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 __init__(self, p, cut_off = 0.25, acc_array = 'Miller', tmp_dir = '/tmp', read_only = False):
'''This function strips a PDB file to one chain and then runs DSSP on this new file.
p should be a PDB object (see pdb.py).
'''
try:
_Popen('.', shlex.split('mkdssp --version'))
except:
raise colortext.Exception('mkdssp does not seem to be installed in a location declared in the environment path.')
self.cut_off = cut_off
self.tmp_dir = tmp_dir
self.residue_max_acc = residue_max_acc[acc_array]
self.read_only = read_only
if not self.read_only:
self.pdb = p.clone() # make a local copy in case this gets modified externally
else:
self.pdb = p
self.chain_order = self.pdb.atom_chain_order
self.dssp_output = None
self.dssp = {}
self.compute()
self.chain_order = [c for c in self.chain_order if c in self.dssp]
self.dsspb = NestedBunch(self.dssp)
