def compute(self):
tmp_dir = self.tmp_dir
if not self.read_only:
pdb_object = self.pdb.clone()
else:
pdb_object = self.pdb # in general, we should not be modifying the structure in this class
input_filepath = write_temp_file(tmp_dir, pdb_object.get_content(), ftype = 'w', prefix = 'dssp_')
output_filepath = write_temp_file(tmp_dir, '', ftype = 'w', prefix = 'dssp_')
try:
p = _Popen('.', shlex.split('mkdssp -i {input_filepath} -o {output_filepath}'.format(**locals())))
if p.errorcode:
if p.stderr.find('empty protein, or no valid complete residues') != -1:
raise MissingAtomException(p.stdout)
else:
raise Exception('An error occurred while calling DSSP:\n%s' % p.stderr)
self.dssp_output = read_file(output_filepath)
self.dssp = self.parse_output()
except MissingAtomException as e:
os.remove(input_filepath)
os.remove(output_filepath)
raise
except Exception as e:
os.remove(input_filepath)
os.remove(output_filepath)
raise colortext.Exception('%s\n%s' % (str(e), traceback.format_exc()))
os.remove(input_filepath)
os.remove(output_filepath)
def compute(self, chain_id):
tmp_dir = self.tmp_dir
pdb_object = self.pdb.clone() # we are immediately modifying the PDB file by stripping chains so we need to make a copy
pdb_object.strip_to_chains(chain_id)
input_filepath = write_temp_file(tmp_dir, pdb_object.get_content(), ftype = 'w', prefix = 'dssp_')
output_filepath = write_temp_file(tmp_dir, '', ftype = 'w', prefix = 'dssp_')
try:
p = _Popen('.', shlex.split('mkdssp -i {input_filepath} -o {output_filepath}'.format(**locals())))
if p.errorcode:
if p.stderr.find('empty protein, or no valid complete residues') != -1:
raise MissingAtomException(p.stdout)
else:
raise Exception('An error occurred while calling DSSP:\n%s' % p.stderr)
self.dssp_output[chain_id] = read_file(output_filepath)
self.dssp[chain_id] = self.parse_output(chain_id)
except MissingAtomException as e:
os.remove(input_filepath)
os.remove(output_filepath)
raise
except Exception as e:
os.remove(input_filepath)
os.remove(output_filepath)
raise colortext.Exception('%s\n%s' % (str(e), traceback.format_exc()))
os.remove(input_filepath)
os.remove(output_filepath)
def _runRScript(r_script_filename, cwd = '.', remove_output = True):
# Reset to new current working directory
tmp_dir = False
if cwd == None:
tmp_dir = True
cwd = tempfile.mkdtemp( prefix = '%s-%s-%s_' % (time.strftime("%y%m%d"), getpass.getuser(), 'plot-working-dir') )
rscriptname = write_temp_file(cwd, r_script_filename)
p = subprocess.Popen(["R", "CMD", "BATCH", rscriptname], cwd = cwd)
while True:
time.sleep(0.3)
errcode = p.poll()
if errcode != None:
break
rout = "%s.Rout" % rscriptname
os.remove(rscriptname)
rout_contents = None
if os.path.exists(rout):
rout_contents = read_file(rout)
os.remove(rout)
if errcode != 0:
print(rout_contents )
raise Exception("The R script failed with error code %d." % errcode)
if tmp_dir and remove_output:
shutil.rmtree(cwd)
return rout_contents
def get_pdb_contents_to_pose_residue_map(pdb_file_contents, rosetta_scripts_path, rosetta_database_path = None, pdb_id = None, extra_flags = ''):
'''Takes a string containing a PDB file, the RosettaScripts executable, and the Rosetta database and then uses the features database to map PDB residue IDs to pose residue IDs.
On success, (True, the residue mapping) is returned. On failure, (False, a list of errors) is returned.
Note: extra_flags should typically include '-ignore_zero_occupancy false' and '-ignore_unrecognized_res'.'''
filename = write_temp_file("/tmp", pdb_file_contents)
success, mapping = get_pdb_to_pose_residue_map(filename, rosetta_scripts_path, rosetta_database_path = rosetta_database_path, pdb_id = pdb_id, extra_flags = extra_flags)
os.remove(filename)
return success, mapping
def create_csv(analysis_table):
contents = '\n'.join(['DatasetID,Experimental,Predicted'] + ['%s,%s,%s' % (str(l['DatasetID']), str(l['Experimental']), str(l['Predicted'])) for l in analysis_table])
return write_temp_file('.', contents)
errors.append('No input files were specified.')
else:
for batch_file_selector in args:
if '*' in batch_file_selector or '?' in batch_file_selector:
batch_files += map(os.path.abspath, glob.glob(batch_file_selector))
elif os.path.isdir(batch_file_selector):
for input_file_wildcard in input_file_wildcards:
batch_files += map(os.path.abspath, glob.glob(os.path.join(batch_file_selector, input_file_wildcard)))
elif not os.path.exists(batch_file_selector):
if len(batch_file_selector) == 4 and batch_file_selector.isalnum():
batch_file_selector = batch_file_selector.lower() # the files are named in lowercase on the cluster
if not os.path.exists('/netapp/database'):
# This script is not being run on the cluster - try to retrieve the file from the RCSB
colortext.message('No file %s exists - assuming that this is a PDB ID and trying to retrieve the associated file from the RCSB.' % batch_file_selector)
try:
fname = write_temp_file('/tmp', retrieve_pdb(batch_file_selector), suffix = '.pdb', prefix = batch_file_selector)
batch_files.append(os.path.abspath(fname))
temp_files.append(os.path.abspath(fname))
except:
errors.append('An error occurred retrieving the PDB file "%s".' % batch_file_selector)
else:
# We are on the cluster so try to retrieve the stored file
colortext.message('No file %s exists - assuming that this is a PDB ID and trying to retrieve the associated file from the cluster mirror of the PDB database.' % batch_file_selector)
if os.path.exists('/netapp/database/pdb/remediated/uncompressed_files/pdb%s.ent' % batch_file_selector):
batch_files.append('/netapp/database/pdb/remediated/uncompressed_files/pdb%s.ent' % batch_file_selector)
elif os.path.exists('/netapp/database/pdb/pre-remediated/uncompressed_files/pdb%s.ent' % batch_file_selector):
batch_files.append('/netapp/database/pdb/pre-remediated/uncompressed_files/pdb%s.ent' % batch_file_selector)
else:
errors.append('Could not find a PDB file for argument "%s".' % batch_file_selector)
missing_files.append(batch_file_selector)
else: