diff --git a/benchmarks/benchmarks/traj_reader.py b/benchmarks/benchmarks/traj_reader.py index 3a203a3707..3e583c9824 100644 --- a/benchmarks/benchmarks/traj_reader.py +++ b/benchmarks/benchmarks/traj_reader.py @@ -28,19 +28,26 @@ except ImportError: pass +try: + from MDAnalysis.coordinates.PDB import PDBReader + from MDAnalysisTests.datafiles import PDB_multiframe +except ImportError: + pass + traj_dict = { "XTC": [XTC, XTCReader], "TRR": [TRR, TRRReader], "DCD": [DCD, DCDReader], "NCDF": [NCDF, NCDFReader], "TRC": [TRC_TRAJ_SOLV, TRCReader], + "PDB": [PDB_multiframe, PDBReader], } class TrajReaderCreation(object): """Benchmarks for trajectory file format reading.""" - params = ["XTC", "TRR", "DCD", "NCDF", "TRC"] + params = ["XTC", "TRR", "DCD", "NCDF", "TRC", "PDB"] param_names = ["traj_format"] def setup(self, traj_format): @@ -57,7 +64,7 @@ def time_reads(self, traj_format): class TrajReaderIteration(object): """Benchmarks for trajectory file format striding.""" - params = ["XTC", "TRR", "DCD", "NCDF", "TRC"] + params = ["XTC", "TRR", "DCD", "NCDF", "TRC", "PDB"] param_names = ["traj_format"] def setup(self, traj_format): diff --git a/package/CHANGELOG b/package/CHANGELOG index 93ef2d158e..b3ccf32241 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -60,6 +60,7 @@ Fixes DSSP by porting upstream PyDSSP 0.9.1 fix (Issue #4913) Enhancements + * Added ASV benchmark for PDB trajectory reading (PR #5394) * Read Linear Angle bonded interaction entries from GROMACS TPR files and add the angles to the topology (Issue #5361, PR #5372) * Enables parallelization for analysis.atomicdistances.AtomicDistances