:bug: fix bug (9f64f555) · Commits · 钟慕尧 / deepchem

deepchem/feat/molecule_featurizers/atomic_coordinates.py

+3 −6

Original line number	Diff line number	Diff line
		@@ -22,12 +22,6 @@ class AtomicCoordinates(MolecularFeaturizer):
		use_bohr: bool, optional (default False)
		Whether to use bohr or angstrom as a coordinate unit.
		"""
		try:
		from rdkit import Chem # noqa
		from rdkit.Chem import AllChem # noqa
		except ModuleNotFoundError:
		raise ImportError("This class requires RDKit to be installed.")

		self.use_bohr = use_bohr

		def _featurize(self, mol: RDKitMol) -> np.ndarray:
		@@ -43,8 +37,11 @@ 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 ImportError("This class requires RDKit to be installed.")

		# Check whether num_confs >=1 or not
		num_confs = len(mol.GetConformers())

+3 −6

Original line number	Diff line number	Diff line
		@@ -55,12 +55,6 @@ class CircularFingerprint(MolecularFeaturizer):
		Whether to calculate SMILES strings for fragment IDs (only applicable
		when calculating sparse fingerprints).
		"""
		try:
		from rdkit import Chem # noqa
		from rdkit.Chem import rdMolDescriptors # noqa
		except ModuleNotFoundError:
		raise ImportError("This class requires RDKit to be installed.")

		self.radius = radius
		self.size = size
		self.chiral = chiral
		@@ -82,8 +76,11 @@ class CircularFingerprint(MolecularFeaturizer):
		np.ndarray
		A numpy array of circular fingerprint.
		"""
		try:
		from rdkit import Chem
		from rdkit.Chem import rdMolDescriptors
		except ModuleNotFoundError:
		raise ImportError("This class requires RDKit to be installed.")

		if self.sparse:
		info: Dict = {}

+3 −6

Original line number	Diff line number	Diff line
		@@ -63,12 +63,6 @@ class CoulombMatrix(MolecularFeaturizer):
		seed: int, optional (default None)
		Random seed to use.
		"""
		try:
		from rdkit import Chem # noqa
		from rdkit.Chem import AllChem # noqa
		except ModuleNotFoundError:
		raise ImportError("This class requires RDKit to be installed.")

		self.max_atoms = int(max_atoms)
		self.remove_hydrogens = remove_hydrogens
		self.randomize = randomize
		@@ -122,8 +116,11 @@ class CoulombMatrix(MolecularFeaturizer):
		np.ndarray
		The coulomb matrices of the given molecule
		"""
		try:
		from rdkit import Chem
		from rdkit.Chem import AllChem
		except ModuleNotFoundError:
		raise ImportError("This class requires RDKit to be installed.")

		# Check whether num_confs >=1 or not
		num_confs = len(mol.GetConformers())

+8 −6

Original line number	Diff line number	Diff line
		@@ -23,12 +23,7 @@ class MACCSKeysFingerprint(MolecularFeaturizer):

		def __init__(self):
		"""Initialize this featurizer."""
		try:
		from rdkit.Chem.AllChem import GetMACCSKeysFingerprint # noqa
		except ModuleNotFoundError:
		raise ImportError("This class requires RDKit to be installed.")

		self.calculator = GetMACCSKeysFingerprint
		self.calculator = None

		def _featurize(self, mol: RDKitMol) -> np.ndarray:
		"""
		@@ -44,4 +39,11 @@ class MACCSKeysFingerprint(MolecularFeaturizer):
		np.ndarray
		1D array of RDKit descriptors for `mol`. The length is 167.
		"""
		if self.calculator is None:
		try:
		from rdkit.Chem.AllChem import GetMACCSKeysFingerprint
		self.calculator = GetMACCSKeysFingerprint
		except ModuleNotFoundError:
		raise ImportError("This class requires RDKit to be installed.")

		return self.calculator(mol)

+3 −5

Original line number	Diff line number	Diff line
		@@ -158,11 +158,6 @@ class MolGraphConvFeaturizer(MolecularFeaturizer):
		Therefore, there is a possibility to fail to featurize for some molecules
		and featurization becomes slow.
		"""
		try:
		from rdkit.Chem import AllChem # noqa
		except ModuleNotFoundError:
		raise ImportError("This method requires RDKit to be installed.")

		self.use_edges = use_edges
		self.use_partial_charge = use_partial_charge
		self.use_chirality = use_chirality
		@@ -185,8 +180,11 @@ class MolGraphConvFeaturizer(MolecularFeaturizer):
		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 method requires RDKit to be installed.")

		# construct atom (node) feature
		h_bond_infos = construct_hydrogen_bonding_info(mol)