Author: bugman Date: Fri Feb 13 18:21:48 2015 New Revision: 27640 URL: http://svn.gna.org/viewcvs/relax?rev=27640&view=rev Log: Merged revisions 27635-27639 via svnmerge from svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk ........ r27635 | bugman | 2015-02-12 19:42:34 +0100 (Thu, 12 Feb 2015) | 10 lines Created new system tests for implementing new functionality for the structure.mean user function. This includes the Structure.test_mean_models and Structure.test_mean_molecules. The idea is to convert the user function to the new pipes/models/molecules/atom_id design. This will allow molecules with non-identical sequences and atomic compositions to be averaged. The set_mol_name and set_model_num arguments from the structure.read_pdb, structure.read_gaussian, and structure.read_xyz user functions will also be implemented to allow the mean structure to be stored alongside the other molecules. ........ r27636 | bugman | 2015-02-13 17:05:57 +0100 (Fri, 13 Feb 2015) | 3 lines Some fixes for the checks in the Structure.test_mean_molecules system test. ........ r27637 | bugman | 2015-02-13 17:06:35 +0100 (Fri, 13 Feb 2015) | 3 lines Fix for the structure.mean user function call in the Structure.test_mean_models system test. ........ r27638 | bugman | 2015-02-13 17:33:19 +0100 (Fri, 13 Feb 2015) | 7 lines Expanded the checking in all the Structure.test_mean* system tests to cover all atomic information. This includes the Structure.test_mean, Structure.test_mean_models, and Structure.test_mean_molecules system tests. All structural data is now carefully checked to make sure that the structure.mean user function operates correctly. ........ r27639 | bugman | 2015-02-13 17:45:08 +0100 (Fri, 13 Feb 2015) | 15 lines Converted the structure.mean user function to the new pipe/model/molecule/atom_id design. This allows the average structure calculation to work on atomic coordinates from different data pipes, different structural models, and different molecules. The user function backend uses the new pipe_control.structure.main.assemble_structural_coordinates() function to assemble the common atom coordinates, molecule names, residue names, residue numbers, atom names and elements. All this information is then used to construct a new molecule container for storing the average structure in the internal structural object. To allow for the averaged structural data to be stored, the internal structural object method add_coordinates() has been created. This is modelled on the PDB, Gaussian, and XYZ format loading methods. The internal structural object mean() method is no longer used, but remains for anyone who might have interest in the future (though as it is untested, bit-rot will be a problem). ........ Modified: branches/frame_order_cleanup/ (props changed) branches/frame_order_cleanup/lib/structure/internal/object.py branches/frame_order_cleanup/pipe_control/structure/main.py branches/frame_order_cleanup/test_suite/system_tests/structure.py branches/frame_order_cleanup/user_functions/structure.py [This mail would be too long, it was shortened to contain the URLs only.] Modified: branches/frame_order_cleanup/lib/structure/internal/object.py URL: http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/structure/internal/object.py?rev=27640&r1=27639&r2=27640&view=diff Modified: branches/frame_order_cleanup/pipe_control/structure/main.py URL: http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/structure/main.py?rev=27640&r1=27639&r2=27640&view=diff Modified: branches/frame_order_cleanup/test_suite/system_tests/structure.py URL: http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/structure.py?rev=27640&r1=27639&r2=27640&view=diff Modified: branches/frame_order_cleanup/user_functions/structure.py URL: http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/user_functions/structure.py?rev=27640&r1=27639&r2=27640&view=diff