Modified MC rotation moves#331
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kamran-haider wants to merge 2 commits intochoderalab:mainfrom
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andrrizzi
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Feb 26, 2018
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Thank you so much! Sorry it took me so long to review. I was in time crunch.
Looks great so far! Just a comment about the docstring. Also, it would be great if you could add a simple unit test in test_mcmc.py. Something like this would be enough:
- If nothing is passed to
rotation_center_indicesall atom positions change. - If the rotation is centered on a single atom, that position won't change.
| ---------- | ||
| positions : nx3 numpy.ndarray simtk.unit.Quantity | ||
| The positions to rotate. | ||
| rotation_center_indices : list |
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Could you add a , optional here? Also, it would be fantastic to document that the center of rotation is chosen to be the center of geometry of this set of atoms, and that the default behavior uses all the atoms in positions.
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No worries at all and thanks so much for the comments. I agree and will get back with the unit test and updated docstring.
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Potential enhancement: Following up on discussion in #330, I modified the
rotate_positionsmethod ofMCRotationMoveto allow a subset of atom positions define the geometric center of rotation. The unit test for metropolized moves wouldn't test for this modification so when running tests locally, everything goes smoothly. I checked the output configurations, as shown in issue thread. Let me know if I should write a unit test for this.