Merge branch 'develop' of github.com:mdanalysis/mdanalysis into ncrst-reader

Author: jeremyleung521

benchmarks/benchmarks/analysis/rms.py

@@ -1,4 +1,5 @@
 import MDAnalysis
+import numpy as np
 
 try:
     from MDAnalysisTests.datafiles import DCD, PSF
@@ -14,23 +15,20 @@
 class SimpleRmsBench(object):
     """Benchmarks for MDAnalysis.analysis.rms.rmsd"""
 
-    params = ([100, 500, 2000], [None, [1.0, 0.5]], [False, True], [False, True])
-    param_names = ["num_atoms", "weights", "center", "superposition"]
+    params = ([100, 500, 2000], [True, False], [False, True], [False, True])
+    param_names = ["num_atoms", "use_weights", "center", "superposition"]
 
-    def setup(self, num_atoms, weights, center, superposition):
+    def setup(self, num_atoms, use_weights, center, superposition):
         # mimic rmsd docstring example code
         self.u = MDAnalysis.Universe(PSF, DCD)
         # ag.positions is the new syntax
         # but older commit hashes will need to use
         # ag.coordinates()
-        try:
-            self.A = self.u.atoms.positions.copy()[:num_atoms]
-            self.u.trajectory[-1]
-            self.B = self.u.atoms.positions.copy()[:num_atoms]
-        except:
-            self.A = self.u.atoms.positions.copy()[:num_atoms]
-            self.u.trajectory[-1]
-            self.B = self.u.atoms.positions.copy()[:num_atoms]
+        self.A = self.u.atoms.positions.copy()[:num_atoms]
+        self.u.trajectory[-1]
+        self.B = self.u.atoms.positions.copy()[:num_atoms]
+        self.atoms = self.u.atoms[:num_atoms]
+        self.weights = self.atoms.masses/np.sum(self.atoms.masses) if use_weights else None
 
     def time_rmsd(self, num_atoms, weights, center, superposition):
         """Benchmark rmsd function using a setup similar to
@@ -40,7 +38,7 @@ def time_rmsd(self, num_atoms, weights, center, superposition):
         rms.rmsd(
             a=self.A,
             b=self.B,
-            weights=weights,
+            weights=self.weights,
             center=center,
             superposition=superposition,
         )

package/CHANGELOG

@@ -15,7 +15,7 @@ The rules for this file:
 
 -------------------------------------------------------------------------------
 ??/??/?? IAlibay, orbeckst, BHM-Bob, TRY-ER, Abdulrahman-PROG, pbuslaev,
-         yuxuanzhuang, yuyuan871111, jpkrowe, jeremyleung521
+         yuxuanzhuang, yuyuan871111, tanishy7777, jpkrowe, jeremyleung521
 
  * 2.10.0
 
@@ -29,7 +29,9 @@ Fixes
  * Reads `segids` column in `PDBParser` from 73-76 instead of 67-76 to 
    align the standard of a PDBReader (e.g., Chimera, CHARMM, Gemmi). 
    (Issue #4948, PR #5001)
-
+ * Fixes the benchmark `SimpleRmsBench` in `benchmarks/analysis/rms.py`
+   by changing the way weights for RMSD are calculated, instead of
+   directly passing them. (Issue #3520, PR #5006)
 Enhancements
  * Allow NCDF reader to read Amber Restart Files with extension `.ncrst`
    (Issue #5030, PR#5031)