def test_frame_mdtraj_read_xtc(self):
logging.disable(logging.WARNING)
frame = Frame(gro="test/data/water.gro", xtc="test/data/water.xtc",
xtc_reader="mdtraj")
logging.disable(logging.NOTSET)
self.assertEqual(663, frame.natoms)
# These are the coordinates from the gro file
np.testing.assert_allclose(np.array([0.696, 1.33, 1.211]),
frame.residues[0].atoms[0].coords)
np.testing.assert_allclose(np.array([1.89868, 1.89868, 1.89868]),
frame.box)
frame.next_frame()
# These coordinates are from the xtc file
np.testing.assert_allclose(np.array([1.176, 1.152, 1.586]),
frame.residues[0].atoms[0].coords)
np.testing.assert_allclose(np.array([1.9052, 1.9052, 1.9052]),
frame.box)
frame.next_frame()
np.testing.assert_allclose(np.array([1.122, 1.130, 1.534]),
frame.residues[0].atoms[0].coords)
np.testing.assert_allclose(np.array([1.90325272, 1.90325272, 1.90325272]),
frame.box)
def test_mapping_pbc(self):
frame = Frame(self.data_dir.joinpath("pbcwater.gro"))
mapping = Mapping(self.data_dir.joinpath("water.map"), DummyOptions)
cg_frame = mapping.apply(frame)
np.testing.assert_allclose(
frame.atom(0).coords,
cg_frame.atom(0).coords)
def test_bondset_boltzmann_invert(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()
self.support_check_mean_fc(measure["ALLA"], 1)
def test_bondset_boltzmann_invert(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()
self.support_check_mean_fc(measure["ALLA"], 1)
def test_frame_output_gro(self):
frame = Frame(self.data_dir.joinpath("water.gro"))
with tempfile.TemporaryDirectory() as tmpdir:
tmp_path = pathlib.Path(tmpdir)
frame.save(tmp_path.joinpath("water-out.gro"))
self.assertTrue(
filecmp.cmp(
self.data_dir.joinpath("water.gro"),
tmp_path.joinpath("water-out.gro"),
))
def test_frame_write_xtc_mdtraj(self):
try:
os.remove("water_test2.xtc")
except IOError:
pass
logging.disable(logging.WARNING)
frame = Frame(gro="test/data/water.gro", xtc="test/data/water.xtc",
xtc_reader="mdtraj")
logging.disable(logging.NOTSET)
while frame.next_frame():
frame.write_xtc("water_test2.xtc")
def test_frame_write_xtc_mdtraj(self):
try:
os.remove("water_test2.xtc")
except IOError:
pass
logging.disable(logging.WARNING)
frame = Frame(gro="test/data/water.gro",
xtc="test/data/water.xtc",
xtc_reader="mdtraj")
logging.disable(logging.NOTSET)
while frame.next_frame():
frame.write_xtc("water_test2.xtc")
def test_frame_write_xtc(self):
"""Test that :class:`Frame` can save a trajectory file."""
frame = Frame(self.data_dir.joinpath("water.gro"),
self.data_dir.joinpath("water.xtc"))
with tempfile.TemporaryDirectory() as tmpdir:
tmp_path = pathlib.Path(tmpdir)
frame.save(tmp_path.joinpath("water.xtc"))
self.assertTrue(
util.compare_trajectories(
self.data_dir.joinpath("water.xtc"),
tmp_path.joinpath("water.xtc"),
topology_file=self.data_dir.joinpath("water.gro"),
))
def test_frame_read_xtc_mdtraj_numframes(self):
logging.disable(logging.WARNING)
frame = Frame(gro="test/data/water.gro",
xtc="test/data/water.xtc",
xtc_reader="mdtraj")
logging.disable(logging.NOTSET)
self.assertEqual(11, frame.numframes)
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 __init__(self, config):
self.config = config
self.in_frame = Frame(
topology_file=self.config.topology,
trajectory_file=self.config.trajectory, # May be None
frame_start=self.config.begin,
frame_end=self.config.end,
)
self.mapping = None
self.out_frame = self.in_frame
if self.config.mapping:
self.mapping, self.out_frame = self.apply_mapping(self.in_frame)
if self.out_frame.natoms == 0:
# The following steps won't work with frames containing no atoms
logger.warning(
"Mapped trajectory contains no atoms - check your mapping file is correct!"
)
return
self.bondset = None
if self.config.bondset:
self.bondset = BondSet(self.config.bondset, self.config)
self.measure_bonds()
if self.config.output_xtc:
self.out_frame.save(self.get_output_filepath("xtc"))
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_pbc(self):
bondset = BondSet("test/data/polyethene.bnd", DummyOptions)
frame = Frame("test/data/pbcpolyethene.gro")
bondset.apply(frame)
bondset.boltzmann_invert()
for bond in bondset.get_bond_lengths("ETH", True):
self.assertAlmostEqual(1., bond.eqm)
self.assertEqual(float("inf"), bond.fconst)
def test_frame_mdtraj_read_xtc(self):
logging.disable(logging.WARNING)
frame = Frame(gro="test/data/water.gro",
xtc="test/data/water.xtc",
xtc_reader="mdtraj")
logging.disable(logging.NOTSET)
self.helper_read_xtc(frame, skip_names=True)
def test_mapping_apply(self):
mapping = Mapping("test/data/water.map", DummyOptions)
frame = Frame("test/data/water.gro")
cgframe = mapping.apply(frame)
self.assertEqual(len(frame), len(cgframe))
cgframe.output("water-cg.gro", format="gro")
self.assertTrue(filecmp.cmp("test/data/water-cg.gro", "water-cg.gro"))
os.remove("water-cg.gro")
def test_bondset_boltzmann_invert_func_forms(self):
class FuncFormOptions(DummyOptions):
length_form = "CosHarmonic"
angle_form = "Harmonic"
dihedral_form = "MartiniDefaultLength"
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"], 3)
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_mapping_weights_geom(self):
frame = Frame(self.data_dir.joinpath("two.gro"))
mapping = Mapping(self.data_dir.joinpath("two.map"), DummyOptions)
cg_frame = mapping.apply(frame)
np.testing.assert_allclose(np.array([[1.5, 1.5, 1.5]]),
cg_frame.residue(0).atom(0).coords)
def test_mapping_charges(self):
mapping = Mapping("test/data/dppc.map", DummyOptions)
self.assertEqual(1, mapping["DPPC"][0].charge)
self.assertEqual(-1, mapping["DPPC"][1].charge)
frame = Frame("test/data/dppc.gro")
cgframe = mapping.apply(frame)
self.assertEqual(1, cgframe[0][0].charge)
self.assertEqual(-1, cgframe[0][1].charge)
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_virtual_mapping_weights_geom(self):
frame = Frame(self.data_dir.joinpath("martini3/four.gro"))
mapping = Mapping(self.data_dir.joinpath("martini3/four.map"),
DummyOptions)
cg_frame = mapping.apply(frame)
np.testing.assert_allclose(np.array([[2.5, 2.5, 2.5]]),
cg_frame.residue(0).atom(2).coords)
def test_mapping_weights_first(self):
frame = Frame("test/data/two.gro")
options = DummyOptions()
options.map_center = "first"
mapping = Mapping("test/data/two.map",
options,
itp="test/data/two.itp")
cg = mapping.apply(frame)
np.testing.assert_allclose(np.array([1., 1., 1.]), cg[0][0].coords)
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_bondset_pbc(self):
bondset = BondSet(self.data_dir.joinpath("polyethene.bnd"),
DummyOptions)
frame = Frame(self.data_dir.joinpath("pbcpolyethene.gro"))
bondset.apply(frame)
bondset.boltzmann_invert()
for bond in bondset.get_bond_lengths("ETH", True):
self.assertAlmostEqual(1.0, bond.eqm)
self.assertEqual(math.inf, bond.fconst)
def test_bondset_polymer(self):
bondset = BondSet("test/data/polyethene.bnd", DummyOptions)
frame = Frame("test/data/polyethene.gro")
bondset.apply(frame)
self.assertEqual(5, len(bondset["ETH"][0].values))
self.assertEqual(4, len(bondset["ETH"][1].values))
self.assertEqual(4, len(bondset["ETH"][2].values))
self.assertEqual(4, len(bondset["ETH"][3].values))
bondset.boltzmann_invert()
self.assertAlmostEqual(0.107, bondset["ETH"][0].eqm, delta=0.107 / 500)
self.assertAlmostEqual(0.107, bondset["ETH"][1].eqm, delta=0.107 / 500)
def test_mapping_weights_guess_mass(self):
frame = Frame("test/data/two.gro")
options = DummyOptions()
options.map_center = "mass"
mapping = Mapping("test/data/two.map", options)
cg = mapping.apply(frame)
np.testing.assert_allclose(np.array([1.922575, 1.922575, 1.922575],
dtype=np.float32),
cg[0][0].coords,
rtol=0.01)
def test_bondset_boltzmann_invert(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()
self.support_check_mean_fc(measure["ALLA"], 1)
def test_empty_result_frame(self):
"""Test that no error is raised when an empty output frame is encountered.
This is instead checked and logged as a warning in the outer script.
"""
frame = Frame(self.data_dir.joinpath("sugar.gro"))
mapping = Mapping(self.data_dir.joinpath("water.map"), DummyOptions)
cg_frame = mapping.apply(frame)
self.assertEqual(0, cg_frame.natoms)
self.assertEqual((1, 0, 3), cg_frame._trajectory.xyz.shape)
def test_mapping_weights_guess_mass(self):
frame = Frame(self.data_dir.joinpath("two.gro"))
options = DummyOptions()
options.map_center = "mass"
mapping = Mapping(self.data_dir.joinpath("two.map"), options)
cg_frame = mapping.apply(frame)
np.testing.assert_allclose(
np.array([[1.922575, 1.922575, 1.922575]], dtype=np.float32),
cg_frame.residue(0).atom(0).coords,
rtol=0.01,
)
def test_virtual_mapping_weights_guess_mass(self):
frame = Frame(self.data_dir.joinpath("martini3/four.gro"))
options = DummyOptions()
options.virtual_map_center = "mass"
mapping = Mapping(self.data_dir.joinpath("martini3/four.map"), options)
cg_frame = mapping.apply(frame)
np.testing.assert_allclose(
np.array([[2.83337, 2.83337, 2.83337]], dtype=np.float32),
cg_frame.residue(0).atom(2).coords,
rtol=0.01,
)
def test_mapping_apply(self):
mapping = Mapping(self.data_dir.joinpath("water.map"), DummyOptions)
frame = Frame(self.data_dir.joinpath("water.gro"))
cg_frame = mapping.apply(frame)
self.assertEqual(frame.natoms / 3, cg_frame.natoms)
cg_frame.save("water-cg.gro")
self.assertTrue(
filecmp.cmp(self.data_dir.joinpath("water-cg.gro"),
"water-cg.gro"))
os.remove("water-cg.gro")
def test_virtual_mapping_weights_mass(self):
frame = Frame(self.data_dir.joinpath("martini3/four.gro"))
options = DummyOptions()
options.virtual_map_center = "mass"
mapping = Mapping(
self.data_dir.joinpath("martini3/four.map"),
options,
itp_filename=self.data_dir.joinpath("martini3/four.itp"),
)
cg_frame = mapping.apply(frame)
np.testing.assert_allclose(np.array([[3.0, 3.0, 3.0]]),
cg_frame.residue(0).atom(2).coords)
def test_mapping_weights_first(self):
frame = Frame(self.data_dir.joinpath("two.gro"))
options = DummyOptions()
options.map_center = "first"
mapping = Mapping(
self.data_dir.joinpath("two.map"),
options,
itp_filename=self.data_dir.joinpath("two.itp"),
)
cg_frame = mapping.apply(frame)
np.testing.assert_allclose(np.array([[1.0, 1.0, 1.0]]),
cg_frame.residue(0).atom(0).coords)
def test_bondset_boltzmann_invert_manual_default_fc(self):
class FuncFormOptions(DummyOptions):
length_form = "MartiniDefaultLength"
angle_form = "MartiniDefaultAngle"
dihedral_form = "MartiniDefaultDihedral"
measure = BondSet(self.data_dir.joinpath("sugar.bnd"), FuncFormOptions)
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()
self.support_check_mean_fc(measure["ALLA"], 2)
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_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_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")