:recycle: refactor (0fa97cb9) · Commits · 钟慕尧 / deepchem

deepchem/dock/binding_pocket.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -6,7 +6,7 @@ import numpy as np
		from typing import Any, List, Optional, Tuple

		from deepchem.models import Model
		from deepchem.utils.rdkit_util import load_molecule
		from deepchem.utils.rdkit_utils import load_molecule
		from deepchem.utils.coordinate_box_utils \
		import CoordinateBox, get_face_boxes, merge_overlapping_boxes
		from deepchem.utils.fragment_utils import get_contact_atom_indices

deepchem/dock/pose_generation.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -15,7 +15,7 @@ from deepchem.dock.binding_pocket import BindingPocketFinder
		from deepchem.utils import download_url, get_data_dir
		from deepchem.utils.typing import RDKitMol
		from deepchem.utils.geometry_utils import compute_centroid, compute_protein_range
		from deepchem.utils.rdkit_util import load_molecule, write_molecule
		from deepchem.utils.rdkit_utils import load_molecule, write_molecule
		from deepchem.utils.vina_utils import load_docked_ligands, write_vina_conf

		logger = logging.getLogger(__name__)

deepchem/dock/tests/test_binding_pocket.py

+2 −2

Original line number	Diff line number	Diff line
		@@ -6,7 +6,7 @@ import unittest
		import os

		import deepchem as dc
		from deepchem.utils import rdkit_util
		from deepchem.utils import rdkit_utils
		from deepchem.utils import coordinate_box_utils as box_utils

		logger = logging.getLogger(__name__)
		@@ -25,7 +25,7 @@ class TestBindingPocket(unittest.TestCase):
		"""Tests that binding pockets are detected."""
		current_dir = os.path.dirname(os.path.realpath(__file__))
		protein_file = os.path.join(current_dir, "1jld_protein.pdb")
		coords = rdkit_util.load_molecule(protein_file)[0]
		coords = rdkit_utils.load_molecule(protein_file)[0]

		boxes = box_utils.get_face_boxes(coords)
		assert isinstance(boxes, list)

deepchem/feat/atomic_coordinates.py

+10 −9

Original line number	Diff line number	Diff line
		@@ -5,8 +5,9 @@ import logging
		import numpy as np
		from deepchem.feat import Featurizer
		from deepchem.feat import ComplexFeaturizer
		from deepchem.utils import rdkit_util, pad_array
		from deepchem.utils.rdkit_util import MoleculeLoadException
		from deepchem.utils import pad_array
		from deepchem.utils.rdkit_utils import MoleculeLoadException, get_xyz_from_mol, \
		load_molecule, merge_molecules_xyz, merge_molecules


		class AtomicCoordinates(Featurizer):
		@@ -172,9 +173,9 @@ class NeighborListComplexAtomicCoordinates(ComplexFeaturizer):
		protein_pdb_file: Str
		Filename for protein pdb file.
		"""
		mol_coords, ob_mol = rdkit_util.load_molecule(mol_pdb_file)
		protein_coords, protein_mol = rdkit_util.load_molecule(protein_pdb_file)
		system_coords = rdkit_util.merge_molecules_xyz([mol_coords, protein_coords])
		mol_coords, ob_mol = load_molecule(mol_pdb_file)
		protein_coords, protein_mol = load_molecule(protein_pdb_file)
		system_coords = merge_molecules_xyz([mol_coords, protein_coords])

		system_neighbor_list = compute_neighbor_list(
		system_coords, self.neighbor_cutoff, self.max_num_neighbors, None)
		@@ -219,17 +220,17 @@ class ComplexNeighborListFragmentAtomicCoordinates(ComplexFeaturizer):

		def _featurize(self, mol_pdb_file, protein_pdb_file):
		try:
		frag1_coords, frag1_mol = rdkit_util.load_molecule(
		frag1_coords, frag1_mol = load_molecule(
		mol_pdb_file, is_protein=False, sanitize=True, add_hydrogens=False)
		frag2_coords, frag2_mol = rdkit_util.load_molecule(
		frag2_coords, frag2_mol = load_molecule(
		protein_pdb_file, is_protein=True, sanitize=True, add_hydrogens=False)
		except MoleculeLoadException:
		# Currently handles loading failures by returning None
		# TODO: Is there a better handling procedure?
		logging.warning("Some molecules cannot be loaded by Rdkit. Skipping")
		return None
		system_mol = rdkit_util.merge_molecules([frag1_mol, frag2_mol])
		system_coords = rdkit_util.get_xyz_from_mol(system_mol)
		system_mol = merge_molecules([frag1_mol, frag2_mol])
		system_coords = get_xyz_from_mol(system_mol)

		frag1_coords, frag1_mol = self._strip_hydrogens(frag1_coords, frag1_mol)
		frag2_coords, frag2_mol = self._strip_hydrogens(frag2_coords, frag2_mol)

deepchem/feat/binding_pocket_features.py

+3 −2

Original line number	Diff line number	Diff line
		@@ -3,8 +3,9 @@ Featurizes proposed binding pockets.
		"""
		import numpy as np
		import logging
		from deepchem.utils import rdkit_util

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

		logger = logging.getLogger(__name__)

		@@ -82,7 +83,7 @@ class BindingPocketFeaturizer(Featurizer):
		A numpy array of shale `(len(pockets), n_residues)`
		"""
		import mdtraj
		protein_coords = rdkit_util.load_molecule(
		protein_coords = load_molecule(
		protein_file, add_hydrogens=False, calc_charges=False)[0]
		mapping = boxes_to_atoms(protein_coords, pockets)
		protein = mdtraj.load(protein_file)

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