Fix PDB load_one for Cl atoms

[tovrstra]

Fixes #282

[tovrstra]

The same fix should work for any atom name, assuming the leading two characters define the symbol. This will not always work, e.g. PDB files often use CA for the alpha carbon, not Calcium. See e.g. https://files.rcsb.org/view/5D3A.pdb

If you want to make sure things work like they should, use PDB files with elements defined in the nearly last columns, instead of relying on atom names. We could add a warning for when the symbol is guessed from the atom name, just to clarify that one is potentially in trouble.

[codecov]

Codecov Report

Merging #284 (5d3b498) into master (bb9415f) will decrease coverage by 0.03%.
The diff coverage is 92.10%.

@@            Coverage Diff             @@
##           master     #284      +/-   ##
==========================================
- Coverage   95.01%   94.99%   -0.03%     
==========================================
  Files          74       74              
  Lines        8811     8828      +17     
  Branches     1213     1216       +3     
==========================================
+ Hits         8372     8386      +14     
- Misses        191      193       +2     
- Partials      248      249       +1     

Impacted Files	Coverage Δ
iodata/formats/pdb.py	97.27% <76.92%> (-2.03%)	⬇️
iodata/test/test_pdb.py	98.61% <100.00%> (+0.13%)	⬆️

📣 We’re building smart automated test selection to slash your CI/CD build times. Learn more

[BradenDKelly]

This seems fine to me. We just need to add a warning if the last column is missing since I have a feeling CA will happen

[tovrstra]

I've pushed a commit with the warnings. I have reorganized a few things to stay closer to the definitions in the PDB format. We should also consider opening an issue to rename some fields return by the PDB loader, eg. atname instead of attype. Usually, these names are not atom types.

[tovrstra]

@FarnazH @evohringer @BradenDKelly This is ready to be merged as far as I am concerned. I'll merge this on May 15 unless there are new comments by then.