From af7b46aae9b408c9fee94619e6a7599470894b6f Mon Sep 17 00:00:00 2001 From: Tanish Yelgoe <23110328@iitgn.ac.in> Date: Fri, 13 Dec 2024 14:31:26 +0530 Subject: [PATCH 1/4] Fixes invalid default unit for convert_density() function --- package/MDAnalysis/analysis/density.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package/MDAnalysis/analysis/density.py b/package/MDAnalysis/analysis/density.py index 8f3f0b33647..f5c270e7dcc 100644 --- a/package/MDAnalysis/analysis/density.py +++ b/package/MDAnalysis/analysis/density.py @@ -826,7 +826,7 @@ def convert_length(self, unit='Angstrom'): self.units['length'] = unit self._update() # needed to recalculate midpoints and origin - def convert_density(self, unit='Angstrom'): + def convert_density(self, unit='Angstrom^{-3}'): """Convert the density to the physical units given by `unit`. Parameters From 52db811d7493b514521dcc7540d7f80abae06cd1 Mon Sep 17 00:00:00 2001 From: Tanish Yelgoe <23110328@iitgn.ac.in> Date: Fri, 13 Dec 2024 14:32:27 +0530 Subject: [PATCH 2/4] Added test for checking for invalid default unit --- testsuite/MDAnalysisTests/analysis/test_density.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/testsuite/MDAnalysisTests/analysis/test_density.py b/testsuite/MDAnalysisTests/analysis/test_density.py index b00a8234c17..a5cae162a6c 100644 --- a/testsuite/MDAnalysisTests/analysis/test_density.py +++ b/testsuite/MDAnalysisTests/analysis/test_density.py @@ -384,6 +384,12 @@ def test_warn_results_deprecated(self, universe): with pytest.warns(DeprecationWarning, match=wmsg): assert_equal(D.density.grid, D.results.density.grid) + def test_density_analysis_invalid_unit(self): + u = mda.Universe(TPR, XTC) + ow = u.select_atoms("name OW") + D = mda.analysis.density.DensityAnalysis(ow, delta=1.0) + D.run() + D.results.density.convert_density() class TestGridImport(object): From 0732b31ad6ac3658918fb4d5c84d8322c7dd3848 Mon Sep 17 00:00:00 2001 From: Tanish Yelgoe <23110328@iitgn.ac.in> Date: Fri, 13 Dec 2024 14:33:06 +0530 Subject: [PATCH 3/4] Updated CHANGELOG and AUTHORS --- package/AUTHORS | 1 + package/CHANGELOG | 3 ++- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/package/AUTHORS b/package/AUTHORS index 1917e6d7059..719eb7b70ce 100644 --- a/package/AUTHORS +++ b/package/AUTHORS @@ -245,6 +245,7 @@ Chronological list of authors - Laksh Krishna Sharma - Matthew Davies - Jia-Xin Zhu + - Tanish Yelgoe External code diff --git a/package/CHANGELOG b/package/CHANGELOG index 83bff740024..63e94854ab7 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -14,11 +14,12 @@ The rules for this file: ------------------------------------------------------------------------------- -??/??/?? IAlibay, ChiahsinChu, RMeli +??/??/?? IAlibay, ChiahsinChu, RMeli, tanishy7777 * 2.9.0 Fixes + * Fixes invalid default unit from Angstrom to Angstrom^{-3} for convert_density() function. (Issue #4829) Enhancements * Add check and warning for empty (all zero) coordinates in RDKit converter (PR #4824) From 69a6d83e2ce03b5be19dbe6d6238671078876783 Mon Sep 17 00:00:00 2001 From: Tanish Yelgoe <143334319+tanishy7777@users.noreply.github.com> Date: Sat, 14 Dec 2024 22:00:24 +0530 Subject: [PATCH 4/4] Update testsuite/MDAnalysisTests/analysis/test_density.py Co-authored-by: Rocco Meli --- testsuite/MDAnalysisTests/analysis/test_density.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/testsuite/MDAnalysisTests/analysis/test_density.py b/testsuite/MDAnalysisTests/analysis/test_density.py index a5cae162a6c..c99b671e3db 100644 --- a/testsuite/MDAnalysisTests/analysis/test_density.py +++ b/testsuite/MDAnalysisTests/analysis/test_density.py @@ -384,7 +384,7 @@ def test_warn_results_deprecated(self, universe): with pytest.warns(DeprecationWarning, match=wmsg): assert_equal(D.density.grid, D.results.density.grid) - def test_density_analysis_invalid_unit(self): + def test_density_analysis_conversion_default_unit(self): u = mda.Universe(TPR, XTC) ow = u.select_atoms("name OW") D = mda.analysis.density.DensityAnalysis(ow, delta=1.0)