def test_get_bond_is_conjugated_one_hot(self):
bonds = self.mol.GetBonds()
one_hot = get_bond_is_conjugated_one_hot(bonds[0])
assert one_hot == [0.0]
bonds = self.mol_benzene.GetBonds()
one_hot = get_bond_is_conjugated_one_hot(bonds[0])
assert one_hot == [1.0]
def _edge_features(self, mol: RDKitMol, path_atoms: Tuple[int, ...],
ring_info) -> np.ndarray:
"""Computes the edge features for a given pair of nodes.
Parameters
----------
mol : : RDKitMol
RDKit molecule instance.
path_atoms: tuple
Shortest path between the given pair of nodes.
ring_info: list
Different rings that contain the pair of atoms
"""
features = []
path_bonds = []
path_length = len(path_atoms)
for path_idx in range(path_length - 1):
bond = mol.GetBondBetweenAtoms(path_atoms[path_idx],
path_atoms[path_idx + 1])
if bond is None:
import warnings
warnings.warn('Valid idx of bonds must be passed')
path_bonds.append(bond)
for path_idx in range(self.max_length):
if path_idx < len(path_bonds):
bond_type = get_bond_type_one_hot(path_bonds[path_idx])
conjugacy = get_bond_is_conjugated_one_hot(
path_bonds[path_idx])
ring_attach = get_bond_is_in_same_ring_one_hot(
path_bonds[path_idx])
features.append(
np.concatenate([bond_type, conjugacy, ring_attach]))
else:
features.append(np.zeros(6))
if path_length + 1 > self.max_length:
path_length = self.max_length + 1
position_feature = np.zeros(self.max_length + 2)
position_feature[path_length] = 1
features.append(position_feature)
if ring_info:
rfeat = [
one_hot_encode(r, allowable_set=self.RING_TYPES)
for r in ring_info
]
# The 1.0 float value represents True Boolean
rfeat = [1.0] + np.any(rfeat, axis=0).tolist()
features.append(rfeat)
else:
# This will return a boolean vector with all entries False
features.append(
[0.0] +
one_hot_encode(ring_info, allowable_set=self.RING_TYPES))
return np.concatenate(features, axis=0)
def _construct_bond_feature(bond: RDKitBond) -> np.ndarray:
"""Construct a bond feature from a RDKit bond object.
Parameters
---------
bond: rdkit.Chem.rdchem.Bond
RDKit bond object
Returns
-------
np.ndarray
A one-hot vector of the bond feature.
"""
bond_type = get_bond_type_one_hot(bond)
same_ring = get_bond_is_in_same_ring_one_hot(bond)
conjugated = get_bond_is_conjugated_one_hot(bond)
stereo = get_bond_stereo_one_hot(bond)
return np.concatenate([bond_type, same_ring, conjugated, stereo])
def _construct_bond_feature(bond: RDKitBond) -> List[float]:
"""Construct a bond feature from a RDKit bond object.
Parameters
---------
bond: rdkit.Chem.rdchem.Bond
RDKit bond object
Returns
-------
List[float]
A one-hot vector of the bond feature.
"""
bond_type = get_bond_type_one_hot(bond)
same_ring = get_bond_is_in_same_ring_one_hot(bond)
conjugated = get_bond_is_conjugated_one_hot(bond)
stereo = get_bond_stereo_one_hot(bond)
return bond_type + same_ring + conjugated + stereo
