def test_map_only(self):
logging.disable(logging.WARNING)
map_only(Args("sugar"), self.config)
logging.disable(logging.NOTSET)
xtc = XtcTrajectory("out.xtc")
xtc_ref = XtcTrajectory("test/data/sugar_out.xtc")
self.assertEqual(xtc_ref.numframes, xtc.numframes)
for i in range(xtc_ref.numframes):
xtc.get_frame(i)
xtc_ref.get_frame(i)
np.testing.assert_array_almost_equal(xtc_ref.box, xtc.box, decimal=3)
np.testing.assert_array_almost_equal(xtc_ref.x, xtc.x, decimal=3)
def test_map_only(self):
logging.disable(logging.WARNING)
map_only(Args("sugar"), self.config)
logging.disable(logging.NOTSET)
xtc = XtcTrajectory("out.xtc")
xtc_ref = XtcTrajectory("test/data/sugar_out.xtc")
self.assertEqual(xtc_ref.numframes, xtc.numframes)
for i in range(xtc_ref.numframes):
xtc.get_frame(i)
xtc_ref.get_frame(i)
np.testing.assert_array_almost_equal(xtc_ref.box,
xtc.box,
decimal=3)
np.testing.assert_array_almost_equal(xtc_ref.x, xtc.x, decimal=3)
("dump_measurements", bool(args.bnd) and not bool(args.map)),
("dump_n_values", 10000),
("output_forcefield", False),
("temperature", 310),
("default_fc", False),
("generate_angles", True),
("generate_dihedrals", False),
("length_form", "harmonic"),
("angle_form", "cosharmonic"),
("dihedral_form", "harmonic"),
],
args,
)
if not args.map and not args.bnd:
parser.error("One or both of -m and -b is required.")
if args.advanced:
try:
config.interactive()
except KeyboardInterrupt:
sys.exit(0)
else:
print("Using GRO: {0}".format(args.gro))
print("Using XTC: {0}".format(args.xtc))
if config.map_only:
map_only(args, config)
else:
main(args, config)
func_forms = FunctionalForms()
args = parser.parse_args()
config = Options(
[("output_name", "out"), ("output", "gro"),
("output_xtc", args.outputxtc), ("map_only", not bool(args.bnd)),
("map_center", "geom"), ("constr_threshold", 100000),
("dump_measurements", bool(args.bnd) and not bool(args.map)),
("dump_n_values", 10000), ("output_forcefield", False),
("temperature", 310), ("default_fc", False),
("generate_angles", True), ("generate_dihedrals", False),
("length_form", "harmonic"), ("angle_form", "cosharmonic"),
("dihedral_form", "harmonic")], args)
if not args.map and not args.bnd:
parser.error("One or both of -m and -b is required.")
if args.advanced:
try:
config.interactive()
except KeyboardInterrupt:
sys.exit(0)
else:
print("Using GRO: {0}".format(args.gro))
print("Using XTC: {0}".format(args.xtc))
if config.map_only:
map_only(args, config)
else:
main(args, config)