def copy_struct(self, struct, chain):
"""Make a copy of the argument structure to use for generating
the animation. Only copy the chain specified in chain_id.
"""
cp_struct = Structure.Structure(structure_id = struct.structure_id)
chain_id = chain.chain_id
for chain in struct.iter_chains():
## TODO: Move "200" to conf.py, 2009-06-19
if chain.chain_id == chain_id or chain.count_fragments() < 200:
include_chain = True
else:
include_chain = False
for frag in chain.iter_fragments():
## skip all waters
if frag.is_water() == True:
continue
elif frag.is_standard_residue() == True and include_chain:
for atm in iter_filter_atoms(frag.iter_atoms()):
cp_atom = Structure.Atom(
chain_id = atm.chain_id,
fragment_id = atm.fragment_id,
res_name = atm.res_name,
element = atm.element,
name = atm.name,
temp_factor = atm.temp_factor,
occupancy = atm.occupancy,
position = atm.position.copy())
cp_struct.add_atom(cp_atom, True)
elif frag.is_standard_residue() == False:
for atm in frag.iter_atoms():
cp_atom = Structure.Atom(
chain_id = atm.chain_id,
fragment_id = atm.fragment_id,
res_name = atm.res_name,
element = atm.element,
name = atm.name,
temp_factor = atm.temp_factor,
occupancy = atm.occupancy,
position = atm.position.copy())
cp_struct.add_atom(cp_atom, True)
cp_struct.sort()
return cp_struct
