Changes (95b9edbf) · Commits · 钟慕尧 / deepchem

deepchem/feat/grid_featurizers.py

+1 −3

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		@@ -8,7 +8,6 @@ from deepchem.utils import rdkit_util
		from deepchem.utils.rdkit_util import get_partial_charge
		from deepchem.feat import ComplexFeaturizer
		from deepchem.utils.hash_utils import hash_ecfp_pair
		from deepchem.utils.hash_utils import vectorize
		from deepchem.utils.voxel_utils import voxelize
		from deepchem.utils.rdkit_util import compute_salt_bridges
		from deepchem.utils.rdkit_util import compute_binding_pocket_cation_pi
		@@ -495,8 +494,7 @@ class HydrogenBondCounter(ComplexFeaturizer):
		#(lig_xyz, lig_rdk), (prot_xyz, prot_rdk) = mol, protein
		#distances = compute_pairwise_distances(prot_xyz, lig_xyz)
		pairwise_features.append(np.concatenate([
		vectorize(
		hash_ecfp_pair, feature_list=hbond_list, size=1)
		np.array([len(hbond_list)])
		for hbond_list in compute_hydrogen_bonds(
		frag1, frag2, distances, self.distance_bins, self.angle_cutoffs)
		], axis=-1))

deepchem/feat/rdkit_grid_featurizer.py

+0 −13

Original line number	Diff line number	Diff line
		@@ -23,26 +23,13 @@ from deepchem.feat.grid_featurizers import CationPiVoxelizer
		from deepchem.feat.grid_featurizers import PiStackVoxelizer
		from deepchem.feat.grid_featurizers import HydrogenBondCounter
		from deepchem.feat.grid_featurizers import HydrogenBondVoxelizer
		from deepchem.utils.rdkit_util import compute_hydrogen_bonds
		from deepchem.utils.rdkit_util import load_molecule
		from deepchem.utils.rdkit_util import compute_centroid
		from deepchem.utils.rdkit_util import subtract_centroid
		from deepchem.utils.rdkit_util import compute_ring_center
		from deepchem.utils.rdkit_util import rotate_molecules
		from deepchem.utils.rdkit_util import compute_pairwise_distances
		from deepchem.utils.rdkit_util import is_salt_bridge
		from deepchem.utils.rdkit_util import compute_salt_bridges
		from deepchem.utils.rdkit_util import compute_pi_stack
		from deepchem.utils.rdkit_util import compute_binding_pocket_cation_pi
		from deepchem.utils.rdkit_util import is_hydrogen_bond
		from deepchem.utils.rdkit_util import compute_all_ecfp
		from deepchem.utils.rdkit_util import MoleculeLoadException
		from deepchem.utils.hash_utils import hash_ecfp
		from deepchem.utils.hash_utils import hash_ecfp_pair
		from deepchem.utils.hash_utils import vectorize
		from deepchem.utils.voxel_utils import voxelize
		from deepchem.utils.voxel_utils import convert_atom_to_voxel
		from deepchem.utils.voxel_utils import convert_atom_pair_to_voxel
		from deepchem.feat import ComplexFeaturizer

		logger = logging.getLogger(__name__)

deepchem/utils/rdkit_util.py

+1 −3

Original line number	Diff line number	Diff line
		@@ -873,9 +873,7 @@ def is_hydrogen_bond(frag1,
		for hydrogen_xyz in hydrogens:
		hydrogen_to_frag2 = frag2_atom_xyz - hydrogen_xyz
		hydrogen_to_frag1 = frag1_atom_xyz - hydrogen_xyz
		#if np.abs(180 - angle_between(hydrogen_to_frag1, hydrogen_to_frag2) * 180.0 / np.pi) <= hbond_angle_cutoff:
		# return True
		return is_angle_within_cutoff(hydrgoen_to_frag2, hydrogen_to_frag1, hbond_angle_cutoff)
		return is_angle_within_cutoff(hydrogen_to_frag2, hydrogen_to_frag1, hbond_angle_cutoff)
		return False

examples/pdbbind/featurize_hydrogen_bond_counter.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -4,7 +4,7 @@ import logging
		from deepchem.molnet.load_function.pdbbind_datasets import get_pdbbind_molecular_complex_files

		complex_files = get_pdbbind_molecular_complex_files(subset="core", version="v2015", interactions="protein-ligand", load_binding_pocket=False)
		n_featurize = 10
		n_featurize = 2
		core_subset = complex_files[:n_featurize]

		featurizer = dc.feat.HydrogenBondCounter()

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