def calculate_binned_contacts_vs_q(args):
trajsfile = args.trajs
function = args.function
coordfile = args.coordfile
coordname = coordfile.split(".")[0]
bins = args.bins
chunksize = args.chunksize
topology = args.topology
periodic = args.periodic
# Data source
trajfiles = ["%s" % x.rstrip("\n") for x in open(trajsfile, "r").readlines()]
dir = os.path.dirname(trajfiles[0])
# Parameterize contact-based reaction coordinate
pairs, contact_params = util.get_contact_params(dir, args)
coord_sources = ["%s/%s" % (os.path.dirname(trajfiles[i]), coordfile) for i in range(len(trajfiles))]
if not all([os.path.exists(x) for x in coord_sources]):
# Parameterize contact-based reaction coordinate
contact_function = util.get_sum_contact_function(pairs, function, contact_params, periodic=periodic)
# Calculate contact function over directories
contacts = util.calc_coordinate_multiple_trajs(
trajfiles,
contact_function,
topology,
chunksize,
save_coord_as=args.coordfile,
savepath=args.savepath,
collect=True,
)
else:
# Load precalculated coordinate
contacts = [np.loadtxt(coord_sources[i]) for i in range(len(coord_sources))]
# Parameterize pairwise contact function
pairwise_contact_function = util.get_pair_contact_function(pairs, function, contact_params, periodic=periodic)
# Calculate pairwise contacts over directories
bin_edges, avgqi_by_bin = util.bin_multiple_coordinates_for_multiple_trajs(
trajfiles, contacts, pairwise_contact_function, pairs.shape[0], bins, topology, chunksize
)
return bin_edges, avgqi_by_bin
args = parser.parse_args()
return args
if __name__ == "__main__":
args = get_args()
trajsfile = args.trajs
topology = args.topology
chunksize = args.chunksize
periodic = args.periodic
if args.saveas is None:
save_coord_as = {"native": "Enative.dat", "nonnative": "Enonnative.dat"}[args.contacts]
else:
save_coord_as = args.saveas
# Data source
trajfiles = ["%s" % (x.rstrip("\n")) for x in open(trajsfile, "r").readlines()]
dir = os.path.dirname(trajfiles[0])
# Parameterize contact energy function.
pairs, pair_type, eps, contact_params = util.get_pair_energy_params(dir, args)
energy_function = util.get_contact_energy_function(pairs, pair_type, eps, contact_params, periodic=periodic)
# Calculate contact function over directories
util.calc_coordinate_multiple_trajs(
trajfiles, energy_function, topology, chunksize, save_coord_as=save_coord_as, savepath=args.savepath
)
