def __on_process_error(self, error):
Logs.warning('Error in nanobabel process:')
Logs.warning(error)
def _on_complex_updated(cls, index, new_complex):
callbacks = _PluginInstance.__complex_updated_callbacks
try:
callbacks[index](new_complex)
except KeyError:
Logs.warning('Received an unknown updated complex index:', index)
def on_advanced_settings(self):
"""
| Called when user presses "Advanced Settings"
"""
Logs.warning('Callback on_advanced_settings not defined. Ignoring')
def _parse_lines(lines):
lines = [line.rstrip() for line in lines]
content = Content()
chain_idx = 0
chain_offset = 0
model_number = 0
model_done = False
line_counter = 0
total_lines = len(lines)
while (line_counter < total_lines):
line = lines[line_counter]
try:
record_type = record_chunk_string(line, 1, 6)
if record_type == "MODEL":
chain_idx = 0
chain_offset = 0
model_number += 1
model_done = False
if not model_done:
rec = None
if record_type == "TER":
ter = record_ter(line, line_counter)
content.records.append(ter)
content.ters.append(ter)
chain_idx += 1
chain_offset = 0
if record_type == "ATOM":
rec = record_atom(line, line_counter)
if record_type == "HETATM":
rec = record_het_atom(line, line_counter)
if not rec == None:
if len(rec.chain_identifier) <= 0:
if rec.residue_serial_number < chain_offset:
chain_idx += 1
chain_offset = 0
elif rec.residue_serial_number >= chain_offset:
chain_offset = rec.residue_serial_number
rec.chain_identifier = str(chain_idx)
model_number = max(model_number, 1)
rec.model_number = model_number
if (not rec.residue_name == "SOL"):
content.records.append(rec)
content.atoms.append(rec)
if (record_type == "COMPND"):
try:
rec = record_compnd(line, line_counter)
content.records.append(rec)
content.compnds.append(rec)
except:
Logs.warning("Error parsing COMPND:",
traceback.format_exc())
if (record_type == "REMARK"):
rec = record_remark(line, line_counter)
content.records.append(rec)
if (rec.num in content._remarks):
content._remarks[
rec.num] = content._remarks[rec.num] + "\n" + rec.text
else:
content._remarks[rec.num] = rec.text
if record_type == "CRYST":
line = "REMARK " + line
rec = record_cryst(line, line_counter)
content.records.append(rec)
content.crysts.append(rec)
if record_type == "ORIGX":
line = "REMARK " + line
rec = record_origx(line, line_counter)
content.records.append(rec)
content.origxs.append(rec)
if record_type == "SCALE":
line = "REMARK " + line
rec = record_scale(line, line_counter)
content.records.append(rec)
content.scales.append(rec)
if record_type == "MTRIX":
rec = record_mtrix(line, line_counter)
content.records.append(rec)
content.mtrixs.append(rec)
if record_type == "HELIX":
rec = record_helix(line, line_counter)
content.records.append(rec)
content.helixs.append(rec)
if record_type == "SHEET":
rec = record_sheet(line, line_counter)
content.records.append(rec)
content.sheets.append(rec)
if record_type == "ENDMDL":
model_done = True
content.raw.append(line)
except:
print("LINE: " + str(line_counter))
print("PDB Parsing error")
raise
line_counter += 1
content.model_count = model_number
return content
def menu(self):
if not self.__set_first:
self.__set_first = True
Logs.warning("The default menu (self.menu) is now deprecated and will be removed in a future version. Please use the ui.Menu() constructor to create the menu.")
return self.__menu
def on_run(self):
"""
| Called when user presses "Run"
"""
Logs.warning('Callback on_run not defined. Ignoring')
def __on_error(self, msg):
Logs.warning("[DSSP]", msg)
def __on_error(self, msg):
if not "molecule converted" in msg:
Logs.warning("[Bond Generation]", msg)
def do_POST(self):
try:
parsed_url = urlparse(self.path)
path = parsed_url.path
path = urllib.parse.unquote(path)
content_len = int(self.headers.get('Content-Length'))
data = self.rfile.read(content_len)
except:
Logs.warning("Error trying to parse request:\n",
traceback.format_exc())
self._send_json_error(400, "Parsing problem")
return
if not path.startswith('/files'):
self._send_json_error(403, "Forbidden")
return
folder = os.path.join(FILES_DIR, path[7:])
# no files provided, create folders
if not content_len:
if os.path.exists(folder):
self._send_json_error(400, "Name already exists")
else:
os.makedirs(folder)
self._send_json_success()
return
data_manager = DataManager()
data_manager.data = data
data_manager.find_boundary()
done = False
while not done:
RequestHandler.read_header(data_manager)
RequestHandler.read_data(data_manager)
done = RequestHandler.check_EOF(data_manager)
file_name = data_manager.file_name
file_body = data_manager.body
if file_name == "":
continue
# If file is not supported
if not WebLoaderServer.file_filter(file_name):
self._send_json_error(400, file_name + " format not supported")
return
subfolder = os.path.join(folder, os.path.dirname(file_name))
if not os.path.exists(subfolder):
os.makedirs(subfolder)
file_path = os.path.join(folder, file_name)
# rename on duplicates: file.txt -> file (n).txt
reg = r'(.+/)([^/]+?)(?: \((\d+)\))?(\.\w+)'
(path, name, copy, ext) = re.search(reg, file_path).groups()
copy = 1 if copy is None else int(copy)
while os.path.isfile(file_path):
copy += 1
file_path = '%s%s (%d)%s' % (path, name, copy, ext)
# Create file
with open(file_path, "wb") as f:
f.write(file_body)
self._send_json_success()
def _write(self, message):
try:
self.wfile.write(message)
except:
Logs.warning("Connection reset while responding",
self.client_address)
async def start_process(self, workspace, ff, steps, steepest):
if sum(1 for _ in workspace.complexes) == 0:
Logs.message('No structures to minimize')
return
input_file = tempfile.NamedTemporaryFile(delete=False,
suffix='.sdf',
dir=self.temp_dir.name)
constraints_file = tempfile.NamedTemporaryFile(delete=False,
suffix='.txt',
dir=self.temp_dir.name)
output_file = tempfile.NamedTemporaryFile(delete=False,
suffix='.pdb',
dir=self.temp_dir.name)
self.__output_lines = []
self.__updates_done = {}
self.__packet_id = 0
(saved_atoms, indices) = self.__save__atoms(input_file.name, workspace)
Logs.debug("Wrote input file:", input_file.name)
self.__save__constraints(constraints_file.name, saved_atoms)
Logs.debug("Wrote constraints file:", constraints_file.name)
self.__stream, error = await self.__plugin.create_writing_stream(
indices, StreamType.position)
if error == StreamCreationError.AtomNotFound:
# User deleted atom in time between start_process() and create_writing_stream().
# so lets update the workspace and try again
Logs.warning(
f"User deleted atoms while setting up process, retrying")
updated_workspace = await self.__plugin.request_workspace()
await self.start_process(updated_workspace, ff, steps, steepest)
return
elif error != StreamCreationError.NoError:
Logs.error(f"Error while creating stream: {error}")
return
self.__data_queue = deque()
cwd_path = self.__nanobabel_dir
exe = 'nanobabel.exe' if IS_WIN else 'nanobabel'
exe_path = os.path.join(cwd_path, exe)
args = [
'minimize', '-h', '-l', '20', '-n',
str(steps), '-ff', ff, '-i', input_file.name, '-cx',
constraints_file.name, '-o', output_file.name
]
if IS_WIN:
args += ['-dd', 'data']
if steepest:
args.append('-sd')
Logs.debug(args)
p = Process(exe_path, args, True)
p.on_error = self.__on_process_error
p.on_output = self.__on_process_output
p.on_done = self.__on_process_done
self.calculation_start_time = time.time()
log_data = {
'exe_path': exe_path,
'force_field': ff,
'steps': steps,
'steepest': steepest
}
Logs.message("Starting Minimization Process", extra=log_data)
p.start()
self.__process = p
self.__process_running = True
self.is_running = True