Author: bugman
Date: Thu Nov 27 19:33:41 2014
New Revision: 26793
URL: http://svn.gna.org/viewcvs/relax?rev=26793&view=rev
Log:
Merged revisions 26746-26747,26760,26768-26771,26782,26791 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r26746 | bugman | 2014-11-26 11:12:30 +0100 (Wed, 26 Nov 2014) | 8 lines
Fixes for the links at the bottom of all HTML manual pages.
This is for the automatically generated documentation at
http://www.nmr-relax.com/manual/index.html,
created using latex2html. The links all require double quotes, and some a
trailing '/'. The links
fixed are http://www.nmr-relax.com, http://www.nmr-relax.com/manual/ and
http://download.gna.org/relax/manual/relax.pdf.
........
r26747 | bugman | 2014-11-26 11:21:53 +0100 (Wed, 26 Nov 2014) | 7 lines
Removed the repository backup file text from the relax manual.
This is for
http://www.nmr-relax.com/manual/Latest_sources_the_relax_repositories.html.
The gzipped
repository dump file has not been created by Gna! for many, many years.
The problem was identified
by the W3C link checker (http://validator.w3.org/checklink).
........
r26760 | bugman | 2014-11-26 14:22:47 +0100 (Wed, 26 Nov 2014) | 5 lines
Updated all of the http://www.nmr-relax.com/manual/ links in the
lib.dispersion package.
This is for all of the individual model pages in the HTML manual.
........
r26768 | bugman | 2014-11-26 18:35:06 +0100 (Wed, 26 Nov 2014) | 3 lines
Improved the description for the relax_fit.select_model user function.
........
r26769 | bugman | 2014-11-26 19:29:54 +0100 (Wed, 26 Nov 2014) | 12 lines
A small code rearrangement to create the new
target_functions.relax_fit_wrapper module.
This follows from the idea at https://gna.org/task/?7415#comment6. The
*func_wrapper() functions of
the specific_analyses.relax_fit.optimisation module have been shifted out
and converted to class
methods to create the target_functions.relax_fit_wrapper module. This will
be used to abstract away
all of the C code, and will form the infrastructure to allow new
exponential curves to be quickly
supported.
The modules of the specific_analyses.relax_fit and
specific_analyses.relax_disp packages now import
the target_functions.relax_fit_wrapper.Relax_fit_opt target function class
and use that instead.
........
r26770 | bugman | 2014-11-26 19:42:20 +0100 (Wed, 26 Nov 2014) | 8 lines
Shifted the C code Jacobian functions into the new
target_functions.relax_fit_wrapper module.
This shifts all of the relaxation curve-fitting C code access into the
target_functions.relax_fit_wrapper module so that the rest of relax does
not need to handle the C
code. This will allow for new models to be very easily supported, as they
would all be set up in
this target function module.
........
r26771 | bugman | 2014-11-27 09:45:09 +0100 (Thu, 27 Nov 2014) | 3 lines
Updated the formula in the description of the relax_fit.select_model user
function.
........
r26782 | bugman | 2014-11-27 15:16:48 +0100 (Thu, 27 Nov 2014) | 8 lines
Modified the printouts from the structure.write_pdb user function if models
are present.
Instead of printing out 'MODEL', 'ATOM, HETATM, TER' and 'ENDMDL' for each
model, the header 'MODEL
records' is printed followed by a single '.' character for each model. For
structures with many models,
this results in a huge speed up of the user function which is strongly
limited by how fast the
terminal can display text.
........
r26791 | bugman | 2014-11-27 19:11:38 +0100 (Thu, 27 Nov 2014) | 11 lines
Added the synthetic saturation-recovery data in the form of Sparky peak
lists to the repository.
These files were created by Andras Boeszoermenyi <Andras_Boeszoermenyi att
hms dott harvard dot
edu>. They are attached to the task at http://gna.org/task/?7415 as the
Relax_sym.tar.gz file at
http://gna.org/task/download.php?file_id=22989. They were created for the
formula I0*(1 -
exp(−R1*t)) where I0 = 1000000000000000.00 and R1 = 0.5. These files and
the associated
relax_sim.py script (which needs to be updated for the latest relax
version) could form the basis of
a basic system test. This system test could then be used to implement the
saturation-recovery
experiment equations in relax.
........
Added:
branches/space_mapping_refactor/target_functions/relax_fit_wrapper.py
- copied unchanged from r26791,
trunk/target_functions/relax_fit_wrapper.py
branches/space_mapping_refactor/test_suite/shared_data/curve_fitting/saturation_recovery/
- copied from r26791,
trunk/test_suite/shared_data/curve_fitting/saturation_recovery/
Modified:
branches/space_mapping_refactor/ (props changed)
branches/space_mapping_refactor/docs/latex/.latex2html-init
branches/space_mapping_refactor/docs/latex/infrastruct.tex
branches/space_mapping_refactor/lib/dispersion/b14.py
branches/space_mapping_refactor/lib/dispersion/cr72.py
branches/space_mapping_refactor/lib/dispersion/dpl94.py
branches/space_mapping_refactor/lib/dispersion/it99.py
branches/space_mapping_refactor/lib/dispersion/lm63.py
branches/space_mapping_refactor/lib/dispersion/lm63_3site.py
branches/space_mapping_refactor/lib/dispersion/m61.py
branches/space_mapping_refactor/lib/dispersion/m61b.py
branches/space_mapping_refactor/lib/dispersion/mmq_cr72.py
branches/space_mapping_refactor/lib/dispersion/mp05.py
branches/space_mapping_refactor/lib/dispersion/ns_cpmg_2site_3d.py
branches/space_mapping_refactor/lib/dispersion/ns_cpmg_2site_expanded.py
branches/space_mapping_refactor/lib/dispersion/ns_cpmg_2site_star.py
branches/space_mapping_refactor/lib/dispersion/ns_mmq_2site.py
branches/space_mapping_refactor/lib/dispersion/ns_mmq_3site.py
branches/space_mapping_refactor/lib/dispersion/ns_r1rho_2site.py
branches/space_mapping_refactor/lib/dispersion/ns_r1rho_3site.py
branches/space_mapping_refactor/lib/dispersion/tap03.py
branches/space_mapping_refactor/lib/dispersion/tp02.py
branches/space_mapping_refactor/lib/dispersion/tsmfk01.py
branches/space_mapping_refactor/lib/structure/internal/object.py
branches/space_mapping_refactor/specific_analyses/relax_disp/estimate_r2eff.py
branches/space_mapping_refactor/specific_analyses/relax_disp/optimisation.py
branches/space_mapping_refactor/specific_analyses/relax_fit/api.py
branches/space_mapping_refactor/specific_analyses/relax_fit/optimisation.py
branches/space_mapping_refactor/test_suite/system_tests/relax_disp.py
branches/space_mapping_refactor/user_functions/relax_fit.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/space_mapping_refactor/docs/latex/.latex2html-init
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/docs/latex/.latex2html-init?rev=26793&r1=26792&r2=26793&view=diff
Modified: branches/space_mapping_refactor/docs/latex/infrastruct.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/docs/latex/infrastruct.tex?rev=26793&r1=26792&r2=26793&view=diff
Modified: branches/space_mapping_refactor/lib/dispersion/b14.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/lib/dispersion/b14.py?rev=26793&r1=26792&r2=26793&view=diff
Modified: branches/space_mapping_refactor/lib/dispersion/cr72.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/lib/dispersion/cr72.py?rev=26793&r1=26792&r2=26793&view=diff
Modified: branches/space_mapping_refactor/lib/dispersion/dpl94.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/lib/dispersion/dpl94.py?rev=26793&r1=26792&r2=26793&view=diff
Modified: branches/space_mapping_refactor/lib/dispersion/it99.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/lib/dispersion/it99.py?rev=26793&r1=26792&r2=26793&view=diff
Modified: branches/space_mapping_refactor/lib/dispersion/lm63.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/lib/dispersion/lm63.py?rev=26793&r1=26792&r2=26793&view=diff
Modified: branches/space_mapping_refactor/lib/dispersion/lm63_3site.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/lib/dispersion/lm63_3site.py?rev=26793&r1=26792&r2=26793&view=diff
Modified: branches/space_mapping_refactor/lib/dispersion/m61.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/lib/dispersion/m61.py?rev=26793&r1=26792&r2=26793&view=diff
Modified: branches/space_mapping_refactor/lib/dispersion/m61b.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/lib/dispersion/m61b.py?rev=26793&r1=26792&r2=26793&view=diff
Modified: branches/space_mapping_refactor/lib/dispersion/mmq_cr72.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/lib/dispersion/mmq_cr72.py?rev=26793&r1=26792&r2=26793&view=diff
Modified: branches/space_mapping_refactor/lib/dispersion/mp05.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/lib/dispersion/mp05.py?rev=26793&r1=26792&r2=26793&view=diff
Modified: branches/space_mapping_refactor/lib/dispersion/ns_cpmg_2site_3d.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/lib/dispersion/ns_cpmg_2site_3d.py?rev=26793&r1=26792&r2=26793&view=diff
Modified:
branches/space_mapping_refactor/lib/dispersion/ns_cpmg_2site_expanded.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/lib/dispersion/ns_cpmg_2site_expanded.py?rev=26793&r1=26792&r2=26793&view=diff
Modified: branches/space_mapping_refactor/lib/dispersion/ns_cpmg_2site_star.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/lib/dispersion/ns_cpmg_2site_star.py?rev=26793&r1=26792&r2=26793&view=diff
Modified: branches/space_mapping_refactor/lib/dispersion/ns_mmq_2site.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/lib/dispersion/ns_mmq_2site.py?rev=26793&r1=26792&r2=26793&view=diff
Modified: branches/space_mapping_refactor/lib/dispersion/ns_mmq_3site.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/lib/dispersion/ns_mmq_3site.py?rev=26793&r1=26792&r2=26793&view=diff
Modified: branches/space_mapping_refactor/lib/dispersion/ns_r1rho_2site.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/lib/dispersion/ns_r1rho_2site.py?rev=26793&r1=26792&r2=26793&view=diff
Modified: branches/space_mapping_refactor/lib/dispersion/ns_r1rho_3site.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/lib/dispersion/ns_r1rho_3site.py?rev=26793&r1=26792&r2=26793&view=diff
Modified: branches/space_mapping_refactor/lib/dispersion/tap03.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/lib/dispersion/tap03.py?rev=26793&r1=26792&r2=26793&view=diff
Modified: branches/space_mapping_refactor/lib/dispersion/tp02.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/lib/dispersion/tp02.py?rev=26793&r1=26792&r2=26793&view=diff
Modified: branches/space_mapping_refactor/lib/dispersion/tsmfk01.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/lib/dispersion/tsmfk01.py?rev=26793&r1=26792&r2=26793&view=diff
Modified: branches/space_mapping_refactor/lib/structure/internal/object.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/lib/structure/internal/object.py?rev=26793&r1=26792&r2=26793&view=diff
Modified:
branches/space_mapping_refactor/specific_analyses/relax_disp/estimate_r2eff.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/specific_analyses/relax_disp/estimate_r2eff.py?rev=26793&r1=26792&r2=26793&view=diff
Modified:
branches/space_mapping_refactor/specific_analyses/relax_disp/optimisation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/specific_analyses/relax_disp/optimisation.py?rev=26793&r1=26792&r2=26793&view=diff
Modified: branches/space_mapping_refactor/specific_analyses/relax_fit/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/specific_analyses/relax_fit/api.py?rev=26793&r1=26792&r2=26793&view=diff
Modified:
branches/space_mapping_refactor/specific_analyses/relax_fit/optimisation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/specific_analyses/relax_fit/optimisation.py?rev=26793&r1=26792&r2=26793&view=diff
Modified:
branches/space_mapping_refactor/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/test_suite/system_tests/relax_disp.py?rev=26793&r1=26792&r2=26793&view=diff
Modified: branches/space_mapping_refactor/user_functions/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/user_functions/relax_fit.py?rev=26793&r1=26792&r2=26793&view=diff
r26793 - in /branches/space_mapping_refactor: ./ docs/latex/ lib/dispersion/ lib/structure/internal/ specific_analyses/relax...