def test_2(self): try: subprocess.Popen('ipcluster start --cluster-id=testclusterid --n=1 --daemonize', shell=True) time.sleep(5) args = self.Args() args.output_dir = tempfile.mkdtemp() args.cluster_id = 'testclusterid' logger = AssignParallel.setup_logger() AssignParallel.main(args, self.metric, logger) assignments = Serializer.load_data(os.path.join(args.output_dir, 'Assignments.h5')) r_assignments = Serializer.load_data(os.path.join(fixtures_dir(), 'Assignments.h5')) distances = Serializer.load_data(os.path.join(args.output_dir, 'Assignments.h5.distances')) r_distances = Serializer.load_data(os.path.join(fixtures_dir(), 'Assignments.h5.distances')) npt.assert_array_equal(assignments, r_assignments) npt.assert_array_almost_equal(distances, r_distances) except: raise finally: shutil.rmtree(args.output_dir) subprocess.Popen('ipcluster stop', shell=True).wait()
def test_2(self): try: subprocess.Popen( 'ipcluster start --cluster-id=testclusterid --n=1 --daemonize', shell=True) time.sleep(5) args = self.Args() args.output_dir = tempfile.mkdtemp() args.cluster_id = 'testclusterid' logger = AssignParallel.setup_logger() AssignParallel.main(args, self.metric, logger) assignments = io.loadh( os.path.join(args.output_dir, 'Assignments.h5'), 'arr_0') r_assignments = io.loadh( os.path.join(fixtures_dir(), 'Assignments.h5'), 'Data') distances = io.loadh( os.path.join(args.output_dir, 'Assignments.h5.distances'), 'arr_0') r_distances = io.loadh( os.path.join(fixtures_dir(), 'Assignments.h5.distances'), 'Data') npt.assert_array_equal(assignments, r_assignments) npt.assert_array_almost_equal(distances, r_distances) except: raise finally: shutil.rmtree(args.output_dir) subprocess.Popen('ipcluster stop --cluster-id=testclusterid', shell=True).wait()
def setup(self): self.metric = metrics.Dihedral() self.pdb_fn = os.path.join(fixtures_dir(), 'native.pdb') self.trj_fn = os.path.join(fixtures_dir(), 'trj0.lh5') self.project = Project({'NumTrajs': 1, 'TrajLengths': [501], 'TrajFileBaseName': 'trj', 'TrajFileType': '.lh5', 'ConfFilename': self.pdb_fn, 'TrajFilePath': fixtures_dir()}) self.vtraj = partition(self.project, chunk_size=501)[0]
def setup(self): self.metric = metrics.Dihedral() self.pdb_fn = os.path.join(fixtures_dir(), 'native.pdb') self.trj_fn = os.path.join(fixtures_dir(), 'trj0.lh5') self.project = Project({'traj_lengths': [501], 'traj_paths': [self.trj_fn], 'conf_filename': self.pdb_fn, 'traj_converted_from': [None], 'traj_errors': [None]}) self.vtraj = partition(self.project, chunk_size=501)[0]
def test_asa_3(): traj_ref = np.loadtxt( os.path.join(reference_dir(),'g_sas_ref.dat')) Conf = Trajectory.load_from_pdb(os.path.join( fixtures_dir(), 'native.pdb')) traj = Trajectory.load_trajectory_file( os.path.join(fixtures_dir(), 'trj0.xtc') , Conf=Conf) traj_asa = calculate_asa(traj, probe_radius=0.14, n_sphere_points = 960) # the algorithm used by gromacs' g_sas is slightly different than the one # used here, so the results are not exactly the same -- see the comments # in src/python/geomtry/asa.py or the readme file src/ext/asa/README.txt # for details npt.assert_array_almost_equal(traj_asa, traj_ref, decimal=2)
def setup(self): self.metric = metrics.Dihedral() self.pdb_fn = os.path.join(fixtures_dir(), 'native.pdb') self.trj_fn = os.path.join(fixtures_dir(), 'trj0.lh5') self.project = Project({ 'NumTrajs': 1, 'TrajLengths': [501], 'TrajFileBaseName': 'trj', 'TrajFileType': '.lh5', 'ConfFilename': self.pdb_fn, 'TrajFilePath': fixtures_dir() }) self.vtraj = partition(self.project, chunk_size=501)[0]
def test_asa_2(): t = Trajectory.load_trajectory_file(os.path.join(fixtures_dir(), 'trj0.lh5')) val1 = np.sum(calculate_asa(t[0])) # calculate only frame 0 val2 = np.sum(calculate_asa(t)[0]) # calculate on all frames true_frame_0_asa = 2.859646797180176 npt.assert_approx_equal(true_frame_0_asa, val1) npt.assert_approx_equal(true_frame_0_asa, val2)
def test_rg_1(): project = Project.load_from(os.path.join(fixtures_dir(), 'ProjectInfo.h5')) traj = project.load_traj(0) xyzlist = traj['XYZList'] a = rgcalc.calculate_rg(xyzlist) b = reference_rg(xyzlist) npt.assert_array_almost_equal(a, b)
def test_traj_0(): aind = np.unique( np.random.randint( 22, size=4) ) stride = np.random.randint(1, 100 ) r_traj = Trajectory.load_from_lhdf( os.path.join( fixtures_dir(), 'trj0.lh5' ), Stride=1 ) r_traj.restrict_atom_indices( aind ) r_traj['XYZList'] = r_traj['XYZList'][ ::stride ] traj = Trajectory.load_from_lhdf( os.path.join( fixtures_dir(), 'trj0.lh5' ), Stride = stride, AtomIndices = aind ) for key in traj.keys(): if key in ['SerializerFilename'] : continue if key in ['IndexList']: for row, r_row in zip( traj[key], r_traj[key] ): npt.assert_array_equal( row, r_row ) elif key == 'XYZList': npt.assert_array_almost_equal( traj[key], r_traj[key]) else: npt.assert_array_equal( traj[key], r_traj[key] )
class Args: project = os.path.join(fixtures_dir(), 'ProjectInfo.h5') generators = os.path.join(fixtures_dir(), 'Gens.lh5') profile = 'default' cluster_id = '' chunk_size = 10