Loading deepchem/feat/complex_featurizers/__init__.pydeleted 100644 → 0 +0 −3 Original line number Diff line number Diff line # flake8: noqa from deepchem.feat.complex_featurizers.atomic_coordinates import NeighborListComplexAtomicCoordinates from deepchem.feat.complex_featurizers.atomic_coordinates import ComplexNeighborListFragmentAtomicCoordinates deepchem/feat/molecule_featurizers/morgan_fingerprint.py→deepchem/feat/molecule_featurizers/circular_fingerprint.py +0 −0 File moved. View file deepchem/feat/molecule_featurizers/one_hot_featurizer.py +16 −16 Original line number Diff line number Diff line Loading @@ -14,13 +14,13 @@ ZINC_CHARSET = [ class OneHotFeaturizer(MolecularFeaturizer): """Encodes a molecule as a one-hot array. This featurizer takes a molecule and encodes its Smiles string as a one-hot array. This featurizer takes a molecule and encodes its SMILES string as a one-hot array. Notes ----- This class requires RDKit to be installed. Note that this featurizer is not thread Safe in initialization of charset Note that this featurizer is not thread safe in initialization of charset. """ def __init__(self, charset: List[str] = ZINC_CHARSET, padlength: int = 120): Loading @@ -47,7 +47,7 @@ class OneHotFeaturizer(MolecularFeaturizer): Returns ------- np.ndarray Vector of RDKit descriptors for `mol` The one hot encoded arrays for each character in SMILES """ try: from rdkit import Chem Loading Loading @@ -90,50 +90,50 @@ class OneHotFeaturizer(MolecularFeaturizer): return self.charset.index(c) def pad_smile(self, smile: str) -> str: """Pad a smile string to `self.pad_length` """Pad a SMILES string to `self.pad_length` Parameters ---------- smile: str The smiles string to be padded. The SMILES string to be padded. Returns ------- str smile string space padded to self.pad_length SMILES string padded to self.pad_length """ return smile.ljust(self.pad_length) def one_hot_encoded(self, smile: str) -> np.ndarray: """One Hot Encode an entire SMILE string """One Hot Encode an entire SMILES string Parameters ---------- smile: str smile string to encode SMILES string to encode Returns ------- np.ndarray The one hot encoded arrays for each character in smile The one hot encoded arrays for each character in SMILES """ return np.array([ self.one_hot_array(self.one_hot_index(x)) for x in self.pad_smile(smile) ]) def untransform(self, one_hot: np.ndarray) -> List[str]: """Convert from one hot representation back to SMILE """Convert from one hot representation back to SMILES Parameters ---------- z: np.ndarray one_hot: np.ndarray A numpy array of one hot encoded features Returns ------- List[str] The List smile Strings picking MAX for each one hot encoded array The List SMILES strings picking MAX for each one hot encoded array """ smiles_list = [] for i in range(len(one_hot)): Loading @@ -145,17 +145,17 @@ class OneHotFeaturizer(MolecularFeaturizer): return smiles_list def _create_charset(self, smiles: List[str]) -> List[str]: """Create the charset from smiles """Create the charset from SMILES Parameters ---------- smiles: List[str] List of smile strings List of SMILES strings Returns ------- List[str] List of length one strings that are characters in smiles. No duplicates List of length one strings that are characters in SMILES. No duplicates """ s = set() for smile in smiles: Loading Loading
deepchem/feat/complex_featurizers/__init__.pydeleted 100644 → 0 +0 −3 Original line number Diff line number Diff line # flake8: noqa from deepchem.feat.complex_featurizers.atomic_coordinates import NeighborListComplexAtomicCoordinates from deepchem.feat.complex_featurizers.atomic_coordinates import ComplexNeighborListFragmentAtomicCoordinates
deepchem/feat/molecule_featurizers/morgan_fingerprint.py→deepchem/feat/molecule_featurizers/circular_fingerprint.py +0 −0 File moved. View file
deepchem/feat/molecule_featurizers/one_hot_featurizer.py +16 −16 Original line number Diff line number Diff line Loading @@ -14,13 +14,13 @@ ZINC_CHARSET = [ class OneHotFeaturizer(MolecularFeaturizer): """Encodes a molecule as a one-hot array. This featurizer takes a molecule and encodes its Smiles string as a one-hot array. This featurizer takes a molecule and encodes its SMILES string as a one-hot array. Notes ----- This class requires RDKit to be installed. Note that this featurizer is not thread Safe in initialization of charset Note that this featurizer is not thread safe in initialization of charset. """ def __init__(self, charset: List[str] = ZINC_CHARSET, padlength: int = 120): Loading @@ -47,7 +47,7 @@ class OneHotFeaturizer(MolecularFeaturizer): Returns ------- np.ndarray Vector of RDKit descriptors for `mol` The one hot encoded arrays for each character in SMILES """ try: from rdkit import Chem Loading Loading @@ -90,50 +90,50 @@ class OneHotFeaturizer(MolecularFeaturizer): return self.charset.index(c) def pad_smile(self, smile: str) -> str: """Pad a smile string to `self.pad_length` """Pad a SMILES string to `self.pad_length` Parameters ---------- smile: str The smiles string to be padded. The SMILES string to be padded. Returns ------- str smile string space padded to self.pad_length SMILES string padded to self.pad_length """ return smile.ljust(self.pad_length) def one_hot_encoded(self, smile: str) -> np.ndarray: """One Hot Encode an entire SMILE string """One Hot Encode an entire SMILES string Parameters ---------- smile: str smile string to encode SMILES string to encode Returns ------- np.ndarray The one hot encoded arrays for each character in smile The one hot encoded arrays for each character in SMILES """ return np.array([ self.one_hot_array(self.one_hot_index(x)) for x in self.pad_smile(smile) ]) def untransform(self, one_hot: np.ndarray) -> List[str]: """Convert from one hot representation back to SMILE """Convert from one hot representation back to SMILES Parameters ---------- z: np.ndarray one_hot: np.ndarray A numpy array of one hot encoded features Returns ------- List[str] The List smile Strings picking MAX for each one hot encoded array The List SMILES strings picking MAX for each one hot encoded array """ smiles_list = [] for i in range(len(one_hot)): Loading @@ -145,17 +145,17 @@ class OneHotFeaturizer(MolecularFeaturizer): return smiles_list def _create_charset(self, smiles: List[str]) -> List[str]: """Create the charset from smiles """Create the charset from SMILES Parameters ---------- smiles: List[str] List of smile strings List of SMILES strings Returns ------- List[str] List of length one strings that are characters in smiles. No duplicates List of length one strings that are characters in SMILES. No duplicates """ s = set() for smile in smiles: Loading
