PDB parser ignores the element column

[jbarnoud]

Related to #2420

Expected behavior

The penultimate field of the ATOM and HETATM records is the element symbol: http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM. The PDB reader should read that field when present and expose it through the elements topology attribute.

Actual behavior

The element field of a PDB file is ignored. This means the element must be guessed even when provided.

Code to reproduce the behavior

import MDAnalysis as mda
from MDAnalysis.tests.datafiles import PDB_full

u = mda.Universe(PDB_full)
u.atoms.elements

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-61-b55fd0543db8> in <module>
      4 
      5 u = mda.Universe(PDB_full)
----> 6 u.atoms.elements

~/dev/mdanalysis/package/MDAnalysis/core/groups.py in __getattr__(self, attr)
   2291             except selection.SelectionError:
   2292                 pass
-> 2293         raise AttributeError("{cls} has no attribute {attr}".format(
   2294             cls=self.__class__.__name__, attr=attr))
   2295 

AttributeError: AtomGroup has no attribute elements

Currently version of MDAnalysis

• Which version are you using? 0.20.2-dev0 4adbd6c
• Which version of Python (python -V)? '3.8.0 | packaged by conda-forge | (default, Nov 22 2019, 19:11:38) \n[GCC 7.3.0]'
• Which operating system? Ubuntu 18.04

[RMeli]

This should be addressed by #2648?

[jbarnoud]

This should be addressed by #2648?

Indeed, it should be.