Merge pull request #987 from rbharath/more-trim (b3ebc4d5) · Commits · 钟慕尧 / deepchem

deepchem/dock/tests/test_docking.py

+6 −4

Original line number	Diff line number	Diff line
		@@ -45,6 +45,7 @@ class TestDocking(unittest.TestCase):
		return
		docker = dc.dock.VinaGridDNNDocker(exhaustiveness=1, detect_pockets=True)

		@attr("slow")
		def test_vina_grid_rf_docker_dock(self):
		"""Test that VinaGridRFDocker can dock."""
		if sys.version_info >= (3, 0):
		@@ -55,8 +56,8 @@ class TestDocking(unittest.TestCase):
		ligand_file = os.path.join(current_dir, "1jld_ligand.sdf")

		docker = dc.dock.VinaGridRFDocker(exhaustiveness=1, detect_pockets=False)
		(score, (protein_docked, ligand_docked)) = docker.dock(protein_file,
		ligand_file)
		(score, (protein_docked, ligand_docked)) = docker.dock(
		protein_file, ligand_file)

		# Check returned files exist
		assert score.shape == (1,)
		@@ -103,6 +104,7 @@ class TestDocking(unittest.TestCase):

		assert score.shape == (1,)

		@attr("slow")
		def test_vina_grid_dnn_docker_dock(self):
		"""Test that VinaGridDNNDocker can dock."""
		current_dir = os.path.dirname(os.path.realpath(__file__))
		@@ -110,8 +112,8 @@ class TestDocking(unittest.TestCase):
		ligand_file = os.path.join(current_dir, "1jld_ligand.sdf")

		docker = dc.dock.VinaGridDNNDocker(exhaustiveness=1, detect_pockets=False)
		(score, (protein_docked, ligand_docked)) = docker.dock(protein_file,
		ligand_file)
		(score, (protein_docked, ligand_docked)) = docker.dock(
		protein_file, ligand_file)

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

+1 −0

Original line number	Diff line number	Diff line
		@@ -33,6 +33,7 @@ class TestPoseGeneration(unittest.TestCase):
		return
		vpg = dc.dock.VinaPoseGenerator(detect_pockets=True, exhaustiveness=1)

		@attr("slow")
		def test_vina_poses(self):
		"""Test that VinaPoseGenerator creates pose files."""
		current_dir = os.path.dirname(os.path.realpath(__file__))

deleted100644 → 0

+0 −13

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		"""
		Convenience classes for assembling graph models.
		"""
		from __future__ import print_function
		from __future__ import division
		from __future__ import unicode_literals

		__author__ = "Han Altae-Tran and Bharath Ramsundar"
		__copyright__ = "Copyright 2016, Stanford University"
		__license__ = "MIT"

		import warnings
		import tensorflow as tf

deleted100644 → 0

+0 −28

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		"""Manages Placeholders for Graph convolution networks.
		"""
		from __future__ import print_function
		from __future__ import division
		from __future__ import unicode_literals

		__author__ = "Han Altae-Tran and Bharath Ramsundar"
		__copyright__ = "Copyright 2016, Stanford University"
		__license__ = "MIT"

		import warnings
		import numpy as np
		import tensorflow as tf
		from deepchem.feat.mol_graphs import ConvMol


		def merge_two_dicts(x, y):
		z = x.copy()
		z.update(y)
		return z


		def merge_dicts(l):
		"""Convenience function to merge list of dictionaries."""
		merged = {}
		for dict in l:
		merged = merge_two_dicts(merged, dict)
		return merged

deleted100644 → 0

+0 −21

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		"""
		Implements a multitask graph convolutional classifier.
		"""
		from __future__ import print_function
		from __future__ import division
		from __future__ import unicode_literals

		__author__ = "Han Altae-Tran and Bharath Ramsundar"
		__copyright__ = "Copyright 2016, Stanford University"
		__license__ = "MIT"

		import warnings
		import os
		import sys
		import numpy as np
		import tensorflow as tf
		import sklearn.metrics
		import tempfile
		from deepchem.data import pad_features
		from deepchem.utils.save import log
		from deepchem.models import Model