Cleanup (6f6b9ad1) · Commits · 钟慕尧 / deepchem

deepchem/feat/grid_featurizer.py

+0 −19

Original line number	Diff line number	Diff line
		@@ -29,11 +29,6 @@ def get_xyz_from_ob(ob_mol):
		returns an m x 3 np array of 3d coords
		of given openbabel molecule
		"""
		######################################################### DEBUG
		#print("get_xyz_from_ob")
		#print("ob_mol.NumAtoms()")
		#print(ob_mol.NumAtoms())
		######################################################### DEBUG
		xyz = np.zeros((ob_mol.NumAtoms(), 3))
		for i, atom in enumerate(ob.OBMolAtomIter(ob_mol)):
		xyz[i, 0] = atom.x()
		@@ -891,10 +886,6 @@ class GridFeaturizer(ComplexFeaturizer):
		def _featurize_complex(self, ligand_ext, ligand_lines, protein_pdb_lines):
		tempdir = tempfile.mkdtemp()

		############################################################### DEBUG
		#print("ligand_lines")
		#print(ligand_lines)
		############################################################### DEBUG
		############################################################## TIMING
		time1 = time.time()
		############################################################## TIMING
		@@ -968,12 +959,6 @@ class GridFeaturizer(ComplexFeaturizer):
		if not self.ligand_only:
		protein_xyz, protein_ob = load_molecule(
		protein_pdb, calc_charges=False)
		############################################################ DEBUG
		#print("protein_pdb")
		#print(protein_pdb)
		#print("protein_xyz")
		#print(protein_xyz)
		############################################################ DEBUG
		############################################################## TIMING
		time2 = time.time()
		log("TIMING: Loading protein coordinates took %0.3f s" % (time2-time1),
		@@ -1026,10 +1011,6 @@ class GridFeaturizer(ComplexFeaturizer):
		_featurize_binding_pocket_ecfp(
		protein_xyz, protein_ob, ligand_xyz, ligand_ob,
		pairwise_distances, cutoff=4.5, ecfp_degree=self.ecfp_degree))
		################################################################ DEBUG
		#print("protein_ecfp_dict")
		#print(protein_ecfp_dict)
		################################################################ DEBUG
		############################################################## TIMING
		time2 = time.time()
		log("TIMING: ecfp voxel computataion took %0.3f s" % (time2-time1),

examples/pdbbind/pdbbind_datasets.py

+1 −18

Original line number	Diff line number	Diff line
		@@ -32,12 +32,6 @@ def compute_pdbbind_features(grid_featurizer, pdb_subdir, pdb_code):
		"""Compute features for a given complex"""
		protein_file = os.path.join(pdb_subdir, "%s_protein.pdb" % pdb_code)
		ligand_file = os.path.join(pdb_subdir, "%s_ligand.sdf" % pdb_code)
		################################################################ DEBUG
		#print("protein_file")
		#print(protein_file)
		#print("ligand_file")
		#print(ligand_file)
		################################################################ DEBUG
		features = grid_featurizer.featurize_complexes(
		[ligand_file], [protein_file])
		features = np.squeeze(features)
		@@ -85,12 +79,8 @@ def load_core_pdbbind_grid(split="index", feat="grid"):
		feature_len = None
		y_inds = []
		for ind, pdb_code in enumerate(ids):
		print("Processing %s" % str(pdb_code))
		print("Processing complex %d, %s" % (ind, str(pdb_code)))
		pdb_subdir = os.path.join(pdbbind_dir, pdb_code)
		######################################################## DEBUG
		#print("pdb_subdir, pdb_code")
		#print(pdb_subdir, pdb_code)
		######################################################## DEBUG
		computed_feature = compute_pdbbind_features(
		featurizer, pdb_subdir, pdb_code)
		if feature_len is None:
		@@ -100,13 +90,6 @@ def load_core_pdbbind_grid(split="index", feat="grid"):
		continue
		y_inds.append(ind)
		features.append(computed_feature)
		######################################################## DEBUG
		#print("np.count_nonzero(computed_feature)")
		#print(np.count_nonzero(computed_feature))
		#print("computed_feature")
		#print(computed_feature)
		##assert 0 == 1
		######################################################## DEBUG
		y = y[y_inds]
		X = np.vstack(features)
		w = np.ones_like(y)

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