relax SVN archive

Fix for the model argument for the frame_order.pdb_model user function.

The deletion of structural models for the Monte Carlo simulations in the average domain position
representation now only happen if more than one model exists.

Fix for the specific_analyses.frame_order.data.pivot_fixed() function.

This was recently introduced (r25763) when the check for PCS data was removed from this function.
To fix the problem, instead of calling base_data_types() to see if PCS data is present, the
cdp.pcs_ids data structure is checked instead.

Modified the frame order auto-analysis to be more fail-safe.

Almost all of the protocol is now within a try-finally block so that the execution lock will always
be released.

Reverted r25767 as this was rubbish, the frame_order.pivot user function updates the model itself.

The command used was:
svn merge -r25767:r25766 .

.....
r25767 | bugman | 2014-09-12 10:08:13 +0200 (Fri, 12 Sep 2014) | 6 lines
Changed paths:
M /branches/frame_order_cleanup/specific_analyses/frame_order/uf.py

Added a call to check_pivot() to the frame_order.select_model user function.

This is to prevent this user function from being called before the pivot has been set, as otherwise
the parameter vector will be incorrectly set up.
.....

The frame_order.pdb_model user function can now properly handle a failed pivot optimisation.

This is when the pivot point optimises to a coordinate outside of the PDB limits.

Now all calls to specific_analyses.frame_order.data.generate_pivot() from the module
specific_analyses.frame_order.geometric set the pdb_limit flag to True. This allows all
representation objects to be within the PDB limits. The algorithm in generate_pivot() has been
extended to allow higher positive values, as the real PDB limits are [-999.999, 9999.999]. And a
RelaxWarning is called when the pivot is outside to tell the user about it.

Created the Frame_order.test_frame_order_pdb_model_failed_pivot system test.

This simply shows how the frame_order.pdb_model user function currently fails if the optimised pivot
point is outside of the PDB coordinate limits of "%8.3f".

Removed the estimate_rx_err module from the specific_analyses.relax_fit.__all__ list.

This module was deleted after merger into the api module.

Modified the frame order sim_init_values() API method to handle missing optimisation data.

The monte_carlo.initial_values user function was failing if optimisation had not been performed.
This is now caught and handled correctly.

Fix for the Frame_order.test_frame_order_pdb_model_ensemble system test.

More needed to be done to set up the Monte Carlo simulations - the monte_carlo.initial_values user
function call was required.

Added support for the model argument for the frame_order.pdb_model user function.

This argument is used to specify which of the models in an ensemble will be used to represent the
average domain position Monte Carlo simulations, as each simulation is encoded as a model, as well
as for the distribution of structures simulating the motion of the system. The argument is
therefore passed into the create_ave_pos() and create_distribution() functions of the
specific_analyses.frame_order.geometric module.

To handle all models being used in the non Monte Carlo simulation PDB file and only one in this
file, the internal structural object is copied twice. The second copy for the MC sims has all but
the chosen model deleted out of it.