Author: bugman
Date: Thu Feb 18 18:54:12 2010
New Revision: 10755
URL: http://svn.gna.org/viewcvs/relax?rev=10755&view=rev
Log:
Merged revisions 10708-10754 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/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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Added:
branches/bieri_gui/auto_analyses/stereochem_analysis.py
- copied unchanged from r10754, 1.3/auto_analyses/stereochem_analysis.py
branches/bieri_gui/sample_scripts/stereochem_analysis.py
- copied unchanged from r10754,
1.3/sample_scripts/stereochem_analysis.py
branches/bieri_gui/test_suite/shared_data/rdc_data/
- copied from r10754, 1.3/test_suite/shared_data/rdc_data/
branches/bieri_gui/test_suite/shared_data/structures/phthalic_acid/
- copied from r10754,
1.3/test_suite/shared_data/structures/phthalic_acid/
branches/bieri_gui/test_suite/system_tests/scripts/n_state_model/
- copied from r10754, 1.3/test_suite/system_tests/scripts/n_state_model/
branches/bieri_gui/test_suite/unit_tests/_auto_analyses/
- copied from r10754, 1.3/test_suite/unit_tests/_auto_analyses/
Removed:
branches/bieri_gui/test_suite/shared_data/structures/gromacs_phthalic_acid.pdb
branches/bieri_gui/test_suite/system_tests/scripts/5_state_xz.py
branches/bieri_gui/test_suite/system_tests/scripts/align_fit.py
branches/bieri_gui/test_suite/system_tests/scripts/lactose_n_state.py
branches/bieri_gui/test_suite/system_tests/scripts/phthalic_acid_noes.py
Modified:
branches/bieri_gui/ (props changed)
branches/bieri_gui/auto_analyses/__init__.py
branches/bieri_gui/generic_fns/pcs.py
branches/bieri_gui/generic_fns/rdc.py
branches/bieri_gui/maths_fns/rotation_matrix.py
branches/bieri_gui/prompt/pcs.py
branches/bieri_gui/prompt/rdc.py
branches/bieri_gui/specific_fns/n_state_model.py
branches/bieri_gui/test_suite/system_tests/load_spins.py
branches/bieri_gui/test_suite/system_tests/n_state_model.py
branches/bieri_gui/test_suite/system_tests/noe_restraints.py
branches/bieri_gui/test_suite/system_tests/scripts/load_spins_from_small_molecule.py
branches/bieri_gui/test_suite/system_tests/structure.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/bieri_gui/auto_analyses/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/auto_analyses/__init__.py?rev=10755&r1=10754&r2=10755&view=diff
Modified: branches/bieri_gui/generic_fns/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/generic_fns/pcs.py?rev=10755&r1=10754&r2=10755&view=diff
Modified: branches/bieri_gui/generic_fns/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/generic_fns/rdc.py?rev=10755&r1=10754&r2=10755&view=diff
Modified: branches/bieri_gui/maths_fns/rotation_matrix.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/maths_fns/rotation_matrix.py?rev=10755&r1=10754&r2=10755&view=diff
Modified: branches/bieri_gui/prompt/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/pcs.py?rev=10755&r1=10754&r2=10755&view=diff
Modified: branches/bieri_gui/prompt/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/rdc.py?rev=10755&r1=10754&r2=10755&view=diff
Modified: branches/bieri_gui/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/specific_fns/n_state_model.py?rev=10755&r1=10754&r2=10755&view=diff
Removed:
branches/bieri_gui/test_suite/shared_data/structures/gromacs_phthalic_acid.pdb
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/test_suite/shared_data/structures/gromacs_phthalic_acid.pdb?rev=10754&view=auto
Modified: branches/bieri_gui/test_suite/system_tests/load_spins.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/test_suite/system_tests/load_spins.py?rev=10755&r1=10754&r2=10755&view=diff
Modified: branches/bieri_gui/test_suite/system_tests/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/test_suite/system_tests/n_state_model.py?rev=10755&r1=10754&r2=10755&view=diff
Modified: branches/bieri_gui/test_suite/system_tests/noe_restraints.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/test_suite/system_tests/noe_restraints.py?rev=10755&r1=10754&r2=10755&view=diff
Removed: branches/bieri_gui/test_suite/system_tests/scripts/5_state_xz.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/test_suite/system_tests/scripts/5_state_xz.py?rev=10754&view=auto
Removed: branches/bieri_gui/test_suite/system_tests/scripts/align_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/test_suite/system_tests/scripts/align_fit.py?rev=10754&view=auto
Removed: branches/bieri_gui/test_suite/system_tests/scripts/lactose_n_state.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/test_suite/system_tests/scripts/lactose_n_state.py?rev=10754&view=auto
Modified:
branches/bieri_gui/test_suite/system_tests/scripts/load_spins_from_small_molecule.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/test_suite/system_tests/scripts/load_spins_from_small_molecule.py?rev=10755&r1=10754&r2=10755&view=diff
Removed:
branches/bieri_gui/test_suite/system_tests/scripts/phthalic_acid_noes.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/test_suite/system_tests/scripts/phthalic_acid_noes.py?rev=10754&view=auto
Modified: branches/bieri_gui/test_suite/system_tests/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/test_suite/system_tests/structure.py?rev=10755&r1=10754&r2=10755&view=diff
r10755 - in /branches/bieri_gui: ./ auto_analyses/ generic_fns/ maths_fns/ prompt/ sample_scripts/ specific_fns/ test_suite/...