From 3a3b92631a704437e62987d410912c1a76d93731 Mon Sep 17 00:00:00 2001
From: Niklaus Johner <nij2003@med.cornell.edu>
Date: Wed, 28 Nov 2012 15:41:07 -0500
Subject: [PATCH] Added a function to calculate a Distance Difference Matrix
from two EntityViews.
---
modules/mol/alg/pymod/structure_analysis.py | 30 +++++++++++++++++++++
1 file changed, 30 insertions(+)
diff --git a/modules/mol/alg/pymod/structure_analysis.py b/modules/mol/alg/pymod/structure_analysis.py
index 7cbd0dd4b..dbbc1d9df 100644
--- a/modules/mol/alg/pymod/structure_analysis.py
+++ b/modules/mol/alg/pymod/structure_analysis.py
@@ -129,3 +129,33 @@ def CalculateHelixAxis(sele1):
f=GetFrameFromEntity(eh)
return f.FitCylinder(sele1)
+
+def CalculateDistanceDifferenceMatrix(sele1,sele2):
+ """
+ This function calculates the pairwise distance differences between two EntityViews.
+ The two EntityViews should have the same number of atoms
+ It returns an NxN DistanceDifferenceMatrix M (where N is the number of atoms in sele1)
+ where M[i,j]=(sele2.atoms[i].pos-sele2.atoms[j].pos)-(sele1.atoms[i].pos-sele1.atoms[j].pos)
+ """
+ try:import numpy as npy
+ except ImportError:
+ LogError("Function needs numpy, but I could not import it.")
+ raise
+ if not sele1.IsValid() and sele2.IsValid():
+ print 'invalid view'
+ return
+ if not sele1.GetAtomCount()==sele2.GetAtomCount():
+ print 'The two views must have the same number of atoms'
+ return
+ n_atoms=sele1.GetAtomCount()
+ M=npy.zeros([n_atoms,n_atoms])
+ for i,a1 in enumerate(sele1.atoms):
+ for j,a2 in enumerate(sele2.atoms):
+ if i>=j:continue
+ d1=geom.Distance(a1.pos,a2.pos)
+ d2=geom.Distance(sele2.atoms[i].pos,sele2.atoms[j].pos)
+ M[i,j]=d2-d1
+ M[j,i]=d2-d1
+ return M
+
+
--
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