def load_jmol_conf(self, file_name, number_of_chains=1):
"""
Load chain configuration from JMOL file
@string file_name: Name of jmol file
@dict map_dict: dict with Monomer class
@int number_of_chains: number of chains in jmol file
"""
f = open(file_name, "r+")
data = f.readlines()
header = int(data[0])
coordinate_data = map(lambda x: x.split(" "), data[2:])
chains = []
for chain_idx in range(number_of_chains):
chain_seq = []
slice_coordinate = coordinate_data[chain_idx * header:]
self.chain_list[chain_idx].positions_list = []
for c_idx in range(len(slice_coordinate)):
c = slice_coordinate[c_idx]
crr = tuple(map(lambda x: float(x)/settings.JMOL_SCALE, tuple(c[1:])))
print "Load", crr
self.chain_list[chain_idx].chain[c_idx]._open = crr
self.chain_list[chain_idx].chain[c_idx].position = Lattice.convert_to_periodic_coordinate(crr)
self.chain_list[chain_idx].positions_list.append(self.chain_list[chain_idx].chain[c_idx]._position)
self.chain_list[chain_idx] = self.rebuild_direction(self.chain_list[chain_idx])
