def test(self):
prep_metric = metrics.Dihedral(angles='phi/psi')
project = get('ProjectInfo.yaml')
os.chdir(self.td)
tICA_train.run(prep_metric, project, delta_time=10, atom_indices=None,
output='tICAtest.h5', min_length=0, stride=1)
ref_tICA = get('tICA_ref_mle.h5')
ref_vals = ref_tICA['vals']
ref_vecs = ref_tICA['vecs']
ref_inds = np.argsort(ref_vals)
ref_vals = ref_vals[ref_inds]
ref_vecs = ref_vecs[:, ref_inds]
test_tICA = load('tICAtest.h5')
test_vals = test_tICA['vals']
test_vecs = test_tICA['vecs']
test_inds = np.argsort(test_vals)
test_vals = test_vals[test_inds]
test_vecs = test_vecs[:, test_inds]
eq(test_vals, ref_vals)
eq(test_vecs, test_vecs)
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 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()