From 2803d6f4fafc1cd9662532bcc84c97e51ffbd3c3 Mon Sep 17 00:00:00 2001
From: noir4201 <bhuprati48@gmail.com>
Date: Tue, 10 Mar 2026 17:22:52 +0530
Subject: [PATCH 1/2] Add benchmarks for MDAnalysis.analysis.align

---
 benchmarks/benchmarks/analysis/bench_align.py | 68 +++++++++++++++++++
 1 file changed, 68 insertions(+)
 create mode 100644 benchmarks/benchmarks/analysis/bench_align.py

diff --git a/benchmarks/benchmarks/analysis/bench_align.py b/benchmarks/benchmarks/analysis/bench_align.py
new file mode 100644
index 0000000000..e1ff5bf60c
--- /dev/null
+++ b/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()
\ No newline at end of file

From a03fb86e07e706106946ae31914d4cb3dae563ca Mon Sep 17 00:00:00 2001
From: noir4201 <bhuprati48@gmail.com>
Date: Tue, 31 Mar 2026 00:41:23 +0530
Subject: [PATCH 2/2] Clean up comments and docstrings in bench_align.py

Removed comments and docstrings from the AlignBenchmark class in bench_align.py.
---
 benchmarks/benchmarks/analysis/bench_align.py | 14 +-------------
 1 file changed, 1 insertion(+), 13 deletions(-)

diff --git a/benchmarks/benchmarks/analysis/bench_align.py b/benchmarks/benchmarks/analysis/bench_align.py
index e1ff5bf60c..e3c241b24e 100644
--- a/benchmarks/benchmarks/analysis/bench_align.py
+++ b/benchmarks/benchmarks/analysis/bench_align.py
@@ -1,25 +1,13 @@
-# 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)
 
@@ -65,4 +53,4 @@ def time_average_structure(self):
             self.reference,
             select="backbone"
         )
-        avg.run()
\ No newline at end of file
+        avg.run()