def one_file(self, pdbinfo):
"""
updates self.data[besename of file_path] withe the pdb_info object
on verbose print the data with more info form the pdb itselef
:param file_path:
:param dir_path:
:return:
"""
_caller = self.__class__.__name__
_pdb = pdbinfo._pdb
_is_verbose = self.is_verbose
if pdbinfo.output_type == 'json':
self.is_verbose = False
self.verbose('')
self.verbose('+---------------------------------------------------')
self.verbose('| {}'.format(os.path.basename(_pdb.file_name)))
self.verbose('+---------------------------------------------------')
self.is_verbose = _is_verbose
try:
if _pdb.has_caveats():
self.cliutils.warn_msg("file:{} - has caveats lines!!!",
caller=_caller)
self.data[os.path.basename(_pdb.file_name)] = pdbinfo
table_data = [["model No", "chain id", "residues", "atoms"]]
for i, model in enumerate(_pdb, 1):
# self.verbose("\t\tmodel No. {}:".format(model.model_number))
for chain in model:
try:
table_data.append(
[model.model_number, None, None, None])
table_data[-1][1] = chain.chain_id
chaiutils = chain_utils(chain)
residues_list = chaiutils.chain2residues_list()
resnames_list = list(
map(lambda r: r.resname, residues_list))
# self.verbose("\t\t\tchains info:{:>2} number of residues: {}".format(chain.chain_id,
# len(resnames_list)))
table_data[-1][2] = len(resnames_list)
table_data[-1][3] = len(chain)
except Exception as e:
msg = "file:{} - model {} - chain {} - {}"
self.cliutils.error_msg(msg.format(
_pdb.file_name, model.model_number, chain.chain_id,
e),
caller=_caller)
self.errors[_pdb.file_name] = e
self.verbose(pdbinfo.info_report(models_table_data=table_data))
except Exception as e:
self.cliutils.error_msg("file:{} - {}".format(_pdb.file_name, e),
caller=_caller)
self.errors[_pdb.file_name] = e
return 1
def remove_atoms_from_every_chain(cls, atoms_to_remove, _pdb):
"""
TODO documentation
:param atoms_to_remove: [(resname, resseq,atom_name)]
:param _pdb:
:return:
"""
for mi, model in enumerate(_pdb):
for ci, chain in enumerate(model):
chainuils = chain_utils(chain)
_pdb[mi][ci] = chainuils.remove_atoms_by_atom_resseq_and_name(atoms_to_remove)
return _pdb
def remove_residues_from_every_chain(cls, missing_residues_per_chain_id, _pdb):
"""
TODO documentation
:param missing_residues_per_chain_id:
:param _pdb:
:return:
"""
missing_residues = []
for chain_id, mis_res_list in missing_residues_per_chain_id.items():
missing_residues.extend(mis_res_list)
for mi, model in enumerate(_pdb):
for ci, chain in enumerate(model):
chainuils = chain_utils(chain)
_pdb[mi][ci] = chainuils.remove_residues_by_resseqs(missing_residues)
return _pdb
def sieve(self, pdb, fix_atoms_serial_number=False):
_pdb = pdb
atoms_to_remove = []
for mi, model in enumerate(_pdb):
for ci, chain in enumerate(model):
for ai, atom in enumerate(chain):
for prefix_name in self.atom_names:
if self.is_match(atom, prefix_name):
atoms_to_remove.append(ai)
for ai in reversed(atoms_to_remove):
del _pdb[mi][ci][ai]
atoms_to_remove = []
if fix_atoms_serial_number:
chinnutils = chain_utils(chain)
chinnutils.fix_atoms_serial_number()
_pdb[mi][ci] = chinnutils.chain
return _pdb
def __init__(self, chain_a, chain_b):
self.residues_list_a = chain_utils(chain_a).chain2residues_list()
self.residues_list_b = chain_utils(chain_b).chain2residues_list()
self.df = None