class PycgtoolTest(unittest.TestCase):
config = Options([("output_name", "out"), ("output", "gro"),
("output_xtc", True), ("map_only", False),
("map_center", "geom"), ("constr_threshold", 100000),
("dump_measurements", False), ("dump_n_values", 10000),
("output_forcefield", False), ("temperature", 310),
("default_fc", False), ("generate_angles", True),
("generate_dihedrals", False)])
def test_run_help(self):
path = os.path.dirname(os.path.dirname(__file__))
self.assertEqual(
0,
subprocess.check_call([os.path.join(path, "pycgtool.py"), "-h"],
stdout=subprocess.PIPE))
@unittest.skipIf(not mdtraj_present, "MDTRAJ or Scipy not present")
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_full(self):
path = os.path.dirname(os.path.dirname(__file__))
self.assertEqual(
0,
subprocess.check_call([
os.path.join(path, "pycgtool.py"),
"-g",
"test/data/sugar.gro",
"-x",
"test/data/sugar.xtc",
"-m",
"test/data/sugar_only.map",
"-b",
"test/data/sugar.bnd",
],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE))
self.assertTrue(
cmp_whitespace_float("out.itp",
"test/data/sugar_out.itp",
float_rel_error=0.001))
self.assertTrue(
cmp_whitespace_float("out.gro",
"test/data/sugar_out.gro",
float_rel_error=0.001))
def test_options_toggle(self):
opt = Options([("a", True), ("b", 10), ("c", "hello")])
opt.toggle_boolean("a")
self.assertEqual(False, opt.a)
def test_options_set(self):
opt = Options([("a", True), ("b", 10), ("c", "hello")])
opt.set("a", False)
opt.set("b", 11)
self.assertEqual(False, opt.a)
self.assertEqual(11, opt.b)
self.assertEqual("hello", opt.c)
opt.set("a", "yEs")
opt.set("b", "12")
self.assertEqual(True, opt.a)
self.assertEqual(12, opt.b)
opt.set("a", "f")
self.assertEqual(False, opt.a)
with self.assertRaises(ValueError):
opt.set("a", "hello")
with self.assertRaises(ValueError):
opt.set("b", "hello")
def test_options_init(self):
opt = Options([("a", True), ("b", 10), ("c", "hello")])
self.assertEqual(True, opt.a)
self.assertEqual(10, opt.b)
self.assertEqual("hello", opt.c)
input_files.add_argument("--end", type=int, default=-1, help="Frame number to end")
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:
type=int,
default=0,
help="Frame number to begin")
input_files.add_argument('--end',
type=int,
default=-1,
help="Frame number to end")
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))
