Author: bugman
Date: Thu Feb 18 19:09:59 2010
New Revision: 10759
URL: http://svn.gna.org/viewcvs/relax?rev=10759&view=rev
Log:
Merged revisions
10330,10404,10431-10435,10443,10450,10461-10462,10611-10612,10626-10631,10645,10652,10668-10671,10674,10676,10680,10684,10688-10689,10691,10694,10699,10703-10704,10708-10754
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
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r10330 | bugman | 2010-01-25 21:01:23 +0100 (Mon, 25 Jan 2010) | 3 lines
As a precaution, the spins will always be named in the automatic model-free
protocol.
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r10404 | bugman | 2010-01-26 18:38:14 +0100 (Tue, 26 Jan 2010) | 3 lines
The generic_fns.state.save_state() pickle arg now defaults to False.
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r10431 | bugman | 2010-01-27 12:54:10 +0100 (Wed, 27 Jan 2010) | 7 lines
Epydoc is now documenting everything!
The whitelist system of selected what to document was not working! Too
many packages are changing,
especially in the branches. Therefore absolutely everything is now being
documented, including the
test suite. This will allow all new packages to be automatically
documented.
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r10432 | bugman | 2010-01-27 13:01:21 +0100 (Wed, 27 Jan 2010) | 3 lines
Epydoc fixes for the dauvergne_protocol module docstring.
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r10433 | bugman | 2010-01-27 13:32:04 +0100 (Wed, 27 Jan 2010) | 3 lines
Epydoc fixes throughout the 'data' package.
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r10434 | bugman | 2010-01-27 13:33:11 +0100 (Wed, 27 Jan 2010) | 3 lines
Epydoc fixes for the 'opendx' package.
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r10435 | bugman | 2010-01-27 13:42:02 +0100 (Wed, 27 Jan 2010) | 3 lines
Epydoc fixes throughout the test suite.
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r10443 | bugman | 2010-01-27 17:22:00 +0100 (Wed, 27 Jan 2010) | 3 lines
The generic_fns.state.save_state() function can now have the verbosity
level changed.
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r10450 | bugman | 2010-01-27 18:24:53 +0100 (Wed, 27 Jan 2010) | 5 lines
Variable name fix for the from_xml() method.
relax_node should have been called pipe_node!
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r10461 | bugman | 2010-01-28 09:37:58 +0100 (Thu, 28 Jan 2010) | 3 lines
The generic_fns.state.load_state() function can now have the verbosity
level changed.
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r10462 | bugman | 2010-01-28 09:38:30 +0100 (Thu, 28 Jan 2010) | 3 lines
Epydoc fix for generic_fns.state.save_state(). Verbosity is a keyword arg!
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r10611 | bugman | 2010-02-01 23:36:57 +0100 (Mon, 01 Feb 2010) | 5 lines
Bug fix for the running of the test suite.
The interpreter _on() and _off() methods are now called on() and off()!
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r10612 | bugman | 2010-02-02 00:19:55 +0100 (Tue, 02 Feb 2010) | 3 lines
Switched from using a cone angle to using an order parameter in the
isotropic cone frame order model.
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r10626 | bugman | 2010-02-03 11:22:00 +0100 (Wed, 03 Feb 2010) | 5 lines
Added the stub function
maths_fns.order_parameters.iso_cone_S_to_cos_theta().
This will be used to convert the order parameter S into the cosine of the
cone angle.
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r10627 | bugman | 2010-02-03 18:00:17 +0100 (Wed, 03 Feb 2010) | 16 lines
Redesigned get_intro_string() to return a container of different strings.
The method is now called get_intro_text() and returns a container with the
following str objects:
- title: The program title 'relax'
- version: For example 'repository checkout' or '1.3.8'.
- desc: The short program description.
- copyright: A list of copyright statements.
- licence: Text pertaining to the licencing.
- errors: A list of import errors.
This is being abstracted so that the different UIs can use this
differently. The prompt/script can
word wrap to 100 char (80 char in Windows), and print this to stdout. The
GUI can use this in the
about prompt and not print to stdout. Other interfaces can use this in any
other way. And the
information content can be expanded for different purposes.
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r10628 | bugman | 2010-02-03 18:09:01 +0100 (Wed, 03 Feb 2010) | 6 lines
Shifted the introductory text object into its own module.
This makes the use of this object more flexible as anything and any part of
the program can import
it.
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r10629 | bugman | 2010-02-03 18:15:59 +0100 (Wed, 03 Feb 2010) | 5 lines
Shifted the spacing() method from relax to the intro module and renamed it
to centre().
The docstring has also been expanded to include epydoc tags.
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r10630 | bugman | 2010-02-03 18:26:28 +0100 (Wed, 03 Feb 2010) | 6 lines
The introductory text for the prompt/script based interface is now
recreated.
The _build_intro_text() method has been added to replicate the formatting
of the deleted
get_intro_text() method of the main relax class. This formatting is only
to be used in these 2 UIs.
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r10631 | bugman | 2010-02-03 18:28:49 +0100 (Wed, 03 Feb 2010) | 7 lines
Changed the program description again.
The program is now described as "Molecular dynamics by NMR data analysis".
This takes into account
that this is for proteins, RNA, DNA, organic molecules, sugars, etc., and
for relaxation data, RDCs,
PCSs, NOEs, and all NMR data.
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r10645 | bugman | 2010-02-04 17:33:24 +0100 (Thu, 04 Feb 2010) | 3 lines
Added the website and a long description to the Intro_text container.
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r10652 | bugman | 2010-02-04 18:31:37 +0100 (Thu, 04 Feb 2010) | 7 lines
Better UI separation in the Intro_text descriptions.
The 'help' assistance message has been shifted directly into
prompt.interpreter as it is only part
of the prompt/script interface. The GPL message has been changed to
specify that it is at the
prompt that you type GPL.
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r10668 | bugman | 2010-02-05 17:54:15 +0100 (Fri, 05 Feb 2010) | 5 lines
Renamed the intro.Intro_text class to info.Info_box.
This is used for introduction strings, but can be used at any point in
relax as well.
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r10669 | bugman | 2010-02-05 18:14:30 +0100 (Fri, 05 Feb 2010) | 3 lines
Updated the d'Auvergne and Gooley, 2008 references to have the full medline
info.
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r10670 | bugman | 2010-02-05 19:56:18 +0100 (Fri, 05 Feb 2010) | 3 lines
Fixes for the d'Auvergne and Gooley, 2008 references.
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r10671 | bugman | 2010-02-05 19:58:02 +0100 (Fri, 05 Feb 2010) | 5 lines
References pertaining to relax have been added to the info box container.
Each reference is a container placed within the 'bib' dictionary of the
info box class.
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r10674 | bugman | 2010-02-06 01:15:52 +0100 (Sat, 06 Feb 2010) | 3 lines
Created the reference base class 'Ref' and added cite_short() to build a
short citation.
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r10676 | bugman | 2010-02-06 01:34:06 +0100 (Sat, 06 Feb 2010) | 3 lines
Fixes for some journal titles. Periods have been added.
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r10680 | bugman | 2010-02-06 02:16:35 +0100 (Sat, 06 Feb 2010) | 6 lines
Created the module for the automatic relaxation curve fitting protocol.
This should better help define the API interface between the UIs and the
core, allowing all UIs to
benefit from advances in this code base.
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r10684 | bugman | 2010-02-06 02:52:44 +0100 (Sat, 06 Feb 2010) | 5 lines
A couple of fixes for the Relax_fit auto analysis class.
The interpreter was not being imported and a class variable was missing the
'self.' part!
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r10688 | bugman | 2010-02-09 11:36:44 +0100 (Tue, 09 Feb 2010) | 5 lines
Added support for using Me pseudo-atom RDCs.
This follows the method of Verdier, et al., JMR, 2003, 163, 353-359.
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r10689 | bugman | 2010-02-11 14:26:13 +0100 (Thu, 11 Feb 2010) | 3 lines
Added the cite_html() method to the citation base class to produce a HTML
formatted citation.
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r10691 | bugman | 2010-02-11 15:03:14 +0100 (Thu, 11 Feb 2010) | 5 lines
Fix for the cite_html() method.
The hyperlinks were incorrectly formed.
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r10694 | bugman | 2010-02-12 10:50:17 +0100 (Fri, 12 Feb 2010) | 5 lines
Fix for the iso cone frame order order parameter.
The c11^2, c12^2, c21^2 and c22^2 element equations were incorrect.
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r10699 | bugman | 2010-02-16 11:01:35 +0100 (Tue, 16 Feb 2010) | 5 lines
Fix for the Lipari and Szabo reference information.
The classes were not being instantiated.
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r10703 | bugman | 2010-02-16 14:16:23 +0100 (Tue, 16 Feb 2010) | 5 lines
The proper function from the order_parameters module is being called to
calc the cone angle.
This allows the code to operate, but the function is not yet implemented.
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r10704 | bugman | 2010-02-16 14:38:47 +0100 (Tue, 16 Feb 2010) | 5 lines
Fix for the cite_html() bibliography method.
The <em> tag was not being closed!
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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/multi_processor_merge/auto_analyses/relax_fit.py
- copied unchanged from r10754, 1.3/auto_analyses/relax_fit.py
branches/multi_processor_merge/auto_analyses/stereochem_analysis.py
- copied unchanged from r10754, 1.3/auto_analyses/stereochem_analysis.py
branches/multi_processor_merge/info.py
- copied unchanged from r10754, 1.3/info.py
branches/multi_processor_merge/maths_fns/order_parameters.py
- copied unchanged from r10754, 1.3/maths_fns/order_parameters.py
branches/multi_processor_merge/sample_scripts/stereochem_analysis.py
- copied unchanged from r10754,
1.3/sample_scripts/stereochem_analysis.py
branches/multi_processor_merge/test_suite/shared_data/rdc_data/
- copied from r10754, 1.3/test_suite/shared_data/rdc_data/
branches/multi_processor_merge/test_suite/shared_data/structures/phthalic_acid/
- copied from r10754,
1.3/test_suite/shared_data/structures/phthalic_acid/
branches/multi_processor_merge/test_suite/system_tests/scripts/n_state_model/
- copied from r10754, 1.3/test_suite/system_tests/scripts/n_state_model/
branches/multi_processor_merge/test_suite/unit_tests/_auto_analyses/
- copied from r10754, 1.3/test_suite/unit_tests/_auto_analyses/
Removed:
branches/multi_processor_merge/test_suite/shared_data/structures/gromacs_phthalic_acid.pdb
branches/multi_processor_merge/test_suite/system_tests/scripts/5_state_xz.py
branches/multi_processor_merge/test_suite/system_tests/scripts/align_fit.py
branches/multi_processor_merge/test_suite/system_tests/scripts/lactose_n_state.py
branches/multi_processor_merge/test_suite/system_tests/scripts/phthalic_acid_noes.py
Modified:
branches/multi_processor_merge/ (props changed)
branches/multi_processor_merge/auto_analyses/__init__.py
branches/multi_processor_merge/auto_analyses/dauvergne_protocol.py
branches/multi_processor_merge/data/__init__.py
branches/multi_processor_merge/data/align_tensor.py
branches/multi_processor_merge/data/diff_tensor.py
branches/multi_processor_merge/data/pipe_container.py
branches/multi_processor_merge/data/relax_xml.py
branches/multi_processor_merge/docs/latex/bibliography.bib
branches/multi_processor_merge/generic_fns/pcs.py
branches/multi_processor_merge/generic_fns/rdc.py
branches/multi_processor_merge/generic_fns/state.py
branches/multi_processor_merge/maths_fns/__init__.py
branches/multi_processor_merge/maths_fns/frame_order.py
branches/multi_processor_merge/maths_fns/frame_order_matrix_ops.py
[... 132 lines stripped ...]
r10759 - in /branches/multi_processor_merge: ./ auto_analyses/ data/ docs/latex/ generic_fns/ maths_fns/ opendx/ prompt/ sam...