452 lines
14 KiB
Python
452 lines
14 KiB
Python
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'''
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PyMOL APBS GUI Plugin
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(c) Schrodinger, Inc.
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'''
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import sys
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import os
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import importlib
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from pymol.Qt import QtCore, QtWidgets
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from pymol.Qt.utils import loadUi, AsyncFunc, MainThreadCaller
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getOpenFileNames = QtWidgets.QFileDialog.getOpenFileNames
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from . import electrostatics
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from .qtwidgets import ResizableMessageBox as QMessageBox
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class SilentAbort(Exception):
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pass
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class StdOutCapture:
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'''
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Redirect stdout and/or stderr to a temporary file until 'release' is called.
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'''
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def __init__(self, stdout=True, stderr=True):
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import tempfile
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self.temp = tempfile.TemporaryFile('w+')
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self.save_stdout = None
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self.save_stderr = None
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if stdout:
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self.save_stdout = sys.stdout
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sys.stdout = self.temp
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if stderr:
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self.save_stderr = sys.stderr
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sys.stderr = self.temp
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def release(self):
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if self.save_stdout is not None:
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sys.stdout = self.save_stdout
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if self.save_stderr is not None:
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sys.stderr = self.save_stderr
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self.temp.seek(0)
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content = self.temp.read()
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self.temp.close()
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return content
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def run_impl(form, _self):
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'''
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Execute the pipeline (prep, apbs, surface vis)
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'''
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selection = form.input_sele.currentText()
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prep_name = ''
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map_name = ''
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ramp_name = ''
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group_name = ['']
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def get_name(lineinput):
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name = lineinput.text()
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if not name:
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name = _self.get_unused_name(lineinput.placeholderText())
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return name
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def do_group(name):
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if form.check_no_group.isChecked():
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return
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if not group_name[0]:
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group_name[0] = _self.get_unused_name('run', 1)
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_self.group(group_name[0], name)
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if form.do_prepare.isChecked():
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from . import creating as pc
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prep_name = get_name(form.prep_name)
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method = form.prep_method.currentText()
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warnings = ''
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get_res_charge = lambda resn: ((-1) if resn in ('GLU', 'ASP') else
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(1) if resn in ('ARG', 'LYS') else 0)
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def get_cb_pseudocharge(resn, name):
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if name != 'CB':
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return 0
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return get_res_charge(resn)
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try:
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state = _self.get_selection_state(selection)
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except BaseException as e:
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state = -1
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if method == 'pdb2pqr':
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warnings = pc.pdb2pqr_cli(prep_name, selection,
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options=form.pdb2pqr_args.text(),
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quiet=0,
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state=state,
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preserve=form.check_preserve.isChecked(),
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fixrna=form.pdb2pqr_fixrna.isChecked(),
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_proclist=form._proclist,
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exe=form.pdb2pqr_exe.text())
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if form.pdb2pqr_ignore_warnings.isChecked():
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warnings = ''
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elif method == 'protein_assign_charges_and_radii':
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_self.create(prep_name, selection)
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_self.util.protein_assign_charges_and_radii(prep_name)
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elif method.startswith('prepwizard'):
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pc.prepwizard(prep_name, selection,
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options=form.prepwizard_args.text(),
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_proclist=form._proclist,
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quiet=0,
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preserve=form.check_preserve.isChecked())
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_self.alter(prep_name, 'elec_radius = vdw')
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elif method.startswith('use formal'):
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_self.create(prep_name, selection)
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_self.alter(prep_name,
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'(elec_radius, partial_charge) = (vdw, formal_charge)')
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elif method.startswith('use CB'):
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_self.create(prep_name, selection)
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_self.alter(
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prep_name,
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'(elec_radius, partial_charge) = (vdw, getpc(resn, name))',
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space={'getpc': get_cb_pseudocharge})
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elif method.startswith('use CA'):
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_self.create(prep_name, '(%s) & name CA' % (selection))
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_self.alter(
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prep_name,
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'(elec_radius, vdw, partial_charge) = (3.0, 3.0, getpc(resn))',
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space={'getpc': get_res_charge})
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elif method.startswith('use vdw'):
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_self.create(prep_name, selection)
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_self.alter(prep_name, 'elec_radius = vdw')
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else:
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raise ValueError('unknown method: ' + method)
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selection = prep_name
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form.input_sele.addItem(prep_name)
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do_group(prep_name)
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if warnings:
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@form._callInMainThread
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def result():
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msgbox = QMessageBox(QMessageBox.Question, 'Continue?',
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method + ' emmitted warnings, do you want to continue?',
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QMessageBox.Yes | QMessageBox.No , form._dialog)
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msgbox.setDetailedText(warnings)
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return msgbox.exec_()
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if result == QMessageBox.No:
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raise SilentAbort
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if form.do_apbs.isChecked():
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map_name = get_name(form.apbs_map)
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template = form.apbs_template.toPlainText()
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electrostatics.map_new_apbs(
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map_name,
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selection,
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grid=form.apbs_grid.value(),
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focus=form.focus_sele.text(),
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quiet=0,
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preserve=form.check_preserve.isChecked(),
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exe=form.apbs_exe.text(),
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_template=template,
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_proclist=form._proclist,
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assign=0)
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form.surf_map.addItem(map_name)
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do_group(map_name)
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if form.do_surface.isChecked():
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if not map_name:
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map_name = form.surf_map.currentText()
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if not map_name:
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raise ValueError('missing map')
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if not prep_name:
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prep_name = _self.get_object_list(selection)[0]
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ramp_name = get_name(form.surf_ramp)
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v = form.surf_range.value()
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_self.ramp_new(ramp_name, map_name, [-v, 0, v])
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do_group(ramp_name)
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sas = 'Accessible' in form.surf_type.currentText()
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_self.set('surface_ramp_above_mode', not sas, prep_name)
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_self.set('surface_solvent', sas, prep_name)
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_self.set('surface_color', ramp_name, prep_name)
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_self.show('surface', selection)
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def dialog(_self=None):
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if _self is None:
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from pymol import cmd as _self
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dialog = QtWidgets.QDialog()
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uifile = os.path.join(os.path.dirname(__file__), 'apbs.ui')
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form = loadUi(uifile, dialog)
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form._dialog = dialog
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form._proclist = []
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def set_apbs_in(contents):
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form.apbs_template.setPlainText(contents.strip())
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# hide options widgets
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form.optarea_prep.setVisible(False)
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form.optarea_apbs.setVisible(False)
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form.optarea_surf.setVisible(False)
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form.optarea_other.setVisible(False)
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# pre-fill form with likely data
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names = _self.get_object_list()
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names += ['(' + n + ')' for n in _self.get_names('public_selections')]
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if names:
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form.input_sele.clear()
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form.input_sele.addItems([('polymer & ' + name)
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if _self.count_atoms('polymer & ' + name) > 0
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else name for name in names])
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form.surf_map.addItems(_self.get_names_of_type('object:map'))
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set_apbs_in(electrostatics.template_apbs_in)
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# executables
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from shutil import which
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form.apbs_exe.setText(electrostatics.find_apbs_exe() or 'apbs')
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form.pdb2pqr_exe.setText(
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which('pdb2pqr') or
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which('pdb2pqr30') or
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# acellera::htmd-pdb2pqr provides pdb2pqr_cli
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which('pdb2pqr_cli') or 'pdb2pqr')
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# for async panels
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form._callInMainThread = MainThreadCaller()
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run_impl_async = AsyncFunc(run_impl)
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# "Run" button callback
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def run():
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form.tabWidget.setEnabled(False)
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form.button_ok.clicked.disconnect()
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form.button_ok.clicked.connect(abort)
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form.button_ok.setText('Abort')
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form._capture = StdOutCapture()
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# detach from main thread
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run_impl_async(form, _self)
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# "Run" button "finally" actions (main thread)
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@run_impl_async.finished.connect
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def run_finally(args):
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_, exception = args
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form._proclist[:] = []
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stdout = form._capture.release()
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print(stdout)
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form.button_ok.setText('Run')
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form.button_ok.clicked.disconnect()
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form.button_ok.clicked.connect(run)
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form.button_ok.setEnabled(True)
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form.tabWidget.setEnabled(True)
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if exception is not None:
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handle_exception(exception, stdout)
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return
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quit_msg = "Finished with Success. Close the APBS dialog?"
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if QMessageBox.Yes == QMessageBox.question(
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form._dialog, 'Finished', quit_msg, QMessageBox.Yes,
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QMessageBox.No):
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form._dialog.close()
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def handle_exception(e, stdout):
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if isinstance(e, SilentAbort):
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return
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msg = str(e) or 'unknown error'
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msgbox = QMessageBox(QMessageBox.Critical, 'Error',
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msg, QMessageBox.Close, form._dialog)
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if stdout.strip():
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msgbox.setDetailedText(stdout)
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msgbox.exec_()
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# "Abort" button callback
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def abort():
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form.button_ok.setEnabled(False)
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while form._proclist:
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p = form._proclist.pop()
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try:
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p.terminate()
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p.returncode = -15 # SIGTERM
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except OSError as e:
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print(e)
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# selection checker
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check_sele_timer = QtCore.QTimer()
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check_sele_timer.setSingleShot(True)
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# grid auto-value
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form.apbs_grid_userchanged = False
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form.apbs_grid.setStyleSheet('background: #ff6')
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@form.apbs_grid.editingFinished.connect
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def _():
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form.apbs_grid_userchanged = True
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form.apbs_grid.setStyleSheet('')
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@check_sele_timer.timeout.connect
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def _():
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has_props = ['no', 'no']
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def callback(partial_charge, elec_radius):
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if partial_charge: has_props[0] = 'YES'
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if elec_radius > 0: has_props[1] = 'YES'
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n = _self.iterate(
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form.input_sele.currentText(),
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'callback(partial_charge, elec_radius)',
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space={'callback': callback})
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# grid auto-value (keep map size in the order of 200x200x200)
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if n > 1 and not form.apbs_grid_userchanged:
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e = _self.get_extent(form.input_sele.currentText())
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volume = (e[1][0] - e[0][0]) * (e[1][1] - e[0][1]) * (e[1][2] - e[0][2])
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grid = max(0.5, volume ** 0.333 / 200.0)
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form.apbs_grid.setValue(grid)
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if n < 1:
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label = 'Selection is invalid'
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color = '#f66'
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elif has_props == ['YES', 'YES']:
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label = 'No preparation necessary, selection has charges and radii'
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form.do_prepare.setChecked(False)
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color = '#6f6'
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else:
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label = 'Selection needs preparation (partial_charge: %s, elec_radius: %s)' % tuple(
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has_props)
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form.do_prepare.setChecked(True)
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color = '#fc6'
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form.label_sele_has.setText(label)
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form.label_sele_has.setStyleSheet('background: %s; padding: 5' % color)
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check_sele_timer.start(0)
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@form.apbs_exe_browse.clicked.connect
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def _():
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fnames = getOpenFileNames(None, filter='apbs (apbs*);;All Files (*)')[0]
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if fnames:
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form.apbs_exe.setText(fnames[0])
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@form.pdb2pqr_exe_browse.clicked.connect
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def _():
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fnames = getOpenFileNames(None, filter='pdb2pqr (pdb2pqr*);;All Files (*)')[0]
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if fnames:
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form.pdb2pqr_exe.setText(fnames[0])
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# hook up events
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form.input_sele.currentIndexChanged.connect(
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lambda: check_sele_timer.start(0))
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form.input_sele.editTextChanged.connect(
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lambda: check_sele_timer.start(1000))
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form.button_ok.clicked.connect(run)
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# "Register" opens a web browser
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@form.button_register.clicked.connect
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|
def _():
|
||
|
|
import webbrowser
|
||
|
|
webbrowser.open("http://www.poissonboltzmann.org/")
|
||
|
|
|
||
|
|
@form.button_load.clicked.connect
|
||
|
|
def _():
|
||
|
|
fnames = getOpenFileNames(
|
||
|
|
None, filter='APBS Input (*.in);;All Files (*)')[0]
|
||
|
|
if fnames:
|
||
|
|
contents = load_apbs_in(form, fnames[0])
|
||
|
|
set_apbs_in(contents)
|
||
|
|
|
||
|
|
@form.button_reset.clicked.connect
|
||
|
|
def _():
|
||
|
|
set_apbs_in(electrostatics.template_apbs_in)
|
||
|
|
|
||
|
|
form._dialog.show()
|
||
|
|
form._dialog.resize(500, 600)
|
||
|
|
|
||
|
|
|
||
|
|
def load_apbs_in(form, filename, contents=''):
|
||
|
|
import shlex
|
||
|
|
from pymol import cmd, importing
|
||
|
|
|
||
|
|
wdir = os.path.dirname(filename)
|
||
|
|
|
||
|
|
if not contents:
|
||
|
|
contents = cmd.file_read(filename)
|
||
|
|
|
||
|
|
if not isinstance(contents, str):
|
||
|
|
contents = contents.decode()
|
||
|
|
|
||
|
|
sectionkeys = ('read', 'elec', 'apolar', 'print')
|
||
|
|
section = ''
|
||
|
|
insert_write_pot = True
|
||
|
|
|
||
|
|
lines = []
|
||
|
|
|
||
|
|
for line in contents.splitlines():
|
||
|
|
a = shlex.split(line)
|
||
|
|
key = a[0].lower() if a else ''
|
||
|
|
|
||
|
|
if not section:
|
||
|
|
if key in sectionkeys:
|
||
|
|
section = key
|
||
|
|
elif key == 'end':
|
||
|
|
if section == 'elec' and insert_write_pot:
|
||
|
|
lines.append('write pot dx "{mapfile}"')
|
||
|
|
section = ''
|
||
|
|
elif section == 'read':
|
||
|
|
if len(a) > 2 and key in ('charge', 'kappa', 'mol', 'parm', 'pot'):
|
||
|
|
filename = os.path.join(wdir, a[2])
|
||
|
|
if os.path.exists(filename):
|
||
|
|
format = a[1].lower()
|
||
|
|
if key == 'mol' and format in ('pqr', 'pdb'):
|
||
|
|
# load into PyMOL and update selection dropdown
|
||
|
|
oname = importing.filename_to_objectname(a[2])
|
||
|
|
oname = cmd.get_unused_name(oname, 0)
|
||
|
|
cmd.load(filename, oname, format=format)
|
||
|
|
form.input_sele.addItem(oname)
|
||
|
|
form.input_sele.setEditText(oname)
|
||
|
|
|
||
|
|
# absolute path in input file
|
||
|
|
a[2] = '"' + filename + '"'
|
||
|
|
line = ' '.join(a)
|
||
|
|
else:
|
||
|
|
QMessageBox.warning(
|
||
|
|
form._dialog, "Warning",
|
||
|
|
f'Warning: File "{filename}" does not exist')
|
||
|
|
|
||
|
|
elif section == 'elec':
|
||
|
|
if key == 'write':
|
||
|
|
if a[1:4] == ['pot', 'dx', "{mapfile}"]:
|
||
|
|
insert_write_pot = False
|
||
|
|
|
||
|
|
lines.append(line)
|
||
|
|
|
||
|
|
return '\n'.join(lines)
|
||
|
|
|
||
|
|
|
||
|
|
def __init_plugin__(app=None):
|
||
|
|
from pymol.plugins import addmenuitemqt as addmenuitem
|
||
|
|
addmenuitem('APBS Electrostatics', dialog)
|