svn+ssh://bugman@.../svn/relax/1.3
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r10708 | bugman | 2010-02-18 10:47:55 +0100 (Thu, 18 Feb 2010) | 3 lines
Alphabetical ordering of the rotation matrix module functions.
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r10709 | bugman | 2010-02-18 10:59:41 +0100 (Thu, 18 Feb 2010) | 3 lines
Added the tilt and torsion angle convention conversions to and from rotation matrices.
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r10710 | bugman | 2010-02-18 11:41:19 +0100 (Thu, 18 Feb 2010) | 6 lines
Shifted the RDC and PCS Q-factor calculation code.
The methods previously in the N-state model specific code have been converted to functions of the
generic_fns.rdc and generic_fns.pcs modules.
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r10711 | bugman | 2010-02-18 13:24:04 +0100 (Thu, 18 Feb 2010) | 6 lines
The Q-factor calculation functions can now accept a spin_id arg.
As there can now be data problems, the functions check if there is any selected spins looped over,
that the is RDC/PCS data, and that there is back-calculated RDC/PCS data.
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r10712 | bugman | 2010-02-18 13:27:07 +0100 (Thu, 18 Feb 2010) | 5 lines
Created the rdc.calc_q_factors() and pcs.calc_q_factors() user functions.
The back-calculated RDC/PCS data must first be generated by the specific code.
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r10713 | bugman | 2010-02-18 13:27:30 +0100 (Thu, 18 Feb 2010) | 3 lines
Docstring fix for pcs.calc_q_factors().
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r10714 | bugman | 2010-02-18 13:35:14 +0100 (Thu, 18 Feb 2010) | 3 lines
Added a directory for the unit tests of the modules of the auto_analyses package.
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r10715 | bugman | 2010-02-18 13:36:13 +0100 (Thu, 18 Feb 2010) | 3 lines
Copied the __init__.py unit tests module from the _specific_fns directory.
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r10716 | bugman | 2010-02-18 13:38:32 +0100 (Thu, 18 Feb 2010) | 3 lines
Added a __ini__ module to the _auto_analyses unit test package.
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r10717 | bugman | 2010-02-18 13:39:02 +0100 (Thu, 18 Feb 2010) | 3 lines
Modified the _auto_analyses.test___init__ module for the auto_analyses package.
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r10718 | bugman | 2010-02-18 13:51:40 +0100 (Thu, 18 Feb 2010) | 6 lines
Added to the auto_analyses the script for determining relative stereochemistry of organic molecules.
This code corresponds to a paper in press. The script will need to be modified to function as an
auto-analysis, and the actual configuration file turned into the real script.
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r10719 | bugman | 2010-02-18 13:53:39 +0100 (Thu, 18 Feb 2010) | 5 lines
Added the relative stereochemistry analysis configuration file.
This will be converted into a relax script.
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r10720 | bugman | 2010-02-18 13:54:12 +0100 (Thu, 18 Feb 2010) | 3 lines
Renamed the stereochem_analysis_config.py file to the stereochem_analysis.py relax script.
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r10721 | bugman | 2010-02-18 14:04:02 +0100 (Thu, 18 Feb 2010) | 5 lines
Converted stereochem_analysis.py into a true relax script.
This now calls the auto_analyses.stereochem_analysi code.
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r10722 | bugman | 2010-02-18 14:10:07 +0100 (Thu, 18 Feb 2010) | 5 lines
Modified the script so that __init__ sets up the class and run() executes the analysis.
This is not implemented on the other side yet.
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r10723 | bugman | 2010-02-18 14:11:26 +0100 (Thu, 18 Feb 2010) | 3 lines
Added a copyright notice to the stereochem_analysis.py sample script.
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r10724 | bugman | 2010-02-18 14:12:28 +0100 (Thu, 18 Feb 2010) | 3 lines
Added a copyright notice to the stereochem_analysis auto-analysis.
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r10725 | bugman | 2010-02-18 14:12:52 +0100 (Thu, 18 Feb 2010) | 3 lines
Module docstring changes. This is no longer a script!
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r10726 | bugman | 2010-02-18 14:13:49 +0100 (Thu, 18 Feb 2010) | 5 lines
Removed some unused code and comments at the top of the ex-script.
A config file is no longer read.
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r10727 | bugman | 2010-02-18 14:14:16 +0100 (Thu, 18 Feb 2010) | 3 lines
Renamed StereoAnalysis to Stereochem_analysis and added 'relative' to the class docstring.
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r10728 | bugman | 2010-02-18 14:17:07 +0100 (Thu, 18 Feb 2010) | 5 lines
Separated the stereochem_analysis auto-analysis execution into the run() method.
This leaves __init__() with the job of setting up the class.
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r10729 | bugman | 2010-02-18 14:19:13 +0100 (Thu, 18 Feb 2010) | 3 lines
Removed the class instantiation from the auto_analyses.stereochem_analysis module.
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r10730 | bugman | 2010-02-18 14:25:05 +0100 (Thu, 18 Feb 2010) | 3 lines
The __init__() method now accepts all the keyword args and stores them in the class namespace.
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r10731 | bugman | 2010-02-18 14:30:35 +0100 (Thu, 18 Feb 2010) | 3 lines
Converted the all-caps module variables into lower case class variables.
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r10732 | bugman | 2010-02-18 14:31:58 +0100 (Thu, 18 Feb 2010) | 3 lines
Fix for the stereochem_analysis.py sample script - the instantiated class run() method must be run!
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r10733 | bugman | 2010-02-18 14:43:04 +0100 (Thu, 18 Feb 2010) | 3 lines
The interpreter is now imported and set up. User function calls are now passed through this class.
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r10734 | bugman | 2010-02-18 14:43:39 +0100 (Thu, 18 Feb 2010) | 3 lines
Missing import of pi.
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r10735 | bugman | 2010-02-18 15:03:55 +0100 (Thu, 18 Feb 2010) | 3 lines
Added a directory to the test suite data for holding phthalic acid structures.
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r10736 | bugman | 2010-02-18 15:13:23 +0100 (Thu, 18 Feb 2010) | 3 lines
Updated the package __all__ list to include all modules.
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r10737 | bugman | 2010-02-18 15:57:22 +0100 (Thu, 18 Feb 2010) | 3 lines
Shifted the Gromacs phthalic acid structure.
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r10738 | bugman | 2010-02-18 16:32:06 +0100 (Thu, 18 Feb 2010) | 5 lines
A results directory can now be specified in the stereochem_analysis auto-analysis.
This is not being used yet.
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r10739 | bugman | 2010-02-18 16:34:08 +0100 (Thu, 18 Feb 2010) | 3 lines
The cwd is used if no results_dir arg is given.
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r10740 | bugman | 2010-02-18 16:48:48 +0100 (Thu, 18 Feb 2010) | 3 lines
The stereochem_analysis auto-analysis is now placing all generated files into the desired results dir.
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r10741 | bugman | 2010-02-18 16:53:13 +0100 (Thu, 18 Feb 2010) | 5 lines
STDOUT is now being restored after each stage.
STDOUT was being lost if logging was turned on!
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r10742 | bugman | 2010-02-18 17:05:55 +0100 (Thu, 18 Feb 2010) | 5 lines
The Grace plots are now being created.
The sorted results files were not been checked for in the results directory.
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r10743 | bugman | 2010-02-18 17:08:35 +0100 (Thu, 18 Feb 2010) | 5 lines
Added a few Gromacs QM/MM snapshots.
This will be used for a stereochemistry analysis system test.
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r10744 | bugman | 2010-02-18 17:10:22 +0100 (Thu, 18 Feb 2010) | 3 lines
Added the phthalic acid RDC data aligned in a PAN gel.
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r10745 | bugman | 2010-02-18 17:12:26 +0100 (Thu, 18 Feb 2010) | 3 lines
Created a directory for collecting all N-state model system test scripts together.
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r10746 | bugman | 2010-02-18 17:16:25 +0100 (Thu, 18 Feb 2010) | 3 lines
Shifted all the N-state model scripts into their directory.
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r10747 | bugman | 2010-02-18 17:30:01 +0100 (Thu, 18 Feb 2010) | 3 lines
Added a system test script for testing the relative stereochemistry analysis.
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r10748 | bugman | 2010-02-18 17:33:34 +0100 (Thu, 18 Feb 2010) | 5 lines
Fixes for all the N-state model system tests.
The scripts were moved to a sub-directory!
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r10749 | bugman | 2010-02-18 17:44:15 +0100 (Thu, 18 Feb 2010) | 3 lines
Fixes for the NOE restraint system tests as these involve the N-state model.
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r10750 | bugman | 2010-02-18 18:04:59 +0100 (Thu, 18 Feb 2010) | 3 lines
Enabled the relative stereochemistry analysis system test.
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r10751 | bugman | 2010-02-18 18:05:15 +0100 (Thu, 18 Feb 2010) | 3 lines
Bug fix for the snapshot paths.
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r10752 | bugman | 2010-02-18 18:06:27 +0100 (Thu, 18 Feb 2010) | 3 lines
Another fix for the stereochem_analysis system test, the results dir is now in ds.tmpdir.
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r10753 | bugman | 2010-02-18 18:24:33 +0100 (Thu, 18 Feb 2010) | 3 lines
Fixes for STDOUT control in the auto_analyses.stereochem_analysis module.
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r10754 | bugman | 2010-02-18 18:43:29 +0100 (Thu, 18 Feb 2010) | 3 lines
Added checks for all of the results files being present in the tmp directory.
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