From de3ba37a397c4c5198432e9a822ed8aa6f4d9a36 Mon Sep 17 00:00:00 2001
From: Niklaus Johner <nij2003@med.cornell.edu>
Date: Sun, 26 Jan 2014 19:52:37 -0500
Subject: [PATCH] Speed up for the AvereageDistanceMatrixFromTraj function
---
modules/mol/alg/pymod/trajectory_analysis.py | 1 +
1 file changed, 1 insertion(+)
diff --git a/modules/mol/alg/pymod/trajectory_analysis.py b/modules/mol/alg/pymod/trajectory_analysis.py
index e46af2756..4fc74233a 100644
--- a/modules/mol/alg/pymod/trajectory_analysis.py
+++ b/modules/mol/alg/pymod/trajectory_analysis.py
@@ -206,6 +206,7 @@ def AverageDistanceMatrixFromTraj(t,sele,first=0,last=-1):
M=npy.zeros([n_atoms,n_atoms])
for i,a1 in enumerate(sele.atoms):
for j,a2 in enumerate(sele.atoms):
+ if j>i:continue
d=ost.mol.alg.AnalyzeDistanceBetwAtoms(t,a1.GetHandle(),a2.GetHandle())[first:last]
M[i,j]=npy.mean(d)
M[j,i]=npy.mean(d)
--
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