analysis.gnm: optimizations and doc/code cleanup#1272
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- optimization
- eliminated costly lookup of residue sizes
- reduces run time of TestGNM.test_closeContactGNMAnalysis by about
a factor of 5 (!) --- should go a long way to improve #1191
- made sure that numpy arrays are used
- argument changes and deprecations
- new weights="size" kwargs
- deprecated MassWeight for 0.17.0 (but have tests until then that
check that it works and overrides weights)
- in GNMAnalysis, replaced skip kwarg with start/stop/step
(without going through deprecation because of limited use)
- added/adapted tests for new kwargs
- code cleanup
- removed unused backup_file() function
- made GNMAnalysis._generate_output() a private method (so that I do not have
to document it...)
- numpy-style docs in whole module
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This was split off from PR #1240 based on @kain88-de 's suggestion. |
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kain88-de
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Mar 30, 2017
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Looks good. Only two minor comments.
package/MDAnalysis/analysis/gnm.py
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| filename to write eigenvectors to, by default no output is written | ||
| (``None``) | ||
| Bonus_groups : tuple | ||
| This is a tuple of selection groups, the com of each which will be |
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You should specify that this has to be selection strrings. Giving an atomgroup doesn't work and will likely produce a Attribute error
package/MDAnalysis/analysis/gnm.py
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| def __init__(self, universe, selection='protein', cutoff=4.5, ReportVector=None, MassWeight=True): | ||
| def __init__(self, universe, selection='protein', cutoff=4.5, ReportVector=None, | ||
| weights="size", | ||
| MassWeight=None): |
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should be on the same line as weights.
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Done as far as I can tell, thanks for the comments. Please squash and merge. |
kain88-de
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Mar 31, 2017
richardjgowers
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Mar 31, 2017
| frame = ts.frame | ||
| timestep = ts.time | ||
| self._timesteps.append(timestep) | ||
| for ts in self.u.trajectory[start:stop:step]: |
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I really like that our API does this now!
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a factor of 5 (!) --- should go a long way to improve Benchmark & Trim unit test time #1191
check that it works and overrides weights)
(without going through deprecation because of limited use)
to document it...)
Fixes #
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