def __init__(self,
ident,
description=None,
is_experimental=False,
structure_path=None,
file_type=None):
StructProp.__init__(self,
ident=ident,
description=description,
chains=None,
mapped_chains=None,
is_experimental=is_experimental,
structure_path=structure_path,
file_type=file_type)
self.subunits = None
"""dict: Subunit composition defined as ``{chain_id: number_of_times_used_in_bioassembly}``"""
def __init__(self,
ident,
description=None,
chains=None,
mapped_chains=None,
structure_path=None,
file_type=None):
StructProp.__init__(self,
ident,
description=description,
chains=chains,
mapped_chains=mapped_chains,
is_experimental=True,
structure_path=structure_path,
file_type=file_type)
self.experimental_method = None
self.resolution = None
self.date = None
self.taxonomy_name = None
def __init__(self,
ident,
description=None,
chains=None,
mapped_chains=None,
structure_path=None,
file_type=None):
StructProp.__init__(self,
ident,
description=description,
chains=chains,
mapped_chains=mapped_chains,
is_experimental=True,
structure_path=structure_path,
file_type=file_type)
self.experimental_method = None
self.resolution = None
self.date = None
self.taxonomy_name = None
self.biological_assemblies = DictList()
"""DictList: A list for storing Bioassembly objects related to this PDB ID"""
def __init__(self, ident, original_results_path, coach_results_folder='model1/coach', model_to_use='model1'):
if not op.exists(original_results_path):
raise OSError('{}: folder does not exist'.format(original_results_path))
StructProp.__init__(self, ident, is_experimental=False)
self._attrs_to_copy = []
self.original_results_path = original_results_path
self.model_to_use = model_to_use
### MODEL
self.model_date = None
original_model_path = op.join(original_results_path, '{}.pdb'.format(model_to_use))
if not op.exists(original_model_path):
raise IOError('{}: no homology model generated'.format(original_model_path))
else:
self.load_structure_path(structure_path=original_model_path, file_type='pdb')
### MODELING RESULTS
self.difficulty = None
self.top_template_pdb = None
self.top_template_chain = None
# Parse init.dat
self._init_dat_path = op.join(original_results_path, 'init.dat')
if op.exists(self._init_dat_path):
self.update(parse_init_dat(self._init_dat_path))
# Parse seq.dat
self._seq_dat_path = op.join(original_results_path, 'seq.dat')
if op.exists(self._seq_dat_path):
self._attrs_to_copy.append('_seq_dat_path')
# TODO: parse seq.dat and store in modeling_results
self.update(parse_seq_dat(self._seq_dat_path))
# Parse exp.dat
self._exp_dat_path = op.join(original_results_path, 'exp.dat')
if op.exists(self._exp_dat_path):
self._attrs_to_copy.append('_exp_dat_path')
# TODO: parse exp.dat and store in modeling_results
self.update(parse_exp_dat(self._exp_dat_path))
# Parse BFP.dat
self._bfp_dat_path = op.join(original_results_path, 'BFP.dat')
if op.exists(self._bfp_dat_path):
self._attrs_to_copy.append('_bfp_dat_path')
# TODO: parse BFP.dat and store in modeling_results
self.update(parse_bfp_dat(self._bfp_dat_path))
# Parse cscore
self.c_score = None
self.tm_score = None
self.tm_score_err = None
self.rmsd = None
self.rmsd_err = None
self._cscore_path = op.join(original_results_path, 'cscore')
if op.exists(self._cscore_path):
self._attrs_to_copy.append('_cscore_path')
self.update(parse_cscore(self._cscore_path))
### COACH RESULTS
self.coach_bsites = []
self.coach_ec = []
self.coach_go_mf = []
self.coach_go_bp = []
self.coach_go_cc = []
coach_folder = op.join(original_results_path, coach_results_folder)
self._coach_bsites_inf_path = op.join(coach_folder, 'Bsites.inf')
self._coach_ec_dat_path = op.join(coach_folder, 'EC.dat')
self._coach_go_mf_dat_path = op.join(coach_folder, 'GO_MF.dat')
self._coach_go_bp_dat_path = op.join(coach_folder, 'GO_BP.dat')
self._coach_go_cc_dat_path = op.join(coach_folder, 'GO_CC.dat')
if op.isdir(coach_folder):
# Parse Bsites.inf
if op.exists(self._coach_bsites_inf_path):
parsed_bsites = parse_coach_bsites_inf(self._coach_bsites_inf_path)
if parsed_bsites:
self._attrs_to_copy.append('_coach_bsites_inf_path')
self.coach_bsites = parsed_bsites
# Parse EC.dat
if op.exists(self._coach_ec_dat_path):
parsed_ec = parse_coach_ec(self._coach_ec_dat_path)
if parsed_ec:
self._attrs_to_copy.append('_coach_ec_dat_path')
self.coach_ec = parsed_ec
# Parse GO_MF.dat
if op.exists(self._coach_go_mf_dat_path):
parsed_go_mf = parse_coach_go(self._coach_go_mf_dat_path)
if parsed_go_mf:
self._attrs_to_copy.append('_coach_go_mf_dat_path')
self.coach_go_mf = parsed_go_mf
# Parse GO_BP.dat
if op.exists(self._coach_go_bp_dat_path):
parsed_go_bp = parse_coach_go(self._coach_go_bp_dat_path)
if parsed_go_bp:
self._attrs_to_copy.append('_coach_go_bp_dat_path')
self.coach_go_bp = parsed_go_bp
# Parse GO_CC.dat
if op.exists(self._coach_go_cc_dat_path):
parsed_go_cc = parse_coach_go(self._coach_go_cc_dat_path)
if parsed_go_cc:
self._attrs_to_copy.append('_coach_go_cc_dat_path')
self.coach_go_cc = parsed_go_cc