Cleanup (fe33e352) · Commits · 钟慕尧 / deepchem

deepchem/dock/binding_pocket.py

+1 −19

Original line number	Diff line number	Diff line
		@@ -235,9 +235,6 @@ class RFConvexHullPocketFinder(BindingPocketFinder):
		examples/binding_pockets/binding_pocket_datasets.py. Find way to refactor
		to avoid code duplication.
		"""
		##################################################### DEBUG
		#print("ENTERING!!!!!!!!!!!!!!!!!!!!")
		##################################################### DEBUG
		if not ligand_file.endswith(".sdf"):
		raise ValueError("Only .sdf ligand files can be featurized.")
		ligand_basename = os.path.basename(ligand_file).split(".")[0]
		@@ -273,19 +270,7 @@ class RFConvexHullPocketFinder(BindingPocketFinder):
		features[:, n_pocket_features:] = ligand_features
		dataset = NumpyDataset(X=features)
		pocket_preds = self.model.predict(dataset)
		############################################################# DEBUG
		pocket_pred_proba = np.squeeze(self.model.predict_proba(dataset))
		#print("pockets")
		#print(pockets)
		#print("pocket_features")
		#print(pocket_features)
		#print("features")
		#print(features)
		#print("n_pockets")
		#print(n_pockets)
		#print("pocket_pred_proba")
		#print(pocket_pred_proba)
		############################################################# DEBUG

		# Find pockets which are active
		active_pockets = []
		@@ -293,11 +278,8 @@ class RFConvexHullPocketFinder(BindingPocketFinder):
		active_pocket_coords = []
		for pocket_ind in range(len(pockets)):
		#################################################### DEBUG
		# TODO(rbharath): FIX THIS! For now since models are broken, using a bogus
		# cutoff.
		# TODO(rbharath): For now, using a weak cutoff. Fix later.
		#if pocket_preds[pocket_ind] == 1:
		#print("pocket_pred_proba.shape")
		#print(pocket_pred_proba.shape)
		if pocket_pred_proba[pocket_ind][1] > .15:
		#################################################### DEBUG
		pocket = pockets[pocket_ind]

examples/binding_pockets/binding_pocket_datasets.py

+1 −12

Original line number	Diff line number	Diff line
		@@ -130,7 +130,7 @@ def featurize_pdbbind_pockets(data_dir=None, subset="core"):
		features, labels = compute_binding_pocket_features(
		pocket_featurizer, ligand_featurizer, pdb_subdir, pdb_code)
		if features is None:
		print("FEATURIZATION FAILED!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!")
		print("Featurization failed!")
		continue
		all_features.append(features)
		all_labels.append(labels)
		@@ -138,21 +138,10 @@ def featurize_pdbbind_pockets(data_dir=None, subset="core"):
		all_ids.append(ids)
		time2 = time.time()
		print("TIMING: PDBBind Pocket Featurization took %0.3f s" % (time2-time1))
		################################################################## DEBUG
		print("[features.shape for features in all_features]")
		print([features.shape for features in all_features])
		print("[labels.shape for labels in all_labels]")
		print([labels.shape for labels in all_labels])
		################################################################## DEBUG
		X = np.vstack(all_features)
		y = np.concatenate(all_labels)
		w = np.ones_like(y)
		ids = np.concatenate(all_ids)
		################################################################## DEBUG
		print("ids.shape")
		print(ids.shape)
		################################################################## DEBUG


		dataset = dc.data.DiskDataset.from_numpy(X, y, w, ids, data_dir=data_dir)
		return dataset, tasks

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