From 5d1f3436d8f863261109bcd9bb0cf85a70be0bd0 Mon Sep 17 00:00:00 2001 From: pranjii Date: Thu, 9 Dec 2021 05:01:25 +0530 Subject: [PATCH] Issue #3467 --- benchmarks/benchmarks/analysis/rms.py | 4 ++-- package/MDAnalysis/analysis/encore/covariance.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/benchmarks/benchmarks/analysis/rms.py b/benchmarks/benchmarks/analysis/rms.py index 3d34f386c5a..bd1040cee04 100644 --- a/benchmarks/benchmarks/analysis/rms.py +++ b/benchmarks/benchmarks/analysis/rms.py @@ -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 diff --git a/package/MDAnalysis/analysis/encore/covariance.py b/package/MDAnalysis/analysis/encore/covariance.py index 352d934f9d5..0887749c010 100644 --- a/package/MDAnalysis/analysis/encore/covariance.py +++ b/package/MDAnalysis/analysis/encore/covariance.py @@ -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 # Flatten reference coordinates reference_coordinates = reference_coordinates.flatten()