Author: bugman Date: Tue Apr 28 14:28:05 2009 New Revision: 9020 URL: http://svn.gna.org/viewcvs/relax?rev=9020&view=rev Log: Merged revisions 8162-8179,8181-8182,8643-8655,8657-8668,8671-8672,8674,8677,8679-8680,8689-8695,8700-8701,8710-8713,8716,9005-9009,9013 via svnmerge from svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/ave_noe ........ r8162 | bugman | 2008-12-08 16:41:32 +0100 (Mon, 08 Dec 2008) | 5 lines Fix for the noe.read_constraints() user function. The noe object is called noe_obj. ........ r8163 | bugman | 2008-12-08 16:46:53 +0100 (Mon, 08 Dec 2008) | 7 lines The noe.read_constraints() user function now calls generic_fns.noesy.read_constraints(). The noe user functions need not all point to the specific NOE object! Maybe later the steady-state NOE can be separated from the NOESY, but for now it isn't too illogical for both to be in the same user function class. ........ r8164 | bugman | 2008-12-08 16:48:34 +0100 (Mon, 08 Dec 2008) | 3 lines Created an empty module for NOESY data. ........ r8165 | bugman | 2008-12-09 10:30:36 +0100 (Tue, 09 Dec 2008) | 3 lines Wrote a stub function generic_fns.noesy.read_constraints(). ........ r8166 | bugman | 2008-12-09 10:37:16 +0100 (Tue, 09 Dec 2008) | 3 lines Added a directory to the test-suite for holding NOE restraint data. ........ r8167 | bugman | 2008-12-09 10:39:00 +0100 (Tue, 09 Dec 2008) | 5 lines Added an RNA H-bond Xplor restraint file. This comes from http://bass.chem.yale.edu/labdocs/packages/xplor.html. ........ r8168 | bugman | 2008-12-09 10:45:58 +0100 (Tue, 09 Dec 2008) | 5 lines Added the system test framework for NOE restraint reading tests. This includes one test for the reading of RNA H-bond restraints from an Xplor formatted input file. ........ r8169 | bugman | 2008-12-09 10:47:29 +0100 (Tue, 09 Dec 2008) | 3 lines Renamed 'constraints' to 'restraints' for the NOEs. ........ r8170 | bugman | 2008-12-09 11:04:24 +0100 (Tue, 09 Dec 2008) | 3 lines The RNA sequence of the noe_rna_hbond.dat file is now generated through a new class method. ........ r8171 | bugman | 2008-12-09 11:06:01 +0100 (Tue, 09 Dec 2008) | 3 lines Renamed all the noe.read_constraints() references in the unit tests to noe.read_restraints(). ........ r8172 | bugman | 2008-12-09 13:31:47 +0100 (Tue, 09 Dec 2008) | 5 lines Completed the test_read_xplor_rna() system test. Checks for the restraint list have now been added. ........ r8173 | bugman | 2008-12-09 13:32:57 +0100 (Tue, 09 Dec 2008) | 3 lines Activated the Noe_restraints system test framework. ........ r8174 | bugman | 2008-12-09 13:33:19 +0100 (Tue, 09 Dec 2008) | 3 lines Bug fix in the rna_seq() method. ........ r8175 | bugman | 2008-12-09 13:36:17 +0100 (Tue, 09 Dec 2008) | 3 lines Another bug fix for the rna_seq() sequence generation method. ........ r8176 | bugman | 2008-12-09 13:49:38 +0100 (Tue, 09 Dec 2008) | 3 lines Final fixes for the rna_seq() sequence generation method. ........ r8177 | bugman | 2008-12-09 13:50:30 +0100 (Tue, 09 Dec 2008) | 3 lines Fix for the call to noe.read_restraints() in test_read_xplor_rna(). ........ r8178 | bugman | 2008-12-09 13:57:32 +0100 (Tue, 09 Dec 2008) | 3 lines Removed the non-existent frq arg and a docstring clarification about the relax formatted file. ........ r8179 | bugman | 2008-12-09 14:02:53 +0100 (Tue, 09 Dec 2008) | 3 lines Missing import! ........ r8181 | bugman | 2008-12-10 14:30:44 +0100 (Wed, 10 Dec 2008) | 3 lines Added a missing import. ........ r8182 | bugman | 2008-12-10 15:18:38 +0100 (Wed, 10 Dec 2008) | 3 lines Added some more code to the read_restraints() function. ........ r8643 | bugman | 2009-01-26 11:52:11 +0100 (Mon, 26 Jan 2009) | 3 lines Wrote the __file_format() function for determining the NOE restraint file format. ........ r8644 | bugman | 2009-01-26 13:30:06 +0100 (Mon, 26 Jan 2009) | 3 lines The non-implemented function generic_fns.xplor.parse_noe_restraints() is now being called. ........ r8645 | bugman | 2009-01-26 13:44:06 +0100 (Mon, 26 Jan 2009) | 3 lines Reverted to calling file.readlines() rather than file.read(). ........ r8646 | bugman | 2009-01-26 15:01:10 +0100 (Mon, 26 Jan 2009) | 6 lines Created the Xplor module for handling Xplor formatted files. The function parse_noe_restraints() has been added to parse the NOE restraints. The function strip_comments() has been written to remove Xplor comments from the input data. ........ r8647 | bugman | 2009-01-26 15:24:53 +0100 (Mon, 26 Jan 2009) | 3 lines Created __convert_to_id() to convert from Xplor atom string to relax atom id. ........ r8648 | bugman | 2009-01-26 15:31:05 +0100 (Mon, 26 Jan 2009) | 3 lines Added checks to make sure spin containers corresponding to the Xplor atom strings exist. ........ r8649 | bugman | 2009-01-26 16:26:45 +0100 (Mon, 26 Jan 2009) | 3 lines Typo fix. 'H4' should have been 'N4'! ........ r8650 | bugman | 2009-01-26 16:32:49 +0100 (Mon, 26 Jan 2009) | 3 lines The NOE restraints are now stored in the current data pipe. ........ r8651 | bugman | 2009-01-26 16:39:22 +0100 (Mon, 26 Jan 2009) | 3 lines Fixes for the test_read_xplor_rna() system test. ........ r8652 | bugman | 2009-01-26 16:40:32 +0100 (Mon, 26 Jan 2009) | 5 lines Modified the NOE restraint list so that some restraints are spread across 2 lines. This should test the Xplor parsing code better. ........ r8653 | bugman | 2009-01-26 16:42:12 +0100 (Mon, 26 Jan 2009) | 5 lines Bug fix for the parse_noe_restraints() function. Xplor restraints spread across 2 lines are now properly handled. ........ r8654 | bugman | 2009-01-26 16:43:23 +0100 (Mon, 26 Jan 2009) | 3 lines Added a few comments to test the Xplor parsing even more. ........ r8655 | bugman | 2009-01-26 18:44:13 +0100 (Mon, 26 Jan 2009) | 3 lines Shifted the checks of the atom id strings from the Xplor parser to the NOE restraint reading fn. ........ r8657 | bugman | 2009-01-27 09:35:53 +0100 (Tue, 27 Jan 2009) | 3 lines Missing RelaxError import. ........ r8658 | bugman | 2009-01-27 09:44:38 +0100 (Tue, 27 Jan 2009) | 3 lines Added some test NOEs, in a generic formatted file, for phthalic acid and testing the NOE reading. ........ r8659 | bugman | 2009-01-27 10:01:41 +0100 (Tue, 27 Jan 2009) | 3 lines Created a system test for the reading of a generically formatted NOE restraint file. ........ r8660 | bugman | 2009-01-27 10:15:15 +0100 (Tue, 27 Jan 2009) | 3 lines Removed an unused import. ........ r8661 | bugman | 2009-01-27 10:16:04 +0100 (Tue, 27 Jan 2009) | 3 lines The generically formatted NOE restraint file is now being parsed. ........ r8662 | bugman | 2009-01-27 11:10:45 +0100 (Tue, 27 Jan 2009) | 3 lines Modified the phthalic acid NOE restraint reading test to include pseudo-atoms. ........ r8663 | bugman | 2009-01-27 13:45:15 +0100 (Tue, 27 Jan 2009) | 3 lines Removed the '@' from the pseudo-atom spin names. ........ r8664 | bugman | 2009-01-27 13:47:35 +0100 (Tue, 27 Jan 2009) | 3 lines Wrote a unit test for the creation of pseudo-atom spin containers. ........ r8665 | bugman | 2009-01-27 13:55:57 +0100 (Tue, 27 Jan 2009) | 3 lines Wrote 5 arg unit tests for the spin.create_pseudo() user function. ........ r8666 | bugman | 2009-01-27 14:00:37 +0100 (Tue, 27 Jan 2009) | 3 lines Wrote the interface for the spin.create_pseudo() user function. ........ r8667 | bugman | 2009-01-27 14:03:18 +0100 (Tue, 27 Jan 2009) | 3 lines Fixes for the arg unit tests of spin.create_pseudo(). ........ r8668 | bugman | 2009-01-27 14:06:13 +0100 (Tue, 27 Jan 2009) | 3 lines Imported the non-existant create_pseudo_spin() function. ........ r8671 | bugman | 2009-01-27 16:14:22 +0100 (Tue, 27 Jan 2009) | 3 lines Wrote the create_pseudo_spin() and __linear_ave() functions for pseudo-atom support. ........ r8672 | bugman | 2009-01-27 16:17:07 +0100 (Tue, 27 Jan 2009) | 5 lines Fix for the phthalic acid NOE restraint reading system test. Pseudo-atom creation was not correctly called. ........ r8674 | bugman | 2009-01-27 16:27:54 +0100 (Tue, 27 Jan 2009) | 3 lines Fixes for the create_pseudo_spin() and __linear_ave() functions. ........ r8677 | bugman | 2009-01-27 16:41:23 +0100 (Tue, 27 Jan 2009) | 3 lines Fixes for the 2 test_create_pseudo_spin() unit tests. ........ r8679 | bugman | 2009-01-27 16:49:58 +0100 (Tue, 27 Jan 2009) | 3 lines Fixes for the test_create_pseudo_spin() unit test. The atomic positions are now set. ........ r8680 | bugman | 2009-01-27 16:51:47 +0100 (Tue, 27 Jan 2009) | 3 lines The __linear_ave() now handles the coordinates as numpy arrays. ........ r8689 | bugman | 2009-01-28 11:24:04 +0100 (Wed, 28 Jan 2009) | 3 lines Added some more checks for the test_create_pseudo_spin() unit test. ........ r8690 | bugman | 2009-01-28 11:30:24 +0100 (Wed, 28 Jan 2009) | 3 lines Wrote a second unit test for the creation of a pseudo-spin. ........ r8691 | bugman | 2009-01-28 11:38:57 +0100 (Wed, 28 Jan 2009) | 3 lines Modified the checks for the pseudo-spin creation unit tests. ........ r8692 | bugman | 2009-01-28 11:40:14 +0100 (Wed, 28 Jan 2009) | 5 lines The pseudo-spin name and number is now stored in the member spin containers. This gives a mapping between from the spin to the pseudo-spin. ........ r8693 | bugman | 2009-01-28 11:40:50 +0100 (Wed, 28 Jan 2009) | 3 lines Fixes for test_create_pseudo_spin() and test_create_pseudo_spin2(). ........ r8694 | bugman | 2009-01-28 11:41:27 +0100 (Wed, 28 Jan 2009) | 3 lines One more fix for test_create_pseudo_spin(). ........ r8695 | bugman | 2009-01-28 11:42:32 +0100 (Wed, 28 Jan 2009) | 3 lines The members list is now stored in the pseudo-spin to map this to the respective spin containers. ........ r8700 | bugman | 2009-01-29 09:42:21 +0100 (Thu, 29 Jan 2009) | 3 lines Added a call to calc() to test the quadratic potential calculation. ........ r8701 | bugman | 2009-01-29 16:40:07 +0100 (Thu, 29 Jan 2009) | 5 lines Created a module for calculating different optimisation/energy potentials. The function quad_pot() has been written to provide a flat-bottom potential. ........ r8710 | bugman | 2009-02-02 10:44:48 +0100 (Mon, 02 Feb 2009) | 3 lines Added tests for the existence of the current data pipe. ........ r8711 | bugman | 2009-02-02 10:49:06 +0100 (Mon, 02 Feb 2009) | 3 lines Modified the RelaxNoModelError print out to be more informative, especially for the N-state model. ........ r8712 | bugman | 2009-02-02 10:51:17 +0100 (Mon, 02 Feb 2009) | 3 lines Added the start of the calculate() method. ........ r8713 | bugman | 2009-02-02 10:51:45 +0100 (Mon, 02 Feb 2009) | 3 lines The N-state model is now selected in the NOESY system test. ........ r8716 | bugman | 2009-02-02 11:05:21 +0100 (Mon, 02 Feb 2009) | 3 lines Modified __base_data_types() to include NOE restraints. ........ r9005 | bugman | 2009-04-09 19:33:13 +0200 (Thu, 09 Apr 2009) | 3 lines Fixed the calls to generic_fns.mol_res_spin.spin.create() function. ........ r9006 | bugman | 2009-04-09 19:46:04 +0200 (Thu, 09 Apr 2009) | 5 lines Fix for the rna_seq() method. The create_residue() and create_molecule() functions were being incorrectly called. ........ r9007 | bugman | 2009-04-10 20:43:00 +0200 (Fri, 10 Apr 2009) | 5 lines Added the calc_ave_dist() method. This doesn't work yet and has been cut and paste from an external relax script. ........ r9008 | bugman | 2009-04-15 11:46:03 +0200 (Wed, 15 Apr 2009) | 3 lines Completed the calculate() and calc_ave_dist() methods for the dynamically averaged NOE analysis. ........ r9009 | bugman | 2009-04-15 14:04:02 +0200 (Wed, 15 Apr 2009) | 3 lines Bug fix in the calc_ave_dist() method for multiple models. ........ r9013 | bugman | 2009-04-15 17:06:54 +0200 (Wed, 15 Apr 2009) | 5 lines Bug fix for the calc_ave_dist() method. The negative of the exponential was being used! ........ Added: 1.3/generic_fns/noesy.py - copied, changed from r8182, branches/ave_noe/generic_fns/noesy.py 1.3/generic_fns/xplor.py - copied unchanged from r8680, branches/ave_noe/generic_fns/xplor.py 1.3/maths_fns/potential.py - copied unchanged from r8713, branches/ave_noe/maths_fns/potential.py 1.3/test_suite/shared_data/noe_restraints/ - copied from r8182, branches/ave_noe/test_suite/shared_data/noe_restraints/ 1.3/test_suite/shared_data/noe_restraints/phthalic_acid - copied unchanged from r8680, branches/ave_noe/test_suite/shared_data/noe_restraints/phthalic_acid 1.3/test_suite/system_tests/noe_restraints.py - copied, changed from r8182, branches/ave_noe/test_suite/system_tests/noe_restraints.py 1.3/test_suite/system_tests/scripts/phthalic_acid_noes.py - copied, changed from r8680, branches/ave_noe/test_suite/system_tests/scripts/phthalic_acid_noes.py Modified: 1.3/ (props changed) 1.3/generic_fns/minimise.py 1.3/generic_fns/mol_res_spin.py 1.3/prompt/noe.py 1.3/prompt/spin.py 1.3/specific_fns/n_state_model.py 1.3/test_suite/shared_data/noe_restraints/noe_rna_hbond.dat 1.3/test_suite/system_tests/__init__.py 1.3/test_suite/unit_tests/_generic_fns/spin.py 1.3/test_suite/unit_tests/_prompt/test_noe.py 1.3/test_suite/unit_tests/_prompt/test_spin.py 1.3/test_suite/unit_tests/spin_testing_base.py [This mail would be too long, it was shortened to contain the URLs only.] Modified: 1.3/generic_fns/minimise.py URL: http://svn.gna.org/viewcvs/relax/1.3/generic_fns/minimise.py?rev=9020&r1=9019&r2=9020&view=diff Modified: 1.3/generic_fns/mol_res_spin.py URL: http://svn.gna.org/viewcvs/relax/1.3/generic_fns/mol_res_spin.py?rev=9020&r1=9019&r2=9020&view=diff Copied: 1.3/generic_fns/noesy.py (from r8182, branches/ave_noe/generic_fns/noesy.py) URL: http://svn.gna.org/viewcvs/relax/1.3/generic_fns/noesy.py?p2=1.3/generic_fns/noesy.py&p1=branches/ave_noe/generic_fns/noesy.py&r1=8182&r2=9020&rev=9020&view=diff Modified: 1.3/prompt/noe.py URL: http://svn.gna.org/viewcvs/relax/1.3/prompt/noe.py?rev=9020&r1=9019&r2=9020&view=diff Modified: 1.3/prompt/spin.py URL: http://svn.gna.org/viewcvs/relax/1.3/prompt/spin.py?rev=9020&r1=9019&r2=9020&view=diff Modified: 1.3/specific_fns/n_state_model.py URL: http://svn.gna.org/viewcvs/relax/1.3/specific_fns/n_state_model.py?rev=9020&r1=9019&r2=9020&view=diff Modified: 1.3/test_suite/shared_data/noe_restraints/noe_rna_hbond.dat URL: http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/noe_restraints/noe_rna_hbond.dat?rev=9020&r1=8182&r2=9020&view=diff Modified: 1.3/test_suite/system_tests/__init__.py URL: http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/__init__.py?rev=9020&r1=9019&r2=9020&view=diff Copied: 1.3/test_suite/system_tests/noe_restraints.py (from r8182, branches/ave_noe/test_suite/system_tests/noe_restraints.py) URL: http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/noe_restraints.py?p2=1.3/test_suite/system_tests/noe_restraints.py&p1=branches/ave_noe/test_suite/system_tests/noe_restraints.py&r1=8182&r2=9020&rev=9020&view=diff Copied: 1.3/test_suite/system_tests/scripts/phthalic_acid_noes.py (from r8680, branches/ave_noe/test_suite/system_tests/scripts/phthalic_acid_noes.py) URL: http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/phthalic_acid_noes.py?p2=1.3/test_suite/system_tests/scripts/phthalic_acid_noes.py&p1=branches/ave_noe/test_suite/system_tests/scripts/phthalic_acid_noes.py&r1=8680&r2=9020&rev=9020&view=diff Modified: 1.3/test_suite/unit_tests/_generic_fns/spin.py URL: http://svn.gna.org/viewcvs/relax/1.3/test_suite/unit_tests/_generic_fns/spin.py?rev=9020&r1=9019&r2=9020&view=diff Modified: 1.3/test_suite/unit_tests/_prompt/test_noe.py URL: http://svn.gna.org/viewcvs/relax/1.3/test_suite/unit_tests/_prompt/test_noe.py?rev=9020&r1=9019&r2=9020&view=diff Modified: 1.3/test_suite/unit_tests/_prompt/test_spin.py URL: http://svn.gna.org/viewcvs/relax/1.3/test_suite/unit_tests/_prompt/test_spin.py?rev=9020&r1=9019&r2=9020&view=diff Modified: 1.3/test_suite/unit_tests/spin_testing_base.py URL: http://svn.gna.org/viewcvs/relax/1.3/test_suite/unit_tests/spin_testing_base.py?rev=9020&r1=9019&r2=9020&view=diff