Merge pull request #2318 from ncfrey/complex-featurizer-fix (f49416be) · Commits · 钟慕尧 / deepchem

deepchem/dock/docking.py

+1 −2

Original line number	Diff line number	Diff line
		@@ -131,8 +131,7 @@ class Docker(object):
		# check whether self.featurizer is instance of ComplexFeaturizer or not
		assert isinstance(self.featurizer, ComplexFeaturizer)
		# TODO: How to handle the failure here?
		(protein_file, ligand_file) = molecular_complex
		features, _ = self.featurizer.featurize([protein_file], [ligand_file])
		features = self.featurizer.featurize([molecular_complex])
		dataset = NumpyDataset(X=features)
		score = self.scoring_model.predict(dataset)
		yield (posed_complex, score)

deepchem/dock/tests/test_docking.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -104,7 +104,7 @@ class TestDocking(unittest.TestCase):
		class DummyFeaturizer(ComplexFeaturizer):

		def featurize(self, complexes, args, *kwargs):
		return np.zeros((len(complexes), 5)), None
		return np.zeros((len(complexes), 5))

		class DummyModel(Model):

deepchem/feat/base_classes.py

+25 −39

Original line number	Diff line number	Diff line
		@@ -4,8 +4,7 @@ Feature calculations.
		import inspect
		import logging
		import numpy as np
		import multiprocessing
		from typing import Any, Dict, List, Iterable, Sequence, Tuple, Union
		from typing import Any, Dict, Iterable, Tuple, Union, cast

		from deepchem.utils import get_print_threshold
		from deepchem.utils.typing import PymatgenStructure
		@@ -150,70 +149,57 @@ class Featurizer(object):
		return self.__class__.__name__ + override_args_info


		class ComplexFeaturizer(object):
		class ComplexFeaturizer(Featurizer):
		""""
		Abstract class for calculating features for mol/protein complexes.
		"""

		def featurize(self, mol_files: Sequence[str],
		protein_pdbs: Sequence[str]) -> Tuple[np.ndarray, List]:
		def featurize(self,
		complexes: Iterable[Tuple[str, str]],
		log_every_n: int = 100) -> np.ndarray:
		"""
		Calculate features for mol/protein complexes.

		Parameters
		----------
		mols: List[str]
		List of PDB filenames for molecules.
		protein_pdbs: List[str]
		List of PDB filenames for proteins.
		complexes: Iterable[Tuple[str, str]]
		List of filenames (PDB, SDF, etc.) for ligand molecules and proteins.
		Each element should be a tuple of the form (ligand_filename,
		protein_filename).

		Returns
		-------
		features: np.ndarray
		Array of features
		failures: List
		Indices of complexes that failed to featurize.
		"""

		pool = multiprocessing.Pool()
		results = []
		for i, (mol_file, protein_pdb) in enumerate(zip(mol_files, protein_pdbs)):
		log_message = "Featurizing %d / %d" % (i, len(mol_files))
		results.append(
		pool.apply_async(ComplexFeaturizer._featurize_callback,
		(self, mol_file, protein_pdb, log_message)))
		pool.close()
		if not isinstance(complexes, Iterable):
		complexes = [cast(Tuple[str, str], complexes)]
		features = []
		failures = []
		for ind, result in enumerate(results):
		new_features = result.get()
		# Handle loading failures which return None
		if new_features is not None:
		features.append(new_features)
		else:
		failures.append(ind)
		for i, point in enumerate(complexes):
		if i % log_every_n == 0:
		logger.info("Featurizing datapoint %i" % i)
		try:
		features.append(self._featurize(point))
		except:
		logger.warning(
		"Failed to featurize datapoint %i. Appending empty array." % i)
		features.append(np.array([]))

		features = np.asarray(features)
		return features, failures
		return features

		def _featurize(self, mol_pdb: str, complex_pdb: str):
		def _featurize(self, complex: Tuple[str, str]):
		"""
		Calculate features for single mol/protein complex.

		Parameters
		----------
		mol_pdb : str
		The PDB filename.
		complex_pdb : str
		The PDB filename.
		complex: Tuple[str, str]
		Filenames for molecule and protein.
		"""
		raise NotImplementedError('Featurizer is not defined.')

		@staticmethod
		def _featurize_callback(featurizer, mol_pdb_file, protein_pdb_file,
		log_message):
		logging.info(log_message)
		return featurizer._featurize(mol_pdb_file, protein_pdb_file)


		class MolecularFeaturizer(Featurizer):
		"""Abstract class for calculating a set of features for a

deepchem/feat/complex_featurizers/complex_atomic_coordinates.py

+9 −7

Original line number	Diff line number	Diff line
		@@ -11,6 +11,8 @@ from deepchem.utils.data_utils import pad_array
		from deepchem.utils.rdkit_utils import MoleculeLoadException, get_xyz_from_mol, \
		load_molecule, merge_molecules_xyz, merge_molecules

		from typing import Tuple


		def compute_neighbor_list(coords, neighbor_cutoff, max_num_neighbors,
		periodic_box_size):
		@@ -98,7 +100,7 @@ class NeighborListComplexAtomicCoordinates(ComplexFeaturizer):
		"""
		Adjacency list of neighbors for protein-ligand complexes in 3-space.

		Neighbors dtermined by user-dfined distance cutoff.
		Neighbors determined by user-defined distance cutoff.
		"""

		def __init__(self, max_num_neighbors=None, neighbor_cutoff=4):
		@@ -112,17 +114,16 @@ class NeighborListComplexAtomicCoordinates(ComplexFeaturizer):
		# Type of data created by this featurizer
		self.dtype = object

		def _featurize(self, mol_pdb_file, protein_pdb_file):
		def _featurize(self, complex: Tuple[str, str]):
		"""
		Compute neighbor list for complex.

		Parameters
		----------
		mol_pdb_file: str
		Filename for ligand pdb file.
		protein_pdb_file: str
		Filename for protein pdb file.
		complex: Tuple[str, str]
		Filenames for molecule and protein.
		"""
		mol_pdb_file, protein_pdb_file = complex
		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])
		@@ -168,7 +169,8 @@ class ComplexNeighborListFragmentAtomicCoordinates(ComplexFeaturizer):
		self.neighborlist_featurizer = NeighborListComplexAtomicCoordinates(
		self.max_num_neighbors, self.neighbor_cutoff)

		def _featurize(self, mol_pdb_file, protein_pdb_file):
		def _featurize(self, complex):
		mol_pdb_file, protein_pdb_file = complex
		try:
		frag1_coords, frag1_mol = load_molecule(
		mol_pdb_file, is_protein=False, sanitize=True, add_hydrogens=False)

deepchem/feat/complex_featurizers/contact_fingerprints.py

+8 −13

Original line number	Diff line number	Diff line
		@@ -93,19 +93,17 @@ class ContactCircularFingerprint(ComplexFeaturizer):
		self.radius = radius
		self.size = size

		def _featurize(self, mol_pdb: str, protein_pdb: str):
		def _featurize(self, complex: Tuple[str, str]):
		"""
		Compute featurization for a molecular complex

		Parameters
		----------
		mol_pdb: str
		Filename for ligand molecule
		protein_pdb: str
		Filename for protein molecule
		complex: Tuple[str, str]
		Filenames for molecule and protein.
		"""
		try:
		fragments = load_complex((mol_pdb, protein_pdb), add_hydrogens=False)
		fragments = load_complex(complex, add_hydrogens=False)

		except MoleculeLoadException:
		logger.warning("This molecule cannot be loaded by Rdkit. Returning None")
		@@ -181,20 +179,17 @@ class ContactCircularVoxelizer(ComplexFeaturizer):
		self.voxels_per_edge = int(self.box_width / self.voxel_width)
		self.flatten = flatten

		def _featurize(self, mol_pdb: str, protein_pdb: str):
		def _featurize(self, complex):
		"""
		Compute featurization for a molecular complex

		Parameters
		----------
		mol_pdb: str
		Filename for ligand molecule
		protein_pdb: str
		Filename for protein molecule
		complex: Tuple[str, str]
		Filenames for molecule and protein.
		"""
		molecular_complex = (mol_pdb, protein_pdb)
		try:
		fragments = load_complex(molecular_complex, add_hydrogens=False)
		fragments = load_complex(complex, add_hydrogens=False)

		except MoleculeLoadException:
		logger.warning("This molecule cannot be loaded by Rdkit. Returning None")

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