From f2bb4a633d79a144887079ca73aa11da6ea50139 Mon Sep 17 00:00:00 2001
From: Niklaus Johner <nij2003@med.cornell.edu>
Date: Tue, 8 May 2012 11:23:35 -0400
Subject: [PATCH] Added function to calculate an RMSD matrix from a trajectory
---
modules/mol/alg/pymod/trajectory_analysis.py | 38 +++++++++++++++++++-
1 file changed, 37 insertions(+), 1 deletion(-)
diff --git a/modules/mol/alg/pymod/trajectory_analysis.py b/modules/mol/alg/pymod/trajectory_analysis.py
index 5e8c452b7..c23603205 100644
--- a/modules/mol/alg/pymod/trajectory_analysis.py
+++ b/modules/mol/alg/pymod/trajectory_analysis.py
@@ -4,7 +4,8 @@ Some functions for analyzing trajectories
Author: Niklaus Johner
"""
-from ost import *
+import ost.mol.alg
+from ost import LogError
import os
def smooth(vec,n):
@@ -46,3 +47,38 @@ def smooth(vec,n):
return vec2
+"""
+From here on the module needs numpy
+"""
+
+def RMSD_Matrix_From_Traj(t,sele,first=0,last=-1):
+ """
+ This function calculates a matrix M such that M[i,j] is the
+ RMSD of the EntityView sele between frames i and j of the trajectory t
+ aligned on sele.
+ Its inputs are:
+ t : the trajectory (CoordGroupHandle)
+ sele : the EntityView used for alignment and RMSD calculation
+ first=0 : the first frame of t to be used
+ last=-1 : the last frame of t to be used
+ Returns a numpy NxN matrix, where n is the number of frames.
+ """
+ try:
+ import numpy as npy
+ if last==-1:last=t.GetFrameCount()
+ n_frames=last-first
+ rmsd_matrix=npy.identity(n_frames)
+ for i in range(n_frames):
+ t=ost.mol.alg.SuperposeFrames(t,sele,begin=first,end=last,ref=i)
+ eh=t.GetEntity()
+ t.CopyFrame(i)
+ rmsd_matrix[i,:]=ost.mol.alg.AnalyzeRMSD(t,sele,sele)
+ if i==0:
+ last=last-first
+ first=0
+ return rmsd_matrix
+ except ImportError:
+ LogError("Function needs numpy, but I could not import it.")
+ raise
+
+
--
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