def test_bondset_boltzmann_invert_mdtraj(self):
logging.disable(logging.WARNING)
frame = Frame("test/data/sugar.gro",
xtc="test/data/sugar.xtc",
xtc_reader="mdtraj")
logging.disable(logging.NOTSET)
measure = BondSet("test/data/sugar.bnd", DummyOptions)
mapping = Mapping("test/data/sugar.map", DummyOptions)
cgframe = mapping.apply(frame)
while frame.next_frame():
cgframe = mapping.apply(frame, cgframe=cgframe)
measure.apply(cgframe)
measure.boltzmann_invert()
self.support_check_mean_fc(measure["ALLA"], 1)
def test_bondset_boltzmann_invert_manual_default_fc(self):
class FuncFormOptions(DummyOptions):
length_form = "MartiniDefaultLength"
angle_form = "MartiniDefaultAngle"
dihedral_form = "MartiniDefaultDihedral"
measure = BondSet("test/data/sugar.bnd", FuncFormOptions)
frame = Frame("test/data/sugar.gro", xtc="test/data/sugar.xtc")
mapping = Mapping("test/data/sugar.map", DummyOptions)
cgframe = mapping.apply(frame)
while frame.next_frame():
cgframe = mapping.apply(frame, cgframe=cgframe)
measure.apply(cgframe)
measure.boltzmann_invert()
self.support_check_mean_fc(measure["ALLA"], 2)
def test_full_itp_sugar(self):
measure = BondSet("test/data/sugar.bnd", DummyOptions)
frame = Frame("test/data/sugar.gro", xtc="test/data/sugar.xtc")
mapping = Mapping("test/data/sugar.map", DummyOptions)
cgframe = mapping.apply(frame)
while frame.next_frame():
cgframe = mapping.apply(frame, cgframe=cgframe)
measure.apply(cgframe)
measure.boltzmann_invert()
logging.disable(logging.WARNING)
measure.write_itp("sugar_out.itp", mapping)
logging.disable(logging.NOTSET)
self.assertTrue(
cmp_whitespace_float("sugar_out.itp",
"test/data/sugar_out.itp",
float_rel_error=0.001))
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_bondset_apply(self):
measure = BondSet("test/data/sugar.bnd", DummyOptions)
frame = Frame("test/data/sugar-cg.gro")
measure.apply(frame)
# First six are bond lengths
self.assertEqual(1, len(measure["ALLA"][0].values))
self.assertAlmostEqual(0.2225376,
measure["ALLA"][0].values[0],
delta=0.2225376 / 500)
# Second six are angles
self.assertEqual(1, len(measure["ALLA"][6].values))
expected = math.radians(77.22779289)
self.assertAlmostEqual(expected,
measure["ALLA"][6].values[0],
delta=expected / 500)
# Final six are dihedrals
self.assertEqual(1, len(measure["ALLA"][12].values))
expected = math.radians(-89.5552903)
self.assertAlmostEqual(expected,
measure["ALLA"][12].values[0],
delta=abs(expected) / 500)
def test_mapping_duplicate_atom_weight(self):
"""Test that an atom can be duplicated in a bead specification to act as a weighting."""
frame = Frame(self.data_dir.joinpath("water.gro"))
mapping = Mapping(self.data_dir.joinpath("water.map"), DummyOptions)
cg_frame = mapping.apply(frame)
np.testing.assert_allclose(
np.array([[0.716, 1.300, 1.198]]),
cg_frame.residue(0).atom(0).coords,
atol=0.0005,
)
mapping = Mapping(self.data_dir.joinpath("water_double_weight.map"),
DummyOptions)
cg_frame = mapping.apply(frame)
np.testing.assert_allclose(
np.array([[0.720, 1.294, 1.195]]),
cg_frame.residue(0).atom(0).coords,
atol=0.0005,
)
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_frame_add_residue(self):
residue = Residue()
frame = Frame()
frame.add_residue(residue)
self.assertEqual(residue, frame.residues[0])
self.assertTrue(residue is frame.residues[0])
def test_frame_simpletraj_read_gro(self):
frame = Frame("test/data/water.gro", xtc_reader="simpletraj")
self.helper_read_xtc(frame, first_only=True)
def test_frame_read_gro(self):
frame = Frame(self.data_dir.joinpath("water.gro"))
self.check_reference_frame(frame)
def test_frame_add_residue(self):
frame = Frame()
residue = frame.add_residue("TEST_RESIDUE")
self.assertTrue(residue is frame.residue(0))
def test_frame_create(self):
Frame()
def test_mapping_pbc(self):
mapping = Mapping("test/data/water.map", DummyOptions)
frame = Frame("test/data/pbcwater.gro")
cgframe = mapping.apply(frame)
np.testing.assert_allclose(frame[0][0].coords, cgframe[0][0].coords)
def test_frame_accept_path(self):
"""Test that Frame accepts :class:`pathlib.Path` arguments."""
_ = Frame(self.data_dir.joinpath("water.gro"),
self.data_dir.joinpath("water.xtc"))
def test_frame_read_xtc_simpletraj_numframes(self):
frame = Frame(gro="test/data/water.gro",
xtc="test/data/water.xtc",
xtc_reader="simpletraj")
self.assertEqual(11, frame.numframes)
def test_frame_any_read_unsupported(self):
with self.assertRaises(UnsupportedFormatException):
_ = Frame(self.data_dir.joinpath("dppc.map"))
def test_frame_read_zero_box(self):
frame = Frame(self.data_dir.joinpath("polyethene.gro"))
self.assertIsNone(frame.unitcell_lengths)
def test_frame_read_pdb_nobox(self):
"""Test reading a PDB with zero box volume."""
frame = Frame(self.data_dir.joinpath("water-nobox.pdb"))
self.check_reference_frame(frame, check_box=False)
def test_mapping_weights_geom(self):
frame = Frame("test/data/two.gro")
mapping = Mapping("test/data/two.map", DummyOptions)
cg = mapping.apply(frame)
np.testing.assert_allclose(np.array([1.5, 1.5, 1.5]), cg[0][0].coords)
def test_frame_simpletraj_read_xtc(self):
frame = Frame(gro="test/data/water.gro",
xtc="test/data/water.xtc",
xtc_reader="simpletraj")
self.helper_read_xtc(frame)
def test_raise_nonmatching_system_mdtraj(self):
with self.assertRaises(NonMatchingSystemError):
_ = Frame(self.data_dir.joinpath("water.gro"),
self.data_dir.joinpath("sugar.xtc"))
def test_frame_read_xtc_numframes(self):
frame = Frame(self.data_dir.joinpath("water.gro"),
self.data_dir.joinpath("water.xtc"))
self.assertEqual(11, frame.n_frames)
def test_frame_mdtraj_read_gro(self):
logging.disable(logging.WARNING)
frame = Frame("test/data/water.gro", xtc_reader="mdtraj")
logging.disable(logging.NOTSET)
self.helper_read_xtc(frame, first_only=True, skip_names=True)
def test_frame_read_xtc(self):
frame = Frame(self.data_dir.joinpath("water.gro"),
self.data_dir.joinpath("water.xtc"))
self.check_reference_trajectory(frame)
def test_frame_output_gro(self):
frame = Frame("test/data/water.gro")
frame.output("water-out.gro", format="gro")
self.assertTrue(filecmp.cmp("test/data/water.gro", "water-out.gro"))
os.remove("water-out.gro")
