def test_full_itp_vsites(self):
"""Test full operation to output of .itp file for molecule with vsites."""
options = DummyOptions()
options.generate_angles = False
measure = BondSet(self.data_dir.joinpath("martini3/naphthalene.bnd"),
options)
frame = Frame(self.data_dir.joinpath("martini3/naphthalene.gro"))
mapping = Mapping(self.data_dir.joinpath("martini3/naphthalene.map"),
options)
cg_frame = mapping.apply(frame)
measure.apply(cg_frame)
measure.boltzmann_invert()
with tempfile.TemporaryDirectory() as tmpdir:
tmp_path = pathlib.Path(tmpdir)
measure.write_itp(tmp_path.joinpath("naphthalene_out.itp"),
mapping)
self.assertTrue(
cmp_file_whitespace_float(
tmp_path.joinpath("naphthalene_out.itp"),
self.data_dir.joinpath("martini3/naphthalene_out.itp"),
rtol=0.005,
verbose=True,
))
def test_forcefield(self):
with tempfile.TemporaryDirectory() as tmpdir:
tmp_path = pathlib.Path(tmpdir)
args = get_args(
"sugar",
tmp_path,
extra={
"output_forcefield": True,
},
)
# Equivalent to
# pycgtool <top> <trj> -m <map> -b <bnd> --output-forcefield
main.PyCGTOOL(args)
# Does not produce itp file
self.assertFalse(tmp_path.joinpath("out.itp").exists())
out_ff_dir = tmp_path.joinpath("ffout.ff")
self.assertTrue(out_ff_dir.is_dir())
# Compare all files in ffout.ff to reference versions
for out_file in out_ff_dir.iterdir():
ref_file = self.data_dir.joinpath(out_file)
self.assertTrue(
util.cmp_file_whitespace_float(ref_file, out_file))
def test_measure_only(self):
with tempfile.TemporaryDirectory() as tmpdir:
tmp_path = pathlib.Path(tmpdir)
args = get_args(
"sugar",
tmp_path,
extra={
"mapping": None,
"trajectory": None,
},
)
# Equivalent to
# pycgtool <top> -b <bnd>
main.PyCGTOOL(args)
# Does not produce itp file
self.assertFalse(tmp_path.joinpath("out.itp").exists())
# Check bond dump files against reference
for bond_type in ["length", "angle", "dihedral"]:
out_file = tmp_path.joinpath(f"ALLA_{bond_type}.dat")
self.assertTrue(out_file.exists())
self.assertTrue(
util.cmp_file_whitespace_float(
self.data_dir.joinpath(f"ALLA_{bond_type}_one.dat"),
out_file))
def test_dump_bonds(self):
measure = BondSet(self.data_dir.joinpath("sugar.bnd"), DummyOptions)
frame = Frame(self.data_dir.joinpath("sugar.gro"),
self.data_dir.joinpath("sugar.xtc"))
mapping = Mapping(self.data_dir.joinpath("sugar.map"), DummyOptions)
cg_frame = mapping.apply(frame)
measure.apply(cg_frame)
measure.boltzmann_invert()
measure.dump_values()
filenames = ("ALLA_length.dat", "ALLA_angle.dat", "ALLA_dihedral.dat")
for filename in filenames:
self.assertTrue(
cmp_file_whitespace_float(self.data_dir.joinpath(filename),
filename,
rtol=0.008,
verbose=True))
os.remove(filename)
def test_full_itp_sugar(self):
measure = BondSet(self.data_dir.joinpath("sugar.bnd"), DummyOptions)
frame = Frame(self.data_dir.joinpath("sugar.gro"),
self.data_dir.joinpath("sugar.xtc"))
mapping = Mapping(self.data_dir.joinpath("sugar.map"), DummyOptions)
cg_frame = mapping.apply(frame)
measure.apply(cg_frame)
measure.boltzmann_invert()
with tempfile.TemporaryDirectory() as tmpdir:
tmp_path = pathlib.Path(tmpdir)
measure.write_itp(tmp_path.joinpath("sugar_out.itp"), mapping)
self.assertTrue(
cmp_file_whitespace_float(
tmp_path.joinpath("sugar_out.itp"),
self.data_dir.joinpath("sugar_out.itp"),
rtol=0.005,
verbose=True,
))
def test_full(self):
with tempfile.TemporaryDirectory() as tmpdir:
tmp_path = pathlib.Path(tmpdir)
args = get_args("sugar", tmp_path)
# Equivalent to
# pycgtool <top> <trj> -m <map> -b <bnd>
main.PyCGTOOL(args)
self.assertTrue(
util.cmp_file_whitespace_float(
tmp_path.joinpath("out.itp"),
self.data_dir.joinpath("sugar_out.itp"),
rtol=0.001,
verbose=True,
))
self.assertTrue(
util.compare_trajectories(
self.data_dir.joinpath("sugar_out.gro"),
tmp_path.joinpath("out.gro"),
rtol=0.001,
))