Author: bugman Date: Thu Dec 11 18:23:48 2008 New Revision: 8197 URL: http://svn.gna.org/viewcvs/relax?rev=8197&view=rev Log: Merged revisions 8160,8180,8183,8186-8189,8191-8193 via svnmerge from svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3 ........ r8160 | bugman | 2008-12-08 14:47:42 +0100 (Mon, 08 Dec 2008) | 3 lines Renamed the noe.read() user function to noe.read_constraints(). ........ r8180 | bugman | 2008-12-10 14:15:47 +0100 (Wed, 10 Dec 2008) | 6 lines Bug fix for the vector_dist() function. The PyMOL structure loading command should not use the file root but the full file name!!! A few unused 'id' file root variables were also deleted. ........ r8183 | bugman | 2008-12-10 18:35:05 +0100 (Wed, 10 Dec 2008) | 3 lines Added a print out for the loading of PDB models. ........ r8186 | bugman | 2008-12-10 18:46:37 +0100 (Wed, 10 Dec 2008) | 3 lines Added tests of structure.load_spins() to all the structure system tests. ........ r8187 | bugman | 2008-12-11 10:33:32 +0100 (Thu, 11 Dec 2008) | 10 lines Partial fix for bug #12735 (https://gna.org/bugs/index.php?12735). The problem fixed here is that of the missing molecule container. This was caused by the weirdness of the Scientific python PDB reader splitting one modified lactose molecule into 2 molecules. The lactose part was unnamed, while the modifier was named after the residues 'UNK'. The generic_fns.mol_res_spin.return_molecule() function was having problems with this concept of the first molecule unnamed and the second named. This is now fixed and the unnamed molecule can be retrieved. ........ r8188 | bugman | 2008-12-11 10:53:22 +0100 (Thu, 11 Dec 2008) | 8 lines Another partial fix for bug #12735 (https://gna.org/bugs/index.php?12735). This problem was trigged by the internal reader (where the problem lies) together with the gromacs_phthalic_acid.pdb file. The issue was that the __fill_object_from_pdb() was operating on all structures currently loaded into relax. Hence with the 2 models of this PDB file, the first molecule had all the atoms of the first and second PDB models combined. ........ r8189 | bugman | 2008-12-11 11:14:00 +0100 (Thu, 11 Dec 2008) | 9 lines Final fixes for bug #12735 (https://gna.org/bugs/index.php?12735). The last problem was again triggered by the Scientific python PDB reader weirdness. Residues ending in '+' were being treated by the PDB reader as a different molecule. But then the molecule names LYS+, ARG+, etc. were causing problems as '+' was being treated as regular expression when matching molecule names. Therefore the '+' character has been stripped from all molecule, residue, and atom names. ........ r8191 | bugman | 2008-12-11 17:24:46 +0100 (Thu, 11 Dec 2008) | 8 lines Fixes for bug #12573 (https://gna.org/bugs/index.php?12573). This bug was reported by Jack Howarth (https://gna.org/users/jhowarth). The problem was simply that the optimisation checks are exact and had to be slightly modified for the Darwin kernel on 32 bit PowerPC. ........ r8192 | bugman | 2008-12-11 17:48:43 +0100 (Thu, 11 Dec 2008) | 11 lines Fixes for the 2 test_atom_loop_spin_selection2() unit tests. This problem was reported by Jack Howarth (https://gna.org/users/jhowarth) in the post at https://mail.gna.org/public/relax-users/2008-10/msg00089.html (Message-id: <20081024141150.GA879@xxxxxxxxxxxxxxxxx>). The problem was with the position array comparison as this was being converted to a string and then compared. The string representations of the numpy arrays is obviously different on the intel vs. powerpc chips. ........ r8193 | bugman | 2008-12-11 18:09:51 +0100 (Thu, 11 Dec 2008) | 10 lines Another PowerPC system test bug fix. This problem was reported by Jack Howarth (https://gna.org/users/jhowarth) in the post at https://mail.gna.org/public/relax-users/2008-10/msg00089.html (Message-id: <20081024141150.GA879@xxxxxxxxxxxxxxxxx>). The string.fromstring() function appears to be useless when switching between big and little endian machines. ........ Modified: branches/multi_processor_merge/ (props changed) branches/multi_processor_merge/generic_fns/mol_res_spin.py branches/multi_processor_merge/generic_fns/pymol.py branches/multi_processor_merge/generic_fns/structure/internal.py branches/multi_processor_merge/generic_fns/structure/main.py branches/multi_processor_merge/prompt/noe.py branches/multi_processor_merge/test_suite/system_tests/angles.py branches/multi_processor_merge/test_suite/system_tests/model_free.py branches/multi_processor_merge/test_suite/system_tests/structure.py branches/multi_processor_merge/test_suite/unit_tests/_generic_fns/_structure/test_internal.py branches/multi_processor_merge/test_suite/unit_tests/_generic_fns/_structure/test_scientific.py branches/multi_processor_merge/test_suite/unit_tests/_prompt/test_noe.py [This mail would be too long, it was shortened to contain the URLs only.] Modified: branches/multi_processor_merge/generic_fns/mol_res_spin.py URL: http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/generic_fns/mol_res_spin.py?rev=8197&r1=8196&r2=8197&view=diff Modified: branches/multi_processor_merge/generic_fns/pymol.py URL: http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/generic_fns/pymol.py?rev=8197&r1=8196&r2=8197&view=diff Modified: branches/multi_processor_merge/generic_fns/structure/internal.py URL: http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/generic_fns/structure/internal.py?rev=8197&r1=8196&r2=8197&view=diff Modified: branches/multi_processor_merge/generic_fns/structure/main.py URL: http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/generic_fns/structure/main.py?rev=8197&r1=8196&r2=8197&view=diff Modified: branches/multi_processor_merge/prompt/noe.py URL: http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/noe.py?rev=8197&r1=8196&r2=8197&view=diff Modified: branches/multi_processor_merge/test_suite/system_tests/angles.py URL: http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/test_suite/system_tests/angles.py?rev=8197&r1=8196&r2=8197&view=diff Modified: branches/multi_processor_merge/test_suite/system_tests/model_free.py URL: http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/test_suite/system_tests/model_free.py?rev=8197&r1=8196&r2=8197&view=diff Modified: branches/multi_processor_merge/test_suite/system_tests/structure.py URL: http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/test_suite/system_tests/structure.py?rev=8197&r1=8196&r2=8197&view=diff Modified: branches/multi_processor_merge/test_suite/unit_tests/_generic_fns/_structure/test_internal.py URL: http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/test_suite/unit_tests/_generic_fns/_structure/test_internal.py?rev=8197&r1=8196&r2=8197&view=diff Modified: branches/multi_processor_merge/test_suite/unit_tests/_generic_fns/_structure/test_scientific.py URL: http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/test_suite/unit_tests/_generic_fns/_structure/test_scientific.py?rev=8197&r1=8196&r2=8197&view=diff Modified: branches/multi_processor_merge/test_suite/unit_tests/_prompt/test_noe.py URL: http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/test_suite/unit_tests/_prompt/test_noe.py?rev=8197&r1=8196&r2=8197&view=diff