Author: bugman Date: Fri Oct 2 12:31:21 2015 New Revision: 27947 URL: http://svn.gna.org/viewcvs/relax?rev=27947&view=rev Log: Merged revisions 24778,24783-24784,24787,24798-24810,24814-24817 via svnmerge from svn+ssh://bug...@svn.gna.org/svn/relax/branches/frame_order_cleanup
........ r24778 | bugman | 2014-07-27 10:40:21 +0200 (Sun, 27 Jul 2014) | 7 lines Fixes for the CaM free-rotor pseudo-ellipse frame order model test data set. This is for the constraint 0 <= theta_x <= theta_y <= pi, as the old data was created with theta_x > theta_y. The new data is also of high quality using 20 million structures and numpy.float128 data averaging. ........ r24783 | bugman | 2014-07-28 14:21:04 +0200 (Mon, 28 Jul 2014) | 5 lines Created the lib.frame_order.rotor_axis.convert_axis_alpha_to_spherical() function. This will convert the axis alpha angle to the equivalent spherical angles theta and phi. ........ r24784 | bugman | 2014-07-28 15:48:50 +0200 (Mon, 28 Jul 2014) | 5 lines Renamed the lib.frame_order.rotor_axis module to lib.frame_order.conversions. This module will be used for all sorts of frame order parameter conversions. ........ r24787 | bugman | 2014-07-28 16:29:59 +0200 (Mon, 28 Jul 2014) | 5 lines Added the pipe_name argument to the specific_analyses.frame_order.data.generate_pivot() function. This allows the pivot from data pipes other than the current one to be assembled and returned. ........ r24798 | bugman | 2014-07-29 11:39:10 +0200 (Tue, 29 Jul 2014) | 8 lines Updated the frame order optimisation results for the CaM free rotor, pseudo-ellipse test data. The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric integration points significantly increased, especially for the Monte Carlo simulations. The new frame order representation files have been added to the repository, as well as the intermediate state files. ........ r24799 | bugman | 2014-07-29 11:40:25 +0200 (Tue, 29 Jul 2014) | 8 lines Updated the frame order optimisation results for the CaM torsionless, pseudo-ellipse test data. The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric integration points significantly increased, especially for the Monte Carlo simulations. The new frame order representation files have been added to the repository, as well as the intermediate state files. ........ r24800 | bugman | 2014-07-29 11:58:19 +0200 (Tue, 29 Jul 2014) | 5 lines Fix for the Frame_order.test_cam_pseudo_ellipse_free_rotor system test. This is for the change of the X and Y cone opening angles. ........ r24801 | bugman | 2014-07-29 13:11:20 +0200 (Tue, 29 Jul 2014) | 14 lines Redesign and expansion of the nested model parameter copying in the frame order auto-analysis. The nested parameter protocol used to allow the analysis to complete in under 1,000,000 years was no longer functional due to the switching to the axis alpha parameter to decrease parameter number and redundancy. The copying of the average domain position for the free rotor models was also incorrect as the dropping of the alpha Euler angle cause the translation parameters and beta and gamma angles to change drastically. The new protocol has been split into four methods for the average domain position, the pivot point, the motional eigenframe and the parameters of ordering. These use the fact that the free rotor and torsionless models are the two extrema of the models where the torsion angle is restricted. The pivot copying is a new addition. ........ r24802 | bugman | 2014-07-29 13:58:14 +0200 (Tue, 29 Jul 2014) | 7 lines Created the Frame_order.test_auto_analysis system test. This will be an extremely quick run through of the frame order auto-analysis as this is not currently tested. 1 Sobol' quasi-random integration point will be used for all models for speed. The system test uses the rigid CaM test data to perform a full analysis. ........ r24803 | bugman | 2014-07-29 13:59:39 +0200 (Tue, 29 Jul 2014) | 3 lines Import fix for the frame order auto-analysis. ........ r24804 | bugman | 2014-07-29 14:01:04 +0200 (Tue, 29 Jul 2014) | 3 lines Alphabetical ordering of the imports in the frame order auto-analysis module. ........ r24805 | bugman | 2014-07-29 14:06:14 +0200 (Tue, 29 Jul 2014) | 5 lines Fixes for the backend script of the Frame_order.test_auto_analysis system test. This includes a missing import and the removal of a long ago deleted user function. ........ r24806 | bugman | 2014-07-29 14:08:11 +0200 (Tue, 29 Jul 2014) | 6 lines Fix for the frame order auto-analysis for the call to the grid search user function. This user function has been renamed to minimise.grid_search, however not all parts of the analysis had been converted to the new name. ........ r24807 | bugman | 2014-07-29 15:13:46 +0200 (Tue, 29 Jul 2014) | 6 lines Created a method in the frame order auto-analysis to reorder the models. This is needed as the nested model parameter copying protocol requires the simpler models to be optimised first. ........ r24808 | bugman | 2014-07-29 15:17:02 +0200 (Tue, 29 Jul 2014) | 5 lines The Frame_order.test_auto_analysis system test now writes all files to the directory of ds.tmpdir. This is to prevent the system test from dumping files in the current directory. ........ r24809 | bugman | 2014-07-29 15:38:41 +0200 (Tue, 29 Jul 2014) | 5 lines Modified the specific_analyses.frame_order.parameters.update_model() function. This will no longer set all parameters to 0.0, excluding the pivot point. ........ r24810 | bugman | 2014-07-29 16:07:28 +0200 (Tue, 29 Jul 2014) | 6 lines Modified the specific_analyses.frame_order.parameters.assemble_param_vector() function. This can now handle the case of no parameters being present. The corresponding elements of the numpy array will consist of NaN values. ........ r24814 | bugman | 2014-07-29 16:41:17 +0200 (Tue, 29 Jul 2014) | 10 lines Better handling of unset parameters in the frame order optimisation functions. The specific_analyses.frame_order.optimisation.target_fn_data_setup() and specific_analyses.frame_order.parameters.assemble_param_vector() function both now accept the unset_fail argument. This is set in both the calculate() and minimise() API methods. When set, a RelaxError will be raised in the assemble_param_vector() function when a parameter has not been set yet. This together with previous changes will prevent the frame order analysis from using 0.0 as a starting value for unset parameters. ........ r24815 | bugman | 2014-07-29 17:01:55 +0200 (Tue, 29 Jul 2014) | 7 lines Fixes for all of the Frame_order.test_rigid_data_to_*_model system tests. The base script now sets all parameter values so that the minimise.calculate user function can operate. The two free rotor model chi-squared values have been updated as these are sensitive to the motional eigenframe parameter values - these models can never approximate a rigid state. ........ r24816 | bugman | 2014-07-29 17:38:31 +0200 (Tue, 29 Jul 2014) | 5 lines Modified the optimisation of the rigid model in the frame order auto-analysis. The grid search is now implemented as a zooming grid search. ........ r24817 | bugman | 2014-07-29 18:03:37 +0200 (Tue, 29 Jul 2014) | 5 lines Missing import in the lib.frame_order.rotor module. This was identified by the new Frame_order.test_auto_analysis system test. ........ Added: trunk/lib/frame_order/conversions.py - copied unchanged from r24817, branches/frame_order_cleanup/lib/frame_order/conversions.py trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/ave_pos_sim.pdb.gz - copied unchanged from r24817, branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/ave_pos_sim.pdb.gz trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_A.pdb.gz - copied unchanged from r24817, branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_A.pdb.gz trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_B.pdb.gz - copied unchanged from r24817, branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_B.pdb.gz trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_fixed_piv.bz2 - copied unchanged from r24817, branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_fixed_piv.bz2 trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_fixed_piv_A.pdb.gz - copied unchanged from r24817, branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_fixed_piv_A.pdb.gz trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_fixed_piv_B.pdb.gz - copied unchanged from r24817, branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_fixed_piv_B.pdb.gz trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_sim_A.pdb.gz - copied unchanged from r24817, branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_sim_A.pdb.gz trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_sim_B.pdb.gz - copied unchanged from r24817, branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_sim_B.pdb.gz trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_true.bz2 - copied unchanged from r24817, branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_true.bz2 trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_true_A.pdb.gz - copied unchanged from r24817, branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_true_A.pdb.gz trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_true_B.pdb.gz - copied unchanged from r24817, branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_true_B.pdb.gz trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/ave_pos_sim.pdb.gz - copied unchanged from r24817, branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/ave_pos_sim.pdb.gz trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_A.pdb.gz - copied unchanged from r24817, branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_A.pdb.gz trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_B.pdb.gz - copied unchanged from r24817, branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_B.pdb.gz trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_fixed_piv.bz2 - copied unchanged from r24817, branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_fixed_piv.bz2 trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_fixed_piv_A.pdb.gz - copied unchanged from r24817, branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_fixed_piv_A.pdb.gz trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_fixed_piv_B.pdb.gz - copied unchanged from r24817, branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_fixed_piv_B.pdb.gz trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_sim_A.pdb.gz - copied unchanged from r24817, branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_sim_A.pdb.gz trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_sim_B.pdb.gz - copied unchanged from r24817, branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_sim_B.pdb.gz trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_true.bz2 - copied unchanged from r24817, branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_true.bz2 trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_true_A.pdb.gz - copied unchanged from r24817, branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_true_A.pdb.gz trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_true_B.pdb.gz - copied unchanged from r24817, branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_true_B.pdb.gz trunk/test_suite/system_tests/scripts/frame_order/cam/auto_analysis_to_rigid.py - copied unchanged from r24817, branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/auto_analysis_to_rigid.py Removed: trunk/lib/frame_order/rotor_axis.py trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order.pdb.gz trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_fixed_piv.pdb.gz trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_true.pdb.gz trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.pdb.gz trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_fixed_piv.pdb.gz trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_true.pdb.gz Modified: trunk/ (props changed) trunk/auto_analyses/frame_order.py trunk/lib/frame_order/__init__.py trunk/lib/frame_order/rotor.py trunk/specific_analyses/frame_order/api.py trunk/specific_analyses/frame_order/data.py trunk/specific_analyses/frame_order/geometric.py trunk/specific_analyses/frame_order/optimisation.py trunk/specific_analyses/frame_order/parameters.py trunk/target_functions/frame_order.py trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/ave_pos.pdb.gz trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/ave_pos_fixed_piv.pdb.gz trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/ave_pos_true.pdb.gz trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/axis.pdb trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order.bz2 trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order.log.bz2 trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order.py trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_matrix trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/generate_distribution.bz2 trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/generate_distribution.log.bz2 trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/generate_distribution.py trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/pcs_dy.txt trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/pcs_dy_subset.txt trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/pcs_er.txt trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/pcs_er_subset.txt trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/pcs_tb.txt trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/pcs_tb_subset.txt trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/pcs_tm.txt trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/pcs_tm_subset.txt trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/rdc_dy.txt trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/rdc_er.txt trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/rdc_tb.txt trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/rdc_tm.txt trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/ave_pos.pdb.gz trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/ave_pos_fixed_piv.pdb.gz trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/ave_pos_true.pdb.gz trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.bz2 trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.log.bz2 trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.py trunk/test_suite/system_tests/frame_order.py trunk/test_suite/system_tests/scripts/frame_order/cam/pseudo_ellipse_free_rotor.py trunk/test_suite/system_tests/scripts/frame_order/rigid_test.py [This mail would be too long, it was shortened to contain the URLs only.] Modified: trunk/auto_analyses/frame_order.py URL: http://svn.gna.org/viewcvs/relax/trunk/auto_analyses/frame_order.py?rev=27947&r1=27946&r2=27947&view=diff Modified: trunk/lib/frame_order/__init__.py URL: http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/__init__.py?rev=27947&r1=27946&r2=27947&view=diff Modified: trunk/lib/frame_order/rotor.py URL: http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/rotor.py?rev=27947&r1=27946&r2=27947&view=diff Removed: trunk/lib/frame_order/rotor_axis.py URL: http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/rotor_axis.py?rev=27946&view=auto Modified: trunk/specific_analyses/frame_order/api.py URL: http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/api.py?rev=27947&r1=27946&r2=27947&view=diff Modified: trunk/specific_analyses/frame_order/data.py URL: http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/data.py?rev=27947&r1=27946&r2=27947&view=diff Modified: trunk/specific_analyses/frame_order/geometric.py URL: http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/geometric.py?rev=27947&r1=27946&r2=27947&view=diff Modified: trunk/specific_analyses/frame_order/optimisation.py URL: http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/optimisation.py?rev=27947&r1=27946&r2=27947&view=diff Modified: trunk/specific_analyses/frame_order/parameters.py URL: http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/parameters.py?rev=27947&r1=27946&r2=27947&view=diff Modified: trunk/target_functions/frame_order.py URL: http://svn.gna.org/viewcvs/relax/trunk/target_functions/frame_order.py?rev=27947&r1=27946&r2=27947&view=diff Modified: trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/ave_pos.pdb.gz URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/ave_pos.pdb.gz?rev=27947&r1=27946&r2=27947&view=diff Modified: trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/ave_pos_fixed_piv.pdb.gz URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/ave_pos_fixed_piv.pdb.gz?rev=27947&r1=27946&r2=27947&view=diff [... 108 lines stripped ...] _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org 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