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made universe for A and B to fix doctest fails #4023

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made universe for A and B to fix doctest fails #4023

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8a06938
made universe for A and B
Telomelonia Feb 11, 2023
b7e1890
added author
Telomelonia Feb 21, 2023
67cc539
Update align.py
Telomelonia Feb 21, 2023
32fdee5
Update align.py
Telomelonia Feb 22, 2023
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changelog updated
Telomelonia Feb 24, 2023
7f6b504
update changelog
Telomelonia Feb 26, 2023
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1 change: 1 addition & 0 deletions package/AUTHORS
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Expand Up @@ -204,6 +204,7 @@ Chronological list of authors
- Mikhail Glagolev
2023
- Christian Pfaendner
- Aryan Shukla


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12 changes: 12 additions & 0 deletions package/CHANGELOG
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Expand Up @@ -13,6 +13,18 @@ The rules for this file:
* release numbers follow "Semantic Versioning" http://semver.org

------------------------------------------------------------------------------
24/02/23 Telomelonia

* 2.5.0

Fixes
* Fix the code for docstring in rotation_matrix method in align.py
which was giving NameError (Issue #3365)

Changes
* Defined the universe for which NameError was raised. (PR #4023)


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??/??/?? IAlibay, pgbarletta, mglagolev, hmacdope, manuel.nuno.melo, chrispfae

* 2.5.0
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6 changes: 4 additions & 2 deletions package/MDAnalysis/analysis/align.py
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Expand Up @@ -245,9 +245,11 @@ def rotation_matrix(a, b, weights=None):
`R` can be used as an argument for
:meth:`MDAnalysis.core.groups.AtomGroup.rotate` to generate a rotated
selection, e.g. ::

>>> from MDAnalysisTests.datafiles import TPR, TRR
>>> A = mda.Universe('topol.tpr','traj.trr')
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fix

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Yeah. I am fixing this, but I am getting errors, and I don't know why, but I need time to understand before debugging

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Show your code, then I can help.

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@orbeckst, thanks, but I am currently having my semester exams 😄. So, I will try to continue after that ✌️

>>> B = A.copy()
>>> R = rotation_matrix(A.select_atoms('backbone').positions,
>>> B.select_atoms('backbone').positions)[0]
... B.select_atoms('backbone').positions)[0]
>>> A.atoms.rotate(R)
>>> A.atoms.write("rotated.pdb")

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