"Fossies" - the Fresh Open Source Software Archive  

Source code changes of the file "modules/pmg_qt/file_dialogs.py" between
pymol-open-source-2.2.0.tar.gz and pymol-open-source-2.3.0.tar.gz

About: PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source version.

file_dialogs.py  (pymol-open-source-2.2.0)	:	file_dialogs.py  (pymol-open-source-2.3.0)
skipping to change at line 31		skipping to change at line 31
'''		'''
if '://' not in fname:		if '://' not in fname:
parent.initialdir = os.path.dirname(fname)		parent.initialdir = os.path.dirname(fname)
parent.recent_filenames_add(fname)		parent.recent_filenames_add(fname)
format = pymol.importing.filename_to_format(fname)[2]		format = pymol.importing.filename_to_format(fname)[2]
if fname[-4:] in ['.dcd', '.dtr']:		if fname[-4:] in ['.dcd', '.dtr']:
load_traj_dialog(parent, fname)		load_traj_dialog(parent, fname)
		elif format in ('aln', 'fasta'):
		load_aln_dialog(parent, fname)
elif format == 'mae':		elif format == 'mae':
load_mae_dialog(parent, fname)		load_mae_dialog(parent, fname)
elif format == 'ccp4':		elif format == 'ccp4':
load_map_dialog(parent, fname, 'ccp4')		load_map_dialog(parent, fname, 'ccp4')
elif format == 'brix':		elif format == 'brix':
load_map_dialog(parent, fname, 'o')		load_map_dialog(parent, fname, 'o')
elif format == 'mtz':		elif format == 'mtz':
load_mtz_dialog(parent, fname)		load_mtz_dialog(parent, fname)
else:		else:
if format in ('pse', 'psw') and not ask_partial(parent, kwargs, fname):		if format in ('pse', 'psw') and not ask_partial(parent, kwargs, fname):
skipping to change at line 181		skipping to change at line 183
form.input_reso_min.value(),		form.input_reso_min.value(),
form.input_reso_max.value(),		form.input_reso_max.value(),
quiet=0)		quiet=0)
except BaseException as e:		except BaseException as e:
QtWidgets.QMessageBox.critical(parent, "Error", str(e))		QtWidgets.QMessageBox.critical(parent, "Error", str(e))
form._dialog.accepted.connect(run)		form._dialog.accepted.connect(run)
form._dialog.setModal(True)		form._dialog.setModal(True)
form._dialog.show()		form._dialog.show()
		def load_aln_dialog(parent, filename):
		_self = parent.cmd
		import numpy
		import difflib
		import pymol.seqalign as seqalign
		try:
		alignment = seqalign.aln_magic_read(filename)
		except ValueError:
		# fails for fasta files which don't contain alignments
		_self.load(filename)
		return
		# alignment record ids and PyMOL model names
		ids = [rec.id for rec in alignment]
		ids_remain = list(ids)
		models = _self.get_object_list()
		models_remain = list(models)
		mapping = {}
		N = len(ids)
		M = len(models)
		# ids -> models similarity matrix
		similarity = numpy.zeros((N, M))
		for i in range(N):
		for j in range(M):
		similarity[i, j] = difflib.SequenceMatcher(None,
		ids[i], models[j], False).ratio()
		# guess mapping
		for _ in range(min(N, M)):
		i, j = numpy.unravel_index(similarity.argmax(), similarity.shape)
		mapping[ids_remain.pop(i)] = models_remain.pop(j)
		similarity = numpy.delete(similarity, i, axis=0)
		similarity = numpy.delete(similarity, j, axis=1)
		form = parent.load_form('load_aln')
		comboboxes = {}
		# mapping GUI
		for row, rec_id in enumerate(ids, 1):
		label = QtWidgets.QLabel(rec_id, form._dialog)
		combobox = QtWidgets.QComboBox(form._dialog)
		combobox.addItem("")
		combobox.addItems(models)
		combobox.setCurrentText(mapping.get(rec_id, ""))
		form.layout_mapping.addWidget(label, row, 0)
		form.layout_mapping.addWidget(combobox, row, 1)
		comboboxes[rec_id] = combobox
		def run():
		mapping = dict((rec_id, combobox.currentText())
		for (rec_id, combobox) in comboboxes.items())
		seqalign.load_aln_multi(filename, mapping=mapping, _self=_self)
		form._dialog.close()
		# hook up events
		form.button_ok.clicked.connect(run)
		form.button_cancel.clicked.connect(form._dialog.close)
		form._dialog.setModal(True)
		form._dialog.show()
def load_mae_dialog(parent, filename):		def load_mae_dialog(parent, filename):
form = parent.load_form('load_mae')		form = parent.load_form('load_mae')
form.input_object_name.setPlaceholderText(		form.input_object_name.setPlaceholderText(
pymol.importing.filename_to_objectname(filename))		pymol.importing.filename_to_objectname(filename))
form.input_object_props.setText(parent.cmd.get('load_object_props_default') or '*')		form.input_object_props.setText(parent.cmd.get('load_object_props_default') or '*')
form.input_atom_props.setText(parent.cmd.get('load_atom_props_default') or ' *')		form.input_atom_props.setText(parent.cmd.get('load_atom_props_default') or ' *')
def get_command(*args):		def get_command(*args):
command = ('load \\\n %s' % (filename))		command = ('load \\\n %s' % (filename))
name = form.input_object_name.text()		name = form.input_object_name.text()
if name:		if name:
command += ', \\\n ' + name		command += ', \\\n ' + name
command += ', \\\n mimic=' + ('1' if form.input_mimic.isChecked() els e '0')		command += ', \\\n mimic=' + ('1' if form.input_mimic.isChecked() els e '0')
command += (		command += (
', \\\n object_props=%s'		', \\\n object_props=%s'
', \\\n atom_props=%s' % (		', \\\n atom_props=%s' % (
form.input_object_props.text(),		form.input_object_props.text(),
form.input_atom_props.text()))		form.input_atom_props.text()))
		multiplex = [-2, 0, 1][form.input_multiplex.currentIndex()]
		if multiplex != -2:
		command += ', \\\n multiplex={}'.format(multiplex)
return command		return command
def update_output_command(*args):		def update_output_command(*args):
form.output_command.setText(get_command())		form.output_command.setText(get_command())
def run():		def run():
parent.cmd.do(get_command())		parent.cmd.do(get_command())
form._dialog.close()		form._dialog.close()
# hook up events		# hook up events
		form.input_multiplex.currentIndexChanged.connect(update_output_command)
form.input_mimic.stateChanged.connect(update_output_command)		form.input_mimic.stateChanged.connect(update_output_command)
form.input_object_name.textChanged.connect(update_output_command)		form.input_object_name.textChanged.connect(update_output_command)
form.input_object_props.textChanged.connect(update_output_command)		form.input_object_props.textChanged.connect(update_output_command)
form.input_atom_props.textChanged.connect(update_output_command)		form.input_atom_props.textChanged.connect(update_output_command)
form.button_ok.clicked.connect(run)		form.button_ok.clicked.connect(run)
update_output_command()		update_output_command()
form._dialog.setModal(True)		form._dialog.setModal(True)
form._dialog.show()		form._dialog.show()
skipping to change at line 427		skipping to change at line 498
formats = [		formats = [
'PDBx/mmCIF (*.cif *.cif.gz)',		'PDBx/mmCIF (*.cif *.cif.gz)',
'PDB (*.pdb *.pdb.gz)',		'PDB (*.pdb *.pdb.gz)',
'PQR (*.pqr)',		'PQR (*.pqr)',
'MOL2 (*.mol2)',		'MOL2 (*.mol2)',
'MDL SD (*.sdf *.mol)',		'MDL SD (*.sdf *.mol)',
'Maestro (*.mae)',		'Maestro (*.mae)',
'MacroModel (*.mmd *.mmod *.dat)',		'MacroModel (*.mmd *.mmod *.dat)',
'ChemPy Pickle (*.pkl)',		'ChemPy Pickle (*.pkl)',
'XYZ (*.xyz)',		'XYZ (*.xyz)',
		'MMTF (*.mmtf)',
'By Extension (*.*)',		'By Extension (*.*)',
]		]
@PopupOnException.decorator		@PopupOnException.decorator
def run(*_):		def run(*_):
selection = form.input_selection.currentText() or default_selection		selection = form.input_selection.currentText() or default_selection
state = int(form.input_state.currentText().split()[0])		state = int(form.input_state.currentText().split()[0])
parent.cmd.set('pdb_conect_nodup', not form.input_no_pdb_conect_nodup .isChecked())		parent.cmd.set('pdb_conect_nodup', not form.input_no_pdb_conect_nodup .isChecked())
parent.cmd.set('pdb_conect_all', form.input_pdb_conect_all.isCh ecked())		parent.cmd.set('pdb_conect_all', form.input_pdb_conect_all.isCh ecked())
End of changes. 5 change blocks.
0 lines changed or deleted		72 lines changed or added

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