def test_atom_pair_featurizer(self):
""" Create an atom pair collectivevariable using MSMSBuilder3 """
atom_pairs = [[0, 1], [10, 14]]
atom_pair_op = op.MSMBFeaturizerCV(
"atom_pairs",
AtomPairsFeaturizer,
topology=self.topology,
pair_indices=atom_pairs)
md_distances = md.compute_distances(self.mdtraj, atom_pairs)
my_distances = atom_pair_op(self.traj_topology)
np.testing.assert_allclose(md_distances, my_distances, rtol=10 ** -6,
atol=10 ** -10)
def test_return_parameters_from_template(self):
atom_pairs = [[0, 1], [10, 14]]
atom_pair_op = op.MSMBFeaturizerCV("atom_pairs",
AtomPairsFeaturizer,
topology=self.topology,
pair_indices=atom_pairs)
# little trick. We just pretend the atom_pairs_op is a function we want
# to use it cannot be stored though, but for from_template it is enough
params = NetCDFPlus.get_value_parameters(
atom_pair_op(self.traj_topology[0]))
assert params['var_type'] == 'numpy.float32'
assert params['simtk_unit'] is None
assert params['dimensions'] == tuple([2])