def initialize_system(dt=0.001,
temperature=100,
forcefield_file='forcefield/smirnoff99Frosst.offxml',
smiles="C1CCCCC1"):
mol = OEMol()
# OEParseSmiles(mol, 'CCOCCSCC')
# OEParseSmiles(mol, 'c1ccccc1')
OEParseSmiles(mol, smiles)
# OEParseSmiles(mol, 'C([C@@H]1[C@H]([C@@H]([C@H](C(O1)O)O)O)O)O')
OEAddExplicitHydrogens(mol)
masses = get_masses(mol)
num_atoms = mol.NumAtoms()
topology = generateTopologyFromOEMol(mol)
ff = ForceField(get_data_filename(forcefield_file))
nrgs, total_params, offsets = system_builder.construct_energies(
ff, mol, False)
# dt = 0.0025
# friction = 10.0
# temperature = 300
# gradient descent
dt = dt
friction = 10.0
temperature = temperature
a, b, c = get_abc_coefficents(masses, dt, friction, temperature)
buf_size = estimate_buffer_size(1e-10, a)
print("BUFFER SIZE", buf_size)
omegaOpts = oeomega.OEOmegaOptions()
omegaOpts.SetMaxConfs(1)
omega = oeomega.OEOmega(omegaOpts)
omega.SetStrictStereo(False)
if not omega(mol):
assert 0
x0 = mol_coords_to_numpy_array(mol) / 10
intg = custom_ops.Integrator_double(dt, buf_size, num_atoms, total_params,
a, b, c)
context = custom_ops.Context_double(nrgs, intg)
x0 = minimizer.minimize_newton_cg(nrgs, x0, total_params)
return nrgs, offsets, intg, context, x0, total_params
def size_and_wbo_fingerprint(mol: oechem.OEMol):
"""Fingerprint with number of atoms in the mol and WBO between central atoms in the t142 param.
(WBO is Wiberg Bond Order.)
Note: The indices are the same in OpenEye and OFF molecules, so the
parameter indices are correct, even though they were calculated for the
OFF mol.
"""
oechem.OEAddExplicitHydrogens(mol)
params = smirnoff_param_utils.read_params_from_mol(mol)
return (
mol.NumAtoms(),
smirnoff_param_utils.calculate_t142_central_wbo(mol, params),
)
def initialize(input_smiles, gp):
train_reference_args = []
train_args = []
train_offset_idxs = []
train_charge_idxs = []
for smi_idx, smiles in enumerate(input_smiles):
print("processing", smiles, smi_idx, "/", len(input_smiles))
mol = OEMol()
OEParseSmiles(mol, smiles)
OEAddExplicitHydrogens(mol)
masses = get_masses(mol)
num_atoms = mol.NumAtoms()
omegaOpts = oeomega.OEOmegaOptions()
omegaOpts.SetMaxConfs(1)
omega = oeomega.OEOmega(omegaOpts)
omega.SetStrictStereo(False)
if not omega(mol):
assert 0
topology = generateTopologyFromOEMol(mol)
reference_forcefield_file = 'forcefield/smirnoff99Frosst_perturbed.offxml'
ff = ForceField(get_data_filename(reference_forcefield_file))
params = system_builder.construct_energies(ff, mol, True)
train_reference_args.append((params[0], params[1], masses, mol))
params = system_builder.construct_energies(ff, mol, False)
# global_params = args[0]
# nrg_params = args[1]
# total_params = args[2]
# masses = args[3]
# mol = args[4]
# charge_idxs = args[5]
train_args.append((gp, params[0], params[1], masses, mol, params[3]))
train_offset_idxs.append(params[2])
train_charge_idxs.append(params[3])
label_confs = [generate_conformations(a) for a in train_reference_args]
return train_args, train_offset_idxs, train_charge_idxs, label_confs
def __init__(self, mol: oechem.OEMol):
"""
mol (oechem.OEMol): OEMol object
"""
self.num_atoms = mol.NumAtoms()
self.adj_mat = self._get_adjacency_matrix(mol)