diff --git a/MD_simulation_on_alanine_dipeptide/current_work/src/molecule_spec_sutils.py b/MD_simulation_on_alanine_dipeptide/current_work/src/molecule_spec_sutils.py index da5877d..f6fa741 100644 --- a/MD_simulation_on_alanine_dipeptide/current_work/src/molecule_spec_sutils.py +++ b/MD_simulation_on_alanine_dipeptide/current_work/src/molecule_spec_sutils.py @@ -29,7 +29,7 @@ def mark_and_modify_pdb_for_calculating_RMSD_for_plumed(pdb_file, out_pdb, temp_bfactors = np.zeros(len(temp_atoms)) temp_bfactors[indices] = 1 - temp_atoms.bfactors = temp_bfactors + temp_atoms.tempfactors = temp_bfactors temp_atoms.occupancies = temp_bfactors temp_atoms.write(out_pdb) return out_pdb diff --git a/MD_simulation_on_alanine_dipeptide/current_work/tests/ANN_simulation_test.py b/MD_simulation_on_alanine_dipeptide/current_work/tests/ANN_simulation_test.py index 32140a9..6a8858a 100644 --- a/MD_simulation_on_alanine_dipeptide/current_work/tests/ANN_simulation_test.py +++ b/MD_simulation_on_alanine_dipeptide/current_work/tests/ANN_simulation_test.py @@ -18,9 +18,9 @@ def test_mark_and_modify_pdb_for_calculating_RMSD_for_plumed(): get_index_list_with_selection_statement('../resources/1l2y.pdb', 'name CA')) a = Universe(temp_out) b = a.select_atoms('name CA') - assert np.all(b.bfactors) and np.all(b.occupancies) + assert np.all(b.tempfactors) and np.all(b.occupancies) b = a.select_atoms('not name CA') - assert not (np.any(b.bfactors) or np.any(b.occupancies)) + assert not (np.any(b.tempfactors) or np.any(b.occupancies)) subprocess.check_output(['rm', temp_out]) return