class XBGFParser:
def __init__(self, PERMISSIVE=1, structure_builder=None):
if structure_builder != None:
self.structure_builder = structure_builder
else:
self.structure_builder = StructureBuilder()
self.PERMISSIVE = PERMISSIVE
# public interface
def parse(self, id, file):
self.structure_builder.init_structure(id)
if isinstance(file, basestring):
file=open(file)
self.charges = dict()
self.chain_suffix = 0
self._parse(file.readlines())
self.structure = self.structure_builder.get_structure()
return self._process_structure()
# private methods
def _parse(self, lines):
self.structure_builder.init_model(0)
self.structure_builder.init_seg("")
self.current_chain_id = None
self.current_residue_id = None
self.current_resname = None
for i in range(0, len(lines)):
self.line_counter = i + 1
self.structure_builder.set_line_counter(self.line_counter)
line = lines[i]
if line[0:6] == 'ATOM ':
self._update_atom(line)
def _update_chain(self, line):
chain_id = self._extract_chain(line)
if self.current_chain_id != chain_id:
try:
self.structure_builder.init_chain(chain_id)
self.current_chain_id = chain_id
self.current_residue_id = None
self.current_resname = None
except PDBConstructionException, message:
self._handle_PDB_exception(message)
class XBGFParser:
def __init__(self, PERMISSIVE=1, structure_builder=None):
if structure_builder != None:
self.structure_builder = structure_builder
else:
self.structure_builder = StructureBuilder()
self.PERMISSIVE = PERMISSIVE
# public interface
def parse(self, id, file):
self.structure_builder.init_structure(id)
if isinstance(file, basestring):
file = open(file)
self.charges = dict()
self.chain_suffix = 0
self._parse(file.readlines())
self.structure = self.structure_builder.get_structure()
return self._process_structure()
# private methods
def _parse(self, lines):
self.structure_builder.init_model(0)
self.structure_builder.init_seg("")
self.current_chain_id = None
self.current_residue_id = None
self.current_resname = None
for i in range(0, len(lines)):
self.line_counter = i + 1
self.structure_builder.set_line_counter(self.line_counter)
line = lines[i]
if line[0:6] == 'ATOM ':
self._update_atom(line)
def _update_chain(self, line):
chain_id = self._extract_chain(line)
if self.current_chain_id != chain_id:
try:
self.structure_builder.init_chain(chain_id)
self.current_chain_id = chain_id
self.current_residue_id = None
self.current_resname = None
except PDBConstructionException, message:
self._handle_PDB_exception(message)
def pdb_extract(structure, **kwargs):
# model to extract from pdb
extract_model = None if not 'model' in kwargs else kwargs['model']
new_model_id = -1 if not 'new_model' in kwargs else kwargs['new_model']
extract_chain = None if not 'chain' in kwargs else kwargs['chain']
first_res = None if not 'first_res' in kwargs else kwargs['first_res']
last_res = None if not 'last_res' in kwargs else kwargs['last_res']
new_first_res = None if not 'new_first_res' in kwargs else kwargs[
'new_first_res']
gap_count = 0 if not 'gap_count' in kwargs else kwargs['gap_count']
water_id = None if not 'water' in kwargs else kwargs['water']
model_rebumber_flag = bool((extract_model is not None)
or new_model_id >= 0)
res_renumber_flag = bool(first_res or last_res or new_first_res
or gap_count)
structure_builder = StructureBuilder()
structure_builder.init_structure('pdb_extract')
structure_builder.set_line_counter(0)
line_counter = 0
start_resseq_by_default = 1 if not new_first_res else new_first_res
for model in structure:
if model_rebumber_flag and \
( extract_model is not None ) and model.get_id() != extract_model:
continue
if model_rebumber_flag and new_model_id >= 0:
this_model_id = new_model_id
new_model_id += 1
else:
this_model_id = model.get_id()
structure_builder.init_model(this_model_id, this_model_id)
for chain in model:
if extract_chain and chain.get_id() != extract_chain:
continue
structure_builder.init_seg(' ')
structure_builder.init_chain(chain.get_id())
resdict = {}
if res_renumber_flag:
# first_res = res_range_tuple[0]
# last_res = res_range_tuple[1]
resdict['before'] = select_residues_from_chain(
chain, first_res=first_res, gap_count=gap_count)
resdict['hit'] = select_residues_from_chain(
chain, first_res=first_res, last_res=last_res)
resdict['after'] = select_residues_from_chain(
chain, last_res=last_res, gap_count=gap_count)
else:
resdict['before'] = []
resdict['hit'] = chain.get_list()
resdict['after'] = []
new_resseq = start_resseq_by_default - len(resdict['before'])
resdict['water'] = chain_water_id(chain, water_id)
for key in ['before', 'hit', 'after', 'water']:
for residue in resdict[key]:
if res_renumber_flag:
new_resid = ' ', new_resseq, ' '
else:
new_resid = residue.get_id()
structure_builder.init_residue(residue.get_resname(),
*new_resid)
residue_atoms = None
if key == 'before':
residue_atoms = [atom for atom in residue if \
(atom.get_name() == 'C' or atom.get_name() == 'O')]
elif key == 'hit' or key == 'water':
residue_atoms = residue.get_list()
elif key == 'after':
residue_atoms = [atom for atom in residue if \
(atom.get_name() == 'N' or atom.get_name() == 'HN')]
for atom in residue_atoms:
structure_builder.init_atom(atom.get_name(),
atom.get_coord(),
atom.get_bfactor(),
atom.get_occupancy(),
atom.get_altloc(),
atom.get_fullname())
structure_builder.set_line_counter(line_counter)
line_counter += 1
new_resseq += 1
if key == 'water' and gap_count and len(
resdict['after']) != gap_count:
new_resseq += gap_count - len(resdict['after'])
out_structure = structure_builder.get_structure()
return out_structure
