Author: bugman
Date: Wed Jul 30 12:22:43 2014
New Revision: 24823
URL: http://svn.gna.org/viewcvs/relax?rev=24823&view=rev
Log:
Added linear constraints for the pivot and average domain translation frame
order parameters.
The pivot coordinates are constrained between -999 and 999 Angstrom and the
translation between -500
and 500 Angstrom. This allows the frame_order.pdb_model user function to
operate in the case of
failed models - often the free rotors fitting to torsionally restricted data
- by preventing the PDB
coordinates from being out of the PDB format range. It should also speed up
optimisation by
stopping the optimisation of failed models earlier.
Modified:
branches/frame_order_cleanup/specific_analyses/frame_order/parameters.py
Modified:
branches/frame_order_cleanup/specific_analyses/frame_order/parameters.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/frame_order/parameters.py?rev=24823&r1=24822&r2=24823&view=diff
==============================================================================
--- branches/frame_order_cleanup/specific_analyses/frame_order/parameters.py
(original)
+++ branches/frame_order_cleanup/specific_analyses/frame_order/parameters.py
Wed Jul 30 12:22:43 2014
@@ -90,7 +90,16 @@
-0.125 <= S <= 1,
0 <= sigma_max <= pi,
- The pivot point parameter, domain position parameters, and eigenframe
parameters are unconstrained.
+ The pivot point and average domain position parameter constraints are::
+
+ -999 <= pivot_x <= 999
+ -999 <= pivot_y <= 999
+ -999 <= pivot_z <= 999
+ -500 <= ave_pos_x <= 500
+ -500 <= ave_pos_y <= 500
+ -500 <= ave_pos_y <= 500
+
+ These are necessary to allow for valid PDB representations to be
created. The eigenframe parameters are unconstrained.
Matrix notation
@@ -120,6 +129,32 @@
| | | |
| 0 0 0 0 -1 | | -pi |
+ The pivot and average position constraints in the A.x >= b notation are::
+
+ | 1 0 0 0 0 0 | | -999.0 |
+ | | | |
+ |-1 0 0 0 0 0 | | -999.0 |
+ | | | |
+ | 0 1 0 0 0 0 | | -999.0 |
+ | | | |
+ | 0 -1 0 0 0 0 | | pivot_x | | -999.0 |
+ | | | | | |
+ | 0 0 1 0 0 0 | | pivot_y | | -999.0 |
+ | | | | | |
+ | 0 0 -1 0 0 0 | | pivot_z | | -999.0 |
+ | | . | | >= | |
+ | 0 0 0 1 0 0 | | ave_pos_x | | -500.0 |
+ | | | | | |
+ | 0 0 0 -1 0 0 | | ave_pos_y | | -500.0 |
+ | | | | | |
+ | 0 0 0 0 1 0 | | ave_pos_z | | -500.0 |
+ | | | |
+ | 0 0 0 0 -1 0 | | -500.0 |
+ | | | |
+ | 0 0 0 0 0 1 | | -500.0 |
+ | | | |
+ | 0 0 0 0 0 -1 | | -500.0 |
+
@keyword scaling_matrix: The diagonal, square scaling matrix.
@type scaling_matrix: numpy rank-2 square matrix
@@ -137,6 +172,28 @@
# Loop over the parameters of the model.
for i in range(n):
+ # The pivot parameters.
+ if cdp.params[i] in ['pivot_x', 'pivot_y', 'pivot_z']:
+ # -999 <= pivot_i <= 999.
+ A.append(zero_array * 0.0)
+ A.append(zero_array * 0.0)
+ A[j][i] = 1.0
+ A[j+1][i] = -1.0
+ b.append(-999.0 / scaling_matrix[i, i])
+ b.append(-999.0 / scaling_matrix[i, i])
+ j = j + 2
+
+ # The average domain translation parameters.
+ if cdp.params[i] in ['ave_pos_x', 'ave_pos_y', 'ave_pos_z']:
+ # -500 <= ave_pos_i <= 500.
+ A.append(zero_array * 0.0)
+ A.append(zero_array * 0.0)
+ A[j][i] = 1.0
+ A[j+1][i] = -1.0
+ b.append(-500.0 / scaling_matrix[i, i])
+ b.append(-500.0 / scaling_matrix[i, i])
+ j = j + 2
+
# The cone opening angles and sigma_max.
if cdp.params[i] in ['cone_theta', 'cone_theta_x', 'cone_theta_y',
'cone_sigma_max']:
# 0 <= theta <= pi.
r24823 - /branches/frame_order_cleanup/specific_analyses/frame_order/parameters.py