Implemented "count in voxel" function #1643
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pytraj/all_actions.py
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| lives_in_voxel = [] | ||
| population = top.atom_indices(mask) |
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use traj.top?
Adding top to function argument was my poor design :(.
| import numpy as np | ||
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| class Test(unittest.TestCase): |
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Since you're making several PRs, so it would be better to follow the "modern" way to write test, by using pytest's style.
- The class is not needed
- Change the name of
test_0to some thing meaningful to you.
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How do I trigger testing locally? Right now I'm making changes directly to the package that is installed, then running the individual test scripts I'm writing. When I remove the class and if __name__ == __main__ clause and run the script with just the function definitions, the tests themselves do not get executed.
| if __name__ == "__main__": | ||
| unittest.main() |
pytraj/all_actions.py
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| mask="", | ||
| voxel_cntr=(0, 0, 0), | ||
| voxel_size=5): | ||
| """for a voxel with center xyz and size voxel_size, find atoms that match a given mask |
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@sastrys1 Looks great to me. I have only several minor comments. |
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Please use pytest
cd tests
python3 -m pytest test_analysys/test_closet_atom.py -vs
…On Thu, Oct 5, 2023 at 4:50 PM sastrys1 ***@***.***> wrote:
***@***.**** commented on this pull request.
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In tests/test_analysis/test_count_in_voxel.py
<#1643 (comment)>:
> @@ -0,0 +1,65 @@
+import unittest
+from pytraj import *
+import pytraj as pt
+from utils import fn
+from pytraj.testing import aa_eq
+import numpy as np
+
+
+class Test(unittest.TestCase):
How do I trigger testing locally? Right now I'm making changes directly to
the package that is installed, then running the individual test scripts I'm
writing. When I remove the class and if __name__ == __main__ clause and
run the script with just the function definitions, the tests themselves do
not get executed.
—
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| # tests to see if function can find an atom if we search with a coordinate | ||
| # very close to the atom's xyz coordinates | ||
| def search_for_atom(self): |
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oh, for each test, you need to add test_ prefix (test_search_for_atom), otherwise, pytest won't be recognise it.
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https://github.com/Amber-MD/pytraj/actions/runs/6424481585/job/17445206646
e.g: click "Test with pytest" and search for your function's names. They are not in there.
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Cool, got the tests to work by adding the prefix and using your python3 -m pytest command
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@sastrys1 here is how github action run the test: |
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Thanks @sastrys1 very much! |
This analysis command is meant to be used with GIST analysis to estimate water residence time for a given region.
When running GIST on a trajectory, we get a list of voxels and their associated rotational/translational entropy of solvent atoms. We can focus on low-entropy voxels (which behave differently from the bulk) and find the population of solvent atoms in a voxel throughout the course of a simulation to measure how long it's taking for solvent molecules to equilibrate in and out of solvent pockets on the macromolecular interface (survival time correlation function).