def test_forcefield(self):
atoms = {'H': 'H', 'C': 'C', 'O': 'O'}
bonds = {(u'C', u'O'): [1000, 1.4115], (u'C', u'H'): [1000, 1.1041],
(u'C', u'C'): [1000, 1.5075]}
angles = {(u'C', u'C', u'H'): [42.9, 110.1],
(u'H', u'C', u'H'): [38.5, 109.47],
(u'H', u'C', u'O'): [56.0, 109.48],
(u'C', u'C', u'O'): [86.0, 108.54],
(u'C', u'O', u'C'): [74.5, 108.05]}
dihedrals = {(u'H', u'C', u'O', u'C'): [0.0, 0.0, -0.73, 0.0],
(u'H', u'C', u'C', u'O'): [0.0, 0.0, 0.28, 0.0],
(u'C', u'C', u'O', u'C'): [1.76, 0.67, 0.04, 0.0],
(u'H', u'C', u'C', u'H'): [0.0, 0.0, 0.28, 0.0],
(u'O', u'C', u'C', u'O'): [0.41, -2.1, -0.6, -0.82]}
pairs = {(u'C', u'C'): [14976.0, 0.3236, 637.6],
(u'H', u'H'): [2649.6, 0.2674, 27.22],
(u'O', u'O'): [75844.8, 0.2461, 396.9]}
self.assertEqual(self.forcefield.atoms, atoms)
self.assertEqual(self.forcefield.bonds, bonds)
self.assertEqual(self.forcefield.angles, angles)
self.assertEqual(self.forcefield.dihedrals, dihedrals)
self.assertEqual(self.forcefield.pairs, pairs)
ff = ForceField.from_dict(self.forcefield.as_dict())
self.assertEqual(ff.atoms, atoms)
self.assertEqual(ff.bonds, bonds)
self.assertEqual(ff.angles, angles)
self.assertEqual(ff.dihedrals, dihedrals)
self.assertEqual(ff.pairs, pairs)
def setUp(self):
self.polymer_linear = Molecule.from_file(
os.path.join(test_dir, "polymer_linear.xyz"))
charges = [-0.1187, 0.0861, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.1187, 0.0861,
0.0861, 0.0861]
ff_map = ["C3", "H3", "H3", "H3", "O", "C2", "H2",
"H2", "C2", "H2", "H2", "O", "C2", "H2",
"H2", "C2", "H2", "H2", "O", "C2", "H2",
"H2", "C2", "H2", "H2", "O", "C2", "H2",
"H2", "C2", "H2", "H2", "O", "C2", "H2",
"H2", "C2", "H2", "H2", "O", "C2", "H2",
"H2", "C2", "H2", "H2", "O", "C3", "H3", "H3", "H3"]
self.polymer_linear.add_site_property("charge", charges)
self.polymer_linear.add_site_property("ff_map", ff_map)
self.topology = Topology.from_molecule(self.polymer_linear)
self.forcefield = ForceField.from_file(
os.path.join(test_dir, "ffmap_data.yaml"))
box_size = [[0.0, 50],
[0.0, 50],
[0.0, 50]]
self.lammps_ff_data = LammpsForceFieldData.from_forcefield_and_topology(
[self.polymer_linear], [1], box_size, self.polymer_linear,
self.forcefield, [self.topology])
def setUpClass(cls):
polymer_chain = Molecule.from_file(os.path.join(test_dir, "polymer_chain.xyz"))
polymer_linear = Molecule.from_file(os.path.join(test_dir, "polymer_linear.xyz"))
cls.polymer_matrix = Molecule.from_file(os.path.join(test_dir, "polymer_matrix.xyz"))
charges = [-0.1187, 0.0861, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.1187, 0.0861,
0.0861, 0.0861]
polymer_linear.add_site_property("charge", charges)
topology = Topology.from_molecule(polymer_linear)
cls.polymer_linear_ff_decorated = Molecule.from_file(
os.path.join(test_dir,"polymer_linear.xyz"))
ff_map = ['C2', 'H3', 'H2', 'H3', 'O', 'C3', 'H2', 'H3', 'C2', 'H3',
'H2', 'O', 'C2', 'H3', 'H2', 'C3', 'H2', 'H3', 'O', 'C3',
'H2', 'H3', 'C2', 'H3', 'H2', 'O', 'C2', 'H3', 'H2', 'C3',
'H2', 'H3', 'O', 'C3', 'H2', 'H3', 'C2', 'H3', 'H2', 'O',
'C2', 'H3', 'H2', 'C3', 'H2', 'H3', 'O', 'C3', 'H2', 'H3', 'H2']
cls.polymer_linear_ff_decorated.add_site_property("ff_map", ff_map)
atoms = OrderedDict([("C", "C"), ("H", "H"), ("O", "O")])
bonds = OrderedDict([((u'C', u'O'), [1000, 1.4115]),
((u'C', u'H'), [1000, 1.1041]),
((u'C', u'C'), [1000, 1.5075])])
pairs = OrderedDict([((u'O', u'O'), [75844.8, 0.2461, 396.9]),
((u'H', u'H'), [2649.6, 0.2674, 27.22]),
((u'C', u'C'), [14976.0, 0.3236, 637.6])])
angles = OrderedDict([((u'C', u'C', u'H'), [42.9, 110.1]),
((u'H', u'C', u'H'), [38.5, 109.47]),
((u'H', u'C', u'O'), [56.0, 109.48]),
((u'C', u'C', u'O'), [86.0, 108.54]),
((u'C', u'O', u'C'), [74.5, 108.05])])
dihedrals = OrderedDict([((u'H', u'C', u'O', u'C'), [0.0, 0.0, -0.73, 0.0]),
((u'H', u'C', u'C', u'H'), [0.0, 0.0, 0.28, 0.0]),
((u'C', u'C', u'O', u'C'), [1.76, 0.67, 0.04, 0.0]),
((u'H', u'C', u'C', u'O'), [0.0, 0.0, 0.28, 0.0]),
((u'O', u'C', u'C', u'O'), [0.41, -2.1, -0.6, -0.82])])
forcefield = ForceField(atoms, bonds, angles, dihedrals=dihedrals, pairs=pairs)
cls.molecules = [polymer_chain] * 3
cls.mols_number = [7, 3, 1]
box_size = [[0.0, 50], [0.0, 50], [0.0, 50]]
cls.topologies = [topology] * len(cls.molecules)
cls.lammps_ff_data_1 = LammpsForceFieldData.from_forcefield_and_topology(
cls.molecules, cls.mols_number, box_size, cls.polymer_matrix,
forcefield, cls.topologies)
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:
top = Topology.from_file('mol.rtf')
except TopCorruptionException:
correct_corrupted_top_files('mol.rtf', 'gaff_data.txt')
top = Topology.from_file('mol.rtf')
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 setUp(self):
# DMOE = Dimethoxyethane
self.dmoe = Molecule.from_file(os.path.join(test_dir, "dmoe.xyz"))
dmoe_charges = [-0.10, 0.09, 0.09, 0.09,
-0.34, -0.01, 0.09, 0.09,
-0.01, 0.09, 0.09, -0.34,
-0.10, 0.09, 0.09, 0.09]
self.dmoe.add_site_property("charge", dmoe_charges)
ff_map = ["C3", "H3", "H3", "H3",
"O", "C2", "H2", "H2",
"C2", "H2", "H2", "O",
"C3", "H3", "H3", "H3"]
self.dmoe.add_site_property("ff_map", ff_map)
self.topology = Topology.from_molecule(self.dmoe, ff_map="ff_map")
self.forcefield = ForceField.from_file(
os.path.join(test_dir, "ffmap_data.yaml"))
self.box_size = [[0.0, 10], [0.0, 10], [0.0, 10]]
self.lammps_ff_data = \
LammpsForceFieldData.from_forcefield_and_topology(
[self.dmoe], [1], self.box_size, self.dmoe, self.forcefield, [self.topology])
def setUpClass(cls):
atoms = OrderedDict([('hw', 'h'), ('ow', 'o')])
bonds = OrderedDict([((u'hw', u'ow'), [553.0, 0.957]),
((u'hw', u'hw'), [553.0, 1.513])])
angles = OrderedDict([((u'hw', u'ow', u'hw'), [0.0, 104.52])])
vdws = OrderedDict([(u'hw', [0.0, 0.0]), (u'ow', [1.7683, 0.1520])])
forcefield = ForceField(atoms, bonds, angles, vdws=vdws)
h2o_coords = [[9.626, 6.787, 12.673], [9.626, 8.420, 12.673],
[10.203, 7.604, 12.673]]
h2o = Molecule(["H", "H", "O"], h2o_coords)
# h2o, h-o, h-o, h=1, h=2, o=3
top_atoms = [['h', 'hw'], ['o', 'ow']]
top_bonds = [[1, 3, ('hw', 'ow')], [2, 3, ('hw', 'ow')]]
top_angles = [[1, 3, 2, ('hw', 'ow', 'hw')]]
topology = Topology(top_atoms, top_bonds, top_angles)
mols = [h2o]
mols_number = [1]
box_size = [[0.0, 10.0], [0.0, 10.0], [0.0, 10.0]]
molecule = h2o
topologies = [topology]
cls.lammps_ff_data = LammpsForceFieldData.from_forcefield_and_topology(
mols, mols_number, box_size, molecule, forcefield, topologies)
def setUpClass(cls):
polymer = Molecule.from_file(os.path.join(test_dir, "polymer.xyz"))
cls.topology = Topology.from_molecule(polymer, tol=0.1)
cls.forcefield = ForceField.from_file(os.path.join(test_dir,
"ff_data.yaml"))
def setUpClass(cls):
polymer = Molecule.from_file(os.path.join(test_dir, "polymer.xyz"))
cls.monomer = Molecule.from_file(os.path.join(test_dir, "monomer.xyz"))
cls.topology = Topology.from_molecule(polymer, tol=0.1)
cls.forcefield = ForceField.from_file(
os.path.join(test_dir, "ff_data.yaml"))
def test_forcefield_serialization(self):
ff = ForceField.from_dict(self.forcefield.as_dict())
self.assertDictEqual(self.forcefield.as_dict(), ff.as_dict())