fixed 2'-hydroxyl dihedral calculation#2231
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- fixes #2218 - RNA 2-hydroxyl selection now agrees with our docs: H2'' (wrong) --> H2' (correct)
- replaced 1k5i.pdb (which had the 2'-OH H in strange positions) with a simulation system of model 1 of 1k5i in CHARMM36m (generated by CHARMM-GUI and equilibrated for 1 ns with Gromacs 2018.6). Octahedral box, K+ counter ions, TIP3P water. - topology datafiles.RNA_PSF data/analysis/1k5i_c36.psf - coordinates datafiles.RNA_PDB data/analysis/1k5i_c36.pdb - added data files as gzipped datafiles (instead of bz2 because of #2232) - removed datafiles.NUCL = data/1k5i - updated all regression tests in test_nucleic.py with numbers appropriate for the new test file; manually confirmed the values for the 2'-hydroxyl dihedrals in the test by manually selecting and calculating in VMD - replaced NUCL in atomselections test (also removed superfluous/outdated utils/test_nuclinfo) - updated CHANGELOG
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Codecov Report
@@ Coverage Diff @@
## develop #2231 +/- ##
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Coverage 90.71% 90.71%
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Files 15 15
Lines 1982 1982
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Hits 1798 1798
Misses 184 184Continue to review full report at Codecov.
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richardjgowers
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Apr 2, 2019
I got a weird failure in PR #2231 in Travis job https://travis-ci.com/MDAnalysis/mdanalysis/jobs/189553940 : Exception occurred: File "/home/travis/miniconda/envs/test/lib/python3.5/site-packages/sphinx/ext/napoleon/docstring.py", line 703, in _parse_raises_section m = self._name_rgx.match(_type).groupdict() AttributeError: 'NoneType' object has no attribute 'groupdict' and the docs build find locally (under Python 3.6)
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CI was failing the doc build in https://travis-ci.com/MDAnalysis/mdanalysis/jobs/189553940 : Locally under 3.6 the docs build just fine. I am trying bumping our doc build environment to the currently "best", i.e., 3.7. |
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Fixes #2218
Changes made in this Pull Request:
datafiles.NUCL; instead usedatafiles.RNA_PSFanddatafiles.RNA_PDBPR Checklist