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ENH: Add PDB reader benchmark to track parsing performance #5394

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e0a787e
ENH: Add PDB reader benchmark to track parsing performance
Dreamstick9 Jun 2, 2026
d2ea984
updated changelog
Dreamstick9 Jun 2, 2026
dddcdf6
simplify PDBReaderBench iteration over PDB_multiframe
Dreamstick9 Jun 4, 2026
625961e
Added time_read for inital parsing
Dreamstick9 Jun 4, 2026
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23 changes: 23 additions & 0 deletions benchmarks/benchmarks/traj_reader.py
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Expand Up @@ -28,6 +28,12 @@
except ImportError:
pass

try:
import MDAnalysis as mda

@orbeckst orbeckst Jun 19, 2026

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from MDAnalysis.coordinates.PDB.PDBReader

from MDAnalysisTests.datafiles import PDB_multiframe
except ImportError:
pass

traj_dict = {
"XTC": [XTC, XTCReader],
"TRR": [TRR, TRRReader],
Expand Down Expand Up @@ -71,3 +77,20 @@ def time_strides(self, traj_format):
"""
for ts in self.reader_object:
pass


class PDBReaderBench(object):

@orbeckst orbeckst Jun 19, 2026

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Do you need to create a separate class? Did you try adding coordinates.PDB.PDBReader and PDB_multiframe in the traj_dict and then handling it through the params?

"""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)
Comment on lines +91 to +92

@orbeckst orbeckst Jun 19, 2026

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This includes time for both topology and setting up PDBReader.

You could try

PDBReader(PDB_multiframe, n_atoms=u.atoms.n_atoms)

By providing n_atoms you avoid parsing the PDB file inside the Reader (see

mdanalysis/package/MDAnalysis/coordinates/PDB.py

Lines 290 to 292 in cec335f

with PDBParser.PDBParser(self.filename) as p:
top = p.parse()
self.n_atoms = top.n_atoms
for the rather ugly code) and so you really only benchmark the actual setup.

You could benchmark the two cases: one with n_atoms, the other without.


def time_iterate(self):
for ts in self.u.trajectory:
pass
1 change: 1 addition & 0 deletions package/CHANGELOG
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Expand Up @@ -22,6 +22,7 @@ The rules for this file:
* 2.11.0

Fixes
* Added ASV benchmark for PDB trajectory reading (PR #1234)

@orbeckst orbeckst Jun 19, 2026

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This would be an enhancement, not a fix.

* `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
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