Author: bugman
Date: Wed Nov 25 18:38:29 2015
New Revision: 28115
URL: http://svn.gna.org/viewcvs/relax?rev=28115&view=rev
Log:
A weighted mean structure can now be calculated.
This is for the calc_mean_structure() function of the relax library module
lib.structure.statistics.
Weights can now be supplied for each structure to allow for a weighted mean to
be calculated and
returned.
Modified:
trunk/lib/structure/statistics.py
Modified: trunk/lib/structure/statistics.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/statistics.py?rev=28115&r1=28114&r2=28115&view=diff
==============================================================================
--- trunk/lib/structure/statistics.py (original)
+++ trunk/lib/structure/statistics.py Wed Nov 25 18:38:29 2015
@@ -1,6 +1,6 @@
###############################################################################
# #
-# Copyright (C) 2011-2013 Edward d'Auvergne #
+# Copyright (C) 2011-2015 Edward d'Auvergne #
# #
# This file is part of the program relax (http://www.nmr-relax.com). #
# #
@@ -23,7 +23,7 @@
"""Module for handling all types of structural statistics."""
# Python module imports.
-from numpy import float64, mean, sqrt, std, zeros
+from numpy import array, float64, mean, ones, sqrt, std, zeros
from numpy.linalg import norm
@@ -84,11 +84,13 @@
return rmsd_mean
-def calc_mean_structure(coord=None, mean=None):
+def calc_mean_structure(coord=None, mean=None, weights=None):
"""Average the coordinates.
@keyword coord: The list of coordinates of all models to superimpose.
The first index is the models, the second is the atomic positions, and the
third is the xyz coordinates.
@type coord: list of numpy rank-2, Nx3 arrays
+ @keyword weights: The weights for each structure.
+ @type weights: list of float
@keyword mean: The data storage for the mean structure.
@type mean: numpy rank-2, Nx3 array
"""
@@ -96,6 +98,10 @@
# The number of atoms.
N = len(coord[0])
M = len(coord)
+ if weights == None:
+ weights = ones(M, float64)
+ else:
+ weights = array(weights, float64)
# Clear the mean data structure.
for i in range(N):
@@ -105,7 +111,7 @@
for i in range(N):
# Loop over the models.
for j in range(M):
- mean[i] += coord[j][i]
+ mean[i] += weights[j] * coord[j][i]
# Average.
- mean[i] = mean[i] / M
+ mean[i] = mean[i] / weights.sum()
_______________________________________________
relax (http://www.nmr-relax.com)
This is the relax-commits mailing list
relax-commits@gna.org
To unsubscribe from this list, get a password
reminder, or change your subscription options,
visit the list information page at
https://mail.gna.org/listinfo/relax-commits
