From 58f6e7039048ebed6726600e2dd386ee1277aab4 Mon Sep 17 00:00:00 2001
From: Niklaus Johner <nij2003@med.cornell.edu>
Date: Sun, 26 Jan 2014 19:51:23 -0500
Subject: [PATCH] Added function to calculate distance fluctuation matrix
---
modules/mol/alg/pymod/trajectory_analysis.py | 20 +++++++++++++++++++-
1 file changed, 19 insertions(+), 1 deletion(-)
diff --git a/modules/mol/alg/pymod/trajectory_analysis.py b/modules/mol/alg/pymod/trajectory_analysis.py
index 064135c32..e46af2756 100644
--- a/modules/mol/alg/pymod/trajectory_analysis.py
+++ b/modules/mol/alg/pymod/trajectory_analysis.py
@@ -211,5 +211,23 @@ def AverageDistanceMatrixFromTraj(t,sele,first=0,last=-1):
M[j,i]=npy.mean(d)
return M
-
+def AnalyzeDistanceFluctuationMatrix(t,sele,first=0,last=-1):
+ try:
+ import numpy as npy
+ except ImportError:
+ LogError("Function needs numpy, but I could not import it.")
+ raise
+ n_atoms=sele.GetAtomCount()
+ M=npy.zeros([n_atoms,n_atoms])
+ for i,a1 in enumerate(sele.atoms):
+ for j,a2 in enumerate(sele.atoms):
+ if i>j:continue
+ d=ost.mol.alg.AnalyzeDistanceBetwAtoms(t,a1.GetHandle(),a2.GetHandle())[first:last]
+ M[j,i]=npy.std(d)
+ M[i,j]=npy.std(d)
+ return M
+
+
+
+
\ No newline at end of file
--
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