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_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
