Streamline angles(), bonds(), dihedrals()

[lilyminium]

Fixes #

Changes made in this Pull Request:

• Wrote an underlying function for angles(), bonds(), dihedrals() to use
• This doesn't really change the code. It adds a little execution time in calling another function, creating a new list of positions, and a bit of string processing for the error messages. It removes a little maintenance time because now any changes only have to be made to one function.

Is there a reason for the _bondsSlow(), _anglesSlow(), etc. functions? They don't appear to be used anywhere.

PR Checklist

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

[pep8speaks]

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

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2021-04-23 04:25:53 UTC

[codecov]

Codecov Report

Merging #3203 (cc9aeae) into develop (bb5d291) will increase coverage by 0.07%.
The diff coverage is 100.00%.

@@             Coverage Diff             @@
##           develop    #3203      +/-   ##
===========================================
+ Coverage    92.73%   92.80%   +0.07%     
===========================================
  Files          168      170       +2     
  Lines        22686    22792     +106     
  Branches      3214     3233      +19     
===========================================
+ Hits         21038    21153     +115     
+ Misses        1600     1591       -9     
  Partials        48       48              

Impacted Files	Coverage Δ
package/MDAnalysis/core/topologyobjects.py	98.56% <100.00%> (-0.05%)	⬇️
package/MDAnalysis/analysis/rms.py	95.06% <0.00%> (ø)
package/MDAnalysis/transformations/fit.py	100.00% <0.00%> (ø)
package/MDAnalysis/transformations/wrap.py	100.00% <0.00%> (ø)
package/MDAnalysis/transformations/rotate.py	100.00% <0.00%> (ø)
package/MDAnalysis/transformations/__init__.py	100.00% <0.00%> (ø)
...ge/MDAnalysis/transformations/positionaveraging.py	100.00% <0.00%> (ø)
...sis/analysis/encore/clustering/ClusteringMethod.py	96.92% <0.00%> (ø)
package/MDAnalysis/transformations/base.py	100.00% <0.00%> (ø)
...ackage/MDAnalysis/transformations/boxdimensions.py	100.00% <0.00%> (ø)
... and 11 more

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[richardjgowers]

The slow versions were for debugging back in the day, if you want to remove them then that would be good