Implementation of CMSParser

[talagayev]

Partially Fixes #4268 Attempt

Changes made in this Pull Request:

• Addition of CMSParser
• Allows reading CMS Files and extracting atomnames, resnames, atomids, resids, segids

Currently the problem that I am facing is, that I have all of the necessary data as arrays, which I give into the
Topology as attrs, but somehow names is recognized correctly, while in the remainder only the first
item is recognized, thus each atom will belong to the first resname, resid and segid and I am not
sure what the reason is for the Topology only recognizing the first item for those and all for the atomnames

PR Checklist

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

Developers certificate of origin

• I certify that this contribution is covered by the LGPLv2.1+ license as defined in our LICENSE and adheres to the Developer Certificate of Origin.

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📚 Documentation preview 📚: https://mdanalysis--4816.org.readthedocs.build/en/4816/

[pep8speaks]

Hello @talagayev! Thanks for opening this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file package/MDAnalysis/topology/CMSParser.py:

Line 21:1: W293 blank line contains whitespace
Line 27:1: W293 blank line contains whitespace
Line 44:80: E501 line too long (89 > 79 characters)
Line 45:1: W293 blank line contains whitespace
Line 53:9: E265 block comment should start with '# '
Line 65:80: E501 line too long (88 > 79 characters)
Line 92:43: W291 trailing whitespace
Line 118:80: E501 line too long (95 > 79 characters)

• In the file package/MDAnalysis/topology/__init__.py:

Line 310:28: E231 missing whitespace after ','

[codecov]

Codecov Report

❌ Patch coverage is 16.66667% with 55 lines in your changes missing coverage. Please review.
✅ Project coverage is 86.21%. Comparing base (557f27d) to head (3602eec).
⚠️ Report is 93 commits behind head on develop.

Files with missing lines	Patch %	Lines
package/MDAnalysis/topology/CMSParser.py	15.38%	55 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4816      +/-   ##
===========================================
+ Coverage    86.08%   86.21%   +0.12%     
===========================================
  Files          177      190      +13     
  Lines        21742    22875    +1133     
  Branches      3055     3065      +10     
===========================================
+ Hits         18717    19722    +1005     
- Misses        2593     2721     +128     
  Partials       432      432              

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