From c22a3e2f3237d9b30cbc63b4818b516b8c82e0ab Mon Sep 17 00:00:00 2001 From: Ananya-vit Date: Sat, 21 Mar 2026 04:08:06 +0530 Subject: [PATCH] Add ASV benchmark for guess_bonds --- benchmarks/__init__.py | 0 benchmarks/time_guess_bonds.py | 12 ++++++++++++ 2 files changed, 12 insertions(+) create mode 100644 benchmarks/__init__.py create mode 100644 benchmarks/time_guess_bonds.py diff --git a/benchmarks/__init__.py b/benchmarks/__init__.py new file mode 100644 index 00000000000..e69de29bb2d diff --git a/benchmarks/time_guess_bonds.py b/benchmarks/time_guess_bonds.py new file mode 100644 index 00000000000..9f7a6816042 --- /dev/null +++ b/benchmarks/time_guess_bonds.py @@ -0,0 +1,12 @@ +class TimeGuessBonds: + def setup(self): + import MDAnalysis as mda + from MDAnalysis.tests.datafiles import PSF, DCD + + self.u = mda.Universe(PSF, DCD) + + # Provide simple vdW radii (dummy but valid) + self.vdwradii = {atom.type: 1.5 + (i % 3)*0.1 for i, atom in enumerate(self.u.atoms)} + + def time_guess_bonds(self): + self.u.atoms.guess_bonds(vdwradii=self.vdwradii)