they modified the API in the new version, MDAnalysis/mdanalysis#1359

weiHelloWorld · Sep 29, 2017 · 7e80f15 · 7e80f15
1 parent ff84795
commit 7e80f15
Show file tree

Hide file tree

Showing 2 changed files with 3 additions and 3 deletions.
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
@@ -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
@@ -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