Add benchmarks for MDAnalysis.analysis.align

benchmarks/benchmarks/analysis/bench_align.py

@@ -0,0 +1,68 @@
+# bench_align.py
+# Benchmarks for MDAnalysis.analysis.align
+# No benchmarks existed for this module before this file
+
+import MDAnalysis as mda
+from MDAnalysis.analysis import align
+from MDAnalysis.tests.datafiles import PSF, DCD, PDB_small
+
+
+class AlignBenchmark:
+    """
+    Benchmarks for MDAnalysis.analysis.align module.
+    Tests alignto() and AlignTraj() which are the two
+    most commonly used functions in this module.
+    """
+
+    def setup(self):
+        # setup() runs ONCE before any timing starts
+        # load data here — never in time_ methods
+        # PSF = protein structure file (topology)
+        # DCD = trajectory file (coordinates over time)
+        # PDB_small = single reference structure
+        self.mobile = mda.Universe(PSF, DCD)
+        self.reference = mda.Universe(PSF, PDB_small)
+
+    def time_alignto_all_atoms(self):
+        """Time aligning all atoms of a single frame"""
+        align.alignto(
+            self.mobile,
+            self.reference,
+            select="all"
+        )
+
+    def time_alignto_backbone(self):
+        """Time aligning backbone atoms only (common in research)"""
+        align.alignto(
+            self.mobile,
+            self.reference,
+            select="backbone"
+        )
+
+    def time_alignto_mass_weighted(self):
+        """Time aligning with mass weighting"""
+        align.alignto(
+            self.mobile,
+            self.reference,
+            select="backbone",
+            weights="mass"
+        )
+
+    def time_aligntraj_all_frames(self):
+        """Time aligning entire trajectory — most expensive operation"""
+        alignment = align.AlignTraj(
+            self.mobile,
+            self.reference,
+            select="backbone",
+            in_memory=True  # avoids writing to disk during benchmark
+        )
+        alignment.run()
+
+    def time_average_structure(self):
+        """Time computing average structure across trajectory"""
+        avg = align.AverageStructure(
+            self.mobile,
+            self.reference,
+            select="backbone"
+        )
+        avg.run()