def setUpClass(cls):
mass_info = [
("A", "H"),
("B", Element("C")),
("C", Element("O")),
("D", 1.00794),
]
nonbond_coeffs = [
[1, 1, 1.1225],
[1, 1.175, 1.31894],
[1, 1.55, 1.73988],
[1, 1, 1.1225],
[1, 1.35, 4],
[1, 1.725, 1.93631],
[1, 1.175, 1.31894],
[1, 2.1, 4],
[1, 1.55, 1.73988],
[1, 1, 1.1225],
]
topo_coeffs = {
"Bond Coeffs": [
{"coeffs": [50, 0.659469], "types": [("A", "B"), ("C", "D")]},
{"coeffs": [50, 0.855906], "types": [("B", "C")]},
]
}
cls.virus = ForceField(mass_info=mass_info, nonbond_coeffs=nonbond_coeffs, topo_coeffs=topo_coeffs)
cls.ethane = ForceField.from_file(os.path.join(test_dir, "ff_ethane.yaml"))
def setUpClass(cls):
mass_info = [("H", Element("H")), ("C", "C")]
pair_coeffs = [[0.0380000011, 2.449971454],
[0.1479999981, 3.6170487995]]
mol_coeffs = {
"Bond Coeffs": [{
"coeffs": [480.0, 1.34],
"types": [("C", "C")]
}, {
"coeffs": [363.4164, 1.08],
"types": [("H", "C")]
}],
"Angle Coeffs": [{
"coeffs": [90.0, 120.0],
"types": [("C", "C", "C")]
}, {
"coeffs": [37.0, 120.0],
"types": [("H", "C", "C")]
}],
"Dihedral Coeffs": [{
"coeffs": [3.0, -1, 2],
"types": [("C", "C", "C", "C"), ("H", "C", "C", "C"),
("H", "C", "C", "H")]
}],
"Improper Coeffs": [{
"coeffs": [0.37, -1, 2],
"types": [("H", "C", "C", "C")]
}]
}
cls.benzene = ForceField(mass_info=mass_info,
pair_coeffs=pair_coeffs,
mol_coeffs=mol_coeffs)
cls.virus = ForceField.from_file(
os.path.join(test_dir, "ff_virus.yaml"))
def _get_gaussian_ff_top_single(self, filename=None):
"""
run antechamber using gaussian output file, then run parmchk
to generate missing force field parameters. Store and return
the force field and topology information in ff_mol.
Args:
filename: gaussian output file of the molecule
Returns:
Amberff namedtuple object that contains information on force field and
topology
"""
scratch = tempfile.gettempdir()
Amberff = namedtuple("Amberff", ["force_field", "topology"])
with ScratchDir(scratch,
copy_from_current_on_enter=True,
copy_to_current_on_exit=True) as d:
# self._convert_to_pdb(mol, 'mol.pdb')
# self.molname = filename.split('.')[0]
self._run_antechamber(filename)
self._run_parmchk()
# if antechamber can't find parameters go to gaff_example.dat
try:
mol = Molecule.from_file('mol.rtf')
print('mol.rtf file exists')
except TopCorruptionException:
correct_corrupted_top_files('mol.rtf', 'gaff_data.txt')
top = Topology.from_file('mol.rtf')
print('mol.rtf file does not exist')
try:
gff = ForceField.from_file('mol.frcmod')
except FFCorruptionException:
correct_corrupted_frcmod_files('ANTECHAMBER.FRCMOD',
'gaff_data.txt')
gff = ForceField.from_file('ANTECHAMBER.FRCMOD')
# gff.set_atom_mappings('ANTECHAMBER_AC.AC')
# gff.read_charges()
# decorate the molecule with the sire property "atomname"
#mol.add_site_property("atomname", (list(gff.atom_index.values())))
return Amberff(gff, top)
def setUpClass(cls):
mass_info = [("A", "H"), ("B", Element("C")),
("C", Element("O")), ("D", 1.00794)]
nonbond_coeffs = [[1, 1, 1.1225], [1, 1.175, 1.31894],
[1, 1.55, 1.73988], [1, 1, 1.1225 ],
[1, 1.35, 4], [1, 1.725, 1.93631],
[1, 1.175, 1.31894], [1, 2.1, 4],
[1, 1.55, 1.73988], [1, 1, 1.1225 ]]
topo_coeffs = {"Bond Coeffs": [{"coeffs": [50, 0.659469],
"types": [("A", "B"), ("C", "D")]},
{"coeffs": [50, 0.855906],
"types": [("B", "C")]}]}
cls.virus = ForceField(mass_info=mass_info,
nonbond_coeffs=nonbond_coeffs,
topo_coeffs=topo_coeffs)
cls.ethane = ForceField.from_file(os.path.join(test_dir,
"ff_ethane.yaml"))
def setUpClass(cls):
mass_info = [("H", Element("H")), ("C", "C")]
pair_coeffs = [[0.0380000011, 2.449971454],
[0.1479999981, 3.6170487995]]
mol_coeffs = {
"Bond Coeffs":
[{"coeffs": [480.0, 1.34], "types": [("C", "C")]},
{"coeffs": [363.4164, 1.08], "types": [("H", "C")]}],
"Angle Coeffs":
[{"coeffs": [90.0, 120.0], "types": [("C", "C", "C")]},
{"coeffs": [37.0, 120.0], "types": [("H", "C", "C")]}],
"Dihedral Coeffs":
[{"coeffs": [3.0, -1, 2], "types": [("C", "C", "C", "C"),
("H", "C", "C", "C"),
("H", "C", "C", "H")]}],
"Improper Coeffs": [{"coeffs": [0.37, -1, 2],
"types": [("H", "C", "C", "C")]}]
}
cls.benzene = ForceField(mass_info=mass_info, pair_coeffs=pair_coeffs,
mol_coeffs=mol_coeffs)
cls.virus = ForceField.from_file(os.path.join(test_dir,
"ff_virus.yaml"))
def test_from_ff_and_topologies(self):
ff = ForceField.from_file(os.path.join(test_dir, "ff_peptide.yaml"))
with open(os.path.join(test_dir, "topologies_peptide.json")) as f:
topo_dicts = json.load(f)
topologies = [Topology.from_dict(d) for d in topo_dicts]
peptide = LammpsData.\
from_ff_and_topologies(ff=ff, topologies=topologies,
box_bounds=[[-50, 150]] * 3)
self.assertListEqual(peptide.masses, ff.masses)
force_field = ff.get_pair_coeffs()
for kw in ff.mol_coeffs.keys():
sec, _ = ff.get_coeffs_and_mapper(kw)
force_field.update(sec)
self.assertDictEqual(peptide.force_field, force_field)
back_atom_map = {v: k for k, v in ff.atom_map.items()}
# test the 1st topology, the peptide
pep = topologies[0]
# atoms and velocities sections
i = random.randint(0, len(pep.sites) - 1)
site = pep.sites[i]
in_atoms = peptide.atoms[i]
self.assertEqual(in_atoms["molecule-ID"], 1)
self.assertEqual(in_atoms["id"], i + 1)
self.assertEqual(in_atoms["type"],
ff.atom_map[site.properties["ff_map"]])
self.assertEqual(in_atoms["q"], pep.charges[i])
self.assertEqual(in_atoms["x"], site.x)
self.assertEqual(in_atoms["y"], site.y)
self.assertEqual(in_atoms["z"], site.z)
in_velos = peptide.velocities[i]
self.assertEqual(in_velos["id"], i + 1)
self.assertListEqual(in_velos["velocity"], pep.velocities[i])
# topology sections
for t in ["Bond", "Angle", "Dihedral", "Improper"]:
topo_sec = "%ss" % t
ff_sec = "%s Coeffs" % t
kw = t.lower()
i = random.randint(0, len(pep.topologies[topo_sec]) - 1)
sample = pep.topologies[topo_sec][i]
in_topos = peptide.topology[topo_sec][i]
self.assertEqual(in_topos["id"], i + 1, "%s" % t)
np.testing.assert_array_equal(in_topos[kw],
np.array(sample) + 1, "%s" % t)
topo_type_id = in_topos["type"]
types = ff.mol_coeffs[ff_sec][topo_type_id - 1]["types"]
sample_type = tuple([pep.sites[j].properties["ff_map"]
for j in sample])
self.assertIn(sample_type, types, "%s" % t)
# test a random solvent (water) molecule
i = random.randint(1, len(topologies) - 1)
solv = topologies[i]
stack = {"Atoms": 0, "Bonds": 0, "Angles": 0}
for topo in topologies[:i]:
stack["Atoms"] += len(topo.sites)
stack["Bonds"] += len(topo.topologies["Bonds"])
stack["Angles"] += len(topo.topologies["Angles"])
# atoms and velocities sections
in_atoms = [d for d in peptide.atoms if d["molecule-ID"] == i + 1]
self.assertEqual(len(in_atoms), len(solv.sites))
aids, types, charges, coords = [], [], [], []
for d in in_atoms:
aids.append(d["id"])
types.append(d["type"])
charges.append(d["q"])
coords.append([d["x"], d["y"], d["z"]])
np.testing.assert_array_equal(aids, np.arange(len(solv.sites))
+ stack["Atoms"] + 1)
self.assertListEqual(types, [ff.atom_map[t] for t in solv.types])
self.assertListEqual(charges, solv.charges)
np.testing.assert_array_equal(coords, solv.sites.cart_coords)
in_velos = peptide.velocities[stack["Atoms"]: stack["Atoms"]
+ len(in_atoms)]
vids, velocities = [], []
for d in in_velos:
vids.append(d["id"])
velocities.append(d["velocity"])
self.assertListEqual(vids, aids)
np.testing.assert_array_equal(velocities, solv.velocities)
# topology sections
for t in ["Bond", "Angle"]:
topo_sec = "%ss" % t
ff_sec = "%s Coeffs" % t
kw = t.lower()
sample = solv.topologies[topo_sec][0]
i = stack[topo_sec]
in_topos = peptide.topology[topo_sec][i]
self.assertEqual(in_topos["id"], i + 1, "%s" % t)
np.testing.assert_array_equal(in_topos[kw], np.array(sample)
+ stack["Atoms"] + 1, "%s" % t)
topo_type_id = in_topos["type"]
types = ff.mol_coeffs[ff_sec][topo_type_id - 1]["types"]
sample_type = tuple([solv.sites[j].properties["ff_map"]
for j in sample])
self.assertIn(sample_type, types, "%s" % t)
def test_from_ff_and_topologies(self):
ff = ForceField.from_file(os.path.join(test_dir, "ff_peptide.yaml"))
with open(os.path.join(test_dir, "topologies_peptide.json")) as f:
topo_dicts = json.load(f)
topologies = [Topology.from_dict(d) for d in topo_dicts]
peptide = LammpsData.\
from_ff_and_topologies(ff=ff, topologies=topologies,
box_bounds=[[-50, 150]] * 3)
self.assertListEqual(peptide.masses, ff.masses)
force_field = ff.get_pair_coeffs()
for kw in ff.mol_coeffs.keys():
sec, _ = ff.get_coeffs_and_mapper(kw)
force_field.update(sec)
self.assertDictEqual(peptide.force_field, force_field)
back_atom_map = {v: k for k, v in ff.atom_map.items()}
# test the 1st topology, the peptide
pep = topologies[0]
# atoms and velocities sections
i = random.randint(0, len(pep.sites) - 1)
site = pep.sites[i]
in_atoms = peptide.atoms[i]
self.assertEqual(in_atoms["molecule-ID"], 1)
self.assertEqual(in_atoms["id"], i + 1)
self.assertEqual(in_atoms["type"],
ff.atom_map[site.properties["ff_map"]])
self.assertEqual(in_atoms["q"], pep.charges[i])
self.assertEqual(in_atoms["x"], site.x)
self.assertEqual(in_atoms["y"], site.y)
self.assertEqual(in_atoms["z"], site.z)
in_velos = peptide.velocities[i]
self.assertEqual(in_velos["id"], i + 1)
self.assertListEqual(in_velos["velocity"], pep.velocities[i])
# topology sections
for t in ["Bond", "Angle", "Dihedral", "Improper"]:
topo_sec = "%ss" % t
ff_sec = "%s Coeffs" % t
kw = t.lower()
i = random.randint(0, len(pep.topologies[topo_sec]) - 1)
sample = pep.topologies[topo_sec][i]
in_topos = peptide.topology[topo_sec][i]
self.assertEqual(in_topos["id"], i + 1, "%s" % t)
np.testing.assert_array_equal(in_topos[kw],
np.array(sample) + 1, "%s" % t)
topo_type_id = in_topos["type"]
types = ff.mol_coeffs[ff_sec][topo_type_id - 1]["types"]
sample_type = tuple(
[pep.sites[j].properties["ff_map"] for j in sample])
self.assertIn(sample_type, types, "%s" % t)
# test a random solvent (water) molecule
i = random.randint(1, len(topologies) - 1)
solv = topologies[i]
stack = {"Atoms": 0, "Bonds": 0, "Angles": 0}
for topo in topologies[:i]:
stack["Atoms"] += len(topo.sites)
stack["Bonds"] += len(topo.topologies["Bonds"])
stack["Angles"] += len(topo.topologies["Angles"])
# atoms and velocities sections
in_atoms = [d for d in peptide.atoms if d["molecule-ID"] == i + 1]
self.assertEqual(len(in_atoms), len(solv.sites))
aids, types, charges, coords = [], [], [], []
for d in in_atoms:
aids.append(d["id"])
types.append(d["type"])
charges.append(d["q"])
coords.append([d["x"], d["y"], d["z"]])
np.testing.assert_array_equal(
aids,
np.arange(len(solv.sites)) + stack["Atoms"] + 1)
self.assertListEqual(types, [ff.atom_map[t] for t in solv.types])
self.assertListEqual(charges, solv.charges)
np.testing.assert_array_equal(coords, solv.sites.cart_coords)
in_velos = peptide.velocities[stack["Atoms"]:stack["Atoms"] +
len(in_atoms)]
vids, velocities = [], []
for d in in_velos:
vids.append(d["id"])
velocities.append(d["velocity"])
self.assertListEqual(vids, aids)
np.testing.assert_array_equal(velocities, solv.velocities)
# topology sections
for t in ["Bond", "Angle"]:
topo_sec = "%ss" % t
ff_sec = "%s Coeffs" % t
kw = t.lower()
sample = solv.topologies[topo_sec][0]
i = stack[topo_sec]
in_topos = peptide.topology[topo_sec][i]
self.assertEqual(in_topos["id"], i + 1, "%s" % t)
np.testing.assert_array_equal(
in_topos[kw],
np.array(sample) + stack["Atoms"] + 1, "%s" % t)
topo_type_id = in_topos["type"]
types = ff.mol_coeffs[ff_sec][topo_type_id - 1]["types"]
sample_type = tuple(
[solv.sites[j].properties["ff_map"] for j in sample])
self.assertIn(sample_type, types, "%s" % t)
