Author: bugman
Date: Fri Aug 22 12:09:52 2014
New Revision: 25207
URL: http://svn.gna.org/viewcvs/relax?rev=25207&view=rev
Log:
Merged revisions 25206 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r25206 | bugman | 2014-08-22 12:08:09 +0200 (Fri, 22 Aug 2014) | 9 lines
Fix for bug #22502 (https://gna.org/bugs/?22502).
This is the problem whereby the geometric prolate diffusion representation
does not align with axis
in PDB, as reported by Martin Ballaschk (https://gna.org/users/mab).
This problem was not the main prolate tensor axis, but that the geometric
object needed to be
rotated 90 degrees about the z-axis to bring the object and axis into the
same frame.
........
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/lib/structure/represent/diffusion_tensor.py
Propchange: branches/frame_order_cleanup/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Fri Aug 22 12:09:52 2014
@@ -1 +1 @@
-/trunk:1-25204
+/trunk:1-25206
Modified:
branches/frame_order_cleanup/lib/structure/represent/diffusion_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/structure/represent/diffusion_tensor.py?rev=25207&r1=25206&r2=25207&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/structure/represent/diffusion_tensor.py
(original)
+++ branches/frame_order_cleanup/lib/structure/represent/diffusion_tensor.py
Fri Aug 22 12:09:52 2014
@@ -68,12 +68,24 @@
# Print out.
print("\nGenerating the geometric object.")
+ # Swap the x and y axes for the prolate spheroid (the vector
distributions are centred on the z-axis).
+ if diff_type == 'prolate':
+ # 90 deg rotation about the diffusion frame z-axis.
+ z_rot = array([[ 0, -1, 0],
+ [ 1, 0, 0],
+ [ 0, 0, 1]], float64)
+
+ # Rotate the tensor and rotation matrix.
+ rotation = dot(transpose(rotation), z_rot)
+ tensor = dot(z_rot, dot(tensor_diag, transpose(z_rot)))
+ tensor = dot(rotation, dot(tensor, transpose(rotation)))
+
# Swap the x and z axes for the oblate spheroid (the vector
distributions are centred on the z-axis).
if diff_type == 'oblate':
# 90 deg rotation about the diffusion frame y-axis.
- y_rot = array([[ 0, 0, 1],
- [ 0, 1, 0],
- [ -1, 0, 0]], float64)
+ y_rot = array([[ 0, 0, 1],
+ [ 0, 1, 0],
+ [ -1, 0, 0]], float64)
# Rotate the tensor and rotation matrix.
rotation = dot(transpose(rotation), y_rot)
r25207 - in /branches/frame_order_cleanup: ./ lib/structure/represent/diffusion_tensor.py