:construction: wip commit (b8504198) · Commits · 钟慕尧 / deepchem

deepchem/feat/binding_pocket_features.py

+21 −7

Original line number	Diff line number	Diff line
		@@ -3,14 +3,17 @@ Featurizes proposed binding pockets.
		"""
		import numpy as np
		import logging
		from typing import Dict, List

		from deepchem.feat import Featurizer
		from deepchem.utils.coordinate_box_utils import CoordinateBox
		from deepchem.utils.rdkit_utils import load_molecule

		logger = logging.getLogger(__name__)


		def boxes_to_atoms(coords, boxes):
		def boxes_to_atoms(coords: np.ndarray, boxes: List[CoordinateBox]
		) -> Dict[CoordinateBox, List[int]]:
		"""Maps each box to a list of atoms in that box.

		Given the coordinates of a macromolecule, and a collection of boxes,
		@@ -20,13 +23,14 @@ def boxes_to_atoms(coords, boxes):
		Parameters
		----------
		coords: np.ndarray
		Of shape `(N, 3)
		A numpy array of shape `(N, 3)`
		boxes: list
		list of `CoordinateBox` objects.
		List of `CoordinateBox` objects.

		Returns
		-------
		dictionary mapping `CoordinateBox` objects to lists of atom coordinates
		Dict[CoordinateBox, List[int]]
		A dictionary mapping `CoordinateBox` objects to lists of atom indices.
		"""
		mapping = {}
		for box_ind, box in enumerate(boxes):
		@@ -57,6 +61,10 @@ class BindingPocketFeaturizer(Featurizer):
		implementation for more sophisticated downstream usecases. Note that
		this class's implementation will only work for proteins and not for
		other macromolecules

		Notes
		-----
		This class requires mdtraj to be installed.
		"""

		residues = [
		@@ -67,7 +75,9 @@ class BindingPocketFeaturizer(Featurizer):

		n_features = len(residues)

		def featurize(self, protein_file, pockets):
		# FIXME: Signature of "featurize" incompatible with supertype "Featurizer"
		def featurize( # type: ignore[override]
		self, protein_file: str, pockets: List[CoordinateBox]) -> np.ndarray:
		"""
		Calculate atomic coodinates.

		@@ -75,14 +85,19 @@ class BindingPocketFeaturizer(Featurizer):
		----------
		protein_file: str
		Location of PDB file. Will be loaded by MDTraj
		pockets: list[CoordinateBox]
		pockets: List[CoordinateBox]
		List of `dc.utils.CoordinateBox` objects.

		Returns
		-------
		np.ndarray
		A numpy array of shale `(len(pockets), n_residues)`
		"""
		try:
		import mdtraj
		except ModuleNotFoundError:
		raise ValueError("This class requires RDKit to be installed.")

		protein_coords = load_molecule(
		protein_file, add_hydrogens=False, calc_charges=False)[0]
		mapping = boxes_to_atoms(protein_coords, pockets)
		@@ -101,6 +116,5 @@ class BindingPocketFeaturizer(Featurizer):
		if residue not in res_map:
		logger.info("Warning: Non-standard residue in PDB file")
		continue
		atomtype = atom_name.split("-")[1]
		all_features[pocket_num, res_map[residue]] += 1
		return all_features

deepchem/feat/molecule_featurizers/init.py

+0 −1

Original line number	Diff line number	Diff line
		@@ -8,4 +8,3 @@ from deepchem.feat.molecule_featurizers.rdkit_descriptors import RDKitDescriptor
		from deepchem.feat.molecule_featurizers.smiles_to_image import SmilesToImage
		from deepchem.feat.molecule_featurizers.smiles_to_seq import SmilesToSeq, create_char_to_idx
		from deepchem.feat.molecule_featurizers.mol_graph_conv_featurizer import MolGraphConvFeaturizer

deepchem/feat/molecule_featurizers/circular_fingerprint.py

+0 −2

Original line number	Diff line number	Diff line
		@@ -3,10 +3,8 @@ Topological fingerprints.
		"""
		from typing import Dict


		import numpy as np


		from deepchem.utils.typing import RDKitMol
		from deepchem.feat.base_classes import MolecularFeaturizer

deepchem/feat/tests/test_binding_pocket_features.py

+0 −1

Original line number	Diff line number	Diff line
		@@ -19,7 +19,6 @@ class TestBindingPocketFeatures(unittest.TestCase):
		current_dir = os.path.dirname(os.path.realpath(__file__))
		protein_file = os.path.join(current_dir,
		"../../dock/tests/1jld_protein.pdb")
		ligand_file = os.path.join(current_dir, "../../dock/tests/1jld_ligand.sdf")

		finder = dc.dock.ConvexHullPocketFinder()
		pocket_featurizer = dc.feat.BindingPocketFeaturizer()

Admin message