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Issue #3467: Replaced .coordinates() with .positions #3479

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Issue #3467: Replaced .coordinates() with .positions #3479

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5d1f343
Issue #3467
pranjii Dec 8, 2021
4436a07
#3467
pranjii Dec 10, 2021
f08867d
pep8 edits
pranjii Dec 10, 2021
63b60f6
pep8 edits 2
pranjii Dec 10, 2021
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4 changes: 2 additions & 2 deletions benchmarks/benchmarks/analysis/rms.py
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Original file line number Diff line number Diff line change
Expand Up @@ -34,9 +34,9 @@ def setup(self, num_atoms, weights, center, superposition):
self.u.trajectory[-1]
self.B = self.u.atoms.positions.copy()[:num_atoms]
except:
self.A = self.u.atoms.coordinates().copy()[:num_atoms]
self.A = self.u.atoms.positions.copy()[:num_atoms]
self.u.trajectory[-1]
self.B = self.u.atoms.coordinates().copy()[:num_atoms]
self.B = self.u.atoms.positions.copy()[:num_atoms]

def time_rmsd(self, num_atoms, weights, center, superposition):
"""Benchmark rmsd function using a setup similar to
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2 changes: 1 addition & 1 deletion package/MDAnalysis/analysis/encore/covariance.py
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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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The failed codecov check is indicating that the this line isn't covered by a test. This explains why tests didn't identify that atoms.coordinates() no longer existed.

If possible could you add a test that checks this code path?


# Flatten reference coordinates
reference_coordinates = reference_coordinates.flatten()
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