def run_script(session):
from chimerax.core.errors import UserError
from chimerax.isolde.parmed import install_parmed_if_necessary
install_parmed_if_necessary(session)
from Qt.QtWidgets import QFileDialog
import os
filter = "AMBER Parameter files (*.mol2 *.frcmod)"
files, _ = QFileDialog.getOpenFileNames(None, "Choose one .mol2 and one .frcmod file", "", filter)
if len(files)!=2:
raise UserError("Please select exactly one .mol2 and one .frcmod file!")
matched_files = {}
for f in files:
matched_files[os.path.splitext(f)[1].lower()] = f
if '.mol2' not in matched_files.keys() or '.frcmod' not in matched_files.keys():
raise UserError('Please select exactly one .mol2 and one .frcmod file!')
mol2, frcmod = matched_files['.mol2'], matched_files['.frcmod']
from chimerax.isolde.openmm.amberff.amber_convert import amber_to_ffxml
try:
ffxml = amber_to_ffxml(frcmod, mol2)
except Exception as e:
raise UserError(f'ParmEd failed to run with the following error. Do your .mol2 and .frcmod match?\n {str(e)}')
session.logger.info(f'Converted AMBER files {mol2} and {frcmod} to OpenMM FFXML file {ffxml}.')
if hasattr(session, 'isolde'):
ff_name = session.isolde.sim_params.forcefield
forcefield = session.isolde.forcefield_mgr[ff_name]
forcefield.loadFile(ffxml, resname_prefix='USER_')
session.logger.info('This has been loaded into ISOLDE\'s forcefield for this session. For '
'future sessions you should add it using the "Load residue MD definition(s)" button.')
else:
session.logger.info('On starting ISOLDE you can add it to the forcefield using the '
'"Load residue MD definition(s)" button.')
def browse_file(self):
filter_list = 'File({})'.format(' '.join(
['*' + e for e in self.filters])) if self.filters else 'Any File(*)'
if self.multiple:
r_files, _ = QFileDialog.getOpenFileNames(self, 'Browse Files',
self.path, filter_list)
if r_files:
self.filesChanged.emit(r_files)
self.path = r_files[0]
else:
r_file, _ = QFileDialog.getOpenFileName(self, 'Browse File', self.path,
filter_list)
if r_file:
self.fileChanged.emit(r_file)
self.path = r_file
def table_clicked(self, row, column):
"""
if the last row is clicked, open a file browser and add
the files to the list
otherwise, if the 2nd column is clicked (the trash can),
remove that row
"""
if row == self.table.rowCount() - 1 or self.table.rowCount() == 1:
filenames = QFileDialog.getOpenFileNames(
filter="Python Files (*.py)")
if filenames[0]:
self.table.setRowCount(self.table.rowCount() - 1)
self.add_files(filenames[0])
elif column == 1:
self.table.removeRow(row)
