def _get_ith_data(data_index, E, N, R, D, Q, Z):
num_atoms = N[data_index].item()
_tmp_data = Data()
_tmp_data.E = E[data_index].view(-1)
_tmp_data.N = N[data_index].view(-1)
_tmp_data.R = R[data_index, :num_atoms, :].view(-1, 3)
_tmp_data.D = D[data_index, :].view(-1, 3)
_tmp_data.Q = Q[data_index].view(-1)
_tmp_data.Z = Z[data_index, :num_atoms].view(-1)
return _tmp_data
def physnet_to_datalist(self,
N,
R,
E,
D,
Q,
Z,
num_mol,
mols,
efgs_batch,
EFG_R,
EFG_Z,
num_efg,
sol_data=None):
"""
load data from PhysNet structure to InMemoryDataset structure (more compact)
:return:
"""
from rdkit.Chem.inchi import MolToInchi
data_array = np.empty(num_mol, dtype=Data)
t0 = time.time()
Z_0 = Z[0, :]
n_heavy = len(Z_0) - (Z_0 == 0).sum() - (Z_0 == 1).sum()
jianing_to_dongdong_map = []
for i in tqdm(range(num_mol)):
if self.bond_atom_sep:
mol = mols[i]
else:
mol = None
# atomic infos
_tmp_Data = Data()
num_atoms = N[i]
_tmp_Data.N = num_atoms.view(-1)
_tmp_Data.R = R[i, :N[i]].view(-1, 3)
_tmp_Data.E = E[i].view(-1)
_tmp_Data.D = D[i].view(-1, 3)
_tmp_Data.Q = Q[i].view(-1)
_tmp_Data.Z = Z[i, :N[i]].view(-1)
if self.cal_efg:
_tmp_Data.atom_to_EFG_batch = efgs_batch[i, :N[i]].view(-1)
_tmp_Data.EFG_R = EFG_R[i, :num_efg[i]].view(-1, 3)
_tmp_Data.EFG_Z = EFG_Z[i, :num_efg[i]].view(-1)
_tmp_Data.EFG_N = num_efg[i].view(-1)
if sol_data is not None:
# find molecule from solvation csv file based on InChI, if found, add it
this_sol_data = sol_data.loc[sol_data["InChI"] == MolToInchi(mol)]
if this_sol_data.shape[0] == 1:
for key in sol_keys:
_tmp_Data.__setattr__(
key,
torch.as_tensor(this_sol_data.iloc[0][key]).view(-1))
jianing_to_dongdong_map.append(1)
else:
jianing_to_dongdong_map.append(0)
continue
_tmp_Data = self.pre_transform(
data=_tmp_Data,
edge_version=self.edge_version,
do_sort_edge=self.sort_edge,
cal_efg=self.cal_efg,
cutoff=self.cutoff,
extended_bond=self.extended_bond,
boundary_factor=self.boundary_factor,
type_3_body=self.type_3_body,
use_center=self.use_center,
mol=mol,
cal_3body_term=self.cal_3body_term,
bond_atom_sep=self.bond_atom_sep,
record_long_range=self.record_long_range)
data_array[i] = _tmp_Data
if sol_data is not None:
torch.save(torch.as_tensor(jianing_to_dongdong_map),
"jianing_to_dongdong_map_{}.pt".format(n_heavy))
data_list = [
data_array[i] for i in range(num_mol) if data_array[i] is not None
]
return data_list