Changes (6bc98744) · Commits · 钟慕尧 / deepchem

deepchem/feat/init.py

+1 −0

Original line number	Diff line number	Diff line
		@@ -18,6 +18,7 @@ from deepchem.feat.rdkit_grid_featurizer import RdkitGridFeaturizer
		from deepchem.feat.binding_pocket_features import BindingPocketFeaturizer
		from deepchem.feat.one_hot import OneHotFeaturizer
		from deepchem.feat.raw_featurizer import RawFeaturizer
		from deepchem.feat.raw_featurizer import RawReactionFeaturizer
		from deepchem.feat.atomic_coordinates import AtomicCoordinates
		from deepchem.feat.atomic_coordinates import NeighborListComplexAtomicCoordinates
		from deepchem.feat.adjacency_fingerprints import AdjacencyFingerprint

deepchem/feat/atomic_coordinates.py

+2 −0

Original line number	Diff line number	Diff line
		@@ -8,6 +8,8 @@ from deepchem.feat import ComplexFeaturizer
		from deepchem.utils import rdkit_util, pad_array
		from deepchem.utils.rdkit_util import MoleculeLoadException

		logger = logging.getLogger(__name__)


		class AtomicCoordinates(Featurizer):
		"""

deepchem/feat/base_classes.py

+15 −0

Original line number	Diff line number	Diff line
		@@ -367,3 +367,18 @@ class UserDefinedFeaturizer(Featurizer):
		def __init__(self, feature_fields):
		"""Creates user-defined-featurizer."""
		self.feature_fields = feature_fields


		class ReactionFeaturizer(Featurizer):
		"""Abstract class that featurizes reactions."""

		def _featurize(self, smarts):
		""""
		Calculate features for a single reaction.

		Parameters
		----------
		smarts: str
		SMARTS string defining reaction.
		"""
		raise NotImplementedError('Featurizer is not defined')

deepchem/feat/raw_featurizer.py

+32 −0

Original line number	Diff line number	Diff line
		@@ -44,3 +44,35 @@ class RawFeaturizer(MolecularFeaturizer):
		return Chem.MolToSmiles(mol)
		else:
		return mol

		class RawReactionFeaturizer(Featurizer):
		"""Featurize SMARTS as RDKit Reaction objects.

		This featurizer uses RDKit's `rdkit.Chem.rdChemReactions.ReactionFromSmarts` to parse in input SMARTS strings.
		"""

		def __init__(self, smarts=True):
		"""
		Parameters
		----------
		smarts: bool, optional
		If True, process smarts into rdkit Reaction objects. Else don't process.
		"""
		self.smarts = smarts

		def _featurize(self, mol):
		"""
		mol: string
		The SMARTS string to process.
		"""
		from rdkit.Chem import rdChemReactions
		if self.smarts:
		smarts = mol
		# Sometimes smarts have extraneous information at end of
		# form " \|f:0" that causes parsing to fail. Not sure what
		# this information is, but just ignoring for now.
		smarts = smarts.split(" ")[0]
		rxn = rdChemReactions.ReactionFromSmarts(smarts)
		return rxn
		else:
		return mol

deepchem/feat/rdkit_grid_featurizer.py

+10 −7

Original line number	Diff line number	Diff line
		"""
		Computes physiochemical descriptors which summarize a 3D molecular complex.
		"""
		import logging
		import os
		import shutil
		import time
		import hashlib
		import multiprocessing
		from collections import Counter
		from warnings import warn
		from deepchem.utils.rdkit_util import load_molecule
		from deepchem.utils.rdkit_util import MoleculeLoadException

		import numpy as np
		from scipy.spatial.distance import cdist
		from copy import deepcopy
		@@ -1233,8 +1239,7 @@ class RdkitGridFeaturizer(ComplexFeaturizer):
		############################################################## TIMING
		time2 = time.time()
		logger.info(
		"TIMING: Loading protein coordinates took %0.3f s" % (time2 - time1),
		self.verbose)
		"TIMING: Loading protein coordinates took %0.3f s" % (time2 - time1))
		############################################################## TIMING
		############################################################## TIMING
		time1 = time.time()
		@@ -1244,8 +1249,7 @@ class RdkitGridFeaturizer(ComplexFeaturizer):
		############################################################## TIMING
		time2 = time.time()
		logger.info(
		"TIMING: Loading ligand coordinates took %0.3f s" % (time2 - time1),
		self.verbose)
		"TIMING: Loading ligand coordinates took %0.3f s" % (time2 - time1))
		############################################################## TIMING
		except MoleculeLoadException:
		logger.warning("Some molecules cannot be loaded by Rdkit. Skipping")
		@@ -1259,8 +1263,7 @@ class RdkitGridFeaturizer(ComplexFeaturizer):
		protein_xyz = subtract_centroid(protein_xyz, centroid)
		############################################################## TIMING
		time2 = time.time()
		logger.info("TIMING: Centroid processing took %0.3f s" % (time2 - time1),
		self.verbose)
		logger.info("TIMING: Centroid processing took %0.3f s" % (time2 - time1))
		############################################################## TIMING

		pairwise_distances = compute_pairwise_distances(protein_xyz, ligand_xyz)

Admin message