def init_chain(self, chain_id):
"""Initiate a new Chain object with given id.
Arguments:
o chain_id - string
"""
if self.current_model.has_chain_with_id(chain_id):
self.current_chain = self.current_model.chains(chain_id)
warnings.warn(
"WARNING: Chain %s is discontinuous at line %i." %
(chain_id, self.line_counter), PDBConstructionWarning)
else:
self.current_chain = Chain(chain_id)
self.current_model.add_chain(self.current_chain)
def _parse_coordinates(self, lines):
self.__chain = Chain(lines[0].split()[4])
for i in range(len(lines)):
items = lines[i].split()
atom_serial_num = int(items[1])
atom_name = items[2]
element = lines[i][13]
residue_name = items[3]
residue_serial_num = int(items[5])
coords = array([items[6], items[7], items[8]], 'f')
if self.__current_residue is None or self.__current_residue.sequence_number(
) != residue_serial_num:
self.__current_residue = Residue(residue_serial_num,
residue_name)
self.__chain.add_residue(self.__current_residue)
self.__current_residue.add_atom(
Atom(atom_serial_num, atom_name, coords, element))
