diff --git a/benchmarks/benchmarks/traj_reader.py b/benchmarks/benchmarks/traj_reader.py index 3a203a3707..b03cd00707 100644 --- a/benchmarks/benchmarks/traj_reader.py +++ b/benchmarks/benchmarks/traj_reader.py @@ -28,6 +28,12 @@ except ImportError: pass +try: + import MDAnalysis as mda + from MDAnalysisTests.datafiles import PDB_multiframe +except ImportError: + pass + traj_dict = { "XTC": [XTC, XTCReader], "TRR": [TRR, TRRReader], @@ -71,3 +77,20 @@ def time_strides(self, traj_format): """ for ts in self.reader_object: pass + + +class PDBReaderBench(object): + """Benchmarks for PDB file format reading and parsing""" + + units = "ms" + timeout = 60.0 + + def setup(self): + self.u = mda.Universe(PDB_multiframe) + + def time_read(self): + mda.Universe(PDB_multiframe) + + def time_iterate(self): + for ts in self.u.trajectory: + pass diff --git a/package/CHANGELOG b/package/CHANGELOG index fd0b869186..537fe1540d 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -22,6 +22,7 @@ The rules for this file: * 2.11.0 Fixes + * Added ASV benchmark for PDB trajectory reading (PR #1234) * `MDAnalysis.analysis.nucleicacids.WatsonCrickDist`, `MinorPairDist`, and `MajorPairDist` now match residue names against the full resname instead of only the first character, fixing incorrect behaviour with