relax SVN archive

Simplified the 'MMQ 2-site' dispersion model target function.

The r2eff_mmq_2site_sq_dq_zq() and r2eff_mmq_2site_mq() functions from lib.dispersion.mmq_2site are
now aliased by the experiment_type_setup() target function method. Both functions now have matching
arguments.

The R20 values are now correctly handled in the dispersion target function for MMQ-type data.

Converted the spin specific 'r2', 'r2a', and 'r2b' dispersion parameters from lists to dictionaries.

The new parameter keys are based on the experiment type and the spectrometer frequency. These keys
are supported by the generate_r20_key() and decompose_r20_key() pair of functions in the
specific_analyses.relax_disp.disp_data module. This enables support for different R20 parameters
for each experiment type - a key piece of infrastructure for the MMQ models.

The relax_disp.select_model user function backend was modified so the parameter list only contains
one instance for each of the 'r2', 'r2a', or 'r2b' strings.

The specific_analyses.relax_disp.parameters.loop_parameters() function was modified so that the R20
key rather than frequency index is returned for the R20 parameters. Many other code changes were
required.

Missing import bug fix - this is a recent bug.

The r2eff_mmq_*() functions of lib.dispersion.mmq_2site now accept different R20A and R20B arguments.

These are set to the same thing within the dispersion target function.

Bug fixes for the previous commit (r21498).

Implemented the 'MMQ 2-site' CPMG model equations from the Korzhnev et al., 2005 reference.

The paper reference is:
- Dmitry M. Korzhnev, Philipp Neudecker, Anthony Mittermaier, Vladislav Yu. Orekhov, and Lewis
E. Kay (2005). Multiple-site exchange in proteins studied with a suite of six NMR relaxation
dispersion experiments: An application to the folding of a Fyn SH3 domain mutant. J. Am. Chem.
Soc., 127, 15602-15611. (doi: http://dx.doi.org/10.1021/ja054550e).

The original code from Mathilde Lescanne and Dominique Marion has only slightly been modified for
this change as the MQ data treatment in the Korzhnev et al., 2004 reference is the same as in the
2005 reference, but using a different notation. This has been renamed to r2eff_mmq_2site_mq().

The new r2eff_mmq_2site_sq_dq_zq() function has been added to the lib.dispersion.mmq_2site module to
allows the SQ, DQ, and ZQ R2eff data to be calculated. This function follows the notation of the
2005 paper.

The populate_matrix() function has been modified to only accept one combined chemical shift
difference value. It can now also accept different values for R20A and R20B, though the mmq_2site
module defaults to R20A=R20B.

Updated the relaxation dispersion target functions for the changes of r21496.

The input data structures have changed type.

Added support for 1H SQ CPMG data for the MMQ-type dispersion models.

The key is to skip the protons in the spin cluster loops and to instead find the proton spin
containers attached to the heteronuclei of the spins of the cluster.

The EXP_TYPE_PROTON_SQ_CPMG and EXP_TYPE_PROTON_MQ_CPMG experiment type variables have been created
to aid this. The MODEL_LIST_MMQ list variable has also been created to more consistently identify
the MMQ-type dispersion models.

The has_disp_data() function has been created to simplify the finding of dispersion data for a given
cluster, experiment type, spectrometer frequency and dispersion point. The has_proton_sq_cpmg() and
has_proton_mq_cpmg() are used to determine if there is proton dispersion data for the given
heteronucleus.

The loop_exp() function has been modified to yield the proton SQ and MQ data if present. Similarly
the num_exp_types() and return_index_from_exp_type() functions exhibit different behaviour if this
data is present. The return_r2eff_arrays() function now assembles all of the proton data on top of
the heteronuclear data by fetching the protons attached to the heteronuclei and aliasing the correct
spin for the given experiment type.

Merged revisions 21492-21494 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r21492 | bugman | 2013-11-17 20:39:27 +0100 (Sun, 17 Nov 2013) | 5 lines

Bug fix for the lib.structure.mass.centre_of_mass() function warning when the element is not known.

This warning was buggy and resulted tracebacks.
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r21493 | bugman | 2013-11-17 20:40:51 +0100 (Sun, 17 Nov 2013) | 5 lines

Created the pipe_control.sequence.return_attached_protons() function.

This is used to return a list of proton spin containers attached to the given spin.
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r21494 | bugman | 2013-11-17 20:42:06 +0100 (Sun, 17 Nov 2013) | 3 lines

Fix for a fatal typo in the previous commit (r21493).
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