Fix bug in m2rotaxis

[RasmusFonseca]

Takes 180deg rotation into account and added some documentation and tests.

[peterjc]

Can I merge #494 from @bertrand-caron first?

Note there are some minor style issues to address, pip install flake8 should let you check this locally:

$ flake8 Bio/
Bio/PDB/Vector.py:17:85: W291 trailing whitespace
Bio/PDB/Vector.py:18:74: W291 trailing whitespace
Bio/PDB/Vector.py:22:5: E265 block comment should start with '# '
Bio/PDB/Vector.py:23:9: E201 whitespace after '('
Bio/PDB/Vector.py:23:17: E231 missing whitespace after ','
Bio/PDB/Vector.py:23:20: E226 missing whitespace around arithmetic operator
Bio/PDB/Vector.py:23:24: E231 missing whitespace after ','
Bio/PDB/Vector.py:23:38: W291 trailing whitespace
Bio/PDB/Vector.py:24:17: E231 missing whitespace after ','
Bio/PDB/Vector.py:24:20: E226 missing whitespace around arithmetic operator
Bio/PDB/Vector.py:24:24: E231 missing whitespace after ','
Bio/PDB/Vector.py:24:38: W291 trailing whitespace
Bio/PDB/Vector.py:25:17: E231 missing whitespace after ','
Bio/PDB/Vector.py:25:20: E226 missing whitespace around arithmetic operator
Bio/PDB/Vector.py:25:24: E231 missing whitespace after ','
Bio/PDB/Vector.py:25:35: E202 whitespace before ')'
Bio/PDB/Vector.py:26:9: E265 block comment should start with '# '
Bio/PDB/Vector.py:27:13: E201 whitespace after '('
Bio/PDB/Vector.py:27:21: E231 missing whitespace after ','
Bio/PDB/Vector.py:27:24: E226 missing whitespace around arithmetic operator
Bio/PDB/Vector.py:27:28: E231 missing whitespace after ','
Bio/PDB/Vector.py:27:42: W291 trailing whitespace
Bio/PDB/Vector.py:28:21: E231 missing whitespace after ','
Bio/PDB/Vector.py:28:24: E226 missing whitespace around arithmetic operator
Bio/PDB/Vector.py:28:28: E231 missing whitespace after ','
Bio/PDB/Vector.py:28:42: W291 trailing whitespace
Bio/PDB/Vector.py:29:21: E231 missing whitespace after ','
Bio/PDB/Vector.py:29:24: E226 missing whitespace around arithmetic operator
Bio/PDB/Vector.py:29:28: E231 missing whitespace after ','
Bio/PDB/Vector.py:30:21: E231 missing whitespace after ','
Bio/PDB/Vector.py:30:24: E226 missing whitespace around arithmetic operator
Bio/PDB/Vector.py:30:28: E231 missing whitespace after ','
Bio/PDB/Vector.py:30:31: E226 missing whitespace around arithmetic operator
Bio/PDB/Vector.py:30:35: E231 missing whitespace after ','
Bio/PDB/Vector.py:30:38: E226 missing whitespace around arithmetic operator
Bio/PDB/Vector.py:30:47: E202 whitespace before ')'
Bio/PDB/Vector.py:309:37: W291 trailing whitespace

[peterjc]

Please put the one-line docstring summary on the same line as the opening triple quote, as per examples in PEP257 https://www.python.org/dev/peps/pep-0257/#multi-line-docstrings

[RasmusFonseca]

@peterjc Yes, you can merge his first, but there will be a minor conflict that needs to be resolved in the beginning of rotmat. Nothing big.

Thanks for pointers on style guide. Ill go through it at some point today.

[codecov]

Codecov Report

Merging #1171 into master will increase coverage by 0.02%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master    #1171      +/-   ##
==========================================
+ Coverage   79.72%   79.75%   +0.02%     
==========================================
  Files         323      323              
  Lines       51452    51454       +2     
==========================================
+ Hits        41020    41035      +15     
+ Misses      10432    10419      -13

Impacted Files	Coverage Δ
Bio/PDB/Vector.py	88.62% <100%> (+9.83%)	⬆️
Bio/GA/Evolver.py	54.54% <0%> (-18.19%)	⬇️
Bio/Restriction/Restriction.py	52.27% <0%> (-0.12%)	⬇️
Bio/NeuralNetwork/Gene/Schema.py	71.9% <0%> (+0.82%)	⬆️

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[peterjc]

OK, I manually applied #494 - the merge conflict was due to a minor docstring change.

Do you want to rebase this branch against the new master, or should I do this?

[RasmusFonseca]

It'd be great if you could. I haven't rebased before, and looking it up indicates there are enough steps that I could mess something up ;) Travis fails because I should have run flake8 Tests as well. Ill fix those first.

[peterjc]

Sorry - this is a new style issue, TravisCI checks for this were enabled only earlier today:

$ flake8 Bio/
Bio/PDB/Vector.py:24:9: E129 visually indented line with same indent as next logical line
Bio/PDB/Vector.py:29:5: E129 visually indented line with same indent as next logical line

See 73896e4 - long lines might be an acceptable solution if you can't see how to break the long line nicely.

[RasmusFonseca]

Haha. The wonders of trying to commit to an active project. I made them single line.

[peterjc]

I've manually applied this to the master branch, and included you in the acknowledgements. Thank you.

Apologies if I already asked, but are you happy to dual licence your contributions under both the Biopython License Agreement AND the BSD 3-Clause License? See #898.

[RasmusFonseca]

You didn't ask, but I'm happy to appear as a contributor and I agree to the licenses.

[peterjc]

Thank you