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BEN: Add HydrogenBondAnalysis benchmark for performance tracking (#5309)
* BEN: Add HydrogenBondAnalysis benchmark for performance tracking * contributes to #1023 * Updated CHANGELOG --------- Co-authored-by: Brady Johnston <36021261+BradyAJohnston@users.noreply.github.com>
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"""
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Benchmark for HydrogenBondAnalysis
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"""
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try:
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from MDAnalysis.analysis.hydrogenbonds.hbond_analysis import HydrogenBondAnalysis as HBA
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from MDAnalysisTests.datafiles import waterPSF , waterDCD
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except ImportError:
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pass
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import MDAnalysis
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class HydrogenBondAnalysisBenchmark:
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"""
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It tests performance of hbond.run() across different
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number of frames using waterPSF/waterDCD test files.
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"""
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unit = "ms"
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timeout = 60.0
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params = [2, 5, 10]
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param_names = ["n_frames"]
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def setup(self, n_frames):
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u = MDAnalysis.Universe(waterPSF, waterDCD)
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self.hbonds = HBA(universe= u)
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def time_run(self, n_frames):
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self.hbonds.run(stop = n_frames)
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package/CHANGELOG

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DSSP by porting upstream PyDSSP 0.9.1 fix (Issue #4913)
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Enhancements
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* Added HydrogenBondAnalysis benchmark for performance tracking (PR #5309)
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* Added `select=None` in `analysis.rms.RMSD` to perform no selection on
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the input `atomgroup` and `reference` (Issue #5300, PR #5296)
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* MOL2Parser now reads unit cell dimensions from @<TRIPOS>CRYSIN records (Issue #3341)

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