Author: bugman
Date: Thu Aug 11 10:57:08 2011
New Revision: 14340
URL: http://svn.gna.org/viewcvs/relax?rev=14340&view=rev
Log:
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@xxxxxxxxxxx/svn/relax/1.3
........
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.
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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.
........
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.
........
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.
........
Modified:
branches/xyz/ (props changed)
branches/xyz/auto_analyses/dauvergne_protocol.py
branches/xyz/auto_analyses/noe.py
branches/xyz/auto_analyses/relax_fit.py
branches/xyz/auto_analyses/stereochem_analysis.py
branches/xyz/data/__init__.py
branches/xyz/generic_fns/grace.py
branches/xyz/generic_fns/pymol_control.py
branches/xyz/generic_fns/structure/main.py
branches/xyz/generic_fns/structure/mass.py
branches/xyz/generic_fns/value.py
branches/xyz/prompt/interpreter.py
branches/xyz/prompt/molmol.py
branches/xyz/relax_warnings.py
branches/xyz/scripts/optimisation_testing.py
branches/xyz/specific_fns/model_free/molmol.py
branches/xyz/status.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/xyz/auto_analyses/dauvergne_protocol.py
URL:
http://svn.gna.org/viewcvs/relax/branches/xyz/auto_analyses/dauvergne_protocol.py?rev=14340&r1=14339&r2=14340&view=diff
Modified: branches/xyz/auto_analyses/noe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/xyz/auto_analyses/noe.py?rev=14340&r1=14339&r2=14340&view=diff
Modified: branches/xyz/auto_analyses/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/xyz/auto_analyses/relax_fit.py?rev=14340&r1=14339&r2=14340&view=diff
Modified: branches/xyz/auto_analyses/stereochem_analysis.py
URL:
http://svn.gna.org/viewcvs/relax/branches/xyz/auto_analyses/stereochem_analysis.py?rev=14340&r1=14339&r2=14340&view=diff
Modified: branches/xyz/data/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/xyz/data/__init__.py?rev=14340&r1=14339&r2=14340&view=diff
Modified: branches/xyz/generic_fns/grace.py
URL:
http://svn.gna.org/viewcvs/relax/branches/xyz/generic_fns/grace.py?rev=14340&r1=14339&r2=14340&view=diff
Modified: branches/xyz/generic_fns/pymol_control.py
URL:
http://svn.gna.org/viewcvs/relax/branches/xyz/generic_fns/pymol_control.py?rev=14340&r1=14339&r2=14340&view=diff
Modified: branches/xyz/generic_fns/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/xyz/generic_fns/structure/main.py?rev=14340&r1=14339&r2=14340&view=diff
Modified: branches/xyz/generic_fns/structure/mass.py
URL:
http://svn.gna.org/viewcvs/relax/branches/xyz/generic_fns/structure/mass.py?rev=14340&r1=14339&r2=14340&view=diff
Modified: branches/xyz/generic_fns/value.py
URL:
http://svn.gna.org/viewcvs/relax/branches/xyz/generic_fns/value.py?rev=14340&r1=14339&r2=14340&view=diff
Modified: branches/xyz/prompt/interpreter.py
URL:
http://svn.gna.org/viewcvs/relax/branches/xyz/prompt/interpreter.py?rev=14340&r1=14339&r2=14340&view=diff
Modified: branches/xyz/prompt/molmol.py
URL:
http://svn.gna.org/viewcvs/relax/branches/xyz/prompt/molmol.py?rev=14340&r1=14339&r2=14340&view=diff
Modified: branches/xyz/relax_warnings.py
URL:
http://svn.gna.org/viewcvs/relax/branches/xyz/relax_warnings.py?rev=14340&r1=14339&r2=14340&view=diff
Modified: branches/xyz/scripts/optimisation_testing.py
URL:
http://svn.gna.org/viewcvs/relax/branches/xyz/scripts/optimisation_testing.py?rev=14340&r1=14339&r2=14340&view=diff
Modified: branches/xyz/specific_fns/model_free/molmol.py
URL:
http://svn.gna.org/viewcvs/relax/branches/xyz/specific_fns/model_free/molmol.py?rev=14340&r1=14339&r2=14340&view=diff
Modified: branches/xyz/status.py
URL:
http://svn.gna.org/viewcvs/relax/branches/xyz/status.py?rev=14340&r1=14339&r2=14340&view=diff
r14340 - in /branches/xyz: ./ auto_analyses/ data/ generic_fns/ generic_fns/structure/ prompt/ scripts/ specific_fns/model_f...