Loading deepchem/feat/__init__.py +2 −0 Original line number Diff line number Diff line Loading @@ -21,10 +21,12 @@ from deepchem.feat.molecule_featurizers import BPSymmetryFunctionInput from deepchem.feat.molecule_featurizers import CircularFingerprint from deepchem.feat.molecule_featurizers import CoulombMatrix from deepchem.feat.molecule_featurizers import CoulombMatrixEig from deepchem.feat.molecule_featurizers import MACCSKeysFingerprint from deepchem.feat.molecule_featurizers import MordredDescriptors from deepchem.feat.molecule_featurizers import Mol2VecFingerprint from deepchem.feat.molecule_featurizers import MolGraphConvFeaturizer from deepchem.feat.molecule_featurizers import OneHotFeaturizer from deepchem.feat.molecule_featurizers import PubChemFingerprint from deepchem.feat.molecule_featurizers import RawFeaturizer from deepchem.feat.molecule_featurizers import RDKitDescriptors from deepchem.feat.molecule_featurizers import SmilesToImage Loading deepchem/feat/molecule_featurizers/__init__.py +2 −0 Original line number Diff line number Diff line Loading @@ -4,9 +4,11 @@ from deepchem.feat.molecule_featurizers.bp_symmetry_function_input import BPSymm from deepchem.feat.molecule_featurizers.circular_fingerprint import CircularFingerprint from deepchem.feat.molecule_featurizers.coulomb_matrices import CoulombMatrix from deepchem.feat.molecule_featurizers.coulomb_matrices import CoulombMatrixEig from deepchem.feat.molecule_featurizers.maccs_keys_fingerprint import MACCSKeysFingerprint from deepchem.feat.molecule_featurizers.mordred_descriptors import MordredDescriptors from deepchem.feat.molecule_featurizers.mol2vec_fingerprint import Mol2VecFingerprint from deepchem.feat.molecule_featurizers.one_hot_featurizer import OneHotFeaturizer from deepchem.feat.molecule_featurizers.pubchem_fingerprint import PubChemFingerprint from deepchem.feat.molecule_featurizers.raw_featurizer import RawFeaturizer from deepchem.feat.molecule_featurizers.rdkit_descriptors import RDKitDescriptors from deepchem.feat.molecule_featurizers.smiles_to_image import SmilesToImage Loading deepchem/feat/molecule_featurizers/maccs_keys_fingerprint.py 0 → 100644 +47 −0 Original line number Diff line number Diff line import numpy as np from deepchem.utils.typing import RDKitMol from deepchem.feat.base_classes import MolecularFeaturizer class MACCSKeysFingerprint(MolecularFeaturizer): """MACCS Keys Fingerprint. The MACCS (Molecular ACCess System) keys are one of the most commonly used structural keys. Please confirm the details in [1]_, [2]_. References ---------- .. [1] Durant, Joseph L., et al. "Reoptimization of MDL keys for use in drug discovery." Journal of chemical information and computer sciences 42.6 (2002): 1273-1280. .. [2] https://github.com/rdkit/rdkit/blob/master/rdkit/Chem/MACCSkeys.py Notes ----- This class requires RDKit to be installed. """ def __init__(self): """Initialize this featurizer.""" try: from rdkit.Chem.AllChem import GetMACCSKeysFingerprint # noqa except ModuleNotFoundError: raise ValueError("This class requires RDKit to be installed.") self.calculator = GetMACCSKeysFingerprint def _featurize(self, mol: RDKitMol) -> np.ndarray: """ Calculate MACCS keys fingerprint. Parameters ---------- mol: rdkit.Chem.rdchem.Mol RDKit Mol object Returns ------- np.ndarray 1D array of RDKit descriptors for `mol`. The length is 167. """ return self.calculator(mol) deepchem/feat/molecule_featurizers/pubchem_fingerprint.py 0 → 100644 +52 −0 Original line number Diff line number Diff line import numpy as np from deepchem.utils.typing import RDKitMol from deepchem.feat.base_classes import MolecularFeaturizer class PubChemFingerprint(MolecularFeaturizer): """PubChem Fingerprint. The PubChem fingerprint is a 881 bit structural key, which is used by PubChem for similarity searching. Please confirm the details in [1]_. References ---------- .. [1] ftp://ftp.ncbi.nlm.nih.gov/pubchem/specifications/pubchem_fingerprints.pdf Notes ----- This class requires RDKit and PubChemPy to be installed. PubChemPy use REST API to get the fingerprint, so you need the internet access. """ def __init__(self): """Initialize this featurizer.""" try: from rdkit import Chem # noqa import pubchempy as pcp # noqa except ModuleNotFoundError: raise ValueError("This class requires PubChemPy to be installed.") self.get_pubchem_compounds = pcp.get_compounds def _featurize(self, mol: RDKitMol) -> np.ndarray: """ Calculate PubChem fingerprint. Parameters ---------- mol: rdkit.Chem.rdchem.Mol RDKit Mol object Returns ------- np.ndarray 1D array of RDKit descriptors for `mol`. The length is 881. """ from rdkit import Chem smiles = Chem.MolToSmiles(mol) pubchem_compound = self.get_pubchem_compounds(smiles, 'smiles')[0] feature = [int(bit) for bit in pubchem_compound.cactvs_fingerprint] return np.asarray(feature) deepchem/feat/tests/test_maccs_keys_finerprint.py 0 → 100644 +25 −0 Original line number Diff line number Diff line import unittest from deepchem.feat import MACCSKeysFingerprint class TestMACCSKeysFingerprint(unittest.TestCase): """ Test MACCSKeyFingerprint. """ def setUp(self): """ Set up tests. """ from rdkit import Chem smiles = 'CC(=O)OC1=CC=CC=C1C(=O)O' self.mol = Chem.MolFromSmiles(smiles) def test_maccs_key_fingerprint(self): """ Test simple fingerprint. """ featurizer = MACCSKeysFingerprint() feature_sum = featurizer([self.mol]) assert feature_sum.shape == (1, 167) Loading
deepchem/feat/__init__.py +2 −0 Original line number Diff line number Diff line Loading @@ -21,10 +21,12 @@ from deepchem.feat.molecule_featurizers import BPSymmetryFunctionInput from deepchem.feat.molecule_featurizers import CircularFingerprint from deepchem.feat.molecule_featurizers import CoulombMatrix from deepchem.feat.molecule_featurizers import CoulombMatrixEig from deepchem.feat.molecule_featurizers import MACCSKeysFingerprint from deepchem.feat.molecule_featurizers import MordredDescriptors from deepchem.feat.molecule_featurizers import Mol2VecFingerprint from deepchem.feat.molecule_featurizers import MolGraphConvFeaturizer from deepchem.feat.molecule_featurizers import OneHotFeaturizer from deepchem.feat.molecule_featurizers import PubChemFingerprint from deepchem.feat.molecule_featurizers import RawFeaturizer from deepchem.feat.molecule_featurizers import RDKitDescriptors from deepchem.feat.molecule_featurizers import SmilesToImage Loading
deepchem/feat/molecule_featurizers/__init__.py +2 −0 Original line number Diff line number Diff line Loading @@ -4,9 +4,11 @@ from deepchem.feat.molecule_featurizers.bp_symmetry_function_input import BPSymm from deepchem.feat.molecule_featurizers.circular_fingerprint import CircularFingerprint from deepchem.feat.molecule_featurizers.coulomb_matrices import CoulombMatrix from deepchem.feat.molecule_featurizers.coulomb_matrices import CoulombMatrixEig from deepchem.feat.molecule_featurizers.maccs_keys_fingerprint import MACCSKeysFingerprint from deepchem.feat.molecule_featurizers.mordred_descriptors import MordredDescriptors from deepchem.feat.molecule_featurizers.mol2vec_fingerprint import Mol2VecFingerprint from deepchem.feat.molecule_featurizers.one_hot_featurizer import OneHotFeaturizer from deepchem.feat.molecule_featurizers.pubchem_fingerprint import PubChemFingerprint from deepchem.feat.molecule_featurizers.raw_featurizer import RawFeaturizer from deepchem.feat.molecule_featurizers.rdkit_descriptors import RDKitDescriptors from deepchem.feat.molecule_featurizers.smiles_to_image import SmilesToImage Loading
deepchem/feat/molecule_featurizers/maccs_keys_fingerprint.py 0 → 100644 +47 −0 Original line number Diff line number Diff line import numpy as np from deepchem.utils.typing import RDKitMol from deepchem.feat.base_classes import MolecularFeaturizer class MACCSKeysFingerprint(MolecularFeaturizer): """MACCS Keys Fingerprint. The MACCS (Molecular ACCess System) keys are one of the most commonly used structural keys. Please confirm the details in [1]_, [2]_. References ---------- .. [1] Durant, Joseph L., et al. "Reoptimization of MDL keys for use in drug discovery." Journal of chemical information and computer sciences 42.6 (2002): 1273-1280. .. [2] https://github.com/rdkit/rdkit/blob/master/rdkit/Chem/MACCSkeys.py Notes ----- This class requires RDKit to be installed. """ def __init__(self): """Initialize this featurizer.""" try: from rdkit.Chem.AllChem import GetMACCSKeysFingerprint # noqa except ModuleNotFoundError: raise ValueError("This class requires RDKit to be installed.") self.calculator = GetMACCSKeysFingerprint def _featurize(self, mol: RDKitMol) -> np.ndarray: """ Calculate MACCS keys fingerprint. Parameters ---------- mol: rdkit.Chem.rdchem.Mol RDKit Mol object Returns ------- np.ndarray 1D array of RDKit descriptors for `mol`. The length is 167. """ return self.calculator(mol)
deepchem/feat/molecule_featurizers/pubchem_fingerprint.py 0 → 100644 +52 −0 Original line number Diff line number Diff line import numpy as np from deepchem.utils.typing import RDKitMol from deepchem.feat.base_classes import MolecularFeaturizer class PubChemFingerprint(MolecularFeaturizer): """PubChem Fingerprint. The PubChem fingerprint is a 881 bit structural key, which is used by PubChem for similarity searching. Please confirm the details in [1]_. References ---------- .. [1] ftp://ftp.ncbi.nlm.nih.gov/pubchem/specifications/pubchem_fingerprints.pdf Notes ----- This class requires RDKit and PubChemPy to be installed. PubChemPy use REST API to get the fingerprint, so you need the internet access. """ def __init__(self): """Initialize this featurizer.""" try: from rdkit import Chem # noqa import pubchempy as pcp # noqa except ModuleNotFoundError: raise ValueError("This class requires PubChemPy to be installed.") self.get_pubchem_compounds = pcp.get_compounds def _featurize(self, mol: RDKitMol) -> np.ndarray: """ Calculate PubChem fingerprint. Parameters ---------- mol: rdkit.Chem.rdchem.Mol RDKit Mol object Returns ------- np.ndarray 1D array of RDKit descriptors for `mol`. The length is 881. """ from rdkit import Chem smiles = Chem.MolToSmiles(mol) pubchem_compound = self.get_pubchem_compounds(smiles, 'smiles')[0] feature = [int(bit) for bit in pubchem_compound.cactvs_fingerprint] return np.asarray(feature)
deepchem/feat/tests/test_maccs_keys_finerprint.py 0 → 100644 +25 −0 Original line number Diff line number Diff line import unittest from deepchem.feat import MACCSKeysFingerprint class TestMACCSKeysFingerprint(unittest.TestCase): """ Test MACCSKeyFingerprint. """ def setUp(self): """ Set up tests. """ from rdkit import Chem smiles = 'CC(=O)OC1=CC=CC=C1C(=O)O' self.mol = Chem.MolFromSmiles(smiles) def test_maccs_key_fingerprint(self): """ Test simple fingerprint. """ featurizer = MACCSKeysFingerprint() feature_sum = featurizer([self.mol]) assert feature_sum.shape == (1, 167)
