Parsing negative values in ATOMIC_NUMBER records of AMBER topologies

[IAlibay]

Fixes #2306

Changes made in this Pull Request:

• Negative values in the ATOMIC_NUMBER records are now read by guessing the atom element using guessers.guess_atom_element.
• As per AMBER topology files with negative ATOMIC_NUMBER fail to be parsed #2306 (comment) element guesses now output user warnings.

Questions:

• Do we want to be warning the users in TOPParser or within the guessers?

PR Checklist

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

[richardjgowers]

Thanks @IAlibay , looks good, is it easy to add a quick test checking that a warning happens? If it's tricky I'll just merge as is

[richardjgowers]

you should be able to write some sort of test that uses assert_warns (or is it with pytest.warns:?)

[codecov]

Codecov Report

Merging #2307 into develop will decrease coverage by 0.01%.
The diff coverage is 100%.

@@             Coverage Diff             @@
##           develop    #2307      +/-   ##
===========================================
- Coverage    89.63%   89.61%   -0.02%     
===========================================
  Files          173      157      -16     
  Lines        21498    19525    -1973     
  Branches      2801     2803       +2     
===========================================
- Hits         19269    17498    -1771     
+ Misses        1628     1431     -197     
+ Partials       601      596       -5

Impacted Files	Coverage Δ
package/MDAnalysis/topology/TOPParser.py	100% <100%> (ø)	⬆️
...age/MDAnalysis/analysis/hbonds/hbond_autocorrel.py	87.8% <0%> (-0.54%)	⬇️
core/util.py
transformations/__init__.py
auxiliary/base.py
util.py
topology/base.py
__init__.py
topology/__init__.py
visualization/__init__.py
... and 16 more

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[IAlibay]

@richardjgowers Thanks for the review, hopefully 8a1295e should cover the warnings 😄

Unfortunately I couldn't find a quick way to not have to duplicate some of the functions.

[richardjgowers]

@IAlibay yep thanks!

[orbeckst]

I ignored AppVeyor and merged. Thanks @IAlibay !