Adding elements attribute to PDB parser and unit tests

[AmeyaHarmalkar]

Fixes #2647

Changes made in this Pull Request:

• Adds elements attribute to check for valid elements and adds them to the Elements class
• Adds suitable unit tests to check for missing, non-valid and valid elements.
• Solves a part of the problem that Parsers should try and provide an Elements attribute #2553 raises.

PR Checklist

• Tests?
• Docs?
• CHANGELOG updated?
• Issue raised/referenced?

[codecov]

Codecov Report

Merging #2648 into develop will increase coverage by 0.39%.
The diff coverage is 100.00%.

@@             Coverage Diff             @@
##           develop    #2648      +/-   ##
===========================================
+ Coverage    90.61%   91.01%   +0.39%     
===========================================
  Files          174      174              
  Lines        23554    23607      +53     
  Branches      3072     3086      +14     
===========================================
+ Hits         21343    21485     +142     
+ Misses        1585     1498      -87     
+ Partials       626      624       -2     

Impacted Files	Coverage Δ
package/MDAnalysis/topology/PDBParser.py	99.44% <100.00%> (+0.03%)	⬆️
package/MDAnalysis/lib/log.py	95.78% <0.00%> (-1.92%)	⬇️
package/MDAnalysis/analysis/pca.py	95.29% <0.00%> (-0.27%)	⬇️
...sis/analysis/encore/clustering/ClusteringMethod.py	96.92% <0.00%> (-0.18%)	⬇️
...age/MDAnalysis/analysis/hbonds/hbond_autocorrel.py	87.34% <0.00%> (-0.16%)	⬇️
package/MDAnalysis/lib/transformations.py	78.47% <0.00%> (-0.15%)	⬇️
package/MDAnalysis/analysis/waterdynamics.py	90.51% <0.00%> (-0.14%)	⬇️
...ckage/MDAnalysis/analysis/hbonds/hbond_analysis.py	81.49% <0.00%> (-0.11%)	⬇️
package/MDAnalysis/analysis/helanal.py	87.93% <0.00%> (-0.07%)	⬇️
package/MDAnalysis/analysis/base.py	100.00% <0.00%> (ø)
... and 9 more

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update e416aa7...ec0b2f5. Read the comment docs.

[AmeyaHarmalkar]

@IAlibay the new PR for the issue like you suggested.
Let me know if I need to do any further changes.

[IAlibay]

@AmeyaHarmalkar I think there has been some misunderstanding, I meant that you should finish PR #2627 solely allowing for elements to be parsed if they are all present & normal (as you are doing here). Then open up a new PR/issue set for dealing with alternative cases where elements are non-normal, including any appropriate changes to guessers.py.

[AmeyaHarmalkar]

Oh, I completely misunderstood you then. Should I do a hard reset on the other branch then do the changes? I will close this PR and delete the issue.

[IAlibay]

Oh, I completely misunderstood you then. Should I do a hard reset on the other branch then do the changes? I will close this PR and delete the issue.

Sorry about that, this is definitely on me for bad communications. Probably closing this PR would be a good idea, however you can keep the issue open, just add it to the header of #2627 and we can close it when we merge the PR.

Re: hard reset -> just revert the one file, you can do that using git checkout: https://stackoverflow.com/questions/215718/how-can-i-reset-or-revert-a-file-to-a-specific-revision