Merged revisions 13961,13983-13984,14008-14009,14011,14013,14071,14103,14107-14110,14146,14157,14179,14181,14185,14249,14262,14285,14292,14324,14329,14331,14333,14335-14336,14338,14341-14343,14347-14352,14354-14355,14361-14366 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3
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r13961 | bugman | 2011-07-28 16:53:26 +0200 (Thu, 28 Jul 2011) | 3 lines
Fix for the overriding of the command line specified mode - the args must be processed anyway.
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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.
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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.
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r14008 | bugman | 2011-07-29 18:36:30 +0200 (Fri, 29 Jul 2011) | 3 lines
Shifted the pedantic flag into the status object.
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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.
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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.
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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.
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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().
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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'.
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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.
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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!
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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.
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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.
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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.
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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@.../svn/relax/branches/xyz
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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@.../svn/relax/branches/xyz
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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()'.
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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.
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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.
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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.
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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()'.
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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.
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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.
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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.
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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.
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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().
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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.
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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.
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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'.
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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.
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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'.
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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.
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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.
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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.
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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.
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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*').
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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().
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r13235 | han87 | 2011-06-27 15:16:46 +0200 (Mon, 27 Jun 2011) | 7 lines
Reverted r13234 as it contains several unrelated changes.
The command used was:
svn merge -r 13234:13227 .
This commit contains several unrelated changes in /generic_fns/structure/main.py and /generic_fns/mol_res_spin.py.
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r13239 | han87 | 2011-06-27 15:21:31 +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().
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r13245 | han87 | 2011-06-27 18:51:42 +0200 (Mon, 27 Jun 2011) | 4 lines
Adding code for extracting the vector in the system test test_read_xyz_internal2()
Code for extracting a vector of two given atoms was added in the system test test_read_xyz_internal2().
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r13246 | han87 | 2011-06-27 18:55:51 +0200 (Mon, 27 Jun 2011) | 4 lines
A new function vector_xyz() was generated.
A new function vector_xyz() was generated in '/prompt/structure.py' for extracting a vector of two given atoms in a xyz file.
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r13249 | han87 | 2011-06-28 10:25:55 +0200 (Tue, 28 Jun 2011) | 7 lines
Reverted r13246 as different approach will be used.
The command used was:
svn merge -r 13246:13239 .
The new function vectors_xyz() in the /prompt/structure.py is not needed. The current code will be fixed for xyz file format suggested in https://mail.gna.org/public/relax-devel/2011-06/msg00244.html.
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r13414 | han87 | 2011-07-04 14:27:05 +0200 (Mon, 04 Jul 2011) | 4 lines
The system test for loading a single spin from a xyz has been changed.
The function return_spin() from the 'mol_res_spin' has been used to load a single spin for the system test 'test_read_xyz_internal2'.
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r13415 | han87 | 2011-07-04 14:30:59 +0200 (Mon, 04 Jul 2011) | 4 lines
Adding a new system test to load a vector.
A system test for loading a vector between two spins has been included in the 'test_read_xyz_internal2'.
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r13416 | han87 | 2011-07-04 14:35:25 +0200 (Mon, 04 Jul 2011) | 4 lines
Changing the keyword argument
The argument of the keyword 'unit' in the function 'vectors' in 'prompt/structure.py' has been changed from 'True' to 'False'.
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r13417 | han87 | 2011-07-04 14:43:10 +0200 (Mon, 04 Jul 2011) | 4 lines
Adding code for extracting a vector of a xyz file.
Code for extracting a vector between specified spins in a xyz file has been included in the '/generic_fns/structure/internal.py'.
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r13891 | han87 | 2011-07-26 17:36:01 +0200 (Tue, 26 Jul 2011) | 4 lines
Debugging in the generic_fns/structure/main.py
Debugging in the function load_spin in order to load a spin for xyz file properly.
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r13894 | han87 | 2011-07-26 17:38:38 +0200 (Tue, 26 Jul 2011) | 4 lines
Changing the code in the test_read_xyz_internal2
Test to load a spin of the already loaded model of the molecule.
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r13900 | han87 | 2011-07-26 18:47:49 +0200 (Tue, 26 Jul 2011) | 4 lines
Changing the code in the generic_fns/structure/main.py
For printing out of modified spins, a test to check whether the spin_name exists or not is added.
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r13924 | han87 | 2011-07-27 11:17:48 +0200 (Wed, 27 Jul 2011) | 4 lines
Deleting the function 'vector_xyz' in the generic_fns/structure/main.py
The code of the function 'vector_xyz' was removed since it will be not used.
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r13931 | han87 | 2011-07-27 17:51:49 +0200 (Wed, 27 Jul 2011) | 4 lines
Changing the value of the unit arg in the function 'vectors' in 'prompt/structure.py'
The argument of the keyword 'unit' in the function 'vectors' in 'prompt/structure.py' has been changed back from 'False' to 'True' since it causes many test failure.
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r13933 | han87 | 2011-07-27 17:58:05 +0200 (Wed, 27 Jul 2011) | 8 lines
Reverted r as it contains several unrelated changes.
The command used was:
svn merge -r 13931:13924 .
This commit contains several unrelated changes in /generic_fns/structure/main.py and /prompt/structure.py.
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r13934 | han87 | 2011-07-27 17:59:07 +0200 (Wed, 27 Jul 2011) | 5 lines
Changing the value of the unit arg in the function 'vectors' in 'prompt/structure.py'
The argument of the keyword 'unit' in the function 'vectors' in 'prompt/structure.py' has been changed back from 'False' to 'True' since it causes many test failure.
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r13944 | han87 | 2011-07-28 10:15:38 +0200 (Thu, 28 Jul 2011) | 3 lines
Initialized merge tracking via "svnmerge" with revisions "1-12830" from
svn+ssh://han87@.../svn/relax/1.3
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r13947 | bugman | 2011-07-28 11:44:06 +0200 (Thu, 28 Jul 2011) | 622 lines
This should have been the commit message of the previous commit (r13946).
This change actually contains a trivial comment modification in the XYZ file reading system tests.
Merged revisions 12937-12941,12943-12945,12947-12952,12954-12957,12959-12960,12965-12967,12969-12975,12982-13022,13028-13029,13045-13046,13153,13258,13357-13359,13411,13510-13512,13577,13631-13632,13641,13655,13660,13683,13686,13706,13742-13743,13748-13749,13780,13835-13836,13845-13857,13904-13906,13909,13919,13926-13927,13929,13932 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3
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r12937 | bugman | 2011-06-09 17:52:04 +0200 (Thu, 09 Jun 2011) | 3 lines
Removed a duplicated self.SetSize() call for the main GUI window.
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r12938 | bugman | 2011-06-09 17:53:10 +0200 (Thu, 09 Jun 2011) | 3 lines
Changed the Frame.SetSize() call to SetMinSize() to prevent the main GUI window becoming too small.
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r12939 | bugman | 2011-06-09 17:54:12 +0200 (Thu, 09 Jun 2011) | 5 lines
Both SetSize() and SetMinSize() are now used for the main GUI window.
This allows for a proper layout.
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r12940 | bugman | 2011-06-09 18:19:37 +0200 (Thu, 09 Jun 2011) | 3 lines
Simplified and localised a variable.
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r12941 | bugman | 2011-06-09 18:31:46 +0200 (Thu, 09 Jun 2011) | 3 lines
Added a hard coded variable for the size of the graphical part of the analysis frames.
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r12943 | bugman | 2011-06-09 19:06:49 +0200 (Thu, 09 Jun 2011) | 3 lines
The text controls are now horizontally expandable.
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r12944 | bugman | 2011-06-09 19:11:05 +0200 (Thu, 09 Jun 2011) | 3 lines
The model-free, Rx, and NOE frame main box sizers all expand horizontally now.
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r12945 | bugman | 2011-06-09 19:33:23 +0200 (Thu, 09 Jun 2011) | 3 lines
A spacer is now used for add_text_sel_element() if no button is present to fill the button space.
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r12947 | bugman | 2011-06-09 20:10:45 +0200 (Thu, 09 Jun 2011) | 5 lines
Big simplification by shifting the widths of the text selection GUI element to hard coded variables.
These hard coded class variables are located in the base class.
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r12948 | bugman | 2011-06-09 20:16:10 +0200 (Thu, 09 Jun 2011) | 3 lines
Added some horizontal spacing between the elements of the text selection GUI element.
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r12949 | bugman | 2011-06-10 09:42:25 +0200 (Fri, 10 Jun 2011) | 5 lines
Created the setup_analysis_element() base method for laying out the main analysis GUI element.
This currently adds a border of 10 px around each analysis.
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r12950 | bugman | 2011-06-10 09:43:01 +0200 (Fri, 10 Jun 2011) | 3 lines
The auto model-free analysis frame now uses the base setup_analysis_element() method.
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r12951 | bugman | 2011-06-10 10:08:05 +0200 (Fri, 10 Jun 2011) | 7 lines
Split the auto model-free build_main_box() method into two.
The left hand box is now created by build_left_box(), to reflect the design of build_right_box()
and to allow build_main_box() to be abstracted into a base class method for all analysis frames to
use.
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r12952 | bugman | 2011-06-10 10:16:14 +0200 (Fri, 10 Jun 2011) | 3 lines
Shifted the model-free window build_main_box() method to the base class.
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r12954 | bugman | 2011-06-10 11:26:14 +0200 (Fri, 10 Jun 2011) | 5 lines
The NOE and Rx analysis windows now use the base class build_main_box() method.
Their build_main_box() methods have been renamed to build_left_box() and modified to suit.
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r12955 | bugman | 2011-06-10 11:31:40 +0200 (Fri, 10 Jun 2011) | 3 lines
The results tab now uses the base setup_analysis_element() method to add borders.
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r12956 | bugman | 2011-06-10 11:58:32 +0200 (Fri, 10 Jun 2011) | 3 lines
The right hand box in the analysis windows now expands vertically with window resizing.
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r12957 | bugman | 2011-06-10 12:09:07 +0200 (Fri, 10 Jun 2011) | 3 lines
Better layout for the base class static text, text control and button addition.
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r12959 | bugman | 2011-06-10 12:17:13 +0200 (Fri, 10 Jun 2011) | 3 lines
The peak list grid GUI element now expands within the box it is given.
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r12960 | bugman | 2011-06-10 12:23:41 +0200 (Fri, 10 Jun 2011) | 3 lines
Added a stretchable spacer to the NOE window so the execute relax button is always at the bottom right.
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r12965 | bugman | 2011-06-10 14:48:51 +0200 (Fri, 10 Jun 2011) | 3 lines
Completely refactored the model-free model buttons code.
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r12966 | bugman | 2011-06-10 14:50:16 +0200 (Fri, 10 Jun 2011) | 3 lines
The model-free model buttons now expand to the correct width.
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r12967 | bugman | 2011-06-10 14:55:17 +0200 (Fri, 10 Jun 2011) | 3 lines
The add_mf_models() method is now using add_static_text() for the text.
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r12969 | bugman | 2011-06-10 15:24:59 +0200 (Fri, 10 Jun 2011) | 3 lines
Shifted the model-free add_execute_relax() method into the base class.
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r12970 | bugman | 2011-06-10 15:28:06 +0200 (Fri, 10 Jun 2011) | 3 lines
The method is now passed into add_execute_relax() to allow derived classes to specify this.
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r12971 | bugman | 2011-06-10 15:30:20 +0200 (Fri, 10 Jun 2011) | 3 lines
Removed the SetName() call (it was for debugging).
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r12972 | bugman | 2011-06-10 15:32:49 +0200 (Fri, 10 Jun 2011) | 3 lines
Fixed the layout of the execute relax button GUI element.
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r12973 | bugman | 2011-06-10 15:35:58 +0200 (Fri, 10 Jun 2011) | 3 lines
The NOE and Rx frames are now using the base method add_execute_relax().
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r12974 | bugman | 2011-06-10 15:38:56 +0200 (Fri, 10 Jun 2011) | 3 lines
The left hand box of the analysis frames/windows now stretches vertically.
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r12975 | bugman | 2011-06-10 15:57:28 +0200 (Fri, 10 Jun 2011) | 3 lines
The peak intensity GUI element is now enclosed within a StaticBox.
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r12982 | bugman | 2011-06-14 12:56:01 +0200 (Tue, 14 Jun 2011) | 5 lines
Shifted the main GUI window layout to the start of the __init__() method.
This is to help with the sizing events.
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r12983 | bugman | 2011-06-14 14:17:01 +0200 (Tue, 14 Jun 2011) | 5 lines
Created the function gui.misc.add_border() for adding borders to generic GUI elements.
The analysis tabs now use this method for their borders.
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r12984 | bugman | 2011-06-14 14:46:39 +0200 (Tue, 14 Jun 2011) | 5 lines
The gui.misc.add_border() function no longer packs the box in the parent and detects orientation.
The parent argument has been replaced by a box sizer argument.
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r12985 | bugman | 2011-06-14 14:48:50 +0200 (Tue, 14 Jun 2011) | 3 lines
All the analysis tab GUI elements now use the new design of the add_border() fn.
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r12986 | bugman | 2011-06-14 14:51:47 +0200 (Tue, 14 Jun 2011) | 5 lines
Added a method for catching resizing events.
It currently does nothing, allowing the event to continue.
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r12987 | bugman | 2011-06-14 14:58:50 +0200 (Tue, 14 Jun 2011) | 3 lines
Added an internal border to the relaxation peak list selection GUI element.
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r12988 | bugman | 2011-06-14 15:26:32 +0200 (Tue, 14 Jun 2011) | 3 lines
Added spacing above and below the peak list GUI element in the Rx tab GUI elements.
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r12989 | bugman | 2011-06-14 15:43:19 +0200 (Tue, 14 Jun 2011) | 3 lines
The resize event is now bound to the grid and the first column now expands with the window.
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r12990 | bugman | 2011-06-14 15:46:17 +0200 (Tue, 14 Jun 2011) | 3 lines
The Rx peak list grid cells can no longer be resized.
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r12991 | bugman | 2011-06-14 16:01:34 +0200 (Tue, 14 Jun 2011) | 3 lines
Horizontal scrolling is turned off in the relaxation peak list grid.
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r12992 | bugman | 2011-06-14 16:06:07 +0200 (Tue, 14 Jun 2011) | 3 lines
Switched the delay time and number of cycles columns in the peak list grid.
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r12993 | bugman | 2011-06-14 16:07:49 +0200 (Tue, 14 Jun 2011) | 14 lines
Reverted r12991, the disabling of horizontal scrolling.
The command used was:
svn merge -r12991:r12990 .
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r12991 | bugman | 2011-06-14 16:01:34 +0200 (Tue, 14 Jun 2011) | 3 lines
Changed paths:
M /1.3/gui/components/spectrum.py
Horizontal scrolling is turned off in the relaxation peak list grid.
....
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r12994 | bugman | 2011-06-14 16:20:30 +0200 (Tue, 14 Jun 2011) | 5 lines
The change_delay_down() and change_delay_up() methods are now bound again.
This allows only numbers in the delay time control and updates the grid once changed.
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r12995 | bugman | 2011-06-14 16:21:37 +0200 (Tue, 14 Jun 2011) | 3 lines
Fixed update_grid() for the swapped columns.
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r12996 | bugman | 2011-06-14 16:22:13 +0200 (Tue, 14 Jun 2011) | 3 lines
Fixed sync_ds() for the swapped columns.
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r12997 | bugman | 2011-06-14 16:23:49 +0200 (Tue, 14 Jun 2011) | 3 lines
The relaxation delay time column is no longer read only.
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r12998 | bugman | 2011-06-14 16:34:20 +0200 (Tue, 14 Jun 2011) | 3 lines
Made the Rx peak list column a little smaller for better scrollbar handling.
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r12999 | bugman | 2011-06-14 16:47:09 +0200 (Tue, 14 Jun 2011) | 3 lines
The relaxation delay times are no longer reset if the number of cycles is not set.
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r13000 | bugman | 2011-06-14 17:44:00 +0200 (Tue, 14 Jun 2011) | 3 lines
Better handling of changes in the relaxation peak list grid.
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r13001 | bugman | 2011-06-14 17:49:02 +0200 (Tue, 14 Jun 2011) | 3 lines
Removed a debugging printout.
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r13002 | bugman | 2011-06-14 17:51:12 +0200 (Tue, 14 Jun 2011) | 3 lines
The font for the grid is now set.
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r13003 | bugman | 2011-06-14 17:56:10 +0200 (Tue, 14 Jun 2011) | 3 lines
Created a new font definition set to 10 pt and bold.
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r13004 | bugman | 2011-06-14 17:56:28 +0200 (Tue, 14 Jun 2011) | 3 lines
The grid fonts are now properly set.
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r13005 | bugman | 2011-06-14 18:04:33 +0200 (Tue, 14 Jun 2011) | 3 lines
The row heights are now set to match the delay time text control.
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r13006 | bugman | 2011-06-14 18:17:32 +0200 (Tue, 14 Jun 2011) | 3 lines
Improved layout of the model-free tab GUI element for resizing.
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r13007 | bugman | 2011-06-14 18:31:10 +0200 (Tue, 14 Jun 2011) | 6 lines
Created the analysis tab base class methods add_spin_control() and add_spin_element().
These are similar to the text control and text selection elements respectively, but use a SpinCtrl
instead.
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r13008 | bugman | 2011-06-14 18:31:51 +0200 (Tue, 14 Jun 2011) | 3 lines
The model-free analysis tab now uses the base class add_spin_element() method for the max iterations.
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r13009 | bugman | 2011-06-14 18:43:49 +0200 (Tue, 14 Jun 2011) | 3 lines
Shifted the model-free list box in the results tab into the new add_list_box() method.
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r13010 | bugman | 2011-06-14 18:50:17 +0200 (Tue, 14 Jun 2011) | 3 lines
The steady-state NOE results box now resizes.
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r13011 | bugman | 2011-06-14 18:50:48 +0200 (Tue, 14 Jun 2011) | 3 lines
Alphabetical ordering of methods.
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r13012 | bugman | 2011-06-14 18:53:46 +0200 (Tue, 14 Jun 2011) | 5 lines
All the result list boxes are now created by add_list_box().
The results tab now nicely resizes.
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r13013 | bugman | 2011-06-14 19:30:46 +0200 (Tue, 14 Jun 2011) | 9 lines
Complete redesign of the relax global settings window to fix the Mac OS X crashing.
This is an attempt at fixing bug #18197 (https://gna.org/bugs/?18197).
The old code has been completely eliminated and replaced with a new set of methods in the base
relax_gui class and a new Global_parameters class in gui.settings which is of the same design as the
free file format settings window.
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r13014 | bugman | 2011-06-14 19:36:56 +0200 (Tue, 14 Jun 2011) | 3 lines
A minimum size is now set to prevent the settings windows from being resized too small.
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r13015 | bugman | 2011-06-14 19:38:20 +0200 (Tue, 14 Jun 2011) | 3 lines
Fix for the global settings window - it needs to inherit from UF_window!
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r13016 | bugman | 2011-06-14 19:44:41 +0200 (Tue, 14 Jun 2011) | 3 lines
Brought the 'Execute relax' text inside the button.
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r13017 | bugman | 2011-06-14 19:53:10 +0200 (Tue, 14 Jun 2011) | 3 lines
Added an icon to the 'Change' buttons throughout the GUI.
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r13018 | bugman | 2011-06-14 19:56:10 +0200 (Tue, 14 Jun 2011) | 3 lines
Added the oxygen icons for opening folders.
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r13019 | bugman | 2011-06-14 19:59:06 +0200 (Tue, 14 Jun 2011) | 3 lines
Added the open folder icons to the paths module.
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r13020 | bugman | 2011-06-14 20:02:21 +0200 (Tue, 14 Jun 2011) | 3 lines
The open folder icons are now used for the 'Results directory' change buttons.
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r13021 | bugman | 2011-06-14 20:03:30 +0200 (Tue, 14 Jun 2011) | 3 lines
Added a space between the relax icon and the text 'Execute relax' on the button.
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r13022 | bugman | 2011-06-14 20:35:01 +0200 (Tue, 14 Jun 2011) | 5 lines
The settings windows are now derived from wx.Dialog rather than wx.Frame.
This is for better operation under MS Windows.
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r13028 | bugman | 2011-06-15 10:52:36 +0200 (Wed, 15 Jun 2011) | 3 lines
Added larger versions of the document-new.png Oxygen icons.
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r13029 | bugman | 2011-06-15 10:53:44 +0200 (Wed, 15 Jun 2011) | 3 lines
Added the new document-new icons to the paths module.
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r13045 | bugman | 2011-06-15 16:29:43 +0200 (Wed, 15 Jun 2011) | 3 lines
Added the document-close Oxygen icons.
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r13046 | bugman | 2011-06-15 16:32:19 +0200 (Wed, 15 Jun 2011) | 3 lines
Added the document-close Oxygen icon to the paths module.
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r13153 | bugman | 2011-06-21 19:18:15 +0200 (Tue, 21 Jun 2011) | 5 lines
Removed a test for the sequence in the user function structure.create_diff_tensor_pdb() backend.
The sequence data is not needed for this.
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r13258 | bugman | 2011-06-28 12:37:30 +0200 (Tue, 28 Jun 2011) | 6 lines
Bug fix for the NOE auto-analysis - the column numbers for the deselected spins file are now assumed.
The residue number is assumed to be in the first column. This is a hack until the spin selection
part is better designed.
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r13357 | bugman | 2011-07-01 13:33:41 +0200 (Fri, 01 Jul 2011) | 3 lines
Added support for old save files in the Peak_intensity.sync_ds() method.
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r13358 | bugman | 2011-07-01 13:35:09 +0200 (Fri, 01 Jul 2011) | 6 lines
Fix for the bug reported as sr #2764 (https://gna.org/support/index.php?2764).
The problem was that the sequence file is now in the variable sequence_file.
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r13359 | bugman | 2011-07-01 13:36:36 +0200 (Fri, 01 Jul 2011) | 5 lines
Another fix for the bug of sr #2764 (https://gna.org/support/?2764).
The sequence file variable is in self.data!!!
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r13411 | michaelbieri | 2011-07-04 01:15:43 +0200 (Mon, 04 Jul 2011) | 2 lines
Argument change_all for deselecting residues in the d'Auvergne protocol has to be boolean.
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r13510 | bugman | 2011-07-08 08:58:14 +0200 (Fri, 08 Jul 2011) | 3 lines
Bug fix for the sequence.read() user function - the force flag is now being passed on.
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r13511 | bugman | 2011-07-08 09:00:06 +0200 (Fri, 08 Jul 2011) | 5 lines
Another fix for the sequence.write() user function - the force flag is passed to open_write_file().
This is from the relax_io.write_spin_data() function.
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r13512 | bugman | 2011-07-08 09:01:05 +0200 (Fri, 08 Jul 2011) | 5 lines
Bug fix for the sequence.write() user function when the column separator is not whitespace.
The column widths are no longer fixed is the separator is not whitespace.
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r13577 | bugman | 2011-07-13 11:44:38 +0200 (Wed, 13 Jul 2011) | 5 lines
Many bug fixes for the functions of the generic_fns.mol_res_spin module.
These fixes are for when a data pipe other than the current data pipe is used.
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r13631 | bugman | 2011-07-14 18:38:10 +0200 (Thu, 14 Jul 2011) | 5 lines
Bug fix for the relax save states - the current data pipe is now saved and restored.
The info about the cdp was being blacklisted, so was not stored in the relax save file.
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r13632 | bugman | 2011-07-14 20:09:47 +0200 (Thu, 14 Jul 2011) | 7 lines
Fix for the loading of saved state files prior to r13631 - the cdp is now set to the last pipe.
The earlier saved state files did not store the current data pipe info, so the current data pipe was
set by default to the last data pipe. This behaviour was broken with r13631 but is now restored for
the old state files.
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r13641 | bugman | 2011-07-15 12:25:21 +0200 (Fri, 15 Jul 2011) | 3 lines
Fix for the new relax save state with current pipe info - the cdp ojbect is now set after loading.
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r13655 | bugman | 2011-07-15 16:37:34 +0200 (Fri, 15 Jul 2011) | 3 lines
Bug fix for the atomic position check in the spin.create_pseudo user function.
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r13660 | bugman | 2011-07-15 19:50:44 +0200 (Fri, 15 Jul 2011) | 6 lines
Bug fix for pseudo-atom support when only a single structure is loaded.
Pseudo-atom support was only working correctly for when multiple models were loaded and atomic
positions were not averaged.
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r13683 | bugman | 2011-07-18 14:00:29 +0200 (Mon, 18 Jul 2011) | 6 lines
Bug fix for the spectrum.read_intensities int_method argument for volumes.
Volume integration should be called 'point sum', but the back end code was checking against the
string 'volume'.
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r13686 | bugman | 2011-07-18 14:24:00 +0200 (Mon, 18 Jul 2011) | 3 lines
Bug fix in one of the relaxation curve-fitting system tests - 'volume' should have been 'point sum'.
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r13706 | bugman | 2011-07-18 20:13:04 +0200 (Mon, 18 Jul 2011) | 6 lines
Fix for the PCS back-calculation function - divide by zero is now avoided.
The PCS back-calculation function was calculating the normalised bond vector between the lanthanide
atom and itself. The normalisation in this case is now avoided.
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r13742 | bugman | 2011-07-19 17:02:29 +0200 (Tue, 19 Jul 2011) | 6 lines
Changed the order of some of the replicated spectra in the test_curve_fitting_height system test.
This triggers a bug in the spectra.error_analysis user function which looks like the replicated
spectra list is order dependent (when it shouldn't be).
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r13743 | bugman | 2011-07-19 17:18:49 +0200 (Tue, 19 Jul 2011) | 7 lines
Bug fix for the spectrum user functions for when the ID order does not match those loaded.
If the order of IDs sent to spectrum.replicated did not match the order they were loaded by
spectrum.read_intensities, then the spectrum.error_analysis user function would fail. The order is
no longer important.
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r13748 | bugman | 2011-07-19 17:58:00 +0200 (Tue, 19 Jul 2011) | 5 lines
The relax_fit overfit_deselect() method now skips deselected spins.
This prevents unnecessary warnings about missing data for deselected spins.
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r13749 | bugman | 2011-07-19 18:00:13 +0200 (Tue, 19 Jul 2011) | 3 lines
All of the overfit_deselect() methods now skip deselected spins, avoiding confusing warnings.
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r13780 | bugman | 2011-07-20 15:56:27 +0200 (Wed, 20 Jul 2011) | 6 lines
Bug fix - the pipe switching flag is now propagated all the way to the data store add() method.
The flag was previously not sent to the method so that the creation of a new data pipe always
resulted in a switch to that pipe. This bug is normally harmless.
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r13835 | bugman | 2011-07-22 16:30:29 +0200 (Fri, 22 Jul 2011) | 6 lines
Fix for the model-free _determine_model_type() method when the spin container has no 'local_tm'.
This code was failing in certain rare circumstances (when the setting up of the diffusion tensor was
forgotten).
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r13836 | bugman | 2011-07-22 16:57:05 +0200 (Fri, 22 Jul 2011) | 3 lines
Created a script for byte compiling the Python source files.
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r13845 | bugman | 2011-07-25 10:07:31 +0200 (Mon, 25 Jul 2011) | 5 lines
Added some old 2004 scripts for creating a uniform vector distribution and calculating relaxation data.
This will be used in the end to build a quick test for the dauvergne_protocol auto-analysis.
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r13846 | bugman | 2011-07-25 10:13:27 +0200 (Mon, 25 Jul 2011) | 3 lines
Modified the spherical vector distribution script in preparation for Python 3.
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r13847 | bugman | 2011-07-25 10:15:19 +0200 (Mon, 25 Jul 2011) | 3 lines
Modified the script to only have 3 incs.
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r13848 | bugman | 2011-07-25 10:15:51 +0200 (Mon, 25 Jul 2011) | 3 lines
Created the PDB representation of the spherical vector distribution for 9 vectors.
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r13849 | bugman | 2011-07-25 10:37:49 +0200 (Mon, 25 Jul 2011) | 3 lines
Converted the relaxation data generation script from relax 1.0 format to relax 1.3.
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r13850 | bugman | 2011-07-25 12:02:17 +0200 (Mon, 25 Jul 2011) | 9 lines
Added initial support for determining protein connectivities in the internal structural reader.
This is currently only for intra-residue connectivities in the protein backbone. A number of new
methods have been added:
_mol_type()
_protein_connect()
_protein_intra_connect()
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r13851 | bugman | 2011-07-25 12:20:43 +0200 (Mon, 25 Jul 2011) | 5 lines
Fixes for the test suite relaxation data creation script.
The code was not fully compatible with the relax 1.3 design.
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r13852 | bugman | 2011-07-25 12:21:13 +0200 (Mon, 25 Jul 2011) | 3 lines
Fixes to the relaxation data generation sample script based on the changes of r13851.
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r13853 | bugman | 2011-07-25 12:22:22 +0200 (Mon, 25 Jul 2011) | 5 lines
The relaxation data is now for 500 and 900 MHz.
This larger difference should hopefully speed up optimisation in the test suite.
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r13854 | bugman | 2011-07-25 12:23:36 +0200 (Mon, 25 Jul 2011) | 3 lines
Added the relaxation data.
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r13855 | bugman | 2011-07-25 13:45:04 +0200 (Mon, 25 Jul 2011) | 5 lines
Added the argument 'bc' to the relax_data.write() user function front end.
This currently doesn't do anything.
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r13856 | bugman | 2011-07-25 14:33:28 +0200 (Mon, 25 Jul 2011) | 5 lines
The 'bc' arg is now part of the value.write() user function, and all of the return_value functions.
The arg is also propagated to the back-end of the relax_data.write() user function.
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r13857 | bugman | 2011-07-25 14:34:12 +0200 (Mon, 25 Jul 2011) | 3 lines
The back calculated data is now written out to file in the synthetic relaxation data script.
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r13904 | bugman | 2011-07-26 21:40:15 +0200 (Tue, 26 Jul 2011) | 5 lines
Added the data_type() method to the specific functions API.
This will be used to determine the type that a given parameter from data_names() should be.
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r13905 | bugman | 2011-07-26 21:52:58 +0200 (Tue, 26 Jul 2011) | 3 lines
Modified the specific functions API method data_type() so that Python type objects should be returned.
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r13906 | bugman | 2011-07-26 21:55:53 +0200 (Tue, 26 Jul 2011) | 3 lines
Implemented the model-free version of the data_type() API method.
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r13909 | bugman | 2011-07-26 22:18:51 +0200 (Tue, 26 Jul 2011) | 3 lines
The data_type() API method is now exposed.
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r13919 | bugman | 2011-07-27 09:37:48 +0200 (Wed, 27 Jul 2011) | 3 lines
The heteronucleus and proton type parameters can now be specified by their parameter names aas well.
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r13926 | bugman | 2011-07-27 16:01:22 +0200 (Wed, 27 Jul 2011) | 5 lines
The create_molecule, create_residue, and create_spin functions now returned the created container.
This should not affect any of the current code using these, as normally None would be returned.
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r13927 | bugman | 2011-07-27 16:05:49 +0200 (Wed, 27 Jul 2011) | 6 lines
Invisible fix for the test_opendx_theta_phi_da() system test.
The spins are extracted from the structure, so they don't need to be read from the relaxation data
file as well. This is causing problems in the xyz branch, but is not an issue in the main line.
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r13929 | bugman | 2011-07-27 16:15:41 +0200 (Wed, 27 Jul 2011) | 3 lines
Modified the create_spin() function to overwrite the first spin if empty.
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r13932 | bugman | 2011-07-27 17:54:24 +0200 (Wed, 27 Jul 2011) | 13 lines
Redesign of the structure.load_spins user function back end.
This redesign is required due to problems encountered by Han in the xyz branch. See the thread
starting at https://mail.gna.org/public/relax-devel/2011-07/msg00021.html.
This commit consists of a number of changes:
- The combine_models argument has been removed as it is a relic, and isn't used at all.
- The spins are now created in the standard way via the generic_fns.mol_res_spin.create_spin()
function, eliminating all of the issues and complications of the old code.
- The atomic positions are now converted to numpy arrays.
- Only the created spins are included in the print out, and not replicated for each model.
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r14038 | han87 | 2011-08-01 17:15:17 +0200 (Mon, 01 Aug 2011) | 4 lines
Declaring the method load_xyz() in API.
The code for declaring load_xyz() in API was added based on the code 'load_pdb' in API and 'load_xyz' in internal.py.
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r14343 | bugman | 2011-08-11 11:06:21 +0200 (Thu, 11 Aug 2011) | 3 lines
Removed merge tracking for "svnmerge" for
svn+ssh://bugman@.../svn/relax/branches/xyz
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r14347 | bugman | 2011-08-11 11:17:22 +0200 (Thu, 11 Aug 2011) | 3 lines
Fix for the molmol_macro() analysis specific API - the first arg should be called data_type.
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r14348 | bugman | 2011-08-11 11:37:27 +0200 (Thu, 11 Aug 2011) | 3 lines
Added the pymol_macro() method to the analysis specific API.
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r14349 | bugman | 2011-08-11 12:01:39 +0200 (Thu, 11 Aug 2011) | 3 lines
Fixes for the molmol_macro() and pymol_macro() analysis specific API method docstrings.
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r14350 | bugman | 2011-08-11 12:02:51 +0200 (Thu, 11 Aug 2011) | 3 lines
Clean up of parameters in the _create_mc_relax_data() specific API common method.
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r14351 | han87 | 2011-08-11 15:14:27 +0200 (Thu, 11 Aug 2011) | 4 lines
Debugging in the system test 'test_read_xyz_internal2'
The code was changed for extracting an unit vector instead of a non unit vector.
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r14352 | bugman | 2011-08-11 15:19:42 +0200 (Thu, 11 Aug 2011) | 3 lines
A number of epydoc docstring fixes.
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r14354 | bugman | 2011-08-11 15:46:58 +0200 (Thu, 11 Aug 2011) | 3 lines
The sconstruct script is only executed when it is the main loaded module or if launched by scons.
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r14355 | bugman | 2011-08-11 15:48:27 +0200 (Thu, 11 Aug 2011) | 5 lines
Improved the list of modules and packages used in the epydoc documentation.
The files and directories which are not python modules or packages are now properly skipped.
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r14361 | bugman | 2011-08-11 16:38:36 +0200 (Thu, 11 Aug 2011) | 5 lines
Bug fix for the data.align_tensor.calc_eta() function - divide by zeros are now avoided.
When Azz is zero, eta is now set to NaN.
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r14362 | bugman | 2011-08-11 16:41:38 +0200 (Thu, 11 Aug 2011) | 3 lines
Typo fix in the unused and incomplete dfunc function.
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r14363 | bugman | 2011-08-11 16:45:31 +0200 (Thu, 11 Aug 2011) | 5 lines
Bug fix for the data.align_tensor.calc_R() function - divide by zeros are now avoided.
When Aa is zero, Ar is now set to NaN.
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r14364 | bugman | 2011-08-11 16:56:16 +0200 (Thu, 11 Aug 2011) | 5 lines
Fix for the test_opt_constr_bfgs_mt_S2_0_970_te_2048_Rex_0_149 model-free system test on MS Windows.
The te parameter check was too strict.
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r14365 | bugman | 2011-08-11 17:04:28 +0200 (Thu, 11 Aug 2011) | 3 lines
Another divide by zero problem is being caught in the RDC Q-factor code.
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r14366 | bugman | 2011-08-11 17:13:28 +0200 (Thu, 11 Aug 2011) | 3 lines
The dipolar_constant() and pcs_constant() functions now catch division by zero problems.
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