Author: bugman Date: Sun Oct 9 16:40:17 2011 New Revision: 14818 URL: http://svn.gna.org/viewcvs/relax?rev=14818&view=rev Log: Merged revisions 13983-13984,14008-14009,14011,14013,14071,14103,14107-14110,14146,14157,14179,14181,14185,14249,14262,14285,14292,14324,14329,14331,14333,14335-14336,14338,14341-14343,14347-14352,14354-14355,14361-14366,14372,14374,14376,14386-14388,14390-14391,14396,14401,14404,14406,14409,14416,14418-14420,14422-14423,14425,14428-14429,14431,14433,14436-14442,14446-14447,14455-14456,14460-14464,14467-14468,14470-14472,14475,14477-14497,14499-14816 via svnmerge from svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3 ................ r13983 | bugman | 2011-07-29 09:59:57 +0200 (Fri, 29 Jul 2011) | 3 lines Created a basic system test checking the reading of a non-PDB file by structure.read_pdb. ................ r13984 | bugman | 2011-07-29 10:06:14 +0200 (Fri, 29 Jul 2011) | 5 lines Fix for structure.read_pdb for when the file contains no PDB data. This is now caught, and a warning is given and the function exists cleanly. ................ r14008 | bugman | 2011-07-29 18:36:30 +0200 (Fri, 29 Jul 2011) | 3 lines Shifted the pedantic flag into the status object. ................ r14009 | bugman | 2011-07-29 18:37:15 +0200 (Fri, 29 Jul 2011) | 3 lines RelaxWarnings now only show a traceback when the pedantic flag is True. ................ r14011 | bugman | 2011-07-29 19:01:35 +0200 (Fri, 29 Jul 2011) | 5 lines The relax state is now saved on a RelaxError when the pedantic rather than debugging flag is turned on. As both flags can be given, this allows for this state saving to be activated or deactivated. ................ r14013 | bugman | 2011-07-29 19:08:13 +0200 (Fri, 29 Jul 2011) | 3 lines The relax_io.read_spin_data() function no longer skips short lines so that a warning is given for it. ................ r14071 | bugman | 2011-08-02 16:54:53 +0200 (Tue, 02 Aug 2011) | 5 lines generic_fns.sequence.validate_sequence() now also checks for the spin ID, data and error columns. This is now used by relax_io.read_spin_data(). ................ r14103 | bugman | 2011-08-04 11:08:58 +0200 (Thu, 04 Aug 2011) | 6 lines Fix for the RelaxWarning system on Mac OS X, the base class __str__ method now returns a simple string. On a Mac, the warning message text was in unicode whereas the __str__() method must return a standard string. So now __str__() is using the str() method to convert. ................ r14107 | bugman | 2011-08-04 11:37:57 +0200 (Thu, 04 Aug 2011) | 6 lines Files created by the grace.write user function are now put into a new list cdp.results_files. This is a list of lists, with the sublist composed of two elements. The first is an identifier string such as 'grace'. The second is the file name. ................ r14108 | bugman | 2011-08-04 11:39:43 +0200 (Thu, 04 Aug 2011) | 3 lines Fix for the addition of grace files to cdp.result_files - the file path is now used. ................ r14109 | bugman | 2011-08-04 11:41:13 +0200 (Thu, 04 Aug 2011) | 5 lines Another fix for the grace.write user function addition to the cdp.result_files list. The proper variable name is now used. ................ r14110 | bugman | 2011-08-04 11:41:31 +0200 (Thu, 04 Aug 2011) | 3 lines The value.write user function now also adds to the cdp.result_files structure. ................ r14146 | bugman | 2011-08-04 18:08:13 +0200 (Thu, 04 Aug 2011) | 5 lines Fix for the structure.vectors user function. It no longer complains about a PDB already loaded when no PDB has been loaded. ................ r14157 | bugman | 2011-08-04 20:24:02 +0200 (Thu, 04 Aug 2011) | 6 lines Modified the execution lock to have a mode. This allows for greater control and avoid string comparison of names to determine if a script or auto-analysis acquired the lock. ................ r14179 | bugman | 2011-08-05 15:01:19 +0200 (Fri, 05 Aug 2011) | 5 lines The dauvergne_protocol is now more robust if the program is interrupted and restarted later. The opt/results.bz2 file is now searched for, and if not the round is assumed incomplete. ................ r14181 | bugman | 2011-08-05 15:40:08 +0200 (Fri, 05 Aug 2011) | 5 lines Fix for the resetting of the global optimisation round in the dauvergne_protocol auto-analysis. The value was being reset to None at every round. ................ r14185 | bugman | 2011-08-05 15:50:37 +0200 (Fri, 05 Aug 2011) | 5 lines Fix for the round determination in the dauvergne_protocol auto-analysis. The 'opt' directory was missing in the path. ................ r14249 | bugman | 2011-08-08 11:12:46 +0200 (Mon, 08 Aug 2011) | 6 lines Bug fix for the saving/loading of a results file in GUI mode. The save files were containing the ds.relax_gui object and restoring it on loading. This caused the data storage of the GUI to change underneath the GUI resulting in a crash or race conditions. ................ r14262 | bugman | 2011-08-08 17:10:15 +0200 (Mon, 08 Aug 2011) | 6 lines Bug fix for the resetting of the relax data store - the cdp structure is now set to None. Previously the data store would be cleared, but the __builtin__.cdp structure would point to the old current data pipe, keeping it in existence. ................ r14285 | bugman | 2011-08-09 12:07:39 +0200 (Tue, 09 Aug 2011) | 3 lines The pymol.tensor_pdb() user function now shows the diffusion tensor using PyMOL sticks. ................ r14292 | bugman | 2011-08-09 14:42:06 +0200 (Tue, 09 Aug 2011) | 3 lines Bug fix for the xydxdy type Grace graphs - the dx data was not being placed in the file. ................ r14324 | bugman | 2011-08-10 22:05:58 +0200 (Wed, 10 Aug 2011) | 6 lines Bug fix for the structure.create_diff_tensor_pdb user function for when no element info is available. These atoms where the element is not in the PDB file or cannot be determined should have been skipped. ................ r14329 | bugman | 2011-08-11 08:45:10 +0200 (Thu, 11 Aug 2011) | 3 lines Bug fix for the molmol macro user functions - one of the args 'param' should have been 'data_type'. ................ r14331 | bugman | 2011-08-11 08:49:24 +0200 (Thu, 11 Aug 2011) | 5 lines Bug fix for the spin_loop() calls when generating Molmol macros. The full_info argument should have been set to True. ................ r14333 | bugman | 2011-08-11 10:08:26 +0200 (Thu, 11 Aug 2011) | 3 lines Fix for the molmol.write macro creation user function - the file arg can be None! ................ r14335 | bugman | 2011-08-11 10:13:18 +0200 (Thu, 11 Aug 2011) | 6 lines Bug fix for the molmol.write user function for model-free parameters. Some of the parameters were using the ancient self.relax code path which was eliminated with the redesign of relax 1.2 to 1.3. ................ r14336 | bugman | 2011-08-11 10:16:24 +0200 (Thu, 11 Aug 2011) | 5 lines Fixes for the old scripts/optimisation_testing.py script. This was also using the ancient self.relax code path. ................ r14338 | bugman | 2011-08-11 10:20:12 +0200 (Thu, 11 Aug 2011) | 3 lines Fix for the molmol macro of the ts parameter, the spin container variable was spelt incorrectly. ................ r14341 | bugman | 2011-08-11 10:57:24 +0200 (Thu, 11 Aug 2011) | 3 lines Initialized merge tracking via "svnmerge" with revisions "1-12831" from svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/xyz ................ r14342 | bugman | 2011-08-11 11:05:46 +0200 (Thu, 11 Aug 2011) | 967 lines Merged revisions 12942,12946,12953,12958,12968,13061,13082,13089-13091,13106,13109-13110,13121-13122,13162-13165,13167,13169,13179-13180,13211,13214-13215,13227,13234-13235,13239,13245-13246,13249,13414-13417,13891,13894,13900,13924,13931,13933-13934,13944,13947,14038 via svnmerge from svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/xyz ................ r12942 | bugman | 2011-06-09 18:49:18 +0200 (Thu, 09 Jun 2011) | 10 lines Creation of a new system test test_read_xyz_internal1(). This is Han's patch http://gna.org/task/download.php?file_id=13143 attached to the task http://gna.org/task/?7404. In order to create a system test for reading the xyz file, a new function 'test_read_xyz_internal1()' has been generated in the xyz/test_suite/system_tests/structure.py. It is based on the function 'test_read_pdb_internal1()'. ................ r12946 | bugman | 2011-06-09 20:02:09 +0200 (Thu, 09 Jun 2011) | 9 lines Modifying the function test 'test_read_xyz_internal1()'. This is Han's patch https://gna.org/task/download.php?file_id=13144 attached to the task http://gna.org/task/?7404. The function 'test_read_xyz_internal1()' was modified so that it is more specific to the XYZ file added to relax and for the new XYZ reader. ................ r12953 | bugman | 2011-06-10 11:14:46 +0200 (Fri, 10 Jun 2011) | 8 lines Modifying the function test 'test_read_xyz_internal1()'. This is Han's patch https://gna.org/task/download.php?file_id=13147 attached to the task http://gna.org/task/?7404. In the 'test_read_xyz_internal1()' option parser='internal' has been removed. ................ r12958 | bugman | 2011-06-10 12:13:16 +0200 (Fri, 10 Jun 2011) | 9 lines Generating new user function 'read_xyz()'. This is Han's patch https://gna.org/task/download.php?file_id=13148 attached to the task http://gna.org/task/?7404. The user function 'read_xyz()' was generated in the prompt/structure.py by duplication of 'read_pdb()' and modified accordingly. ................ r12968 | bugman | 2011-06-10 15:08:46 +0200 (Fri, 10 Jun 2011) | 9 lines Generating new user function 'read_xyz()'. This is Han's patch https://gna.org/task/download.php?file_id=13153 attached to the task http://gna.org/task/?7404. The user function 'read_xyz()' was generated and modified in the generic_fns/structure/main.py based on the function 'read_pdb()'. ................ r13061 | bugman | 2011-06-16 11:37:42 +0200 (Thu, 16 Jun 2011) | 11 lines Adding a new test xyz file. This is Han's patch https://gna.org/task/download.php?file_id=13224 attached to the task http://gna.org/task/?7404. This is a new xyz file, which contains several different models. This file should be put in the directory: test_suite/shared_data/structures. ................ r13082 | bugman | 2011-06-17 10:38:40 +0200 (Fri, 17 Jun 2011) | 8 lines Modifying the user function 'read_xyz()'. This is Han's patch https://gna.org/task/download.php?file_id=13243 attached to the task http://gna.org/task/?7404. In the user function generic_fns/structure/main.py a single blank line was removed. ................ r13089 | bugman | 2011-06-17 11:17:27 +0200 (Fri, 17 Jun 2011) | 9 lines Modifying test_suite/shared_data/structures/Indol_test.xyz This is Han's patch https://gna.org/task/download.php?file_id=13245 attached to the task http://gna.org/task/?7404. In the test_suite/shared_data/structures/Indol_test.xyz 0.00000 after the molecule name was removed. The reason for that is because in a typical xyz file the second line is just the molecule name. ................ r13090 | bugman | 2011-06-17 11:39:57 +0200 (Fri, 17 Jun 2011) | 9 lines Generating new system test 'test_read_xyz_internal2()'. This is Han's patch https://gna.org/task/download.php?file_id=13246 attached to the task http://gna.org/task/?7404. The new system test was generated in test_suite/system_tests/structure.py for reading a xyz file 'SSS-cluster4-new-test.xyz' with multiple models. ................ r13091 | bugman | 2011-06-17 12:05:06 +0200 (Fri, 17 Jun 2011) | 9 lines Generating new user functions load_xyz() and __parse_models_xyz(). This is Han's patch https://gna.org/task/download.php?file_id=13247 attached to the task http://gna.org/task/?7404. New user functions load_xyz() and __parse_models_xyz() were generated in generic_fns/structures/internal.py based on the functions load_pdb() and __parse_models(). ................ r13106 | bugman | 2011-06-17 14:50:41 +0200 (Fri, 17 Jun 2011) | 9 lines Changing the name of the user function __parse_models() to __parse_models_pdb() This is Han's patch https://gna.org/task/download.php?file_id=13250 attached to the task http://gna.org/task/?7404. The name of the user function __parse_models() in 'generic_fns/structure/internal.py' has been changed to __parse_models_pdb(). This function is specific for reading the pdb files. ................ r13109 | bugman | 2011-06-17 15:57:30 +0200 (Fri, 17 Jun 2011) | 9 lines Debugging and cleaning up the user functions load_xyz() and __parse_models_xyz(). This is Han's patch https://gna.org/task/download.php?file_id=13251 attached to the task http://gna.org/task/?7404. Debugging and several print outs in the user functions load_xyz() and __parse_models_xyz() in generic_fns/structures/internal.py have been removed. ................ r13110 | bugman | 2011-06-17 16:10:19 +0200 (Fri, 17 Jun 2011) | 9 lines Generating two new functions '__parse_xyz_record()' and 'fill_object_from_xyz()'. This is Han's patchhttps://gna.org/task/download.php?file_id=13252 attached to the task http://gna.org/task/?7404. Two new functions '__parse_xyz_record()' and 'fill_object_from_xyz()' were generated in the class 'MolContainer()' in the file 'generic_fns/structure/internal.py'. ................ r13121 | han87 | 2011-06-20 10:07:35 +0200 (Mon, 20 Jun 2011) | 4 lines Debugging the user functions load_xyz() and test_read_xyz_internal2(). The user functions load_xyz() in 'generic_fns/structure/internal.py' and test_read_xyz_internal2() in 'test_suite/system_tests/structure.py' have been changed so that the molecule name can be read properly. ................ r13122 | han87 | 2011-06-20 15:52:58 +0200 (Mon, 20 Jun 2011) | 5 lines changing the description in the user functions load_spins() and read_xyz(). An example for loading the spins for xyz file format was added in the description of the user function load_spins() and the description of the user function read_xyz() was changed. Both user functions are located in 'prompt/structure.py'. ................ r13162 | han87 | 2011-06-22 16:11:25 +0200 (Wed, 22 Jun 2011) | 4 lines Debugging in the system_test test_read_xyz_internal2(). In the function to load a single spin, the sign for recognizing the molecule "#" was added and the second atom was loaded instead of loading all C atoms. ................ r13163 | han87 | 2011-06-22 16:15:11 +0200 (Wed, 22 Jun 2011) | 4 lines Debugging the user function fill_object_from_xyz().. In the user function fill_object_from_xyz() in generic_fns/structure/internal.py the initialisation of the atom number was changed from 0 to 1. ................ r13164 | han87 | 2011-06-22 16:17:25 +0200 (Wed, 22 Jun 2011) | 5 lines Debugging in the system_test test_read_xyz_internal2(). In the function to load a single spin, the sign for recognizing the molecule "#" was added and the second atom was loaded instead of loading all C atoms. ................ r13165 | han87 | 2011-06-22 17:11:05 +0200 (Wed, 22 Jun 2011) | 4 lines Debugging the user function load_spins() and add_item(). In the function load_spins() in generic_fns/structure/main.py a parameter 'res_num_exist' was added to check whether in the structural data the residue number exists or not. Normally in the pdb file there is a residue number and in the xyz file not. And then this parameter was used as a flag in the add_item() to avoid the Error message 'RelaxError("The residue number '" + repr(res_num) + "' already exists in the sequence.")' in case for xyz file when residue number does not exist. ................ r13167 | han87 | 2011-06-22 17:16:17 +0200 (Wed, 22 Jun 2011) | 4 lines Changing the description in the user function load_spins(). In description of the funtion load_spins() in prompt/structure.py the example for loading all C atoms was changed from 'relax> structure.load_spins(spin_id='@C')' to relax> structure.load_spins(spin_id='@*C*'). ................ r13169 | han87 | 2011-06-22 17:23:16 +0200 (Wed, 22 Jun 2011) | 4 lines Debugging the system test 'test_read_xyz_internal1()'. In the system test 'test_read_xyz_internal1()' the molecule name and the spin name were changed. ................ r13179 | han87 | 2011-06-23 11:26:46 +0200 (Thu, 23 Jun 2011) | 7 lines Reverted r13165 as this change could break other part of the relax. The command used was: svn merge -r 13165:13164 The changing of the user functions "load_spins" and "add_item" could break other part of relax. This was pointed out by Edward in the email: https://mail.gna.org/public/relax-devel/2011-06/msg00226.html. ................ r13180 | han87 | 2011-06-23 15:19:45 +0200 (Thu, 23 Jun 2011) | 4 lines Debugging the user function load_spins() and changing the system test test_read_xyz_internal2(). In the user function load_spins() in generic_fns/structure/main.py a check whether the residue name exists or not has been included. The code is similiar to the molecule check. Also see email: https://mail.gna.org/public/relax-devel/2011-06/msg00226.html. And in the system test 'test_read_xyz_internal2()' all models were loaded instead of 2 and the line for loading proton was removed. ................ r13211 | han87 | 2011-06-24 11:06:46 +0200 (Fri, 24 Jun 2011) | 4 lines Debugging the user function load_spins() Debugging the user function load_spins() in generic_fns/structure/main.py for a proper residue check as suggest in: https://mail.gna.org/public/relax-devel/2011-06/msg00231.html. ................ r13214 | han87 | 2011-06-24 11:50:33 +0200 (Fri, 24 Jun 2011) | 4 lines Debugging the user function load_xyz() and changing the system test_read_xyz_internal2(). Debugging the user function load_xyz() in generic_fns/structure/internal.py and changing the system test test_read_xyz_internal2() so that loading a desired model can be achieved. ................ r13215 | han87 | 2011-06-24 11:55:46 +0200 (Fri, 24 Jun 2011) | 4 lines Debugging the user function load_spins(). Debugging the user function load_spins() in generic_fns/structure/main.py by using the residue number instead of the residue name for a proper residue check as suggest in: https://mail.gna.org/public/relax-devel/2011-06/msg00235.html. ................ r13227 | han87 | 2011-06-27 09:59:35 +0200 (Mon, 27 Jun 2011) | 4 lines Debugging the user function load_spins(). Changing the name from model_increment to xyz_model_increment in the user function load_spins() in generic_fns/structure/main.py as suggest in: https://mail.gna.org/public/relax-devel/2011-06/msg00240.html. ................ r13234 | han87 | 2011-06-27 15:10:31 +0200 (Mon, 27 Jun 2011) | 4 lines Adding code for checking the atomic positions in the system test test_read_xyz_internal2() Code for checking the atomic position (x, y and z) of the last spin was added in the system test test_read_xyz_internal2(). ................ r13235 | han87 | 2011-06-27 15:16:46 +0200 (Mon, 27 Jun 2011) | 7 lines [... 11205 lines stripped ...]