Loading .travis.yml +1 −2 Original line number Diff line number Diff line Loading @@ -2,7 +2,6 @@ language: python python: - '2.7' - '3.5' - '3.6' sudo: required dist: trusty install: Loading @@ -20,7 +19,7 @@ install: - pip install coveralls - python setup.py install script: - nosetests --with-flaky -a '!slow' --with-timer --with-coverage --cover-package=deepchem - nosetests -q --with-flaky -a '!slow' --with-coverage --cover-package=deepchem -v deepchem --nologcapture - if [ $TRAVIS_PYTHON_VERSION == '3.5' ]; then find ./deepchem | grep .py$ |xargs python -m doctest -v; Loading deepchem/dock/pose_generation.py +1 −1 Original line number Diff line number Diff line Loading @@ -68,7 +68,7 @@ class VinaPoseGenerator(PoseGenerator): logger.info("Vina not available. Downloading") # TODO(rbharath): May want to move this file to S3 so we can ensure it's # always available. wget_cmd = "wget -nv -c http://vina.scripps.edu/download/autodock_vina_1_1_2_linux_x86.tgz" wget_cmd = "wget -nv -c -T 15 http://vina.scripps.edu/download/autodock_vina_1_1_2_linux_x86.tgz" call(wget_cmd.split()) logger.info("Downloaded Vina. Extracting") download_cmd = "tar xzvf autodock_vina_1_1_2_linux_x86.tgz" Loading deepchem/dock/tests/test_docking.py +3 −0 Original line number Diff line number Diff line Loading @@ -21,12 +21,14 @@ class TestDocking(unittest.TestCase): Does sanity checks on pose generation. """ @nottest def test_vina_grid_rf_docker_init(self): """Test that VinaGridRFDocker can be initialized.""" if sys.version_info >= (3, 0): return docker = dc.dock.VinaGridRFDocker(exhaustiveness=1, detect_pockets=False) @nottest def test_pocket_vina_grid_rf_docker_init(self): """Test that VinaGridRFDocker w/pockets can be initialized.""" if sys.version_info >= (3, 0): Loading Loading @@ -65,6 +67,7 @@ class TestDocking(unittest.TestCase): assert os.path.exists(protein_docked) assert os.path.exists(ligand_docked) @nottest def test_vina_grid_rf_docker_specified_pocket(self): """Test that VinaGridRFDocker can dock into spec. pocket.""" if sys.version_info >= (3, 0): Loading deepchem/dock/tests/test_pose_generation.py +2 −0 Original line number Diff line number Diff line Loading @@ -20,11 +20,13 @@ class TestPoseGeneration(unittest.TestCase): Does sanity checks on pose generation. """ @attr("slow") def test_vina_initialization(self): """Test that VinaPoseGenerator can be initialized.""" # Note this may download autodock Vina... vpg = dc.dock.VinaPoseGenerator(detect_pockets=False, exhaustiveness=1) @attr("slow") def test_pocket_vina_initialization(self): """Test that VinaPoseGenerator can be initialized.""" # Note this may download autodock Vina... Loading deepchem/feat/rdkit_grid_featurizer.py +22 −0 Original line number Diff line number Diff line Loading @@ -1313,6 +1313,28 @@ class RdkitGridFeaturizer(ComplexFeaturizer): channel_power=None, nb_channel=16, dtype="np.int8"): """Private helper function to voxelize inputs. Parameters ---------- get_voxels: function Function that voxelizes inputs hash_function: function Used to map feature choices to voxel channels. coordinates: np.ndarray Contains the 3D coordinates of a molecular system. feature_dict: Dictionary Keys are atom indices. feature_list: list List of available features. channel_power: int If specified, nb_channel is set to 2**channel_power. TODO: This feels like a redundant parameter. nb_channel: int The number of feature channels computed per voxel dtype: type The dtype of the numpy ndarray created to hold features. """ if channel_power is not None: if channel_power == 0: Loading Loading
.travis.yml +1 −2 Original line number Diff line number Diff line Loading @@ -2,7 +2,6 @@ language: python python: - '2.7' - '3.5' - '3.6' sudo: required dist: trusty install: Loading @@ -20,7 +19,7 @@ install: - pip install coveralls - python setup.py install script: - nosetests --with-flaky -a '!slow' --with-timer --with-coverage --cover-package=deepchem - nosetests -q --with-flaky -a '!slow' --with-coverage --cover-package=deepchem -v deepchem --nologcapture - if [ $TRAVIS_PYTHON_VERSION == '3.5' ]; then find ./deepchem | grep .py$ |xargs python -m doctest -v; Loading
deepchem/dock/pose_generation.py +1 −1 Original line number Diff line number Diff line Loading @@ -68,7 +68,7 @@ class VinaPoseGenerator(PoseGenerator): logger.info("Vina not available. Downloading") # TODO(rbharath): May want to move this file to S3 so we can ensure it's # always available. wget_cmd = "wget -nv -c http://vina.scripps.edu/download/autodock_vina_1_1_2_linux_x86.tgz" wget_cmd = "wget -nv -c -T 15 http://vina.scripps.edu/download/autodock_vina_1_1_2_linux_x86.tgz" call(wget_cmd.split()) logger.info("Downloaded Vina. Extracting") download_cmd = "tar xzvf autodock_vina_1_1_2_linux_x86.tgz" Loading
deepchem/dock/tests/test_docking.py +3 −0 Original line number Diff line number Diff line Loading @@ -21,12 +21,14 @@ class TestDocking(unittest.TestCase): Does sanity checks on pose generation. """ @nottest def test_vina_grid_rf_docker_init(self): """Test that VinaGridRFDocker can be initialized.""" if sys.version_info >= (3, 0): return docker = dc.dock.VinaGridRFDocker(exhaustiveness=1, detect_pockets=False) @nottest def test_pocket_vina_grid_rf_docker_init(self): """Test that VinaGridRFDocker w/pockets can be initialized.""" if sys.version_info >= (3, 0): Loading Loading @@ -65,6 +67,7 @@ class TestDocking(unittest.TestCase): assert os.path.exists(protein_docked) assert os.path.exists(ligand_docked) @nottest def test_vina_grid_rf_docker_specified_pocket(self): """Test that VinaGridRFDocker can dock into spec. pocket.""" if sys.version_info >= (3, 0): Loading
deepchem/dock/tests/test_pose_generation.py +2 −0 Original line number Diff line number Diff line Loading @@ -20,11 +20,13 @@ class TestPoseGeneration(unittest.TestCase): Does sanity checks on pose generation. """ @attr("slow") def test_vina_initialization(self): """Test that VinaPoseGenerator can be initialized.""" # Note this may download autodock Vina... vpg = dc.dock.VinaPoseGenerator(detect_pockets=False, exhaustiveness=1) @attr("slow") def test_pocket_vina_initialization(self): """Test that VinaPoseGenerator can be initialized.""" # Note this may download autodock Vina... Loading
deepchem/feat/rdkit_grid_featurizer.py +22 −0 Original line number Diff line number Diff line Loading @@ -1313,6 +1313,28 @@ class RdkitGridFeaturizer(ComplexFeaturizer): channel_power=None, nb_channel=16, dtype="np.int8"): """Private helper function to voxelize inputs. Parameters ---------- get_voxels: function Function that voxelizes inputs hash_function: function Used to map feature choices to voxel channels. coordinates: np.ndarray Contains the 3D coordinates of a molecular system. feature_dict: Dictionary Keys are atom indices. feature_list: list List of available features. channel_power: int If specified, nb_channel is set to 2**channel_power. TODO: This feels like a redundant parameter. nb_channel: int The number of feature channels computed per voxel dtype: type The dtype of the numpy ndarray created to hold features. """ if channel_power is not None: if channel_power == 0: Loading
