Author: bugman
Date: Fri Dec 19 16:42:53 2014
New Revision: 27147
URL: http://svn.gna.org/viewcvs/relax?rev=27147&view=rev
Log:
Added the 'parallax shift' measure to the structure.atomic_fluctuations user
function.
The parallax shift is defined as the length of the average vector minus the
interatomic vector. It
is similar to the angle measure however, importantly, it is independent of the
distance between the
two atoms.
Modified:
trunk/pipe_control/structure/main.py
trunk/user_functions/structure.py
Modified: trunk/pipe_control/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/main.py?rev=27147&r1=27146&r2=27147&view=diff
==============================================================================
--- trunk/pipe_control/structure/main.py (original)
+++ trunk/pipe_control/structure/main.py Fri Dec 19 16:42:53 2014
@@ -254,7 +254,7 @@
# Checks.
check_pipe()
check_structure()
- allowed_measures = ['distance', 'angle']
+ allowed_measures = ['distance', 'angle', 'parallax shift']
if measure not in allowed_measures:
raise RelaxError("The measure '%s' must be one of %s." % (measure,
allowed_measures))
@@ -278,6 +278,7 @@
matrix = zeros((n, n), float64)
dist = zeros(m, float64)
vectors = zeros((m, 3), float64)
+ parallax_vectors = zeros((m, 3), float64)
angles = zeros(m, float64)
# Generate the pairwise distance SD matrix.
@@ -317,6 +318,29 @@
# Calculate and store the corrected sample standard deviation.
matrix[i, j] = matrix[j, i] = std(angles, ddof=1)
+
+ # Generate the pairwise parallax shift SD matrix.
+ elif measure == 'parallax shift':
+ # Loop over the atom pairs.
+ for i in range(n):
+ for j in range(n):
+ # Only calculate the upper triangle to avoid duplicate
calculations.
+ if j > i:
+ continue
+
+ # The interatomic vectors between each structure.
+ for k in range(m):
+ vectors[k] = coord[k, i] - coord[k, j]
+
+ # The average vector.
+ ave_vect = average(vectors, axis=0)
+
+ # The parallax shift.
+ for k in range(m):
+ dist[k] = norm(vectors[k] - ave_vect)
+
+ # Calculate and store the corrected sample standard deviation.
+ matrix[i, j] = matrix[j, i] = std(dist, ddof=1)
# Call the plotting API.
correlation_matrix(format=format, matrix=matrix, labels=labels, file=file,
dir=dir, force=force)
Modified: trunk/user_functions/structure.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/structure.py?rev=27147&r1=27146&r2=27147&view=diff
==============================================================================
--- trunk/user_functions/structure.py (original)
+++ trunk/user_functions/structure.py Fri Dec 19 16:42:53 2014
@@ -341,6 +341,7 @@
uf.desc[-1].add_paragraph("This is used to visualise the interatomic
fluctuations between different structures. By setting the measure argument,
this can be set to either the fluctuations of the interatomic distances or the
fluctuations of the interatomic vector angles:")
uf.desc[-1].add_item_list_element("'distance'", "This is the default. The
corrected sample standard deviation (SD) is calculated for the distances
between all atom pairs, resulting in a pairwise matrix of SD values.")
uf.desc[-1].add_item_list_element("'angle'", "The corrected sample standard
deviation (SD) is calculated for the angles between the inter atom vectors all
atom pairs to an average vector. This also produces a pairwise matrix of SD
values.")
+uf.desc[-1].add_item_list_element("'parallax shift'", "The corrected sample
standard deviation (SD) is calculated for the parallax shift between the inter
atom vectors all atom pairs to an average vector. This also produces a
pairwise matrix of SD values. The parallax shift is the length of the average
vector minus the interatomic vector. It is similar to the angle measure
however, importantly, it is independent of the distance between the two atoms.")
uf.desc[-1].add_paragraph("For the output file, the currently supported
formats are:")
uf.desc[-1].add_item_list_element("'text'", "This is the default value and
will result in a single text file being created.")
uf.desc[-1].add_item_list_element("'gnuplot'", "This will create a both a text
file with the data and a script for visualising the correlation matrix using
gnuplot. The script will have the same name as the text file, however the file
extension will be changed to *.gnu.")
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