Loading deepchem/feat/molecule_featurizers/mat_featurizer.py +14 −1 Original line number Diff line number Diff line Loading @@ -15,17 +15,30 @@ except: class MATFeaturizer(MolecularFeaturizer): """ This class is a featurizer for the Molecule Attention Transformer. """ def __init__( self, add_dummy_node=True, one_hot_formal_charge=True, ): """ Parameters ---------- mol (rdchem.Mol): An RDKit Mol object. add_dummy_node (bool): If True, a dummy node will be added to the molecular graph. one_hot_formal_charge (bool): If True, formal charges on atoms are one-hot encoded. """ self.mol = mol self.add_dummy_node = add_dummy_node self.one_hot_formal_charge = one_hot_formal_charge def atom_features(self, atom, one_hot_formal_charge=True): """ Deepchem already contains an atom_features function, however we are defining a new one here due to the need to handle features specific to MAT. """ attrib = [] attrib += one_hot_encode(atom.GetAtomicNumber(), [5, 6, 7, 8, 9, 15, 16, 17, 35, 53, 999]) Loading Loading
deepchem/feat/molecule_featurizers/mat_featurizer.py +14 −1 Original line number Diff line number Diff line Loading @@ -15,17 +15,30 @@ except: class MATFeaturizer(MolecularFeaturizer): """ This class is a featurizer for the Molecule Attention Transformer. """ def __init__( self, add_dummy_node=True, one_hot_formal_charge=True, ): """ Parameters ---------- mol (rdchem.Mol): An RDKit Mol object. add_dummy_node (bool): If True, a dummy node will be added to the molecular graph. one_hot_formal_charge (bool): If True, formal charges on atoms are one-hot encoded. """ self.mol = mol self.add_dummy_node = add_dummy_node self.one_hot_formal_charge = one_hot_formal_charge def atom_features(self, atom, one_hot_formal_charge=True): """ Deepchem already contains an atom_features function, however we are defining a new one here due to the need to handle features specific to MAT. """ attrib = [] attrib += one_hot_encode(atom.GetAtomicNumber(), [5, 6, 7, 8, 9, 15, 16, 17, 35, 53, 999]) Loading
