Add intra_connections (intra_bonds, intra_angles, etc) #3200
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Hello @lilyminium! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:
Comment last updated at 2021-05-02 17:03:39 UTC |
Codecov Report
@@ Coverage Diff @@
## develop #3200 +/- ##
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Coverage 92.85% 92.86%
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Files 170 170
Lines 22840 22865 +25
Branches 3240 3243 +3
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+ Hits 21208 21233 +25
Misses 1584 1584
Partials 48 48
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lilyminium
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| ugroup = getattr(self.universe.atoms, typename) | ||
| if not len(ugroup): | ||
| return ugroup | ||
| func = np.any if outside else np.all |
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I'd prefer a more explicit name for that. logic_comparator maybe?
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I see the conversation marked as resolved, but the variable is still named func.
| @@ -2296,14 +2309,22 @@ def set_atoms(self, ag): | |||
| return NotImplementedError("Cannot set bond information") | |||
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| def get_atoms(self, ag): | |||
| """ | |||
| Get subset for atoms. | |||
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It is good to add a docstring, but I am not sure this one helps much: what subset of the atoms?
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I hope this new one is more helpful, although I'm not certain users will ever really see it
Co-authored-by: Jonathan Barnoud <[email protected]>
Fixes MDAnalysis#3037 Co-authored-by: Lily Wang <[email protected]>
Towards MDAnalysis#2468 ## Work done in this PR * Add aromaticity and Gasteiger charges guessers which work via the RDKIT converter.
Fixes MDAnalysis#3109 ## Work done in this PR * gracefully handle the case where `gcc` toolchain in use on MacOS has been built from source using `clang` by `spack` (so it really is `gcc` in use, not `clang`) ## Notes * we could try to add regression testing, but a few problems: - `using_clang()` is inside `setup.py`, which probably can't be safely imported because it has unguarded statements/ code blocks that run right away - testing build issues is typically tricky with mocking, etc. (though in this case, probably just need to move `using_clang()` somewhere else and then test it against a variety of compiler metadata strings
* Fixes MDAnalysis#2974 * Python 3.9 officially supported * Add Python 3.9 to testing matrix * Adds macOS CI entry, formalises 3.9 support
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…lysis into get_connections_develop
…lysis into get_connections_develop
| ugroup = getattr(self.universe.atoms, typename) | ||
| if not len(ugroup): | ||
| return ugroup | ||
| func = np.any if outside else np.all |
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I see the conversation marked as resolved, but the variable is still named func.
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Sorry, I thought I clicked the button already. |
Fixes #1264
Fixes #2821
Changes made in this Pull Request:
After PR Added get_connections #3160, sets the defaultget_atomsto only return connections where all atoms are within the queried AtomGroup (i.e.outside=False)However, it still returns all connections involving the atom in Atom.bonds/angles/dihedrals etc (i.e.outside=True)I would expect Atom.bonds to include all the bonds involving that Atom, but AtomGroup to only include the bonds within the group.Also changes various parsers and writers to useget_connectionsinstead of.bondsetc to get the previous dataChanges a bunch of tests to passPR Checklist