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Changes
Links to the API documentation (part 7 - the end).
* Introduced the nested_params_ave_dom_pos argument to the [http://www.nmr-relax.com/api/4.0/auto_analyses.frame_order-module.html frame order auto-analysis]. This allows the average domain position to be set to no rotations and translations rather than taking the average position from the rotor or free-rotor model. This can be useful when large motions are present causing the rigid model to have unreasonable domain positions.
* Fix for the [http://www.nmr-relax.com/manual/frame_order_permute_axes.html frame_order.permute_axes user function] description to allow the manual to be compiled. The table caption containing the user function name was causing the LaTeX compilation to fail. Therefore the captions have been rewritten to avoid the user function name.
* Modified the [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.frame_order.Frame_order-class.html#check_chi2 frame order system test check_chi2() method ] to test the [http://www.nmr-relax.com/manual/statistics_model.html statistics.model user function]. This causes all of the Frame_order.test_cam_* system tests to fail, as the user function backend is not implemented for the frame order analysis.* Implemented the frame order analysis backend for the [http://www.nmr-relax.com/manual/statistics_model.html statistics.model] and [http://www.nmr-relax.com/manual/statistics_aic.html statistics.aic] user functions. This simply required aliasing the specific analysis API common [http://www.nmr-relax.com/api/4.0/specific_analyses.api_common.API_common-class.html#_get_model_container_cdp _get_model_container_cdp() method ] to get_model_container().* Bug fix for the [http://www.nmr-relax.com/api/4.0/specific_analyses.frame_order.api.Frame_order-class.html#base_data_loop frame order specific analysis API base_data_loop() method]. This was looping over non-existent PCS and RDC data. Now the alignment ID is checked for in the interatomic data container 'rdc' data structure and the spin container 'pcs' data structure, as well as values of None, before yielding the data.* Created a large set of system tests for implementing the [http://www.nmr-relax.com/manual/frame_order_distribute.html frame_order.distribute user function]. This user function will be similar to [http://www.nmr-relax.com/manual/frame_order_simulate.html frame_order.simulate]. However instead of creating a PDB file with models from a pseudo-Brownian simulation, the [http://www.nmr-relax.com/manual/frame_order_distribute.html frame_order.distribute user function] will generate a PDB file of models forming a uniform distribution of structures covering the full frame order motional space. The new system tests are: Frame_order.test_distribute_double_rotor_mode1_xz_plane_tilt, Frame_order.test_distribute_double_rotor_mode1_z_axis, Frame_order.test_distribute_double_rotor_mode2_xz_plane_tilt, Frame_order.test_distribute_double_rotor_mode2_z_axis, [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.frame_order.Frame_order-class.html#test_distribute_free_rotor_z_axisFrame_order.test_distribute_free_rotor_z_axis], [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.frame_order.Frame_order-class.html#test_distribute_iso_cone_z_axis Frame_order.test_distribute_iso_cone_z_axis], [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.frame_order.Frame_order-class.html#test_distribute_iso_cone_xz_plane_tiltFrame_order.test_distribute_iso_cone_xz_plane_tilt], [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.frame_order.Frame_order-class.html#test_distribute_iso_cone_torsionless_z_axisFrame_order.test_distribute_iso_cone_torsionless_z_axis], [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.frame_order.Frame_order-class.html#test_distribute_pseudo_ellipse_xz_plane_tiltFrame_order.test_distribute_pseudo_ellipse_xz_plane_tilt], [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.frame_order.Frame_order-class.html#test_distribute_pseudo_ellipse_z_axisFrame_order.test_distribute_pseudo_ellipse_z_axis], [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.frame_order.Frame_order-class.html#test_distribute_pseudo_ellipse_free_rotor_z_axisFrame_order.test_distribute_pseudo_ellipse_free_rotor_z_axis], [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.frame_order.Frame_order-class.html#test_distribute_pseudo_ellipse_torsionless_z_axisFrame_order.test_distribute_pseudo_ellipse_torsionless_z_axis], [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.frame_order.Frame_order-class.html#test_distribute_rotor_z_axisFrame_order.test_distribute_rotor_z_axis]. These are aliases for the equivalent Frame_order.test_simulate_* system tests which have had the 'type' keyword argument added, defaulting to 'sim', which allows to switch between the [http://www.nmr-relax.com/manual/frame_order_simulate.html frame_order.simulate] and [http://www.nmr-relax.com/manual/frame_order_distribute.html frame_order.distribute] user functions. The concept behind these system tests are the same for both user functions, so the code is shared.
* Created the front-end of the [http://www.nmr-relax.com/manual/frame_order_distribute.html frame_order.distribute user function]. This is a copy and modification of the [http://www.nmr-relax.com/manual/frame_order_simulate.html frame_order.simulate user function], as the concepts are similar.
* Small modification of the [http://www.nmr-relax.com/manual/frame_order_simulate.html frame_order.simulate user function]. The GUI file opening dialog wildcard selectors are now set to all PDB file types (plain text, bzip2 compressed, and gzip compressed).
* Added the [http://www.nmr-relax.com/manual/frame_order_distribute.html frame_order.distribute user function] to the auto-analysis results output. This will allow both the pseudo-Brownian simulation and uniform distribution PDB files to be available to the user in all results directories (excluding the intermediate results for speed).
* Implemented the back-end of the [http://www.nmr-relax.com/manual/frame_order_distribute.html frame_order.distribute user function]. This follows the design of the pseudo-Brownian simulation [http://www.nmr-relax.com/manual/frame_order_simulate.html frame_order.simulate user function]. The [http://www.nmr-relax.com/api/4.0/specific_analyses.frame_order.uf-module.html#distribute specific_analyses.frame_order.uf.distribute() function ] has been created as a modified copy of the [http://www.nmr-relax.com/api/4.0/specific_analyses.frame_order.uf-module.html#simulate simulate() function ] of the same module. This simply performs checks and assembles the data, passing into the new [http://www.nmr-relax.com/api/4.0/lib.frame_order.simulation-module.html#uniform_distribution lib.frame_order.simulate.uniform_distribution() function], which itself is a modified copy of the [http://www.nmr-relax.com/api/4.0/lib.frame_order.simulation-module.html#brownian brownian() function] in the same module.
* Introduced the max_rotations argument into the [http://www.nmr-relax.com/manual/frame_order_distribute.html frame_order.distribute user function]. This is used to prevent the user function from running forever. This happens whenever a cone opening angle or torsion angle is zero, and hence the random sampling of the rotational space will never find rotations within the motional distribution.
* Improved control of the [http://www.nmr-relax.com/manual/frame_order_distribute.html frame_order.distribute user function] in the [http://www.nmr-relax.com/api/4.0/auto_analyses.frame_order-module.html frame order auto-analysis]. The maximum number of rotations can now be set, and the argument for the total states for the distribution has been shortened.
* Fix of a fatal bug preventing the frame order analysis to be run on a multi-processor system. The multi-processor code was calling the [http://www.nmr-relax.com/api/4.0/specific_analyses.frame_order.optimisation-module.html#count_sobol_points count_sobol_points() function] of the [http://www.nmr-relax.com/api/4.0/specific_analyses.frame_order.optimisation-module.html specific_analyses.frame_order.optimisation module] to give feedback when calling the [http://www.nmr-relax.com/manual/minimise_execute.html minimise.execute] or [http://www.nmr-relax.com/manual/minimise_calculate.html minimise.calculate] user functions. However this was run in the slave command run() method, hence would be executed on the slave. The problem is that [http://www.nmr-relax.com/api/4.0/specific_analyses.frame_order.optimisation-module.html#count_sobol_points count_sobol_points()] performs a number of checks on the current data pipe, however the slaves do not have any data pipes set up.
* Added the new 'atom_id' argument to the [http://www.nmr-relax.com/manual/frame_order_distribute.html frame_order.distribute user function]. This uses the new inverse selection functionality recently introduced into the trunk to delete all structural data not matching the atom_id from the copy of the loaded structural data string prior to generating the distribution of structures.
* Bug fix for the frame order target function (introduced recently). The copy.deepcopy() function is now used for all numpy input data to avoid the data from being modified between function calls. This is important for missing RDC and PCS data which is sent in as NaN values. In the [http://www.nmr-relax.com/api/4.0/target_functions.frame_order.Frame_order-class.html#__init__ target function __init__() method], the NaN values are replaced by 0.0 after the self.missing_rdc and self.missing_pcs structures have been by checking for NaN values. However the recent [http://www.nmr-relax.com/api/4.0/specific_analyses.frame_order.optimisation-module.html specific_analyses.frame_order.optimisation ] change in the [http://www.nmr-relax.com/api/4.0/specific_analyses.frame_order.optimisation.Frame_order_minimise_command-class.html Frame_order_minimise_command slave command] to printout the number of integration points resulted in the target function being initialised twice, causing all NaN values to be 0.0 in the second initialisation. Hence all missing data was being treated as real data with values of 0.0.
* Created a new skeleton chapter in the relax manual for the frame order analysis.
* Added a theory section to the new frame order chapter. This is taken from an in-preparation supplement.
* Removed the printout of pylint STDERR messages in the find_unused_imports.py developer script.
* Elimination of a number of wildcard imports from some frame order timing scripts. This is to avoid excessive function imports.
* Removal of an unused import from the [http://www.nmr-relax.com/api/4.0/user_functions.frame_order-module.html user_functions.frame_order module].
* Removal of unused imports from the test_suite/shared_data/frame_order/simulation scripts.
* Updated some unused frame order scripts to use the new minimise user function design.
* Unused import cleanup of all scripts in the test_suite/shared_data/dispersion/ directories. This both removes unused imports, or uncomments but deactivates temporarily unused code.
* Removed unused imports from the scripts in the test_suite/shared_data/frame_order subdirectories.
* Removed unused imports from the Spectrum [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.spectrum-module.html spectrum system test base module].* Removed unused imports from the Relax_disp [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.relax_disp-module.html relax_disp system test base module].
* Clean up of all unused imports in the system test scripts.
* Removed unused imports from the Structure [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.structure-module.html structure system test base module].* Changed how the import of [http://www.nmr-relax.com/api/4.0/lib.regex-module.html lib.regex ] in the Test_regex [http://www.nmr-relax.com/api/4.0/test_suite.unit_tests._lib.test_regex-module.html test_regex unit tests ] is used. The module is no longer stored in the TestCase class namespace, but is rather called directly within the unit test.* Changed the import of [http://www.nmr-relax.com/api/4.0/pipe_control.state-module.html pipe_control.state ] in the [http://www.nmr-relax.com/api/4.0/test_suite.unit_tests._pipe_control.test_state-module.html test_state unit test module].
* Removed unused imports from the unit tests.
* Added another exception to the find_unused_imports.py devel script. This is for the [http://www.nmr-relax.com/api/4.0/test_suite.unit_tests._lib._geometry.test_rotations -module .html test_suite.unit_tests._lib._geometry.test_rotations module] which programatically obtains the imports using globals().* Added a workaround or hack for exceptions for circular imports in the find_unused_imports.py script. This is currently for the [http://www.nmr-relax.com/api/4.0/test_suite.unit_tests._lib.test___init__ -module.html test_suite.unit_tests._lib.test___init__] and [http://www.nmr-relax.com/api/4.0/test_suite.unit_tests._lib._geometry.test___init__-module.html test_suite.unit_tests._lib._geometry.test___init__ ] modules.* Removal of unused imports from the [http://www.nmr-relax.com/api/4.0/test_suite.gui_tests-module.html GUI test modules].* Removed all unused imports from the [http://www.nmr-relax.com/api/4.0/pipe_control-module.html pipe_control package].* Added import exceptions for the [http://www.nmr-relax.com/api/4.0/lib.compat -module .html lib.compat module] in the find_unused_imports.py devel script.* Added import exceptions for the [http://www.nmr-relax.com/api/4.0/lib.xml -module .html lib.xml module] in the find_unused_imports.py devel script. These are needed because of eval() function calls on XML stored Python data structures.* Removed all unused imports from the [http://www.nmr-relax.com/api/4.0/lib-module.html relax library package].* Removed all unused imports from the [http://www.nmr-relax.com/api/4.0/target_functions-module.html target_functions package].
* Removed unused imports from the developer scripts.
* Removed all unused imports from the [http://www.nmr-relax.com/api/4.0/specific_analyses-module.html specific_analyses package].* Removed all unused imports from the [http://www.nmr-relax.com/api/4.0/auto_analyses-module.html auto_analyses package].
* Removed all unused imports from the numdifftools extern package.
* Removal of the last unused import from the [http://www.nmr-relax.com/api/4.0/target_functions-module.html target_functions package].
* Fix for the PCS system tests on old Python versions. The self.assertAlmostEqual() function cannot compare None values in earlier Python versions.
* MS Windows fix for the [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.frame_order.Frame_order-class.html#test_generate_rotor2_distribution Frame_order.test_generate_rotor2_distribution system test]. The locale.setlocale() function call for correctly setting up a spinning progress meter was failing on MS Windows. The error is now caught and the local setting skipped.
* Added Python 3.5 to the manual C module compilation script.
* Added Python 3.5 to the Python multiversion test suite script.