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)
def main(traj_required=True):
if "--help" in sys.argv or "-h" in sys.argv:
print(HELP_STR)
exit(1)
# Parse required and optional arguments
parser = argparse.ArgumentParser(add_help=False)
parser.add_argument('--topology',
type=str,
required=True,
help='path to topology file ')
parser.add_argument('--trajectory',
type=str,
required=traj_required,
default=None,
help='path to trajectory file')
parser.add_argument('--output',
type=str,
required=True,
help='path to output file')
parser.add_argument('--cores',
type=int,
default=6,
help='number of cpu cores to parallelize upon')
parser.add_argument('--solv',
type=str,
default="TIP3",
help='resname of solvent molecule')
parser.add_argument('--sele',
type=str,
default=None,
help='atom selection query in VMD')
parser.add_argument('--stride',
type=int,
default=1,
help='skip frames with specified frequency')
parser.add_argument('--ligand',
type=str,
nargs="+",
default=[],
help='resname of ligand molecule')
# Parse geometric criterion arguments
parser.add_argument(
'--sb_cutoff_dist',
type=float,
default=4.0,
help=
'cutoff for distance between anion and cation atoms [default = 4.0 angstroms]'
)
parser.add_argument(
'--pc_cutoff_dist',
type=float,
default=6.0,
help=
'cutoff for distance between cation and centroid of aromatic ring [default = 6.0 angstroms]'
)
parser.add_argument(
'--pc_cutoff_ang',
type=float,
default=60,
help=
'cutoff for angle between normal vector projecting from aromatic plane and vector from aromatic center to cation atom [default = 60 degrees]'
)
parser.add_argument(
'--ps_cutoff_dist',
type=float,
default=7.0,
help=
'cutoff for distance between centroids of two aromatic rings [default = 7.0 angstroms]'
)
parser.add_argument(
'--ps_cutoff_ang',
type=float,
default=30,
help=
'cutoff for angle between the normal vectors projecting from each aromatic plane [default = 30 degrees]'
)
parser.add_argument(
'--ps_psi_ang',
type=float,
default=45,
help=
'cutoff for angle between normal vector projecting from aromatic plane 1 and vector between the two aromatic centroids [default = 45 degrees]'
)
parser.add_argument(
'--ts_cutoff_dist',
type=float,
default=5.0,
help=
'cutoff for distance between centroids of two aromatic rings [default = 5.0 angstroms]'
)
parser.add_argument(
'--ts_cutoff_ang',
type=float,
default=30,
help=
'cutoff for angle between the normal vectors projecting from each aromatic plane minus 90 degrees [default = 30 degrees]'
)
parser.add_argument(
'--ts_psi_ang',
type=float,
default=45,
help=
'cutoff for angle between normal vector projecting from aromatic plane 1 and vector between the two aromatic centroids [default = 45 degrees]'
)
parser.add_argument(
'--hbond_cutoff_dist',
type=float,
default=3.5,
help=
'cutoff for distance between donor and acceptor atoms [default = 3.5 angstroms]'
)
parser.add_argument(
'--hbond_cutoff_ang',
type=float,
default=70,
help=
'cutoff for angle between donor hydrogen acceptor [default = 70 degrees]'
)
parser.add_argument(
'--vdw_epsilon',
type=float,
default=0.5,
help=
'amount of padding for calculating vanderwaals contacts [default = 0.5 angstroms]'
)
parser.add_argument(
'--vdw_res_diff',
type=int,
default=2,
help=
'minimum residue distance for which to consider computing vdw interactions'
)
parser.add_argument(
'--itypes',
required=True,
type=str,
nargs="+",
metavar="ITYPE",
help='Compute only these interaction types. Valid choices are: \n'
'* all (default), \n'
'* sb (salt-bridges), \n'
'* pc (pi-cation), \n'
'* ps (pi-stacking), \n'
'* ts (t-stacking), \n'
'* vdw (van der Waals), \n'
'* hb (hydrogen bonds)\n'
'* lhb (ligand hydrogen bonds)')
args, unknown = parser.parse_known_args()
top = args.topology
traj = args.trajectory
output = args.output
cores = args.cores
ligand = args.ligand
solv = args.solv
sele = args.sele
stride = args.stride
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:
print("Error: " + itype + " is not a valid interaction type")
exit(1)
itypes = args.itypes
# Begin computation
tic = datetime.datetime.now()
compute_contacts(top, traj, output, itypes, geom_criterion_values, cores,
stride, solv, sele, ligand)
toc = datetime.datetime.now()
print("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)