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_mapping_create(self):
mapping = Mapping("test/data/water.map", DummyOptions)
self.assertEqual(1, len(mapping))
self.assertTrue("SOL" in mapping)
self.assertEqual(1, len(mapping["SOL"]))
self.assertEqual(3, len(mapping["SOL"][0].atoms))
self.assertEqual("OW", mapping["SOL"][0].atoms[0])
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_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_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_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_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_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_mapping_itp_multi(self):
mapping = Mapping(
self.data_dir.joinpath("membrane/membrane.map"),
DummyOptions,
itp_filename=self.data_dir.joinpath("membrane/membrane.top"),
)
self.assertAlmostEqual(-1.2, mapping["POPE"][0].charge, delta=0.0001)
self.assertAlmostEqual(0, mapping["POPG"][0].charge, delta=0.0001)
self.assertAlmostEqual(94.9716, mapping["POPE"][0].mass, delta=0.0001)
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_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_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_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_virtual_mapping_create(self):
mapping = Mapping(self.data_dir.joinpath("martini3/naphthalene.map"),
DummyOptions)
self.assertEqual(1, len(mapping))
self.assertTrue("NAPH" in mapping)
self.assertEqual(5, len(mapping["NAPH"]))
self.assertTrue(isinstance(mapping["NAPH"][2], VirtualMap))
self.assertEqual(4, len(mapping["NAPH"][2].atoms))
self.assertEqual("R1", mapping["NAPH"][2].atoms[0])
self.assertEqual(1, [
isinstance(bead, VirtualMap) for bead in mapping["NAPH"]
].count(True))
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_mapping_create(self):
"""Test that a mapping can be correctly read from a file."""
mapping = Mapping(self.data_dir.joinpath("water.map"), DummyOptions)
self.assertEqual(2, len(mapping)) # SOL and HOH
self.assertTrue("SOL" in mapping)
sol_map = mapping["SOL"]
self.assertEqual(1, len(sol_map))
self.assertEqual(3, len(sol_map[0].atoms))
self.assertEqual("OW", sol_map[0].atoms[0])
self.assertEqual("HW1", sol_map[0].atoms[1])
self.assertEqual("HW2", sol_map[0].atoms[2])
def test_mapping_rename(self):
"""Test that an alternate mapping is created using MDTraj conventions."""
mapping = Mapping(self.data_dir.joinpath("water.map"), DummyOptions)
self.assertEqual(2, len(mapping)) # SOL and HOH
self.assertTrue("HOH" in mapping)
sol_map = mapping["HOH"]
self.assertEqual(1, len(sol_map))
self.assertEqual(3, len(sol_map[0].atoms))
self.assertEqual("O", sol_map[0].atoms[0])
self.assertEqual("H1", sol_map[0].atoms[1])
self.assertEqual("H2", sol_map[0].atoms[2])
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_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_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 apply_mapping(self, in_frame: Frame) -> typing.Tuple[Mapping, Frame]:
"""Map input frame to output using requested mapping file."""
mapping = Mapping(self.config.mapping,
self.config,
itp_filename=self.config.itp)
out_frame = mapping.apply(in_frame)
out_frame.save(self.get_output_filepath("gro"), frame_number=0)
if self.config.backmapper_resname and self.out_frame.n_frames > 1:
try:
self.train_backmapper(self.config.resname)
except ImportError:
logger.error("MDPlus must be installed to perform backmapping")
return mapping, out_frame
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_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_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_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_mapping_charges(self):
mapping = Mapping(self.data_dir.joinpath("dppc.map"), DummyOptions)
self.assertEqual(1, mapping["DPPC"][0].charge)
self.assertEqual(-1, mapping["DPPC"][1].charge)