Loading .travis.yml +0 −1 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 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 scripts/install_deepchem_conda.sh +1 −1 Original line number Diff line number Diff line Loading @@ -42,6 +42,7 @@ if [[ "$unamestr" == 'Darwin' ]]; then fi conda install -y -q -c omnia pdbfixer=1.4 yes | pip install --upgrade pip conda install -y -q -c deepchem mdtraj=1.9.1 conda install -y -q -c rdkit rdkit=2017.09.1 conda install -y -q -c conda-forge joblib=0.11 \ Loading @@ -57,7 +58,6 @@ conda install -y -q -c conda-forge joblib=0.11 \ requests=2.18.4 \ xgboost=0.6a2 \ simdna=0.4.2 \ jupyter=1.0.0 \ pbr=3.1.1 \ setuptools=39.0.1 \ biopython=1.71 \ Loading Loading
.travis.yml +0 −1 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
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
scripts/install_deepchem_conda.sh +1 −1 Original line number Diff line number Diff line Loading @@ -42,6 +42,7 @@ if [[ "$unamestr" == 'Darwin' ]]; then fi conda install -y -q -c omnia pdbfixer=1.4 yes | pip install --upgrade pip conda install -y -q -c deepchem mdtraj=1.9.1 conda install -y -q -c rdkit rdkit=2017.09.1 conda install -y -q -c conda-forge joblib=0.11 \ Loading @@ -57,7 +58,6 @@ conda install -y -q -c conda-forge joblib=0.11 \ requests=2.18.4 \ xgboost=0.6a2 \ simdna=0.4.2 \ jupyter=1.0.0 \ pbr=3.1.1 \ setuptools=39.0.1 \ biopython=1.71 \ Loading
