
self.form.btn_browse_lip.clicked.connect(self.browse_filename_lip)
self.form.btn_browse_scaffold.clicked.connect(self.browse_filename_scaffold)
self.form.btn_browse_data.clicked.connect(self.browse_filename_data)
self.form.button_close.clicked.connect(self.dialog.close)
# change GUI depending upon the choice of assembly type
self.form.input_type.currentIndexChanged.connect(self.change_assembly)
# emptyAssembly = assemble complex without transmembrane protein component
self.form.checkBox_emptyAssembly.toggled.connect(self.emptyAssembly)
# preOriProt = pre-oriented protein
self.form.checkBox_3.toggled.connect(self.preOriProt)
self.form.checkBox_prebuild_bilayer.toggled.connect(self.preBuildBilayer)
# CRYSOL options
self.form.checkBox_expHyd.toggled.connect(self.explicitHydrogens)
self.form.checkBox_const.toggled.connect(self.constantSubtraction)