Author: bugman
Date: Fri Jan 17 12:23:16 2014
New Revision: 22028
URL: http://svn.gna.org/viewcvs/relax?rev=22028&view=rev
Log:
Merged revisions 21980,21983-22012,22016,22024-22027 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r21980 | bugman | 2014-01-15 10:40:53 +0100 (Wed, 15 Jan 2014) | 3 lines
Fix for the parameters listed for the IT99 dispersion model in the manual.
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r21983 | bugman | 2014-01-15 15:55:32 +0100 (Wed, 15 Jan 2014) | 6 lines
Improvements and addition of many links to the lib.dispersion.cr72 API
documentation.
This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.cr72-module.html.
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r21984 | bugman | 2014-01-15 15:57:31 +0100 (Wed, 15 Jan 2014) | 3 lines
Spacing fix for the lib.dispersion.cr72 module docstring.
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r21985 | bugman | 2014-01-15 16:00:51 +0100 (Wed, 15 Jan 2014) | 6 lines
Improvements and addition of many links to the lib.dispersion.dpl94 API
documentation.
This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.dpl94-module.html.
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r21986 | bugman | 2014-01-15 16:05:26 +0100 (Wed, 15 Jan 2014) | 6 lines
Improvements and addition of many links to the lib.dispersion.it99 API
documentation.
This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.it99-module.html.
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r21987 | bugman | 2014-01-15 16:10:19 +0100 (Wed, 15 Jan 2014) | 6 lines
Improvements and addition of many links to the lib.dispersion.lm63_3site
API documentation.
This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.lm63_3site-module.html.
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r21988 | bugman | 2014-01-15 16:15:23 +0100 (Wed, 15 Jan 2014) | 6 lines
Improvements and addition of many links to the lib.dispersion.lm63 API
documentation.
This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.lm63-module.html.
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r21989 | bugman | 2014-01-15 16:20:07 +0100 (Wed, 15 Jan 2014) | 6 lines
Improvements and addition of many links to the lib.dispersion.m61b API
documentation.
This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.m61b-module.html.
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r21990 | bugman | 2014-01-15 16:26:03 +0100 (Wed, 15 Jan 2014) | 6 lines
Improvements and addition of many links to the lib.dispersion.m61 API
documentation.
This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.m61-module.html.
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r21991 | bugman | 2014-01-15 16:31:41 +0100 (Wed, 15 Jan 2014) | 6 lines
Improvements and addition of many links to the lib.dispersion.mmq_cr72 API
documentation.
This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.mmq_cr72-module.html.
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r21992 | bugman | 2014-01-15 16:42:33 +0100 (Wed, 15 Jan 2014) | 6 lines
Improvements and addition of many links to the lib.dispersion.mp05 API
documentation.
This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.mp05-module.html.
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r21993 | bugman | 2014-01-15 16:50:56 +0100 (Wed, 15 Jan 2014) | 6 lines
Improvements and addition of many links to the
lib.dispersion.ns_cpmg_2site_3d API documentation.
This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_cpmg_2site_3d-module.html.
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r21994 | bugman | 2014-01-15 16:55:01 +0100 (Wed, 15 Jan 2014) | 3 lines
Epydoc URL simplifications.
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r21995 | bugman | 2014-01-15 16:59:09 +0100 (Wed, 15 Jan 2014) | 6 lines
Improvements and addition of many links to the
lib.dispersion.ns_cpmg_2site_expanded API documentation.
This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_cpmg_2site_expanded-module.html.
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r21996 | bugman | 2014-01-15 17:14:49 +0100 (Wed, 15 Jan 2014) | 6 lines
Improvements and addition of many links to the
lib.dispersion.ns_cpmg_2site_star API documentation.
This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_cpmg_2site_star-module.html.
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r21997 | bugman | 2014-01-15 17:16:45 +0100 (Wed, 15 Jan 2014) | 3 lines
Added the 'NS CPMG 2-site 3D full' model to the
lib.dispersion.ns_cpmg_2site_3d module docstring.
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r21998 | bugman | 2014-01-15 17:33:31 +0100 (Wed, 15 Jan 2014) | 6 lines
Improvements and addition of many links to the lib.dispersion.ns_mmq_2site
API documentation.
This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_mmq_2site-module.html.
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r21999 | bugman | 2014-01-15 17:46:40 +0100 (Wed, 15 Jan 2014) | 6 lines
Improvements and addition of many links to the lib.dispersion.ns_mmq_3site
API documentation.
This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_mmq_3site-module.html.
........
r22000 | bugman | 2014-01-15 17:53:00 +0100 (Wed, 15 Jan 2014) | 6 lines
Improvements and addition of many links to the
lib.dispersion.ns_r1rho_2site API documentation.
This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_r1rho_2site-module.html.
........
r22001 | bugman | 2014-01-15 17:58:09 +0100 (Wed, 15 Jan 2014) | 6 lines
Improvements and addition of many links to the
lib.dispersion.ns_r1rho_3site API documentation.
This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_r1rho_3site-module.html.
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r22002 | bugman | 2014-01-15 17:59:22 +0100 (Wed, 15 Jan 2014) | 3 lines
Small docstring edit for the lib.dispersion.mp05 module.
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r22003 | bugman | 2014-01-15 18:03:09 +0100 (Wed, 15 Jan 2014) | 6 lines
Improvements and addition of many links to the lib.dispersion.tap03 API
documentation.
This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.tap03-module.html.
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r22004 | bugman | 2014-01-15 18:20:18 +0100 (Wed, 15 Jan 2014) | 6 lines
Improvements and addition of many links to the lib.dispersion.tp02 API
documentation.
This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.tp02-module.html.
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r22005 | bugman | 2014-01-15 18:20:37 +0100 (Wed, 15 Jan 2014) | 3 lines
Epydoc URL simplifications in the lib.dispersion.mp05 module.
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r22006 | bugman | 2014-01-15 18:24:35 +0100 (Wed, 15 Jan 2014) | 3 lines
Epydoc docstring edit in the lib.dispersion.mmq_cr72 module.
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r22007 | bugman | 2014-01-15 18:30:44 +0100 (Wed, 15 Jan 2014) | 6 lines
Improvements and addition of many links to the lib.dispersion.tsmfk01 API
documentation.
This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.tsmfk01-module.html.
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r22008 | bugman | 2014-01-15 18:32:16 +0100 (Wed, 15 Jan 2014) | 3 lines
Copyright notice updates for the lib.dispersion modules changed today.
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r22009 | bugman | 2014-01-16 15:36:04 +0100 (Thu, 16 Jan 2014) | 85 lines
Added links to the relax wiki, API documentation, and relax website to all
dispersion models in the manual.
This is to make it easier to find additional information about each of the
models.
For reference, the relax wiki links are:
http://wiki.nmr-relax.com/R2eff
http://wiki.nmr-relax.com/No_Rex
http://wiki.nmr-relax.com/LM63
http://wiki.nmr-relax.com/LM63_3-site
http://wiki.nmr-relax.com/CR72_full
http://wiki.nmr-relax.com/CR72
http://wiki.nmr-relax.com/IT99
http://wiki.nmr-relax.com/TSMFK01
http://wiki.nmr-relax.com/NS_CPMG_2-site_expanded
http://wiki.nmr-relax.com/NS_CPMG_2-site_3D_full
http://wiki.nmr-relax.com/NS_CPMG_2-site_3D
http://wiki.nmr-relax.com/NS_CPMG_2-site_star_full
http://wiki.nmr-relax.com/NS_CPMG_2-site_star
http://wiki.nmr-relax.com/MMQ_CR72
http://wiki.nmr-relax.com/NS_MMQ_2-site
http://wiki.nmr-relax.com/NS_MMQ_3-site_linear
http://wiki.nmr-relax.com/NS_MMQ_3-site
http://wiki.nmr-relax.com/M61
http://wiki.nmr-relax.com/M61_skew
http://wiki.nmr-relax.com/DPL94
http://wiki.nmr-relax.com/TP02
http://wiki.nmr-relax.com/TAP03
http://wiki.nmr-relax.com/MP05
http://wiki.nmr-relax.com/NS_R1rho_2-site
http://wiki.nmr-relax.com/NS_R1rho_3-site
http://wiki.nmr-relax.com/NS_R1rho_3-site_linear
The API documentation links are:
http://www.nmr-relax.com/api/3.1/specific_analyses.relax_disp.optimisation-module.html#back_calc_r2eff
http://www.nmr-relax.com/api/3.1/lib.dispersion.two_point-module.html#calc_two_point_r2eff
http://www.nmr-relax.com/api/3.1/target_functions.relax_disp.Dispersion-class.html#func_NOREX
http://www.nmr-relax.com/api/3.1/lib.dispersion.lm63-module.html
http://www.nmr-relax.com/api/3.1/lib.dispersion.lm63_3site-module.html
http://www.nmr-relax.com/api/3.1/lib.dispersion.cr72-module.html
http://www.nmr-relax.com/api/3.1/lib.dispersion.it99-module.html
http://www.nmr-relax.com/api/3.1/lib.dispersion.tsmfk01-module.html
http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_cpmg_2site_expanded-module.html
http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_cpmg_2site_3d-module.html
http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_cpmg_2site_star-module.html
http://www.nmr-relax.com/api/3.1/lib.dispersion.mmq_cr72-module.html
http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_mmq_2site-module.html
http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_mmq_3site-module.html
http://www.nmr-relax.com/api/3.1/lib.dispersion.m61-module.html
http://www.nmr-relax.com/api/3.1/lib.dispersion.m61b-module.html
http://www.nmr-relax.com/api/3.1/lib.dispersion.dpl94-module.html
http://www.nmr-relax.com/api/3.1/lib.dispersion.tp02-module.html
http://www.nmr-relax.com/api/3.1/lib.dispersion.tap03-module.html
http://www.nmr-relax.com/api/3.1/lib.dispersion.mp05-module.html
http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_r1rho_2site-module.html
http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_r1rho_3site-module.html
The relax website links are:
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#R2eff
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#No_Rex
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#LM63
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#LM63_3-site
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#CR72_full
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#CR72
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#IT99
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#TSMFK01
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#NS_CPMG_2-site_expanded
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#NS_CPMG_2-site_3D_full
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#NS_CPMG_2-site_3D
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#NS_CPMG_2-site_star_full
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#NS_CPMG_2-site_star
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#MMQ_CR72
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#NS_MMQ_2-site
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#NS_MMQ_3-site_linear
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#NS_MMQ_3-site
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#M61
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#M61_skew
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#DPL94
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#TP02
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#TAP03
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#MP05
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#NS_R1rho_2-site
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#NS_R1rho_3-site
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#NS_R1rho_3-site_linear
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r22010 | bugman | 2014-01-16 16:06:40 +0100 (Thu, 16 Jan 2014) | 3 lines
Updated the author list for the submitted paper for the relaxation
dispersion analysis.
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r22011 | bugman | 2014-01-16 16:07:41 +0100 (Thu, 16 Jan 2014) | 5 lines
Added the primary reference for relaxation dispersion in relax to the
dispersion chapter of the manual.
This is the paper which is not published yet.
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r22012 | bugman | 2014-01-16 16:09:49 +0100 (Thu, 16 Jan 2014) | 5 lines
Removed the single quantum R1rho-type data reference in the introduction of
the dispersion chapter of the manual.
This is redundant as R1rho data is always single quantum.
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r22016 | bugman | 2014-01-16 16:19:10 +0100 (Thu, 16 Jan 2014) | 6 lines
Backported the relax 3.1.3 CHANGES file addition to trunk.
The command used was:
svn merge -r22014:22015 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/3.1.3 .
........
r22024 | bugman | 2014-01-17 11:51:16 +0100 (Fri, 17 Jan 2014) | 12 lines
Created the Frame_order.test_generate_rotor2_distribution system test.
This is to test the Frame Order distribution generating base script, used
for creating the synthetic
Frame Order test data, and to demonstrate a failure in handling
back-calculated RDC data.
To implement this, the test_suite/shared_data/frame_order/cam/ path has
been converted into a Python
package (with the addition of the __init__.py files). The base data
generation script
test_suite/shared_data/frame_order/cam/generate_base.py has also been
modified to use the absolute
path for the data files and its run() method now accepts the save_path
argument to allow the files
to be saved into a temporary directory.
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r22025 | bugman | 2014-01-17 11:57:50 +0100 (Fri, 17 Jan 2014) | 6 lines
Fix for bug #21499 (https://gna.org/bugs/?21499), the failure of the
rdc.write user function.
The rdc.write user function fails for back-calculated RDC data. The fix
was to handle the missing
interatom.rdc_data_types variable.
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r22026 | bugman | 2014-01-17 12:00:43 +0100 (Fri, 17 Jan 2014) | 7 lines
Fixes for the Frame_order.test_generate_rotor2_distribution system test.
The test_suite/shared_data/frame_order/cam/generate_base.py script now
saves the program state files
into the self.save_path directory, preventing the system test from
attempting to save files into the
relax test suite directories.
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r22027 | bugman | 2014-01-17 12:02:58 +0100 (Fri, 17 Jan 2014) | 7 lines
Another fix for the Frame_order.test_generate_rotor2_distribution system
test.
The test_suite/shared_data/frame_order/cam/generate_base.py script no
longer prints its progress
indicator to sys.__stderr__ but to sys.stderr instead. This avoids the
progress text from appearing
during the relax test suite execution.
........
Added:
branches/double_rotor/test_suite/shared_data/frame_order/__init__.py
- copied unchanged from r22027,
trunk/test_suite/shared_data/frame_order/__init__.py
branches/double_rotor/test_suite/shared_data/frame_order/cam/__init__.py
- copied unchanged from r22027,
trunk/test_suite/shared_data/frame_order/cam/__init__.py
branches/double_rotor/test_suite/system_tests/scripts/frame_order/cam/generate_rotor2_distribution.py
- copied unchanged from r22027,
trunk/test_suite/system_tests/scripts/frame_order/cam/generate_rotor2_distribution.py
Modified:
branches/double_rotor/ (props changed)
branches/double_rotor/docs/CHANGES
branches/double_rotor/docs/latex/bibliography.bib
branches/double_rotor/docs/latex/dispersion.tex
branches/double_rotor/lib/dispersion/cr72.py
branches/double_rotor/lib/dispersion/dpl94.py
branches/double_rotor/lib/dispersion/it99.py
branches/double_rotor/lib/dispersion/lm63.py
branches/double_rotor/lib/dispersion/lm63_3site.py
branches/double_rotor/lib/dispersion/m61.py
branches/double_rotor/lib/dispersion/m61b.py
branches/double_rotor/lib/dispersion/mmq_cr72.py
branches/double_rotor/lib/dispersion/mp05.py
branches/double_rotor/lib/dispersion/ns_cpmg_2site_3d.py
branches/double_rotor/lib/dispersion/ns_cpmg_2site_expanded.py
branches/double_rotor/lib/dispersion/ns_cpmg_2site_star.py
branches/double_rotor/lib/dispersion/ns_mmq_2site.py
branches/double_rotor/lib/dispersion/ns_mmq_3site.py
branches/double_rotor/lib/dispersion/ns_r1rho_2site.py
branches/double_rotor/lib/dispersion/ns_r1rho_3site.py
branches/double_rotor/lib/dispersion/tap03.py
branches/double_rotor/lib/dispersion/tp02.py
branches/double_rotor/lib/dispersion/tsmfk01.py
branches/double_rotor/pipe_control/rdc.py
branches/double_rotor/test_suite/shared_data/__init__.py
branches/double_rotor/test_suite/shared_data/frame_order/cam/generate_base.py
branches/double_rotor/test_suite/system_tests/frame_order.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/double_rotor/docs/CHANGES
URL:
http://svn.gna.org/viewcvs/relax/branches/double_rotor/docs/CHANGES?rev=22028&r1=22027&r2=22028&view=diff
Modified: branches/double_rotor/docs/latex/bibliography.bib
URL:
http://svn.gna.org/viewcvs/relax/branches/double_rotor/docs/latex/bibliography.bib?rev=22028&r1=22027&r2=22028&view=diff
Modified: branches/double_rotor/docs/latex/dispersion.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/double_rotor/docs/latex/dispersion.tex?rev=22028&r1=22027&r2=22028&view=diff
Modified: branches/double_rotor/lib/dispersion/cr72.py
URL:
http://svn.gna.org/viewcvs/relax/branches/double_rotor/lib/dispersion/cr72.py?rev=22028&r1=22027&r2=22028&view=diff
Modified: branches/double_rotor/lib/dispersion/dpl94.py
URL:
http://svn.gna.org/viewcvs/relax/branches/double_rotor/lib/dispersion/dpl94.py?rev=22028&r1=22027&r2=22028&view=diff
Modified: branches/double_rotor/lib/dispersion/it99.py
URL:
http://svn.gna.org/viewcvs/relax/branches/double_rotor/lib/dispersion/it99.py?rev=22028&r1=22027&r2=22028&view=diff
Modified: branches/double_rotor/lib/dispersion/lm63.py
URL:
http://svn.gna.org/viewcvs/relax/branches/double_rotor/lib/dispersion/lm63.py?rev=22028&r1=22027&r2=22028&view=diff
Modified: branches/double_rotor/lib/dispersion/lm63_3site.py
URL:
http://svn.gna.org/viewcvs/relax/branches/double_rotor/lib/dispersion/lm63_3site.py?rev=22028&r1=22027&r2=22028&view=diff
Modified: branches/double_rotor/lib/dispersion/m61.py
URL:
http://svn.gna.org/viewcvs/relax/branches/double_rotor/lib/dispersion/m61.py?rev=22028&r1=22027&r2=22028&view=diff
Modified: branches/double_rotor/lib/dispersion/m61b.py
URL:
http://svn.gna.org/viewcvs/relax/branches/double_rotor/lib/dispersion/m61b.py?rev=22028&r1=22027&r2=22028&view=diff
Modified: branches/double_rotor/lib/dispersion/mmq_cr72.py
URL:
http://svn.gna.org/viewcvs/relax/branches/double_rotor/lib/dispersion/mmq_cr72.py?rev=22028&r1=22027&r2=22028&view=diff
Modified: branches/double_rotor/lib/dispersion/mp05.py
URL:
http://svn.gna.org/viewcvs/relax/branches/double_rotor/lib/dispersion/mp05.py?rev=22028&r1=22027&r2=22028&view=diff
Modified: branches/double_rotor/lib/dispersion/ns_cpmg_2site_3d.py
URL:
http://svn.gna.org/viewcvs/relax/branches/double_rotor/lib/dispersion/ns_cpmg_2site_3d.py?rev=22028&r1=22027&r2=22028&view=diff
Modified: branches/double_rotor/lib/dispersion/ns_cpmg_2site_expanded.py
[... 38 lines stripped ...]
r22028 - in /branches/double_rotor: ./ docs/ docs/latex/ lib/dispersion/ pipe_control/ test_suite/shared_data/ test_suite/sh...