def main(argv=None):
# Parse arguments
parser = ap.build_getcontact_parser(__doc__, True)
args = parser.parse_args(argv)
top = args.topology
traj = args.trajectory
output = args.output
cores = args.cores
ligand = args.ligand
solv = args.solv
lipid = args.lipid
sele1 = args.sele
sele2 = args.sele2
beg = args.beg
end = args.end if args.end else sys.maxsize
stride = args.stride
distout = args.distout
geom_criteria = process_geometric_criterion_args(args)
# If sele2 is None set it to sele1
if sele2 is None:
sele2 = sele1
# Check interaction types
all_itypes = ["hp", "sb", "pc", "ps", "ts", "vdw", "hb"]
if "all" in args.itypes:
itypes = all_itypes
else:
for itype in args.itypes:
if itype not in all_itypes:
parser.error(itype + " is not a valid interaction type")
itypes = args.itypes
# Begin computation
tic = datetime.datetime.now()
compute_contacts(top, traj, output, itypes, geom_criteria, cores, beg, end,
stride, distout, ligand, solv, lipid, sele1, sele2)
toc = datetime.datetime.now()
total_time = (toc - tic).total_seconds()
print("\nTotal computation time:", total_time, "seconds")
print("topology=%s" % top)
print("trajectory=%s" % traj)
print("output=%s" % output)
print("cores=%s" % cores)
print("solv=%s" % solv)
print("sele=%s" % sele1)
print("sele2=%s" % sele2)
print("stride=%s" % stride)
def main(argv=None):
# Parse arguments
parser = ap.build_getcontact_parser(__doc__, False)
args, unknown = parser.parse_known_args(argv)
top = args.structure
traj = args.structure
output = args.output
cores = 1
solv = args.solv
lipids = args.lipids
sele1 = args.sele
sele2 = args.sele2
beg = 0
end = 0
stride = 1
geom_criteria = process_geometric_criterion_args(args)
# If sele2 is None set it to sele1
if sele2 is None:
sele2 = sele1
# Check interaction types
all_itypes = ["hp", "sb", "pc", "ps", "ts", "vdw", "hb", "lhb"]
if "all" in args.itypes:
itypes = all_itypes
else:
for itype in args.itypes:
if itype not in all_itypes:
parser.error(itype + " is not a valid interaction type")
itypes = args.itypes
# Begin computation
tic = datetime.datetime.now()
compute_contacts(top, traj, output, itypes, geom_criteria, cores, beg, end,
stride, solv, lipids, sele1, sele2)
toc = datetime.datetime.now()
print("\nTotal computation time: " + str((toc - tic).total_seconds()) +
" seconds")
print("topology=%s" % top)
print("trajectory=%s" % traj)
print("output=%s" % output)
print("solv=%s" % solv)
print("sele=%s" % sele1)
print("sele2=%s" % sele2)
def main(argv=None):
# Parse arguments
parser = ap.build_getcontact_parser(__doc__, False)
args, unknown = parser.parse_known_args(argv)
top = args.structure
traj = args.structure
output = args.output
cores = 1
ligand = args.ligand
solv = args.solv
sele = args.sele
beg = 0
end = 0
stride = 1
geom_criterion_values = process_geometric_criterion_args(args)
# Check interaction types
all_itypes = ["sb", "pc", "ps", "ts", "vdw", "hb", "lhb"]
if "all" in args.itypes:
itypes = all_itypes
else:
for itype in args.itypes:
if itype not in all_itypes:
parser.error(itype + " is not a valid interaction type")
itypes = args.itypes
# Begin computation
tic = datetime.datetime.now()
compute_contacts(top, traj, output, itypes, geom_criterion_values, cores,
beg, end, stride, solv, sele, ligand)
toc = datetime.datetime.now()
print("\nTotal computation time: " + str((toc - tic).total_seconds()) +
" seconds")
print("topology=%s" % top)
print("trajectory=%s" % traj)
print("output=%s" % output)
print("cores=%s" % cores)
print("ligand=%s" % ",".join(ligand))
print("solv=%s" % solv)
print("sele=%s" % sele)
print("stride=%s" % stride)