def file_fetch_pdb(parent):
form = parent.load_form('fetch')
form.input_assembly.setEditText(parent.cmd.get('assembly'))
def get_command(*args):
code = form.input_code.text()
if len(code) != 4:
return ''
def get_name(w):
name = w.text()
if name:
return ', ' + name
return ''
if form.input_check_pdb.isChecked():
command = 'set assembly, "%s"\nfetch %s%s%s' % (
form.input_assembly.currentText(), code,
form.input_chain.currentText(), get_name(form.input_name))
else:
command = ''
if form.input_check_2fofc.isChecked():
command += '\nfetch %s%s, type=2fofc' % (
code, get_name(form.input_name_2fofc))
if form.input_check_fofc.isChecked():
command += '\nfetch %s%s, type=fofc' % (
code, get_name(form.input_name_fofc))
return command
def update_output_command(*args):
form.output_command.setText(get_command())
def code_changed(code):
for combo in [form.input_assembly, form.input_chain]:
if combo.count() != 1:
text = combo.currentText()
combo.clear()
combo.addItem('')
combo.setEditText(text)
if len(code) == 4:
update_assemblies(code)
update_chains(code)
update_output_command()
def run():
if len(form.input_code.text()) != 4:
QtWidgets.QMessageBox.warning(parent, "Error",
"Need 4 letter PDB code")
return
parent.cmd.do(get_command())
form._dialog.close()
# async events
update_assemblies = AsyncFunc(_get_assemblies,
form.input_assembly.addItems)
update_chains = AsyncFunc(_get_chains, form.input_chain.addItems)
# hook up events
form.input_code.textChanged.connect(code_changed)
form.input_chain.editTextChanged.connect(update_output_command)
form.input_assembly.editTextChanged.connect(update_output_command)
form.input_name.textChanged.connect(update_output_command)
form.input_name_2fofc.textChanged.connect(update_output_command)
form.input_name_fofc.textChanged.connect(update_output_command)
form.input_check_pdb.stateChanged.connect(update_output_command)
form.input_check_2fofc.stateChanged.connect(update_output_command)
form.input_check_fofc.stateChanged.connect(update_output_command)
form.button_ok.clicked.connect(run)
update_output_command()
form._dialog.show()
def dialog(_self=None):
if _self is None:
from pymol import cmd as _self
dialog = QtWidgets.QDialog()
uifile = os.path.join(os.path.dirname(__file__), 'apbs.ui')
form = loadUi(uifile, dialog)
form._dialog = dialog
form._proclist = []
def set_apbs_in(contents):
form.apbs_template.setPlainText(contents.strip())
# hide options widgets
form.optarea_prep.setVisible(False)
form.optarea_apbs.setVisible(False)
form.optarea_surf.setVisible(False)
form.optarea_other.setVisible(False)
# pre-fill form with likely data
names = _self.get_object_list()
names += ['(' + n + ')' for n in _self.get_names('public_selections')]
if names:
form.input_sele.clear()
form.input_sele.addItems([
('polymer & ' +
name) if _self.count_atoms('polymer & ' + name) > 0 else name
for name in names
])
form.surf_map.addItems(_self.get_names_of_type('object:map'))
set_apbs_in(electrostatics.template_apbs_in)
# executables
from distutils.spawn import find_executable
form.apbs_exe.setText(electrostatics.find_apbs_exe() or 'apbs')
form.pdb2pqr_exe.setText(
find_executable('pdb2pqr') or
# acellera::htmd-pdb2pqr provides pdb2pqr_cli
find_executable('pdb2pqr_cli') or find_executable(
'share/pdb2pqr/pdb2pqr.py', os.getenv('FREEMOL', '/usr'))
or 'pdb2pqr')
# for async panels
form._callInMainThread = MainThreadCaller()
run_impl_async = AsyncFunc(run_impl)
# "Run" button callback
def run():
form.tabWidget.setEnabled(False)
form.button_ok.clicked.disconnect()
form.button_ok.clicked.connect(abort)
form.button_ok.setText('Abort')
form._capture = StdOutCapture()
# detach from main thread
run_impl_async(form, _self)
# "Run" button "finally" actions (main thread)
@run_impl_async.finished.connect
def run_finally(args):
_, exception = args
form._proclist[:] = []
stdout = form._capture.release()
print(stdout)
form.button_ok.setText('Run')
form.button_ok.clicked.disconnect()
form.button_ok.clicked.connect(run)
form.button_ok.setEnabled(True)
form.tabWidget.setEnabled(True)
if exception is not None:
handle_exception(exception, stdout)
return
quit_msg = "Finished with Success. Close the APBS dialog?"
if QMessageBox.Yes == QMessageBox.question(form._dialog, 'Finished',
quit_msg, QMessageBox.Yes,
QMessageBox.No):
form._dialog.close()
def handle_exception(e, stdout):
if isinstance(e, SilentAbort):
return
msg = str(e) or 'unknown error'
msgbox = QMessageBox(QMessageBox.Critical, 'Error', msg,
QMessageBox.Close, form._dialog)
if stdout.strip():
msgbox.setDetailedText(stdout)
msgbox.exec_()
# "Abort" button callback
def abort():
form.button_ok.setEnabled(False)
while form._proclist:
p = form._proclist.pop()
try:
p.terminate()
p.returncode = -15 # SIGTERM
except OSError as e:
print(e)
# selection checker
check_sele_timer = QtCore.QTimer()
check_sele_timer.setSingleShot(True)
# grid auto-value
form.apbs_grid_userchanged = False
form.apbs_grid.setStyleSheet('background: #ff6')
@form.apbs_grid.editingFinished.connect
def _():
form.apbs_grid_userchanged = True
form.apbs_grid.setStyleSheet('')
@check_sele_timer.timeout.connect
def _():
has_props = ['no', 'no']
def callback(partial_charge, elec_radius):
if partial_charge: has_props[0] = 'YES'
if elec_radius > 0: has_props[1] = 'YES'
n = _self.iterate(form.input_sele.currentText(),
'callback(partial_charge, elec_radius)',
space={'callback': callback})
# grid auto-value (keep map size in the order of 200x200x200)
if n > 1 and not form.apbs_grid_userchanged:
e = _self.get_extent(form.input_sele.currentText())
volume = (e[1][0] - e[0][0]) * (e[1][1] - e[0][1]) * (e[1][2] -
e[0][2])
grid = max(0.5, volume**0.333 / 200.0)
form.apbs_grid.setValue(grid)
if n < 1:
label = 'Selection is invalid'
color = '#f66'
elif has_props == ['YES', 'YES']:
label = 'No preparation necessary, selection has charges and radii'
form.do_prepare.setChecked(False)
color = '#6f6'
else:
label = 'Selection needs preparation (partial_charge: %s, elec_radius: %s)' % tuple(
has_props)
form.do_prepare.setChecked(True)
color = '#fc6'
form.label_sele_has.setText(label)
form.label_sele_has.setStyleSheet('background: %s; padding: 5' % color)
check_sele_timer.start(0)
@form.apbs_exe_browse.clicked.connect
def _():
fnames = getOpenFileNames(None,
filter='apbs (apbs*);;All Files (*)')[0]
if fnames:
form.apbs_exe.setText(fnames[0])
@form.pdb2pqr_exe_browse.clicked.connect
def _():
fnames = getOpenFileNames(
None, filter='pdb2pqr (pdb2pqr*);;All Files (*)')[0]
if fnames:
form.pdb2pqr_exe.setText(fnames[0])
# hook up events
form.input_sele.currentIndexChanged.connect(
lambda: check_sele_timer.start(0))
form.input_sele.editTextChanged.connect(
lambda: check_sele_timer.start(1000))
form.button_ok.clicked.connect(run)
# "Register" opens a web browser
@form.button_register.clicked.connect
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)