--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()
if cmd.quiet:
_stdout = sys.stdout
sys.stdout = open(os.devnull, 'w')
struct_path = _check_path(cmd.structf)
# Parse structure
structure, n_chains, n_res = parse_structure(struct_path)
print('[+] Parsed structure file {0} ({1} chains, {2} residues)'.format(
structure.id, n_chains, n_res))
# Make selection dict from user option or PDB chains
if cmd.selection:
selection_dict = {}
for igroup, group in enumerate(cmd.selection):
chains = group.split(',')
for chain in chains:
if chain in selection_dict:
errmsg = 'Selections must be disjoint sets: {0} is repeated'.format(
chain)
raise ValueError(errmsg)
selection_dict[chain] = igroup
else:
--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, stream=sys.stdout, format="%(message)s")
logger = logging.getLogger('Prodigy')
struct_path = _check_path(cmd.structf)
# Parse structure
structure, n_chains, n_res = parse_structure(struct_path)
logger.info('[+] Parsed structure file {0} ({1} chains, {2} residues)'.format(structure.id, n_chains, n_res))
prodigy = Prodigy(structure, cmd.selection, cmd.temperature)
prodigy.predict(distance_cutoff=cmd.distance_cutoff, acc_threshold=cmd.acc_threshold)
prodigy.print_prediction(quiet=cmd.quiet)
# Print out interaction network
if cmd.contact_list:
fname = struct_path[:-4] + '.ic'
prodigy.print_contacts(fname)
# Print out interaction network
if cmd.pymol_selection:
fname = struct_path[:-4] + '.pml'
prodigy.print_pymol_script(fname)