Author: bugman
Date: Thu Jun 12 10:53:55 2014
New Revision: 23859
URL: http://svn.gna.org/viewcvs/relax?rev=23859&view=rev
Log:
Removed the 2nd pivot point infrastructure from the frame order analysis.
This change is almost the same as reverting r22177 of the deleted
double_rotor branch. The 2nd
pivot is now defined via the pivot_disp parameter.
Modified:
branches/frame_order_cleanup/specific_analyses/frame_order/optimisation.py
branches/frame_order_cleanup/target_functions/frame_order.py
Modified:
branches/frame_order_cleanup/specific_analyses/frame_order/optimisation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/frame_order/optimisation.py?rev=23859&r1=23858&r2=23859&view=diff
==============================================================================
---
branches/frame_order_cleanup/specific_analyses/frame_order/optimisation.py
(original)
+++
branches/frame_order_cleanup/specific_analyses/frame_order/optimisation.py
Thu Jun 12 10:53:55 2014
@@ -658,11 +658,6 @@
if hasattr(cdp, 'pivot_x'):
pivot = array([cdp.pivot_x, cdp.pivot_y, cdp.pivot_z])
- # The second pivot.
- pivot2 = None
- if hasattr(cdp, 'pivot_x_2'):
- pivot2 = array([cdp.pivot_x_2, cdp.pivot_y_2, cdp.pivot_z_2])
-
# Pivot optimisation.
pivot_opt = True
if pivot_fixed():
@@ -701,7 +696,7 @@
sys.stdout.write("Base data: %s\n" % repr(base_data))
# Set up the optimisation function.
- target = frame_order.Frame_order(model=cdp.model,
init_params=param_vector, full_tensors=full_tensors,
full_in_ref_frame=full_in_ref_frame, rdcs=rdcs, rdc_errors=rdc_err,
rdc_weights=rdc_weight, rdc_vect=rdc_vect, dip_const=rdc_const, pcs=pcs,
pcs_errors=pcs_err, pcs_weights=pcs_weight, atomic_pos=atomic_pos, temp=temp,
frq=frq, paramag_centre=paramag_centre, scaling_matrix=scaling_matrix,
com=com, ave_pos_pivot=ave_pos_pivot, pivot=pivot, pivot2=pivot2,
pivot_opt=pivot_opt, num_int_pts=cdp.num_int_pts)
+ target = frame_order.Frame_order(model=cdp.model,
init_params=param_vector, full_tensors=full_tensors,
full_in_ref_frame=full_in_ref_frame, rdcs=rdcs, rdc_errors=rdc_err,
rdc_weights=rdc_weight, rdc_vect=rdc_vect, dip_const=rdc_const, pcs=pcs,
pcs_errors=pcs_err, pcs_weights=pcs_weight, atomic_pos=atomic_pos, temp=temp,
frq=frq, paramag_centre=paramag_centre, scaling_matrix=scaling_matrix,
com=com, ave_pos_pivot=ave_pos_pivot, pivot=pivot, pivot_opt=pivot_opt,
num_int_pts=cdp.num_int_pts)
# Return the data.
return target, param_vector, scaling_matrix
Modified: branches/frame_order_cleanup/target_functions/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/target_functions/frame_order.py?rev=23859&r1=23858&r2=23859&view=diff
==============================================================================
--- branches/frame_order_cleanup/target_functions/frame_order.py
(original)
+++ branches/frame_order_cleanup/target_functions/frame_order.py Thu
Jun 12 10:53:55 2014
@@ -57,7 +57,7 @@
class Frame_order:
"""Class containing the target function of the optimisation of Frame
Order matrix components."""
- def __init__(self, model=None, init_params=None, full_tensors=None,
full_in_ref_frame=None, rdcs=None, rdc_errors=None, rdc_weights=None,
rdc_vect=None, dip_const=None, pcs=None, pcs_errors=None, pcs_weights=None,
atomic_pos=None, temp=None, frq=None, paramag_centre=zeros(3),
scaling_matrix=None, num_int_pts=500, com=None, ave_pos_pivot=zeros(3),
pivot=None, pivot2=None, pivot_opt=False):
+ def __init__(self, model=None, init_params=None, full_tensors=None,
full_in_ref_frame=None, rdcs=None, rdc_errors=None, rdc_weights=None,
rdc_vect=None, dip_const=None, pcs=None, pcs_errors=None, pcs_weights=None,
atomic_pos=None, temp=None, frq=None, paramag_centre=zeros(3),
scaling_matrix=None, num_int_pts=500, com=None, ave_pos_pivot=zeros(3),
pivot=None, pivot_opt=False):
"""Set up the target functions for the Frame Order theories.
@keyword model: The name of the Frame Order model.
@@ -102,8 +102,6 @@
@type ave_pos_pivot: numpy 3D rank-1 array
@keyword pivot: The pivot point for the ball-and-socket
joint motion. This is needed if PCS or PRE values are used.
@type pivot: numpy rank-1, 3D array or None
- @keyword pivot2: The second pivot point for the motion.
This is needed if PCS or PRE values are used and if a double-motional model
is to be optimised.
- @type pivot2: numpy rank-1, 3D array or None
@keyword pivot_opt: A flag which if True will allow the
pivot point of the motion to be optimised.
@type pivot_opt: bool
"""
@@ -134,7 +132,6 @@
self.com = com
self.ave_pos_pivot = ave_pos_pivot
self._param_pivot = pivot
- self._param_pivot2 = pivot2
self.pivot_opt = pivot_opt
# Tensor setup.
@@ -383,9 +380,8 @@
# Unpack the parameters.
if self.pivot_opt:
self._param_pivot = params[:3]
- self._param_pivot2 = params[3:6]
- self._translation_vector = params[6:9]
- ave_pos_alpha, ave_pos_beta, ave_pos_gamma, axis_theta,
axis_phi, axis_theta_2, axis_phi_2, sigma_max, sigma_max_2 = params[9:]
+ self._translation_vector = params[3:6]
+ ave_pos_alpha, ave_pos_beta, ave_pos_gamma, axis_theta,
axis_phi, axis_theta_2, axis_phi_2, sigma_max, sigma_max_2 = params[6:]
else:
self._translation_vector = params[:3]
ave_pos_alpha, ave_pos_beta, ave_pos_gamma, axis_theta,
axis_phi, axis_theta_2, axis_phi_2, sigma_max, sigma_max_2 = params[3:]
r23859 - in /branches/frame_order_cleanup: specific_analyses/frame_order/optimisation.py target_functions/frame_order.py