Loading deepchem/feat/molecule_featurizers/atomic_coordinates.py +6 −3 Original line number Diff line number Diff line Loading @@ -22,6 +22,12 @@ class AtomicCoordinates(MolecularFeaturizer): use_bohr: bool, optional (default False) Whether to uss bohr or angstrom as a coordinate unit. """ try: from rdkit import Chem # noqa from rdkit.Chem import AllChem # noqa except ModuleNotFoundError: raise ValueError("This class requires RDKit to be installed.") self.use_bohr = use_bohr def _featurize(self, mol: RDKitMol) -> np.ndarray: Loading @@ -37,11 +43,8 @@ class AtomicCoordinates(MolecularFeaturizer): np.ndarray A numpy array of atomic coordinates. The shape is `(n_atoms, 3)`. """ try: from rdkit import Chem from rdkit.Chem import AllChem except ModuleNotFoundError: raise ValueError("This class requires RDKit to be installed.") # Check whether num_confs >=1 or not num_confs = len(mol.GetConformers()) Loading deepchem/feat/molecule_featurizers/bp_symmetry_function_input.py +17 −5 Original line number Diff line number Diff line import numpy as np from deepchem.utils.typing import RDKitMol from deepchem.utils.data_utils import pad_array from deepchem.feat.base_classes import MolecularFeaturizer from deepchem.feat.molecule_featurizers.atomic_coordinates import AtomicCoordinates class BPSymmetryFunctionInput(MolecularFeaturizer): """Calculate Symmetry Function for each atom in the molecules """Calculate symmetry function for each atom in the molecules This method is described in [1]_ Loading @@ -31,13 +32,24 @@ class BPSymmetryFunctionInput(MolecularFeaturizer): process. """ self.max_atoms = max_atoms self.coordfeat = AtomicCoordinates(use_bohr=True) def _featurize(self, mol: RDKitMol) -> np.ndarray: coordfeat = AtomicCoordinates(use_bohr=True) coordinates = coordfeat._featurize(mol)[0] """Calculate symmetry function. Parameters ---------- mol: rdkit.Chem.rdchem.Mol RDKit Mol object Returns ------- np.ndarray A numpy array of symmetry function. The shape is `(max_atoms, 4)`. """ coordinates = self.coordfeat._featurize(mol) atom_numbers = np.array([atom.GetAtomicNum() for atom in mol.GetAtoms()]) atom_numbers = np.expand_dims(atom_numbers, axis=1) assert atom_numbers.shape[0] == coordinates.shape[0] n_atoms = atom_numbers.shape[0] features = np.concatenate([atom_numbers, coordinates], axis=1) return np.pad(features, ((0, self.max_atoms - n_atoms), (0, 0)), 'constant') return pad_array(features, (self.max_atoms, 4)) Loading
deepchem/feat/molecule_featurizers/atomic_coordinates.py +6 −3 Original line number Diff line number Diff line Loading @@ -22,6 +22,12 @@ class AtomicCoordinates(MolecularFeaturizer): use_bohr: bool, optional (default False) Whether to uss bohr or angstrom as a coordinate unit. """ try: from rdkit import Chem # noqa from rdkit.Chem import AllChem # noqa except ModuleNotFoundError: raise ValueError("This class requires RDKit to be installed.") self.use_bohr = use_bohr def _featurize(self, mol: RDKitMol) -> np.ndarray: Loading @@ -37,11 +43,8 @@ class AtomicCoordinates(MolecularFeaturizer): np.ndarray A numpy array of atomic coordinates. The shape is `(n_atoms, 3)`. """ try: from rdkit import Chem from rdkit.Chem import AllChem except ModuleNotFoundError: raise ValueError("This class requires RDKit to be installed.") # Check whether num_confs >=1 or not num_confs = len(mol.GetConformers()) Loading
deepchem/feat/molecule_featurizers/bp_symmetry_function_input.py +17 −5 Original line number Diff line number Diff line import numpy as np from deepchem.utils.typing import RDKitMol from deepchem.utils.data_utils import pad_array from deepchem.feat.base_classes import MolecularFeaturizer from deepchem.feat.molecule_featurizers.atomic_coordinates import AtomicCoordinates class BPSymmetryFunctionInput(MolecularFeaturizer): """Calculate Symmetry Function for each atom in the molecules """Calculate symmetry function for each atom in the molecules This method is described in [1]_ Loading @@ -31,13 +32,24 @@ class BPSymmetryFunctionInput(MolecularFeaturizer): process. """ self.max_atoms = max_atoms self.coordfeat = AtomicCoordinates(use_bohr=True) def _featurize(self, mol: RDKitMol) -> np.ndarray: coordfeat = AtomicCoordinates(use_bohr=True) coordinates = coordfeat._featurize(mol)[0] """Calculate symmetry function. Parameters ---------- mol: rdkit.Chem.rdchem.Mol RDKit Mol object Returns ------- np.ndarray A numpy array of symmetry function. The shape is `(max_atoms, 4)`. """ coordinates = self.coordfeat._featurize(mol) atom_numbers = np.array([atom.GetAtomicNum() for atom in mol.GetAtoms()]) atom_numbers = np.expand_dims(atom_numbers, axis=1) assert atom_numbers.shape[0] == coordinates.shape[0] n_atoms = atom_numbers.shape[0] features = np.concatenate([atom_numbers, coordinates], axis=1) return np.pad(features, ((0, self.max_atoms - n_atoms), (0, 0)), 'constant') return pad_array(features, (self.max_atoms, 4))
