Fixing type errors (35288b8f) · Commits · 钟慕尧 / deepchem

deepchem/feat/complex_featurizers/contact_fingerprints.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -211,10 +211,10 @@ class ContactCircularVoxelizer(ComplexFeaturizer):
		sum([
		voxelize(
		convert_atom_to_voxel,
		hash_ecfp,
		xyz,
		self.box_width,
		self.voxel_width,
		hash_function=hash_ecfp,
		feature_dict=ecfp_dict,
		nb_channel=self.size) for xyz, ecfp_dict in zip(
		xyzs,

deepchem/feat/complex_featurizers/grid_featurizers.py

+29 −25

Original line number	Diff line number	Diff line
		@@ -19,12 +19,12 @@ from deepchem.utils.geometry_utils import compute_pairwise_distances
		from deepchem.utils.geometry_utils import subtract_centroid
		from deepchem.utils.fragment_utils import get_partial_charge
		from deepchem.utils.fragment_utils import reduce_molecular_complex_to_contacts
		from typing import List, Tuple
		from typing import List, Tuple, Optional

		logger = logging.getLogger(__name__)

		HBOND_DIST_BINS = [(2.2, 2.5), (2.5, 3.2), (3.2, 4.0)]
		HBOND_ANGLE_CUTOFFS = [5, 50, 90]
		HBOND_ANGLE_CUTOFFS = [5., 50., 90.]


		def compute_charge_dictionary(molecule):
		@@ -435,16 +435,21 @@ class HydrogenBondCounter(ComplexFeaturizer):
		that computes the total number of hydrogen bonds.
		"""

		def __init__(self,
		def __init__(
		self,
		cutoff: float = 4.5,
		distance_bins: List[Tuple] = None,
		angle_cutoffs: List[float] = None,
		reduce_to_contacts: bool = True):
		reduce_to_contacts: bool = True,
		distance_bins: Optional[List[Tuple[float, float]]] = None,
		angle_cutoffs: Optional[List[float]] = None,
		):
		"""
		Parameters
		----------
		cutoff: float (default 4.5)
		Distance cutoff in angstroms for molecules in complex.
		reduce_to_contacts: bool, optional
		If True, reduce the atoms in the complex to those near a contact
		region.
		distance_bins: list[tuple]
		List of hydgrogen bond distance bins. If not specified is
		set to default
		@@ -454,9 +459,6 @@ class HydrogenBondCounter(ComplexFeaturizer):
		deviation from the ideal (180 deg) angle between
		hydrogen-atom1, hydrogen-atom2 vectors.If not specified
		is set to default `[5, 50, 90]`
		reduce_to_contacts: bool, optional
		If True, reduce the atoms in the complex to those near a contact
		region.
		"""
		self.cutoff = cutoff
		if distance_bins is None:
		@@ -533,18 +535,28 @@ class HydrogenBondVoxelizer(ComplexFeaturizer):
		of hydrogen bonds at each voxel.
		"""

		def __init__(self,
		def __init__(
		self,
		cutoff: float = 4.5,
		distance_bins: List[Tuple] = None,
		angle_cutoffs: List[float] = None,
		box_width: float = 16.0,
		voxel_width: float = 1.0,
		reduce_to_contacts: bool = True):
		reduce_to_contacts: bool = True,
		distance_bins: Optional[List[Tuple[float, float]]] = None,
		angle_cutoffs: Optional[List[float]] = None,
		):
		"""
		Parameters
		----------
		cutoff: float (default 4.5)
		Distance cutoff in angstroms for contact atoms in complex.
		box_width: float, optional (default 16.0)
		Size of a box in which voxel features are calculated. Box
		is centered on a ligand centroid.
		voxel_width: float, optional (default 1.0)
		Size of a 3D voxel in a grid.
		reduce_to_contacts: bool, optional
		If True, reduce the atoms in the complex to those near a contact
		region.
		distance_bins: list[tuple]
		List of hydgrogen bond distance bins. If not specified is
		set to default
		@@ -554,14 +566,6 @@ class HydrogenBondVoxelizer(ComplexFeaturizer):
		deviation from the ideal (180 deg) angle between
		hydrogen-atom1, hydrogen-atom2 vectors.If not specified
		is set to default `[5, 50, 90]`
		box_width: float, optional (default 16.0)
		Size of a box in which voxel features are calculated. Box
		is centered on a ligand centroid.
		voxel_width: float, optional (default 1.0)
		Size of a 3D voxel in a grid.
		reduce_to_contacts: bool, optional
		If True, reduce the atoms in the complex to those near a contact
		region.
		"""
		self.cutoff = cutoff
		if distance_bins is None:

deepchem/utils/rdkit_utils.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -172,7 +172,7 @@ def compute_charges(mol):
		def load_complex(molecular_complex: OneOrMany[str],
		add_hydrogens: bool = True,
		calc_charges: bool = True,
		sanitize: bool = True) -> List[Tuple]:
		sanitize: bool = True) -> List[Tuple[np.ndarray, RDKitMol]]:
		"""Loads a molecular complex.

		Given some representation of a molecular complex, returns a list of

deepchem/utils/test/test_voxel_utils.py

+2 −2

Original line number	Diff line number	Diff line
		@@ -40,10 +40,10 @@ class TestVoxelUtils(unittest.TestCase):
		nb_channel = 16
		features = voxel_utils.voxelize(
		get_voxels,
		hash_function,
		coordinates,
		box_width,
		voxel_width,
		hash_function,
		feature_dict,
		nb_channel=nb_channel)
		assert features.shape == (voxels_per_edge, voxels_per_edge, voxels_per_edge,
		@@ -64,10 +64,10 @@ class TestVoxelUtils(unittest.TestCase):
		nb_channel = 16
		features = voxel_utils.voxelize(
		get_voxels,
		hash_function,
		coordinates,
		box_width,
		voxel_width,
		hash_function,
		feature_dict,
		nb_channel=nb_channel)
		assert features.shape == (voxels_per_edge, voxels_per_edge, voxels_per_edge,

deepchem/utils/voxel_utils.py

+3 −3

Original line number	Diff line number	Diff line
		@@ -77,10 +77,10 @@ def convert_atom_pair_to_voxel(coordinates_tuple: Tuple[np.ndarray, np.ndarray],


		def voxelize(get_voxels: Callable[..., Any],
		hash_function: Callable[..., Any],
		coordinates: np.ndarray,
		box_width: float = 16.0,
		voxel_width: float = 1.0,
		hash_function: Optional[Callable[..., Any]] = None,
		feature_dict: Optional[Dict[Any, Any]] = None,
		feature_list: Optional[List[Union[int, Tuple[int]]]] = None,
		nb_channel: int = 16,
		@@ -96,8 +96,6 @@ def voxelize(get_voxels: Callable[..., Any],
		----------
		get_voxels: Function
		Function that voxelizes inputs
		hash_function: Function
		Used to map feature choices to voxel channels.
		coordinates: np.ndarray
		Contains the 3D coordinates of a molecular system.
		box_width: float, optional (default 16.0)
		@@ -105,6 +103,8 @@ def voxelize(get_voxels: Callable[..., Any],
		is centered on a ligand centroid.
		voxel_width: float, optional (default 1.0)
		Size of a 3D voxel in a grid in Angstroms.
		hash_function: Function
		Used to map feature choices to voxel channels.
		feature_dict: Dict, optional (default None)
		Keys are atom indices or tuples of atom indices, the values are
		computed features. If `hash_function is not None`, then the values

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