Merge pull request #992 from rbharath/deprem (9c9e7b29) · Commits · 钟慕尧 / deepchem

deepchem/dock/init.py

+0 −1

Original line number	Diff line number	Diff line
		@@ -11,6 +11,5 @@ from deepchem.dock.pose_scoring import PoseScorer
		from deepchem.dock.pose_scoring import GridPoseScorer
		from deepchem.dock.docking import Docker
		from deepchem.dock.docking import VinaGridRFDocker
		from deepchem.dock.docking import VinaGridDNNDocker
		from deepchem.dock.binding_pocket import ConvexHullPocketFinder
		from deepchem.dock.binding_pocket import RFConvexHullPocketFinder

deepchem/dock/docking.py

+6 −4

Original line number	Diff line number	Diff line
		@@ -14,7 +14,7 @@ import os
		import tempfile
		from deepchem.data import DiskDataset
		from deepchem.models import SklearnModel
		from deepchem.models import TensorflowMultiTaskRegressor
		from deepchem.models import MultiTaskRegressor
		from deepchem.dock.pose_scoring import GridPoseScorer
		from deepchem.dock.pose_generation import VinaPoseGenerator
		from sklearn.ensemble import RandomForestRegressor
		@@ -71,6 +71,7 @@ class VinaGridRFDocker(Docker):
		return (score, (protein_docked, ligand_docked))


		'''
		class VinaGridDNNDocker(object):
		"""Vina pose-generation, DNN-models on grid-featurization of complexes."""

		@@ -88,14 +89,14 @@ class VinaGridDNNDocker(object):
		# Fit model on dataset
		pdbbind_tasks = ["-logKd/Ki"]
		n_features = 2052
		model = TensorflowMultiTaskRegressor(
		model = MultiTaskRegressor(
		len(pdbbind_tasks),
		n_features,
		logdir=self.model_dir,
		dropouts=[.25],
		learning_rate=0.0003,
		weight_init_stddevs=[.1],
		batch_size=64)
		batch_size=64,
		model_dir=self.model_dir)
		model.reload()

		self.pose_scorer = GridPoseScorer(model, feat="grid")
		@@ -116,3 +117,4 @@ class VinaGridDNNDocker(object):
		else:
		score = np.zeros((1,))
		return (score, (protein_docked, ligand_docked))
		'''

deepchem/dock/tests/test_docking.py

+4 −0

Original line number	Diff line number	Diff line
		@@ -34,6 +34,7 @@ class TestDocking(unittest.TestCase):
		return
		docker = dc.dock.VinaGridRFDocker(exhaustiveness=1, detect_pockets=True)

		'''
		@attr("slow")
		def test_vina_grid_dnn_docker_init(self):
		"""Test that VinaGridDNNDocker can be initialized."""
		@@ -44,6 +45,7 @@ class TestDocking(unittest.TestCase):
		if sys.version_info >= (3, 0):
		return
		docker = dc.dock.VinaGridDNNDocker(exhaustiveness=1, detect_pockets=True)
		'''

		@attr("slow")
		def test_vina_grid_rf_docker_dock(self):
		@@ -104,6 +106,7 @@ class TestDocking(unittest.TestCase):

		assert score.shape == (1,)

		'''
		@attr("slow")
		def test_vina_grid_dnn_docker_dock(self):
		"""Test that VinaGridDNNDocker can dock."""
		@@ -136,3 +139,4 @@ class TestDocking(unittest.TestCase):

		# Check returned files exist
		assert score.shape == (1,)
		'''

deepchem/hyper/tests/test_hyperparam_opt.py

+2 −2

Original line number	Diff line number	Diff line
		@@ -145,8 +145,8 @@ class TestHyperparamOpt(unittest.TestCase):
		params_dict = {"layer_sizes": [(10,), (100,)]}

		def model_builder(model_params, model_dir):
		return dc.models.TensorflowMultiTaskClassifier(
		len(tasks), n_features, model_dir, **model_params)
		return dc.models.MultiTaskClassifier(
		len(tasks), n_features, model_dir=model_dir, **model_params)

		optimizer = dc.hyper.HyperparamOpt(model_builder)
		best_model, best_hyperparams, all_results = optimizer.hyperparam_search(

deepchem/models/init.py

+0 −9

Original line number	Diff line number	Diff line
		@@ -10,18 +10,9 @@ from deepchem.models.sklearn_models import SklearnModel
		from deepchem.models.xgboost_models import XGBoostModel
		from deepchem.models.multitask import SingletaskToMultitask

		from deepchem.models.tensorflow_models.fcnet import TensorflowMultiTaskRegressor
		from deepchem.models.tensorflow_models.fcnet import TensorflowMultiTaskClassifier
		from deepchem.models.tensorflow_models.fcnet import TensorflowMultiTaskFitTransformRegressor
		from deepchem.models.tensorflow_models.fcnet import MultiTaskRegressor
		from deepchem.models.tensorflow_models.fcnet import MultiTaskClassifier
		from deepchem.models.tensorflow_models.fcnet import MultiTaskFitTransformRegressor
		from deepchem.models.tensorflow_models.robust_multitask import RobustMultitaskRegressor
		from deepchem.models.tensorflow_models.robust_multitask import RobustMultitaskClassifier
		from deepchem.models.tensorflow_models.lr import TensorflowLogisticRegression
		from deepchem.models.tensorflow_models.progressive_multitask import ProgressiveMultitaskRegressor
		from deepchem.models.tensorflow_models.progressive_joint import ProgressiveJointRegressor
		from deepchem.models.tensorflow_models.IRV import TensorflowMultiTaskIRVClassifier
		from deepchem.models.tensorgraph.tensor_graph import TensorGraph
		from deepchem.models.tensorgraph.models.graph_models import WeaveTensorGraph, DTNNTensorGraph, DAGTensorGraph, GraphConvTensorGraph, MPNNTensorGraph
		from deepchem.models.tensorgraph.models.symmetry_function_regression import BPSymmetryFunctionRegression, ANIRegression

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