def test_mol_broken_ids_whole_molecule_large():
univ = MDAnalysis.Universe(TPR_xvf, PDB_xvf)
mol_group = univ.select_atoms(sel_spec_nowall)
assert not mol_broken(mol_group)
def test_mol_broken_ids_whole_molecule_small():
ref_top_filepath = os.path.join(root_dir, 'test_data/top.tpr')
struct_filepath = os.path.join(root_dir, 'test_data/ala_shifted_whole.gro')
univ = MDAnalysis.Universe(ref_top_filepath, struct_filepath)
mol_group = univ.select_atoms(sel_spec_nowall)
assert not mol_broken(mol_group)
def test_mol_broken_ids_single_broken_water():
univ = MDAnalysis.Universe(
'test_data/broken_mols/single_water/single_water.tpr',
'test_data/broken_mols/single_water/single_water_broken.gro')
mol_group = univ.select_atoms('resname SOL')
assert mol_group.n_atoms == 3
assert mol_broken(mol_group)
def test_mol_broken_ids_broken_molecule_large():
univ = MDAnalysis.Universe(TPR, GRO)
mol_group = univ.select_atoms(sel_spec_nowall)
assert mol_broken(mol_group)