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Added ASV benchmark for Contacts analysis
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import MDAnalysis as mda
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from MDAnalysis.analysis import contacts
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from MDAnalysisTests.datafiles import PSF, DCD
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class ContactsBench:
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params = [4.5, 6.0]
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param_names = ["radius"]
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def setup(self, radius):
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self.u = mda.Universe(PSF, DCD)
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self.sel1 = "protein"
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self.sel2 = "name CA"
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g1 = self.u.select_atoms(self.sel1)
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g2 = self.u.select_atoms(self.sel2)
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self.analysis = contacts.Contacts(
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self.u,
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select=(self.sel1, self.sel2),
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refgroup=(g1, g2),
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radius=radius,
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)
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def time_contacts_run(self, radius):
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self.analysis.run()

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