def _featurize(self, mol: RDKitMol) -> GraphData:
"""Calculate molecule graph features from RDKit mol object.
Parameters
----------
mol: rdkit.Chem.rdchem.Mol
RDKit mol object.
Returns
-------
graph: GraphData
A molecule graph with some features.
"""
if self.use_partial_charge:
try:
mol.GetAtomWithIdx(0).GetProp('_GasteigerCharge')
except:
# If partial charges were not computed
try:
from rdkit.Chem import AllChem
AllChem.ComputeGasteigerCharges(mol)
except ModuleNotFoundError:
raise ImportError(
"This class requires RDKit to be installed.")
# construct atom (node) feature
h_bond_infos = construct_hydrogen_bonding_info(mol)
atom_features = np.asarray(
[
_construct_atom_feature(atom, h_bond_infos, self.use_chirality,
self.use_partial_charge)
for atom in mol.GetAtoms()
],
dtype=float,
)
# construct edge (bond) index
src, dest = [], []
for bond in mol.GetBonds():
# add edge list considering a directed graph
start, end = bond.GetBeginAtomIdx(), bond.GetEndAtomIdx()
src += [start, end]
dest += [end, start]
# construct edge (bond) feature
bond_features = None # deafult None
if self.use_edges:
features = []
for bond in mol.GetBonds():
features += 2 * [_construct_bond_feature(bond)]
bond_features = np.asarray(features, dtype=float)
return GraphData(node_features=atom_features,
edge_index=np.asarray([src, dest], dtype=int),
edge_features=bond_features)
def _featurize(self, mol: RDKitMol) -> GraphData:
"""Calculate molecule graph features from RDKit mol object.
Parameters
----------
mol: rdkit.Chem.rdchem.Mol
RDKit mol object.
Returns
-------
graph: GraphData
A molecule graph with some features.
"""
from rdkit import Chem
from rdkit.Chem import AllChem
# construct atom and bond features
try:
mol.GetAtomWithIdx(0).GetProp('_GasteigerCharge')
except:
# If partial charges were not computed
AllChem.ComputeGasteigerCharges(mol)
h_bond_infos = construct_hydrogen_bonding_info(mol)
sssr = Chem.GetSymmSSSR(mol)
# construct atom (node) feature
atom_features = np.array(
[
_construct_atom_feature(atom, h_bond_infos, sssr)
for atom in mol.GetAtoms()
],
dtype=np.float,
)
# construct edge (bond) information
src, dest, bond_features = [], [], []
for bond in mol.GetBonds():
# add edge list considering a directed graph
start, end = bond.GetBeginAtomIdx(), bond.GetEndAtomIdx()
src += [start, end]
dest += [end, start]
bond_features += 2 * [_construct_bond_feature(bond)]
if self.add_self_edges:
num_atoms = mol.GetNumAtoms()
src += [i for i in range(num_atoms)]
dest += [i for i in range(num_atoms)]
# add dummy edge features
bond_fea_length = len(bond_features[0])
bond_features += num_atoms * [[0 for _ in range(bond_fea_length)]]
return GraphData(node_features=atom_features,
edge_index=np.array([src, dest], dtype=np.int),
edge_features=np.array(bond_features, dtype=np.float))
def _featurize(self, datapoint: RDKitMol, **kwargs) -> GraphData:
"""Calculate molecule graph features from RDKit mol object.
Parameters
----------
datapoint: rdkit.Chem.rdchem.Mol
RDKit mol object.
Returns
-------
graph: GraphData
A molecule graph with some features.
"""
assert datapoint.GetNumAtoms(
) > 1, "More than one atom should be present in the molecule for this featurizer to work."
if 'mol' in kwargs:
datapoint = kwargs.get("mol")
raise DeprecationWarning(
'Mol is being phased out as a parameter, please pass "datapoint" instead.'
)
if self.use_partial_charge:
try:
datapoint.GetAtomWithIdx(0).GetProp('_GasteigerCharge')
except:
# If partial charges were not computed
try:
from rdkit.Chem import AllChem
AllChem.ComputeGasteigerCharges(datapoint)
except ModuleNotFoundError:
raise ImportError(
"This class requires RDKit to be installed.")
# construct atom (node) feature
h_bond_infos = construct_hydrogen_bonding_info(datapoint)
atom_features = np.asarray(
[
_construct_atom_feature(atom, h_bond_infos, self.use_chirality,
self.use_partial_charge)
for atom in datapoint.GetAtoms()
],
dtype=float,
)
# construct edge (bond) index
src, dest = [], []
for bond in datapoint.GetBonds():
# add edge list considering a directed graph
start, end = bond.GetBeginAtomIdx(), bond.GetEndAtomIdx()
src += [start, end]
dest += [end, start]
# construct edge (bond) feature
bond_features = None # deafult None
if self.use_edges:
features = []
for bond in datapoint.GetBonds():
features += 2 * [_construct_bond_feature(bond)]
bond_features = np.asarray(features, dtype=float)
return GraphData(node_features=atom_features,
edge_index=np.asarray([src, dest], dtype=int),
edge_features=bond_features)
