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Fix Dihedral box #198

Merged
merged 19 commits into from
Sep 14, 2021
Merged

Fix Dihedral box #198

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abda324
Add dihedral.py and test_dihedral.py
ALescoulie Sep 9, 2021
fcad293
Merge branch 'Becksteinlab:develop' into analysis
ALescoulie Sep 9, 2021
07590d4
Add test
ALescoulie Sep 10, 2021
9d7293b
Merge remote-tracking branch 'origin/analysis' into analysis
ALescoulie Sep 10, 2021
03330c4
modify dihedral.py to accept list
ALescoulie Sep 10, 2021
e0c1116
Merge branch 'Becksteinlab:develop' into analysis
ALescoulie Sep 10, 2021
6e4d5de
Merge branch 'develop' into analysis
orbeckst Sep 10, 2021
7f47384
fix dihedral.py Ensemble call
ALescoulie Sep 10, 2021
2d5a90e
add check_input and tests
ALescoulie Sep 10, 2021
d12dc2c
add docs
ALescoulie Sep 10, 2021
fe20e51
reformat exceptions
ALescoulie Sep 11, 2021
3bf3488
reformat data for _single_frame
ALescoulie Sep 11, 2021
e75430b
convert result to degree
ALescoulie Sep 11, 2021
f7a4a55
add tests
ALescoulie Sep 11, 2021
058cc78
fix EnsembleAnalysis common ensemble function
ALescoulie Sep 11, 2021
5be9e61
fix EnsembleAnalysis common ensemble function
ALescoulie Sep 11, 2021
ec20ceb
finalize docs
ALescoulie Sep 12, 2021
2efd9f7
add box
ALescoulie Sep 14, 2021
a191e82
Merge branch 'develop' into analysis
ALescoulie Sep 14, 2021
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3 changes: 2 additions & 1 deletion mdpow/analysis/dihedral.py
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Original file line number Diff line number Diff line change
Expand Up @@ -99,7 +99,8 @@ def _single_frame(self):
cord2 = np.concatenate(tuple([cord_dict2[k] for k in key_list]))
cord3 = np.concatenate(tuple([cord_dict3[k] for k in key_list]))
cord4 = np.concatenate(tuple([cord_dict4[k] for k in key_list]))
angle = calc_dihedrals(cord1, cord2, cord3, cord4)
angle = calc_dihedrals(cord1, cord2, cord3, cord4,
box=self.g1[key_list[0]].dimensions)
angle = np.rad2deg(angle)
for i in range(len(self.names)):
result = list(key_list[i]) + [self._ts.time, angle[i]]
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