Merge pull request #2039 from nd-02110114/improve-more (a48fbdb2) · Commits · 钟慕尧 / deepchem

deepchem/dock/binding_pocket.py

+2 −2

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
		@@ -50,7 +50,7 @@ def extract_active_site(protein_file: str,
		z_min = int(np.floor(np.amin(pocket_coords[:, 2])))
		z_max = int(np.ceil(np.amax(pocket_coords[:, 2])))
		box = CoordinateBox((x_min, x_max), (y_min, y_max), (z_min, z_max))
		return (box, pocket_coords)
		return box, pocket_coords


		class BindingPocketFinder(object):

deepchem/dock/pose_generation.py

+2 −2

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__)
		@@ -47,7 +47,7 @@ class PoseGenerator(object):

		Parameters
		----------
		molecular_complexes: Tuple[str]
		molecular_complexes: Tuple[str, str]
		A representation of a molecular complex. This tuple is
		(protein_file, ligand_file).
		centroid: np.ndarray, optional (default None)

deepchem/dock/tests/test_binding_pocket.py

+8 −8

Original line number	Diff line number	Diff line
		"""
		Tests for binding pocket detection.
		"""
		import os
		import logging
		import unittest
		import os
		import numpy as np

		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 +26,7 @@ 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)
		@@ -53,9 +54,8 @@ class TestBindingPocket(unittest.TestCase):
		protein_file = os.path.join(current_dir, "1jld_protein.pdb")
		ligand_file = os.path.join(current_dir, "1jld_ligand.sdf")

		active_site_box, active_site_coords = (
		dc.dock.binding_pocket.extract_active_site(protein_file, ligand_file))
		finder = dc.dock.ConvexHullPocketFinder()
		pockets = finder.find_pockets(protein_file)
		active_site_box, active_site_coords = \
		dc.dock.binding_pocket.extract_active_site(protein_file, ligand_file)

		assert len(pockets) > 0
		assert isinstance(active_site_box, box_utils.CoordinateBox)
		assert isinstance(active_site_coords, np.ndarray)

deepchem/dock/tests/test_pose_scoring.py

+0 −2

Original line number	Diff line number	Diff line
		@@ -4,7 +4,6 @@ Tests for Pose Scoring

		import logging
		import unittest
		import pytest
		import numpy as np

		from deepchem.dock.pose_scoring import vina_nonlinearity
		@@ -19,7 +18,6 @@ from deepchem.dock.pose_scoring import vina_energy_term
		logger = logging.getLogger(__name__)


		@pytest.mark.linux_only
		class TestPoseScoring(unittest.TestCase):
		"""
		Does sanity checks on pose generation.

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)

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