MDAnalysis 2.0.0: Structures fetched by PDB code do not contain elements

[dominiquesydow]

https://github.com/MDAnalysis/mdanalysis/releases/tag/release-2.0.0

From @schallerdavid volkamerlab/teachopencadd#106 (comment)

With the new release of MDAnalysis 2.0.0 the OpenCADD fetch of PDB structures by PDB codes will not have elements assigned in the mda.Universe. So by default this will not be written to a PDB file. However openbabel requires this information. I found a workaround to add the element information to the mda.Universe in case it is not present:

# retrieve structure from the Protein Data Bank
pdb_id = "2ito"
structure = Structure.from_pdbid(pdb_id)
# element information maybe missing, but important for subsequent PDBQT conversion
if not hasattr(structure.atoms, "elements"):
    structure.add_TopologyAttr('elements', structure.atoms.types)
structure

[dominiquesydow]

Before 2.0.0

ATOM      1  N   ALA A 702       5.243  11.333 -39.231  1.00  0.00      A    N
ATOM      2  CA  ALA A 702       3.878  11.924 -39.337  1.00  0.00      A    C
ATOM      3  C   ALA A 702       3.882  13.125 -40.277  1.00  0.00      A    C

With 2.0.0

ATOM      1  N   ALA X 702       5.243  11.333 -39.231  1.00 48.95      A     
ATOM      2  CA  ALA X 702       3.878  11.924 -39.337  1.00 48.46      A     
ATOM      3  C   ALA X 702       3.882  13.125 -40.277  1.00 48.29      A