def __init__(self, PERMISSIVE=True, get_header=False,
structure_builder=None, QUIET=False):
"""
The PDB parser call a number of standard methods in an aggregated
StructureBuilder object. Normally this object is instanciated by the
PDBParser object itself, but if the user provides his/her own
StructureBuilder object, the latter is used instead.
Arguments:
o PERMISSIVE - Evaluated as a Boolean. If false, exceptions in
constructing the SMCRA data structure are fatal. If true (DEFAULT),
the exceptions are caught, but some residues or atoms will be missing.
THESE EXCEPTIONS ARE DUE TO PROBLEMS IN THE PDB FILE!.
o structure_builder - an optional user implemented StructureBuilder class.
o QUIET - Evaluated as a Boolean. If true, warnings issued in constructing
the SMCRA data will be suppressed. If false (DEFAULT), they will be shown.
These warnings might be indicative of problems in the PDB file!
"""
if structure_builder is not None:
self.structure_builder = structure_builder
else:
self.structure_builder = StructureBuilder()
self.header = None
self.trailer = None
self.line_counter = 0
self.PERMISSIVE = bool(PERMISSIVE)
self.QUIET = bool(QUIET)
def set_structure(self, pdb_object):
# Check what the user is providing and build a structure appropriately
if pdb_object.level == "S":
structure = pdb_object
else:
sb = StructureBuilder()
sb.init_structure('pdb')
sb.init_seg(' ')
# Build parts as necessary
if pdb_object.level == "M":
sb.structure.add(pdb_object)
self.structure = sb.structure
else:
sb.init_model(0)
if pdb_object.level == "C":
sb.structure[0].add(pdb_object)
else:
sb.init_chain('A')
if pdb_object.level == "R":
try:
parent_id = pdb_object.parent.id
sb.structure[0]['A'].id = parent_id
except Exception:
pass
sb.structure[0]['A'].add(pdb_object)
else:
# Atom
sb.init_residue('DUM', ' ', 1, ' ')
try:
parent_id = pdb_object.parent.parent.id
sb.structure[0]['A'].id = parent_id
except Exception:
pass
sb.structure[0]['A'].child_list[0].add(pdb_object)
# Return structure
structure = sb.structure
self.structure = structure
def get_structure(self, structure_id, filename):
self._mmcif_dict = MMCIF2Dict(filename)
self._structure_builder = StructureBuilder()
self._build_structure(structure_id)
return self._structure_builder.get_structure()
