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)