relax SVN archive

Initialized merge tracking via "svnmerge" with revisions "1-12831" from
svn+ssh://bugman@.../svn/relax/branches/xyz

Merged revisions 14103,14107-14110,14146,14157,14179,14181,14185,14249,14262,14285,14292,14324,14329,14331,14333,14335-14336,14338 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

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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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Merged revisions 14338 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

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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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Fix for the molmol macro of the ts parameter, the spin container variable was spelt incorrectly.

Merged revisions 14335-14336 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

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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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Fixes for the old scripts/optimisation_testing.py script.

This was also using the ancient self.relax code path.

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.

Merged revisions 14331,14333 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

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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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Fix for the molmol.write macro creation user function - the file arg can be None!

The dauvergne_protocol auto-analysis now generates molmol macros and text files with the parameters.

After the addition of the PyMOL macros, this will fully shift the original GUI code of
gui.analyses.results_analysis into the core of relax (the original model_free_results() function from
gui.res.results_analysis).