def load_struct(self, args, struct_var, mirror_var, strip_water, strip_hydrogen):
struct_id = getattr(args, struct_var)
if getattr(args, mirror_var) is not None:
mirror_path = getattr(args, mirror_var)
struct = load_cif_from_mirror(struct_id, mirror_path)
else:
struct = load_cif_from_file(struct_id)
if strip_water:
for model in struct:
preprocess.strip_water(model)
if strip_hydrogen:
for model in struct:
preprocess.strip_hydrogen(model)
setattr(args, struct_var, struct)
(i1, i2) for i1 in lst1 for i2 in lst2
if id(i1) != id(i2) and #not the same object
self._dist(i1[0], i2[0])
]
return (pair
for xi in range(self.min_coords[0], self.max_coords[0] + 1)
for xj in range(self.min_coords[1], self.max_coords[1] + 1)
for xk in range(self.min_coords[1], self.max_coords[1] + 1)
for di in range(0, 2) for dj in range(0, 2)
for dk in range(0, 2) for pair in _all_neighbors(
self.coord_sparse_mat.get((xi, xj, xk), []),
self.coord_sparse_mat.get((xi + di, xj + dj,
xk + dk), [])))
if __name__ == '__main__':
import sys
from mmstructlib.IO import load_cif_from_mirror
if len(sys.argv) != 2:
exit("usage: {} <struct id>".format(sys.argv[0]))
struct = load_cif_from_mirror(sys.argv[1])
gridhash = GridHash([(a.coordinates, a) for a in struct[0].atoms], 10)
for (ac1, a1), (ac2, a2) in gridhash.all_neighbors_iter():
print("{}.{}/{}/{}-{}.{}/{}/{}".format(a1.molecule.id, a1.monomer.id,
a1.monomer.type, a1.name,
a2.molecule.id, a2.monomer.id,
a2.monomer.type, a2.name))
print("\n".join([
"options:",
" -c <chains> limit return to these chains (comma seperated)",
" -f interpret <struct> as file name",
" -m set pdb mirror directory, default: {0}".format(mirror)
]))
sys.exit(1)
chains = optdict.get('-c', None)
if chains:
chains = chains.split(",")
mirror = optdict.get('-m', mirror)
if '-f' in optdict:
loader = load_cif_from_file
else:
loader = lambda x: load_cif_from_mirror(x, mirror)
struct = loader(args[0])
chains = [
m for m in struct[0].molecules
if m.is_protein() and (not chains or m.pdb_id in chains)
]
for chain in chains:
seq = [
c321(s) if a is not None else c321(s).lower() for s, a in chain.seq_res
]
print(">{0}_{1}".format(struct.id, chain.pdb_id))
print("".join(seq))