def test_tautomer_transformation():
print(os.getcwd())
with open('data/exp_results.pickle', 'rb') as f:
exp_results = pickle.load(f)
name = 'molDWRow_298'
t1_smiles = exp_results[name]['t1-smiles']
t2_smiles = exp_results[name]['t2-smiles']
from_mol_tautomer_idx = 1
to_mol_tautomer_idx = 2
# generate both rdkit mol
mols = {
't1': neutromeratio.generate_rdkit_mol(t1_smiles),
't2': neutromeratio.generate_rdkit_mol(t2_smiles)
}
from_mol = mols[f"t{from_mol_tautomer_idx}"]
to_mol = mols[f"t{to_mol_tautomer_idx}"]
ani_input = neutromeratio.from_mol_to_ani_input(from_mol)
tautomer_transformation = neutromeratio.get_tautomer_transformation(
from_mol, to_mol)
atom_list = ani_input['ligand_atoms']
assert (atom_list == 'CCCCCOOHHHHHHHH')
assert (tautomer_transformation['hydrogen_idx'] == 11)
assert (tautomer_transformation['acceptor_idx'] == 5)
assert (tautomer_transformation['donor_idx'] == 2)
def test_neutromeratio_energy_calculations_with_dummy_atom():
# read in pregenerated traj
traj = neutromeratio.equilibrium.read_precalculated_md(
'neutromeratio/data/structure.pdb', 'neutromeratio/data/structure.dcd')
# read in exp_results.pickle
with open('data/exp_results.pickle', 'rb') as f:
exp_results = pickle.load(f)
# generate smiles
name = 'molDWRow_298'
t1_smiles = exp_results[name]['t1-smiles']
t2_smiles = exp_results[name]['t2-smiles']
from_mol_tautomer_idx = 1
to_mol_tautomer_idx = 2
# generate both rdkit mol
mols = {
't1': neutromeratio.generate_rdkit_mol(t1_smiles),
't2': neutromeratio.generate_rdkit_mol(t2_smiles)
}
from_mol = mols[f"t{from_mol_tautomer_idx}"]
to_mol = mols[f"t{to_mol_tautomer_idx}"]
ani_input = neutromeratio.from_mol_to_ani_input(from_mol)
# generate tautomer transformation
tautomer_transformation = neutromeratio.get_tautomer_transformation(
from_mol, to_mol)
atom_list = ani_input['ligand_atoms']
hydrogen_idx = tautomer_transformation['hydrogen_idx']
# overwrite the coordinates that rdkit generated with the first frame in the traj
x0 = traj[0]
platform = 'cpu'
device = torch.device(platform)
model = neutromeratio.ani.LinearAlchemicalANI(
alchemical_atoms=[hydrogen_idx], ani_input=ani_input, device=device)
model = model.to(device)
torch.set_num_threads(1)
energy_function = neutromeratio.ANI1_force_and_energy(
device=device,
model=model,
atom_list=atom_list,
platform=platform,
tautomer_transformation=tautomer_transformation)
energy_function.lambda_value = 0.0
x = energy_function.calculate_energy(x0)
x = x.value_in_unit(unit.kilocalorie_per_mole)
assert (x == -216698.91137287067)
def test_hybrid_topology():
with open('data/exp_results.pickle', 'rb') as f:
exp_results = pickle.load(f)
# specify the system you want to simulate
name = 'molDWRow_590'
from_mol_tautomer_idx = 1
to_mol_tautomer_idx = 2
t1_smiles = exp_results[name]['t1-smiles']
t2_smiles = exp_results[name]['t2-smiles']
# generate both rdkit mol
mols = {
't1': neutromeratio.generate_rdkit_mol(t1_smiles),
't2': neutromeratio.generate_rdkit_mol(t2_smiles)
}
from_mol = mols[f"t{from_mol_tautomer_idx}"]
to_mol = mols[f"t{to_mol_tautomer_idx}"]
ani_input = neutromeratio.from_mol_to_ani_input(from_mol)
tautomer_transformation = neutromeratio.get_tautomer_transformation(
from_mol, to_mol)
neutromeratio.generate_hybrid_structure(
ani_input, tautomer_transformation,
neutromeratio.ani.ANI1_force_and_energy)
assert (ani_input['hybrid_atoms'] == 'OCCCNCCCCCCHHHHHHHH')
ani_traj = md.Trajectory(
ani_input['hybrid_coords'].value_in_unit(unit.nanometer),
ani_input['hybrid_topology'])
e = ani_input['min_e']
assert (type(e) == unit.Quantity)
assert (type(tautomer_transformation['donor_hydrogen_idx']) == int)
e = e.value_in_unit(unit.kilocalorie_per_mole)
assert (e < -216698.91137612148 + 5)
def test_tautomer_class():
from neutromeratio.tautomers import Tautomer
print(os.getcwd())
with open("data/test_data/exp_results.pickle", "rb") as f:
exp_results = pickle.load(f)
name = "molDWRow_298"
t1_smiles = exp_results[name]["t1-smiles"]
t2_smiles = exp_results[name]["t2-smiles"]
from_mol_tautomer_idx = 1
to_mol_tautomer_idx = 2
# generate both rdkit mol
mols = {
"t1": neutromeratio.generate_rdkit_mol(t1_smiles),
"t2": neutromeratio.generate_rdkit_mol(t2_smiles),
}
from_mol = mols[f"t{from_mol_tautomer_idx}"]
to_mol = mols[f"t{to_mol_tautomer_idx}"]
t = Tautomer(name=name, initial_state_mol=from_mol, final_state_mol=to_mol)
t.perform_tautomer_transformation()
# name of the system
name = str(sys.argv[1])
# lambda state
lambda_value = float(sys.argv[2])
# platform
platform = str(sys.argv[3])
# number of steps
n_steps = int(sys.argv[4])
exp_results = pickle.load(open('../data/exp_results.pickle', 'rb'))
t1_smiles = exp_results[name]['t1-smiles']
t2_smiles = exp_results[name]['t2-smiles']
# generate both rdkit mol
mols = { 't1' : neutromeratio.generate_rdkit_mol(t1_smiles), 't2' : neutromeratio.generate_rdkit_mol(t2_smiles) }
from_mol = mols['t1']
to_mol = mols['t2']
ani_input = neutromeratio.from_mol_to_ani_input(from_mol)
tautomer_transformation = neutromeratio.get_tautomer_transformation(from_mol, to_mol)
neutromeratio.generate_hybrid_structure(ani_input, tautomer_transformation, neutromeratio.ani.ANI1_force_and_energy)
# define the alchemical atoms
alchemical_atoms=[tautomer_transformation['acceptor_hydrogen_idx'], tautomer_transformation['donor_hydrogen_idx']]
np.random.seed(0)
# extract hydrogen donor idx and hydrogen idx for from_mol
platform = 'cpu'
device = torch.device(platform)