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updated atoms.coordinates() with atoms.positions #3467 #3576

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updated atoms.coordinates() with atoms.positions #3467 #3576

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2 changes: 1 addition & 1 deletion package/MDAnalysis/analysis/encore/covariance.py
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Original file line number Diff line number Diff line change
Expand Up @@ -215,7 +215,7 @@ def covariance_matrix(ensemble,
# Select the same atoms in reference structure
reference_atom_selection = reference.select_atoms(
ensemble.get_atom_selection_string())
reference_coordinates = reference_atom_selection.atoms.coordinates()
reference_coordinates = reference_atom_selection.atoms.positions
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Could you please add a test that check this fix works?

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can you tell me please, how to add test?

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@manishsaini6421 please write a function with code that uses this pathway. It should fail with the original .coordinates() and succeed with the new .positions. Have a look at the tests in https://github.com/MDAnalysis/mdanalysis/blob/develop/testsuite/MDAnalysisTests/analysis/test_encore.py and more generally throughout https://github.com/MDAnalysis/mdanalysis/tree/develop/testsuite/MDAnalysisTests for ideas :)


# Flatten reference coordinates
reference_coordinates = reference_coordinates.flatten()
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