def test_parse_structure():
"""Test the structure parser."""
pdb_path = Path(DATA_FOLDER, "complex.pdb")
s, n_chains, n_res = parse_structure(pdb_path)
assert isinstance(s, Structure)
assert n_chains == 2
assert n_res == 252
with pytest.raises(Exception):
parse_structure("nothing.pdb")
pdb_w_gaps_path = Path(DATA_FOLDER, "ens_w_gaps.pdb")
s_gaps, n_chains_gaps, n_res_gaps = parse_structure(pdb_w_gaps_path)
assert isinstance(s_gaps, Structure)
assert n_chains_gaps == 2
assert n_res_gaps == 247
def contact_list():
pdb_path = Path(DATA_FOLDER, "complex.pdb")
s, _, _ = parse_structure(pdb_path)
return [(s[0]["I"][1], s[0]["E"][20])]
def parsed_structure_w_gaps():
pdb_path = Path(DATA_FOLDER, "ens_w_gaps.pdb")
s, _, _ = parse_structure(pdb_path)
return s
def parsed_structure():
pdb_path = Path(DATA_FOLDER, "complex.pdb")
s, _, _ = parse_structure(pdb_path)
return s
be considered for the calculation. Separate by a space the chains that
are to be considered _different_ molecules. Use commas to include multiple
chains as part of a single group:
--selection A B => Contacts calculated (only) between chains A and B.
--selection A,B C => Contacts calculated (only) between chains A and C; and B and C.
--selection A B C => Contacts calculated (only) between chains A and B; B and C; and A and C.
"""
sel_opt = ap.add_argument_group("Selection Options", description=_co_help)
sel_opt.add_argument("--selection", nargs="+", metavar=("A B", "A,B C"))
cmd = ap.parse_args()
# setup logging
log_level = logging.ERROR if cmd.quiet else logging.INFO
logging.basicConfig(level=log_level, format="%(message)s")
logger = logging.getLogger("Prodigy")
struct_path = _check_path(cmd.structf)
# Parse structure
structure, n_chains, n_res = parse_structure(struct_path)
prodigy = ProdigyCrystal(structure, cmd.selection)
prodigy.predict()
prodigy.print_prediction(quiet=cmd.quiet)
# Print out interaction network
if cmd.contact_list:
fname = struct_path[:-4] + ".ic"
prodigy.print_contacts(fname)