def test_pairwise_ring_info(self):
from rdkit import Chem
mol = Chem.MolFromSmiles("c1ccccc1")
predict_dict = rdkit_utils.compute_pairwise_ring_info(mol)
assert all(pair == [(6, True)] for pair in predict_dict.values())
mol = Chem.MolFromSmiles("c1c2ccccc2ccc1")
predict_dict = rdkit_utils.compute_pairwise_ring_info(mol)
assert all(pair == [(6, True)] for pair in predict_dict.values())
mol = Chem.MolFromSmiles("CN=C=O")
predict_dict = rdkit_utils.compute_pairwise_ring_info(mol)
assert not predict_dict
def _pagtn_edge_featurizer(self,
mol: RDKitMol) -> Tuple[np.ndarray, np.ndarray]:
"""Calculate bond features from RDKit mol object.
Parameters
----------
mol: rdkit.Chem.rdchem.Mol
RDKit mol object.
Returns
-------
np.ndarray
Source and Destination node indexes of each bond.
np.ndarray
numpy vector of bond features.
"""
n_atoms = mol.GetNumAtoms()
# To get the shortest paths between two nodes.
paths_dict = compute_all_pairs_shortest_path(mol)
# To get info if two nodes belong to the same ring.
rings_dict = compute_pairwise_ring_info(mol)
# Featurizer
feats = []
src = []
dest = []
for i in range(n_atoms):
for j in range(n_atoms):
src.append(i)
dest.append(j)
if (i, j) not in paths_dict:
feats.append(np.zeros(7 * self.max_length + 7))
continue
ring_info = rings_dict.get(self.ordered_pair(i, j), [])
feats.append(
self._edge_features(mol, paths_dict[(i, j)], ring_info))
return np.array([src, dest], dtype=np.int), np.array(feats,
dtype=np.float)