From 4728655d22c5ef5a47284588921a99687f3d9b1a Mon Sep 17 00:00:00 2001
From: Niklaus Johner <nij2003@med.cornell.edu>
Date: Mon, 9 Jun 2014 17:12:03 -0400
Subject: [PATCH] Added additional argument and flag in the
RMSD_Matrix_From_Traj function to allow for alignment and RMSD calulation
from different EntityViews
---
modules/mol/alg/pymod/trajectory_analysis.py | 8 +++++---
1 file changed, 5 insertions(+), 3 deletions(-)
diff --git a/modules/mol/alg/pymod/trajectory_analysis.py b/modules/mol/alg/pymod/trajectory_analysis.py
index 23c53b5a7..ddd2c4173 100644
--- a/modules/mol/alg/pymod/trajectory_analysis.py
+++ b/modules/mol/alg/pymod/trajectory_analysis.py
@@ -52,7 +52,7 @@ def smooth(vec,n):
From here on the module needs numpy
"""
-def RMSD_Matrix_From_Traj(t,sele,first=0,last=-1):
+def RMSD_Matrix_From_Traj(t,sele,first=0,last=-1,align=True,align_sele=None):
"""
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
@@ -64,14 +64,16 @@ def RMSD_Matrix_From_Traj(t,sele,first=0,last=-1):
last=-1 : the last frame of t to be used
Returns a numpy NxN matrix, where n is the number of frames.
"""
+ if not align_sele:align_sele=sele
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()
+ if align:
+ t=ost.mol.alg.SuperposeFrames(t,align_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:
--
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