Add ASV benchmark for Contacts analysis

benchmarks/benchmarks/analysis/contacts.py

@@ -0,0 +1,62 @@
+import MDAnalysis as mda
+from MDAnalysis.analysis import contacts
+from MDAnalysisTests.datafiles import PSF, DCD
+
+
+class ContactsBench(object):
+    """
+    Benchmarks for MDAnalysis.analysis.contacts.Contacts
+    """
+
+    # Parameter combinations tested in the benchmark.
+    # radius : cutoff distance used to define a contact
+    # method : algorithm used to compute contacts
+    # pbc    : whether periodic boundary conditions are applied
+    params = [
+        [4.5, 6.0],
+        ["hard_cut", "soft_cut", "radius_cut"],
+        [True, False],
+    ]
+
+    # Names corresponding to the parameters above
+    param_names = ["radius", "method", "pbc"]
+
+    def setup(self, radius, method, pbc):
+        """
+        Prepare the Universe and contact analysis object
+        for benchmarking.
+        """
+
+        # Load test trajectory
+        self.u = mda.Universe(PSF, DCD)
+
+        # Define atom selections
+        self.sel1 = "protein"
+        self.sel2 = "name CA"
+
+        # Create atom groups from the selections
+        g1 = self.u.select_atoms(self.sel1)
+        g2 = self.u.select_atoms(self.sel2)
+
+        # Initialize the Contacts analysis
+        # select   : atom selection strings
+        # refgroup : reference atom groups used for contacts
+        # radius   : contact cutoff distance
+        # method   : contact calculation method
+        # pbc      : periodic boundary conditions flag
+        self.analysis = contacts.Contacts(
+            self.u,
+            select=(self.sel1, self.sel2),
+            refgroup=(g1, g2),
+            radius=radius,
+            method=method,
+            pbc=pbc,
+        )
+
+    def time_contacts_run(self, radius, method, pbc):
+        """
+        Benchmark execution of Contacts.run()
+        over the full trajectory.
+        """
+
+        self.analysis.run()

package/AUTHORS

@@ -276,6 +276,7 @@ Chronological list of authors
   - Kunj Sinha
   - Ayush Agarwal
   - Parth Uppal
+  - Amarendra Mohan
 
 External code
 -------------

package/CHANGELOG

@@ -42,6 +42,7 @@ Fixes
    DSSP by porting upstream PyDSSP 0.9.1 fix (Issue #4913)
 
 Enhancements
+ * Added ASV benchmark for `MDAnalysis.analysis.contacts` (PR #5291)
  * MOL2Parser now reads unit cell dimensions from @<TRIPOS>CRYSIN records (Issue #3341)
  * Reduces duplication of code in _apply() function (Issue #5247, PR #5294)
  * Added new top-level `MDAnalysis.fetch` module (PR #4943)