Author: bugman
Date: Wed Sep 10 14:24:58 2014
New Revision: 25735
URL: http://svn.gna.org/viewcvs/relax?rev=25735&view=rev
Log:
Many fixes for the frame_order.permute_axes user function.
The z-axis inversion is now encoded into a 3D numpy array as the index of the
new z-axis position
needs to be stored. The cone_theta_x, cone_theta_y and cone_sigma_max
parameters are now permuted
in reverse 'perm' data structure by calling its index() method. And the
cone_theta_x - cone_theta_y
to y-axis - x-axis switch has been removed (this may need to be reintroduced
later).
Modified:
branches/frame_order_cleanup/specific_analyses/frame_order/uf.py
Modified: branches/frame_order_cleanup/specific_analyses/frame_order/uf.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/frame_order/uf.py?rev=25735&r1=25734&r2=25735&view=diff
==============================================================================
--- branches/frame_order_cleanup/specific_analyses/frame_order/uf.py
(original)
+++ branches/frame_order_cleanup/specific_analyses/frame_order/uf.py Wed Sep
10 14:24:58 2014
@@ -23,7 +23,7 @@
"""Module for all of the frame order specific user functions."""
# Python module imports.
-from numpy import array, float64, transpose, zeros
+from numpy import array, float64, ones, transpose, zeros
from warnings import warn
# relax module imports.
@@ -116,12 +116,12 @@
if not hasattr(cdp, 'cone_theta_y') or not is_float(cdp.cone_theta_y):
raise RelaxError("The parameter values are not set up.")
- # The angles. Note that cone_theta_x corresponds to a rotation about the
y-axis!
+ # The angles.
cone_sigma_max = 0.0
if cdp.model == MODEL_PSEUDO_ELLIPSE:
cone_sigma_max = cdp.cone_sigma_max
- angles = array([cdp.cone_theta_y, cdp.cone_theta_x, cone_sigma_max],
float64)
- y, x, z = angles
+ angles = array([cdp.cone_theta_x, cdp.cone_theta_y, cone_sigma_max],
float64)
+ x, y, z = angles
# Generate the eigenframe of the motion.
frame = zeros((3, 3), float64)
@@ -138,6 +138,9 @@
print("%-20s\n%s" % ("eigenframe", frame))
print("\nPermutation '%s':" % permutation)
+ # The axis inversion structure.
+ inv = ones(3, float64)
+
# The starting condition x <= y <= z.
if x <= y and y <= z:
# Printout.
@@ -146,10 +149,10 @@
# The permutation and axis inversion.
if permutation == 'A':
perm = [0, 2, 1]
- z_factor = -1.0
+ inv[1] = -1.0
else:
perm = [2, 0, 1]
- z_factor = 1.0
+ inv[0] = 1.0
# The starting condition x <= z <= y.
elif x <= z and z <= y:
@@ -159,10 +162,10 @@
# The permutation and axis inversion.
if permutation == 'A':
perm = [0, 2, 1]
- z_factor = -1.0
+ inv[1] = -1.0
else:
- perm = [1, 2, 0]
- z_factor = -1.0
+ perm = [2, 1, 0]
+ inv[0] = -1.0
# The starting condition z <= x <= y.
elif z <= x and x <= y:
@@ -172,10 +175,10 @@
# The permutation and axis inversion.
if permutation == 'A':
perm = [1, 2, 0]
- z_factor = 1.0
+ inv[1] = 1.0
else:
perm = [2, 1, 0]
- z_factor = -1.0
+ inv[0] = -1.0
# Cannot be here.
else:
@@ -183,16 +186,16 @@
# Printout.
print("%-20s %-20s" % ("permutation", perm))
- print("%-20s %-20s" % ("z-axis inversion", z_factor))
+ print("%-20s %-20s" % ("z-axis inversion", inv))
# Permute the angles.
- cdp.cone_theta_y = angles[perm[0]]
- cdp.cone_theta_x = angles[perm[1]]
+ cdp.cone_theta_x = angles[perm.index(0)]
+ cdp.cone_theta_y = angles[perm.index(1)]
if cdp.model == MODEL_PSEUDO_ELLIPSE:
- cdp.cone_sigma_max = angles[perm[2]]
+ cdp.cone_sigma_max = angles[perm.index(2)]
# Permute the axes and invert the z-axis as necessary.
- frame_new = transpose(array([frame[:, perm[0]], frame[:, perm[1]],
z_factor*frame[:, perm[2]]], float64))
+ frame_new = transpose(array([inv[0]*frame[:, perm[0]], inv[1]*frame[:,
perm[1]], inv[2]*frame[:, perm[2]]], float64))
# Convert the permuted frame to Euler angles and store them.
cdp.eigen_alpha, cdp.eigen_beta, cdp.eigen_gamma =
R_to_euler_zyz(frame_new)
_______________________________________________
relax (http://www.nmr-relax.com)
This is the relax-commits mailing list
[email protected]
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
