def run(self):
file_traf = self.file_TRAF
file_seq = self.file_SEQ
self.setup_job()
if self.reference_pdb:
self.parse_reference(self.reference_pdb)
with_cabs = None in (file_traf, file_seq)
if with_cabs:
self.setup_cabs_run()
self.execute_cabs_run()
if self.save_cabs_files:
self.save_cabs_res()
self.load_output(file_traf, file_seq)
self.score_results(n_filtered=self.filtering_count,
number_of_medoids=self.clustering_medoids,
number_of_iterations=self.clustering_iterations)
self.save_models()
if self.reference_pdb:
try:
self.calculate_rmsd()
except (ValueError, AlignError) as e:
logger.critical(module_name=_name, msg=e.message)
self.save_config_file()
self.draw_plots(colors=self.colors)
if self.load_cabs_files:
for _file in _CABS_files:
os.remove(os.path.join(self.work_dir, _file))
logger.info(module_name=_name, msg='Simulation completed successfully')
def run(cabs_cmd, cmd_line=sys.argv[1:]):
if cabs_cmd not in ['dock', 'flex']:
raise IndexError
module_name = 'CABS' + cabs_cmd
parser = getattr(optparser, cabs_cmd + '_parser')
pre_parser = argparse.ArgumentParser(add_help=False)
pre_parser.add_argument('-c', '--config')
pre_parser.add_argument('--version', action='store_true')
pre_parser.add_argument('-h', '--help', action='store_true')
pre_args, remains = pre_parser.parse_known_args(cmd_line)
if pre_args.help:
_help = parser.format_help()
print re.sub('\n( *)\n( *)\n', '\n\n', _help)
sys.exit(0)
elif pre_args.version:
print __version__
sys.exit(0)
elif pre_args.config:
remains = optparser.ConfigFileParser(pre_args.config).args + remains
config = vars(parser.parse_args(remains))
import CABS.job
task = getattr(CABS.job, cabs_cmd.title() + 'Task')
job = task(**config)
try:
job.run()
except KeyboardInterrupt:
logger.critical(module_name, 'Interrupted by user.')
except Exception as e:
logger.exit_program(module_name,
'Error occurred',
traceback=_tr.format_exc(),
exc=e)
finally:
logger.close_log()
for _file in _JUNK:
rmtree(_file, ignore_errors=True)
def build_exe(params,
src,
exe='cabs',
build_command=FORTRAN_COMMAND,
destination='.'):
with open(src) as f:
lines = f.read()
names = ['NDIM', 'NREPS', 'NMOLS', 'MAXRES']
for name, value in zip(names, params):
lines = re.sub(name + '=\d+', name + '=%i' % value, lines)
run_cmd = join(destination, exe)
cmd = build_command.split() + ['-o', run_cmd, '-x', 'f77', '-']
try:
out, err = Popen(cmd, stdin=PIPE, stderr=PIPE).communicate(lines)
if err:
raise Exception(err)
except Exception as e:
logger.critical(_name, msg=e.message)
return run_cmd
def load_cabs_results(self):
if not os.path.exists(self.load_cabs_files):
logger.exit_program(
module_name=_name,
msg="Provided CABS files path does not exist (%s)" %
self.load_cabs_files,
traceback=False)
try:
files = glob.glob(os.path.join(self.load_cabs_files, "*.cbs"))
if len(files) > 1:
logger.critical(
module_name=_name,
msg="More than one .cbs file in provided directory %s " %
" \n".join(files))
logger.exit_program(
module_name=_name,
msg="Please re-run with --load-cabs-files <filename> "
"or remove the files you do not need. Quiting.",
traceback=False)
elif len(files) == 1:
logger.info(module_name=_name,
msg="Loading CABS files from %s" % files[0])
with tarfile.open(files[0], "r:gz") as f:
f.extractall(os.path.join(self.work_dir))
else:
raise IOError
except IOError:
files_loc = self.load_cabs_files
try:
with tarfile.open(files_loc, "r:gz") as f:
logger.info(module_name=_name,
msg="Loading CABS files from %s" % files_loc)
f.extractall(os.path.join(self.work_dir))
except IOError:
raise
return
def dssp(self, output=''):
"""Runs dssp on the read pdb file and returns a dictionary with secondary structure"""
out = err = None
try:
proc = Popen([self.DSSP_COMMAND, '/dev/stdin'], stdin=PIPE, stdout=PIPE, stderr=PIPE)
out, err = proc.communicate(input=self.body)
logger.debug(
module_name=_name,
msg='Running DSSP'
)
except OSError:
logger.warning(
module_name=_name,
msg='DSSP not found.'
)
tempfile = mkstemp(suffix='.pdb', prefix='.tmp.dssp.', dir=PDB_CACHE)[1]
with open(tempfile, 'wb') as f:
f.write(self.body)
try:
logger.debug(
module_name=_name,
msg='Submitting structure to the DSSP server'
)
out, err = self.xssp(tempfile)
except (HTTPError, ConnectionError):
logger.warning(
module_name=_name,
msg='Cannot connect to the DSSP server. DSSP was not ran at all.'
)
return None
finally:
try:
os.remove(tempfile)
except OSError:
pass
if err:
logger.critical(
module_name=_name,
msg='DSSP ERROR: %s' % err.replace('\n', ' ')
)
return None
else:
logger.debug(_name, 'DSSP successful')
if logger.log_files() and output:
output = os.path.join(output, 'output_data', 'DSSP_output_%s.txt' % self.name)
d = os.path.dirname(output)
if not isdir(d):
os.makedirs(d)
logger.to_file(
filename=output,
content=out,
msg='Saving DSSP output to %s' % output
)
sec = OrderedDict()
p = '^([0-9 ]{5}) ([0-9 ]{4}.)([A-Z ]) ([A-Z]) ([HBEGITS ])(.*)$'
for line in out.split('\n'):
m = re.match(p, line)
if m:
key = str(m.group(2).strip() + ':' + m.group(3))
if m.group(5) in 'HGI':
val = 'H'
elif m.group(5) in 'BE':
val = 'E'
elif m.group(5) in 'T':
val = 'T'
else:
val = 'C'
sec[key] = val
return sec