relax SVN archive

Added the 'MP05' R2eff calculating function to the relax library.

This is the Miloushev and Palmer 2005 R1rho analytic model for 2-site off-resonance exchange.

This follows the tutorial for adding relaxation dispersion models at:
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_library.

Just in case git-svn does not preserve the file copying history, the lib/dispersion/mp05.py file was
copied from the tp02.py file.

Created the 'MP05' model target function.

This is the Miloushev and Palmer 2005 R1rho analytic model for 2-site off-resonance exchange.

This follows the tutorial for adding relaxation dispersion models at:
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_target_function

Added support for the 'MP05' model to the relax_disp.select_model user function back end.

This is the Miloushev and Palmer 2005 R1rho analytic model for 2-site off-resonance exchange.

This follows the tutorial for adding relaxation dispersion models at:
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_disp.select_model_user_function_back_end

Added the 'MP05' model to the relax_disp.select_model user function frontend.

This is the Miloushev and Palmer 2005 R1rho analytic model for 2-site off-resonance exchange.

This follows the tutorial for adding relaxation dispersion models at:
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_disp.select_model_user_function_front_end

Added the 'MP05' model to the dispersion variables.

This is the Miloushev and Palmer 2005 R1rho analytic model for 2-site off-resonance exchange.

This follows the tutorial for adding relaxation dispersion models at:
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Adding_the_model_to_the_list

Created the Relax_disp.test_tp02_data_to_mp05 system test.

This was copied from the Relax_disp.test_tp02_data_to_tp02 system test. The r1rho_off_res_tp02.py
system test script was modified to handle both tests by allowing the list of models to optimise to
be set via the ds.models variable.

This follows the tutorial for adding relaxation dispersion models at:
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_test_suite

The dispersion GUI analysis now uses graphics.fetch_icon() for all icons.

The gui.paths module no longer exists.

Removal of an unused import of the now non-existent gui.paths module.

More fixes for the elimination of the gui.paths module.

Merged revisions 21436-21453 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r21436 | bugman | 2013-11-13 22:06:46 +0100 (Wed, 13 Nov 2013) | 6 lines

Created the N_state_model.test_pyrotartaric_anhydride_mix system test.

This is used to demonstrate a bug in the N-state analysis using mixed RDC and long range absolute
J+D data.
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r21437 | bugman | 2013-11-14 10:48:08 +0100 (Thu, 14 Nov 2013) | 9 lines

Movement of N-state model specific code to the analysis neutral pipe_control package.

Many of the functions of the specific_analyses.n_state_model.data module relating to alignment
tensors, RDC data and PCS data have been shifted in to the pipe_control package modules
align_tensor, rdc, and pcs respectively. This allows these functions to be made more general and
allow the code to be shared with the frame order analysis or any future analysis using such data,
and hence remove some code duplication.
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r21438 | bugman | 2013-11-14 11:23:52 +0100 (Thu, 14 Nov 2013) | 3 lines

Create two new warnings RelaxNucleusWarning and RelaxSpinTypeWarning to match the equivalent errors.
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r21439 | bugman | 2013-11-14 11:34:18 +0100 (Thu, 14 Nov 2013) | 5 lines

Added some RDC data checks to the N_state_model.test_pyrotartaric_anhydride_rdcs system test.

This is to demonstrate a problem with the data assembly function pipe_control.rdc.return_rdc_data().
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r21440 | bugman | 2013-11-14 11:54:27 +0100 (Thu, 14 Nov 2013) | 6 lines

Clean ups and improvements for the pipe_control.rdc.check_rdcs() function.

Pseudo-atoms are now handled much better and correctly in all cases. And many RelaxErrors have been
converted to RelaxWarnings followed by a 'return False' statement.
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r21441 | bugman | 2013-11-14 11:56:30 +0100 (Thu, 14 Nov 2013) | 7 lines

Created the pipe_control.rdc.setup_pseudoatom_rdcs() function.

This is used to make sure that the pseudo-atom interatomic systems (the containers from heternucleus
to pseudo-atom and heteronucleus to pseudo-atom members) are properly set up. It will deselect the
interatomic containers if incorrectly set up or if they are not part of the main pair.
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r21442 | bugman | 2013-11-14 13:12:24 +0100 (Thu, 14 Nov 2013) | 3 lines

Typo fix in a warning message.
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r21443 | bugman | 2013-11-14 13:27:48 +0100 (Thu, 14 Nov 2013) | 3 lines

Removed a debugging printout.
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r21444 | bugman | 2013-11-14 13:34:07 +0100 (Thu, 14 Nov 2013) | 5 lines

Added quotation marks around a number of spin IDs with molecule names in some RDC data files.

This is for the N-state model population model data used in the test suite.
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r21445 | bugman | 2013-11-14 13:43:21 +0100 (Thu, 14 Nov 2013) | 6 lines

The rdc.read and j_coupling.read user functions now ignore all lines starting with the # character.

This is to remove all comment lines silently. Therefore if spin IDs are used which contain the
molecule name, then they should be wrapped in quotation marks.
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r21446 | bugman | 2013-11-14 13:44:17 +0100 (Thu, 14 Nov 2013) | 5 lines

Updated a number of RDC test suite data files to have quotation marks around the spin IDs.

This is to allow the molecule identifier to be present while not being mistaken for a comment line.
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r21447 | bugman | 2013-11-14 14:06:05 +0100 (Thu, 14 Nov 2013) | 6 lines

Updated some of the RDC data files used in the frame order system tests.

The spin IDs are now in quotation marks as the molecule name is included. This is to prevent the
line being removed as a comment.
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r21448 | bugman | 2013-11-14 14:38:19 +0100 (Thu, 14 Nov 2013) | 6 lines

Changes to the setup_pseudoatom_rdcs() function and renamed it to setup_pseudoatom_rdc().

The interatomic loop is now within the function to make sure that all is completed before the
containers are accessed.
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r21449 | bugman | 2013-11-14 14:39:13 +0100 (Thu, 14 Nov 2013) | 3 lines

Fix for the setup_pseudoatom_rdc() function which should have been part of r21448.
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r21450 | bugman | 2013-11-14 15:00:49 +0100 (Thu, 14 Nov 2013) | 8 lines

Started to add better pseudo-atom support for the PCS.

The new pipe_control.pcs.setup_pseudoatom_pcs() function has been added to deselect the spins which
are members of a pseudo-atom. The return_pcs_data() function in the same module now calls this
function and builds a list of pseudo-atom flags for use in the target function (though it is still
unused).
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r21451 | bugman | 2013-11-14 15:01:37 +0100 (Thu, 14 Nov 2013) | 3 lines

Fix for the N-state model _target_fn_setup() method for when no PCS data is present.
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r21452 | bugman | 2013-11-14 15:18:27 +0100 (Thu, 14 Nov 2013) | 3 lines

Fix for a recent bug in the pipe_control.rdc.setup_pseudoatom_rdc() function.
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r21453 | bugman | 2013-11-14 17:22:56 +0100 (Thu, 14 Nov 2013) | 5 lines

Finally eliminated the gui.paths module, replacing it with graphics.fetch_icon() calls.

The GUI was using a mix of the old gui.paths module and the fetch_icon() function.
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