Author: semor Date: Thu Feb 5 16:28:33 2009 New Revision: 8747 URL: http://svn.gna.org/viewcvs/relax?rev=8747&view=rev Log: Merged revisions 8714,8717,8723,8725-8732,8734-8746 via svnmerge from svn+ssh://semor@xxxxxxxxxxx/svn/relax/1.3 ........ r8714 | bugman | 2009-02-02 04:58:41 -0500 (Mon, 02 Feb 2009) | 3 lines Added some printouts stating which file the relax saved state is placed in when in Debug mode. ........ r8717 | bugman | 2009-02-02 05:30:54 -0500 (Mon, 02 Feb 2009) | 11 lines Fixed an annoying bug in the RelaxError debugging mode. The problem here is that the relax state was being saved in the __init__() methods if in debug mode. The result was that in try statements which catch and allow for RelaxErrors, the relax state was being saved even though the error message and exception was suppressed. The fix was to shift the state saving code into the __str__() method. A side effect of this change is a simplification of all the RelaxError classes as the debug code is no longer duplicated in each class. ........ r8723 | bugman | 2009-02-03 12:05:58 -0500 (Tue, 03 Feb 2009) | 6 lines Wrote 2 new system tests for the new structural data design. In test_read_pdb_internal6(), 2 different structures are loaded as 2 molecules. In test_read_pdb_internal7(), 2 identical structures are loaded as 2 molecules. ........ r8725 | bugman | 2009-02-04 04:33:25 -0500 (Wed, 04 Feb 2009) | 3 lines Duplicated 5 systems tests of the internal PDB reader for the Scientific python PDB reader. ........ r8726 | bugman | 2009-02-04 04:37:40 -0500 (Wed, 04 Feb 2009) | 5 lines Bug fix for the load_pdb() method. When set_model_num is None, this is now handled properly. ........ r8727 | bugman | 2009-02-04 04:51:40 -0500 (Wed, 04 Feb 2009) | 6 lines Fixes for the test_read_pdb_mol_2_model_scientific() system test. The Scientific python PDB reader somehow decided to split the single structures in 'lactose_MCMM4_S1_*.pdb' into 2. ........ r8728 | bugman | 2009-02-04 09:55:49 -0500 (Wed, 04 Feb 2009) | 5 lines Fixes for the load_pdb() method. Previously loaded structures were not being taken into account. ........ r8729 | bugman | 2009-02-04 10:16:25 -0500 (Wed, 04 Feb 2009) | 5 lines More fixes for load_pdb(). Collapsing 2 models into 1 was failing. ........ r8730 | bugman | 2009-02-04 11:22:01 -0500 (Wed, 04 Feb 2009) | 5 lines Another fix for the load_pdb() method. The mol_offset value should be calculated at all times! ........ r8731 | bugman | 2009-02-04 11:22:38 -0500 (Wed, 04 Feb 2009) | 3 lines Added error checking to load_pdb() for when the number of molecules exceeds the set_mol_name list. ........ r8732 | bugman | 2009-02-04 11:24:47 -0500 (Wed, 04 Feb 2009) | 3 lines The read_mol arg now does something in load_pdb()!!! ........ r8734 | bugman | 2009-02-04 11:32:36 -0500 (Wed, 04 Feb 2009) | 6 lines Fix for the test_read_pdb_complex_scientific() system test. Retarded Scientific python splitting a perfectly good molecule into 2 when it can't recognise a residue type! ........ r8735 | bugman | 2009-02-05 04:00:21 -0500 (Thu, 05 Feb 2009) | 6 lines Modified test_read_pdb_internal1() to catch a molecule name identification bug. The test_read_pdb_scientific1() was similarly modified, but there is no bug in the Scientific python code. ........ r8736 | bugman | 2009-02-05 04:18:17 -0500 (Thu, 05 Feb 2009) | 5 lines Bug fix for the atom_loop() method. The molecule name was not being checked! ........ r8737 | bugman | 2009-02-05 04:22:02 -0500 (Thu, 05 Feb 2009) | 3 lines Added a check for the molecule name. ........ r8738 | bugman | 2009-02-05 04:22:35 -0500 (Thu, 05 Feb 2009) | 3 lines Modified a print out to make it clearer. ........ r8739 | bugman | 2009-02-05 05:30:37 -0500 (Thu, 05 Feb 2009) | 3 lines Modified the get_pipe() function to check if a data pipe exists. ........ r8740 | bugman | 2009-02-05 05:43:43 -0500 (Thu, 05 Feb 2009) | 3 lines Modified 2 system tests for the loading of N-Ca vectors. ........ r8741 | bugman | 2009-02-05 08:41:36 -0500 (Thu, 05 Feb 2009) | 22 lines Massive speed up of the bond_vectors() method. The algorithm used was very, very poorly designed. Now when setting the profile flag to 1 gives the following. Before in one test: 11168736 function calls (10986641 primitive calls) in 76.750 CPU seconds ncalls tottime percall cumtime percall filename:lineno(function) 758954 12.160 0.000 51.060 0.000 /home/edau/relax/relax-1.3/generic_fns/relax_re.py:31(search) 141 0.890 0.006 67.620 0.480 /home/edau/relax/relax-1.3/generic_fns/structure/internal.py:444(bond_vectors) All other function call info lines have been removed. After the changes: 2586419 function calls (2579305 primitive calls) in 21.370 CPU seconds ncalls tottime percall cumtime percall filename:lineno(function) 62803 1.180 0.000 5.020 0.000 /home/edau/relax/relax-1.3/generic_fns/relax_re.py:31(search) 141 0.060 0.000 12.020 0.085 /home/edau/relax/relax-1.3/generic_fns/structure/internal.py:444(bond_vectors) The difference is that the selection object is no longer used, as it is completely unnecessary. ........ r8742 | bugman | 2009-02-05 08:42:51 -0500 (Thu, 05 Feb 2009) | 3 lines Modified the base API bond_vectors() method. ........ r8743 | bugman | 2009-02-05 08:46:28 -0500 (Thu, 05 Feb 2009) | 3 lines Added the atoms 'NZ' and 'OH' as nitrogens and oxygens of amino acids respectively. ........ r8744 | bugman | 2009-02-05 08:54:50 -0500 (Thu, 05 Feb 2009) | 8 lines Fixes for the bond_vectors() method. The atom_id string is now generated as it is no longer passed in. This is a temporary fix and this function is very inefficient, just as the internal object bond_vectors() method was (which was fixed in r8741). ........ r8745 | bugman | 2009-02-05 09:00:36 -0500 (Thu, 05 Feb 2009) | 5 lines Fix for the test_read_pdb_scientific1() system test. The current data pipe was not aliased. ........ r8746 | bugman | 2009-02-05 09:03:40 -0500 (Thu, 05 Feb 2009) | 3 lines Removed some debugging print statements. ........ Modified: branches/relax_disp/ (props changed) branches/relax_disp/generic_fns/pipes.py branches/relax_disp/generic_fns/structure/api_base.py branches/relax_disp/generic_fns/structure/internal.py branches/relax_disp/generic_fns/structure/main.py branches/relax_disp/generic_fns/structure/scientific.py branches/relax_disp/relax_errors.py branches/relax_disp/test_suite/system_tests/structure.py [This mail would be too long, it was shortened to contain the URLs only.] Modified: branches/relax_disp/generic_fns/pipes.py URL: http://svn.gna.org/viewcvs/relax/branches/relax_disp/generic_fns/pipes.py?rev=8747&r1=8746&r2=8747&view=diff Modified: branches/relax_disp/generic_fns/structure/api_base.py URL: http://svn.gna.org/viewcvs/relax/branches/relax_disp/generic_fns/structure/api_base.py?rev=8747&r1=8746&r2=8747&view=diff Modified: branches/relax_disp/generic_fns/structure/internal.py URL: http://svn.gna.org/viewcvs/relax/branches/relax_disp/generic_fns/structure/internal.py?rev=8747&r1=8746&r2=8747&view=diff Modified: branches/relax_disp/generic_fns/structure/main.py URL: http://svn.gna.org/viewcvs/relax/branches/relax_disp/generic_fns/structure/main.py?rev=8747&r1=8746&r2=8747&view=diff Modified: branches/relax_disp/generic_fns/structure/scientific.py URL: http://svn.gna.org/viewcvs/relax/branches/relax_disp/generic_fns/structure/scientific.py?rev=8747&r1=8746&r2=8747&view=diff Modified: branches/relax_disp/relax_errors.py URL: http://svn.gna.org/viewcvs/relax/branches/relax_disp/relax_errors.py?rev=8747&r1=8746&r2=8747&view=diff Modified: branches/relax_disp/test_suite/system_tests/structure.py URL: http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/structure.py?rev=8747&r1=8746&r2=8747&view=diff