relax 3.1.0

Official relax releases
	relax version 3.1.0
← relax 3.0.2	relax 3.1.1 →
Keywords	Initial relaxation dispersion
Release type	Major feature
Release date	28 November 2013
	The relax 3.1.0 user manual

Description

After four years of development by numerous NMR spectroscopists, the relaxation dispersion analysis in relax is finally ready for release [Morin et al., 2014]! This support is complete and includes almost all analytic and numeric dispersion models in existence. These have been labelled as R2eff, No Rex, LM63 [Luz and Meiboom 1963], LM63 3-site [Luz and Meiboom 1963], CR72 [Carver and Richards 1972], IT99 [Ishima and Torchia 1999], TSMFK01 [Tollinger et al., 2001], NS CPMG 2-site expanded, NS CPMG 2-site 3D, NS CPMG 2-site star, M61 [Meiboom 1961], DPL94 [Davis et al., 1994], TP02 [Trott and Palmer 2002], TAP03 [Trott et al., 2003], MP05 [Miloushev and Palmer 2005], NS R1rho 2-site, MQ CR72, and MMQ 2-site, mainly named after the authors and publication date. It includes support for single, zero, double, and multiple quantum CPMG data, including combined proton-heteronuclear data, and off-resonance R_1ρ data. An automated protocol has been developed to simplify the analysis and a GUI has been designed around this auto-analysis. Calculations have been parallelised at the spin cluster and Monte Carlo simulation level for speed.

Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).

CHANGES file

Version 3.1.0
(28 November 2013, from /trunk)
http://svn.gna.org/svn/relax/tags/3.1.0

Features

Full support for the analysis of relaxation dispersion data in the prompt, scripting, and graphical user interfaces.
Support for single quantum (SQ), zero quantum (ZQ), double quantum (DQ), and multiple quantum (MQ) CPMG-type data.
Support for R_1ρ-type data.
Support for combined proton-heteronuclear SQ, ZQ, DQ, and MQ CPMG-type data (multiple-MQ or MMQ data).
The R2eff model - used to determine the R_2eff or R_1ρ values and errors required as the base data for all other models.
The No Rex model - the model for no chemical exchange being present.
The LM63 SQ CPMG-type analytic model - the original Luz and Meiboom 1963 2-site fast exchange equation with parameters {R₂⁰, …, φ_ex, k_ex} [Luz and Meiboom 1963].
The LM63 3-site SQ CPMG-type analytic model - the original Luz and Meiboom 1963 3-site fast exchange equation with parameters {R₂⁰, …, φ_ex,B, k_B, φ_ex,C, k_C} [Luz and Meiboom 1963].
The CR72 SQ CPMG-type analytic model - the reduced Carver and Richards 1972 2-site equation for most time scales whereby the simplification R_2A⁰ = R_2B⁰ is assumed with the parameters {R₂⁰, …, p_A, δω, k_ex} [Carver and Richards 1972].
The CR72 full SQ CPMG-type analytic model - the full Carver and Richards 1972 2-site equation for most time scales with parameters {R_2A⁰, R_2B⁰, …, p_A, δω, k_ex} [Carver and Richards 1972].
The IT99 SQ CPMG-type analytic model - the Ishima and Torchia 1999 2-site model for all time scales with p_A ≫ p_B and with parameters {R₂⁰, …, φ_ex, p_A.δω², k_ex} [Ishima and Torchia 1999].
The TSMFK01 SQ CPMG-type analytic model - the Tollinger et al., 2001 2-site very-slow exchange model for time scales within range of microsecond to second time scale with parameters are {R_2A⁰, …, δω, k_AB} [Tollinger et al., 2001].
The NS CPMG 2-site expanded SQ CPMG-type numeric model - A model for 2-site exchange expanded using Maple by Nikolai Skrynnikov (Tollinger et al., 2001) with the parameters {R₂⁰, …, p_A, δω, k_ex}.
The NS CPMG 2-site 3D SQ CPMG-type numeric model - the reduced model for 2-site exchange using 3D magnetisation vectors whereby the simplification R_2A⁰ = R_2B⁰ is assumed with the parameters {R₂⁰, …, p_A, δω, k_ex}.
The NS CPMG 2-site 3D full SQ CPMG-type numeric model - the full model for 2-site exchange using 3D magnetisation vectors with parameters {R_2A⁰, R_2B⁰, …, p_A, δω, k_ex}.
The NS CPMG 2-site star SQ CPMG-type numeric model - the reduced model for 2-site exchange using complex conjugate matrices whereby the simplification R_2A⁰ = R_2B⁰ is assumed with the parameters {R₂⁰, …, p_A, δω, k_ex}.
The NS CPMG 2-site star full SQ CPMG-type numeric model - the full model for 2-site exchange using complex conjugate matrices with parameters {R_2A⁰, R_2B⁰, …, p_A, δω, k_ex}.
The M61 R_1ρ-type analytic model - the Meiboom 1961 2-site fast exchange equation for on-resonance data with parameters {R_1ρ', …, φ_ex, k_ex} [Meiboom 1961].
The M61 skew R_1ρ-type analytic model - the Meiboom 1961 2-site equation for all time scales with p_A ≫ p_B and with parameters {R_1ρ', …, p_A, δω, k_ex} [Meiboom 1961].
The DPL94 R_1ρ-type analytic model - the Davis et al., 1994 2-site fast exchange equation extending the M61 model for off-resonance data with parameters {R_1ρ', …, φ_ex, k_ex} [Davis et al., 1994].
The TP02 R_1ρ-type analytic model - the Trott and Palmer 2002 2-site equation for all time scales with p_A ≫ p_B and with parameters {R_1ρ', …, p_A, δω, k_ex} [Trott and Palmer 2002].
The TAP03 R_1ρ-type analytic model - the Trott et al., 2003 off-resonance 2-site equation for all time scales with the weak condition p_A ≫ p_B and with parameters {R_1ρ', …, p_A, δω, k_ex} [Trott et al., 2003].
The MP05 R_1ρ-type analytic model - the Miloushev and Palmer 2005 off-resonance 2-site equation for all time scales with parameters {R_1ρ', …, p_A, δω, k_ex} [Miloushev and Palmer 2005].
The NS R1rho 2-site R_1ρ numeric model - the model for 2-site exchange using 3D magnetisation vectors with the parameters {R_1ρ', …, p_A, δω, k_ex}.
The MQ CR72 MMQ-type analytic model - the Carver and Richards 1972 2-site model for most time scales expanded for MMQ CPMG data by Korzhnev et al., 2004 with the parameters {R₂⁰, …, p_A, δω, δω_H, k_ex}.
The MMQ 2-site MMQ-type numeric model - the model for 2-site exchange whereby the simplification R_2A⁰ = R_2B⁰ is assumed with the parameters {R₂⁰, …, p_A, δω, δω_H, k_ex}.
An automated protocol for relaxation dispersion which includes sequential optimisation of the models, fixed model elimination rules to remove failed models and failed MC simulations increasing both parameter reliability and accuracy [d'Auvergne and Gooley 2006], and a final run whereby AIC model selection is used to judge statistical significance.
Additional methods to speed up the auto-analysis by skipping the grid search: Model nesting, the more complex model starts with the optimised parameters of the simpler; Model equivalence, when two models have the same parameters; And spin clustering, the analysis starts with the averaged parameter values from a completed non-clustered analysis.
Parallelisation of the dispersion analysis at the level of the spin cluster and Monte Carlo simulation for fast optimisation on computer clusters using OpenMPI.

Changes

Started to implement the framework for relaxation dispersion system tests.
Copied 'test_suite/system_tests/relax_fit.py' for relaxation dispersion.
Started to implement relaxation dispersion system tests.
Created the user_functions.relax_disp module by copying user_functions.relax_fit. This file now needs to be modified to suit the needs of relaxation dispersion.
Manually created the relax_disp user functions. This is equivalent to Seb's commit for the prompt.relax_disp module. The equivalent changes to the user_functions.relax_disp were hand edited. Added functions to select the experiment type and mathematical model used. These functions allow the user to select the experiment type (cpmg or r1rho) as well as the mathematical model to fit the data (fast or slow).
Copied the 'relax_fit.py' script to 'relax_disp.py'. This file, obviously, will need to be modified to suit the needs of the relaxation dispersion code.
Modified the script so it will test for fast-exchange curve fitting from CPMG data. Data and functions to treat it are still missing.
Added a test for CPMG data in slow-exchange and changed the name of the test for fast-exchange.
Copied the 'relax_fit.py' specific functions to 'relax_disp.py'. The code will now need many many many changes to suit the needs of relaxation dispersion.
Made a few changes towards a functional relaxation dispersion code. This includes several modifications as well as the addition of the exp_type() function.
Moved the relax_time() function to cpmg_frq() and made other small changes. Still much (!) work is needed for this code to be complete.
Renamed 'cdp.frq' to 'cdp.cpmg_frqs' so it is not confusing with the spectrometer frequency. Indeed, 'cdp.cpmg_frqs' points to the CPMG pulse train frequency (nu_cpmg).
Changed all instances of 'relax_times' to 'cpmg_frqs' and made other small changes.
Changed 'relax_time' instances to 'cpmg_frq'.
Changed the index name and description. The description might change later to be more appropriate when the code is more mature…
Included the setting of the spectrometer frequency and uncommented a few lines of code. Of course, this won't work until the sample data has been introduced and the right names for the different files be input in the system test script…
Fixed many formatting errors and made the 'relax_disp' code accessible (pipes, interpreter, etc.). These changes also include a coming back to using the C code 'math_fns/relax_fit.py' since there is still no such code associated to relaxation dispersion. This will allow working in the code without relax crashing and complaining about the lack of a C module name 'relax_disp.py'.
Added the user function cpmg_delayT() which allows setting the CPMG constant time delay T used for the analysed dataset. This follows a post at https://mail.gna.org/public/relax-devel/2009-01/msg00027.html.
Made a few changes so the cpmg_delayT() function now works.
Added the user function cpmg_frq() and added examples to the user function cpmg_delayT().
Corrected remaining frq instances to cpmg_frq when appropriate to avoid confusion and corrected a few related things in the system test script.
Made the cpmg_frq() function accept only None for the reference spectrum and corrected a typo.
Added the parameters for the slow- and fast-exchange regime.
Added the parameters for the slow- and fast-exchange regime in the function data_names().
Corrected a few formatting issues and still added parameters for the slow- and fast-exchange regime.
Corrected a few formatting issues and still added parameters for the slow- and fast-exchange regime. Formatting issues corrected were spotted by Ed in a post at https://mail.gna.org/public/relax-devel/2009-01/msg00045.html.
A bit more changes to introduce parameters for CPMG relaxation dispersion.
Introduced CPMG parameters into the function return_grace_string() and corrected formatting issues.
Introduced relaxation dispersion parameters in the function return_data_name().
Changed the default cpmg_frq value in cpmg_frq() from 0 to None.
Added a relaxation dispersion dataset in the system-test. This was kindly provided by Dr Flemming Hansen (flemming AT pound DOT med DOT utoronto DOT ca) and was previously published in Hansen, Vallurupalli & Kay (2008) J. Phys. Chem. B, 112, 5898-5904. The original format was different and was modified to better suit the way relax handles datasets. Finally, the information contained here were written in a 'readme' file placed in the same directory as the dataset itself to allow referencing and acknowledgments.
Added 'Sparky' formatted files to the system-test so the files can be input and development of the branch continued.
Changed the format of the CPMG frequency and corrected the names of some input files.
Added an unresolved file to meet the script requirements.
Copied the script for the fast-exchange regime to the slow-exchange regime.
Modified the newly copied script so it is effectively for the slow-exchange regime.
Added details to the readme file and changed the directory name where the sample data is located. The directory is now named 'dataset_1-a'. This contains data recorded at 500 MHz. Data recorded at 800 MHz will be put in a directory called 'dataset_1-b'.
Created a directory for the data recorded at 800 MHz and put a readme file explaining its origin.
Added the relaxation dispersion dataset recorded at 800 MHz in the system-test. This was kindly provided by Dr Flemming Hansen (flemming AT pound DOT med DOT utoronto DOT ca) and was previously published in Hansen, Vallurupalli & Kay (2008) J. Phys. Chem. B, 112, 5898-5904. The original format was different and two formats were made ('generic' and 'sparky'), as for the dataset recorded at 500 MHz.
Renamed the directories containing the sample datasets provided by Flemming Hansen. The names are now more obvious as to their content… This was proposed by Ed in a post at https://mail.gna.org/public/relax-devel/2009-01/msg00056.html.
Added an 'unresolved' file to the 800 MHz data and moved (and modified) some files (sequence and readme) so there is only one copy for the 500 and 800 MHz data. This prevents duplicated files.
Changed the object names so they are lower case as they should be, based on the rest of the code. Made the equivalent change in the function assemble_param_vector() to allow the system-test to go further.. This was spotted by Ed in a post at https://mail.gna.org/public/relax-devel/2009-01/msg00058.html.
Corrected capitalisation issues for param names. These were spotted by Ed in a thread starting at https://mail.gna.org/public/relax-devel/2009-01/msg00059.html.
Rearranged commands in the scripts. The experiment type and exchange regime will have to be input before the cpmg pulse train delay T.
Introduced a RelaxError when chosing 'r1rho' as experiment type as this won't be implemented now. Efforts will be concentrated on the CPMG code first, then on the R_1ρ code.
Added tests, print statements and other code to the relaxation dispersion specific functions. Tests were proposed by Ed in a post at https://mail.gna.org/public/relax-devel/2009-01/msg00065.html.
Started to implement a function for calculating the effective transversal relaxation rate (R_2eff). This follows a thread at https://mail.gna.org/public/relax-devel/2009-01/msg00067.html.
Converted the function linear_constraints() for relaxation dispersion needs.
Started to implement the scaling matrix for scaling the 'R_2eff' values. This might change in the future as other possible curve fitting parameters ('R2', 'Rex', 'k_ex', 'R_2A⁰', 'kA', 'δω') might need some scaling.
Completed the scaling matrix code. This follows a thread at https://mail.gna.org/public/relax-devel/2009-01/msg00073.html.
Imported relaxation dispersion in grace user functions.
Added a missing quote which prevented the user manual to be sconstructed. This was discussed in a thread starting at https://mail.gna.org/public/relax-devel/2009-01/msg00082.html.
Started to implement a function for reading 'R_2eff' values directly. This is as proposed in a post at https://mail.gna.org/public/relax-devel/2009-01/msg00020.html. The function does not contain code yet.
Started to put equations and references in the user function docstrings and also corrected a small typo. This was proposed by Ed in a post at https://mail.gna.org/public/relax-devel/2009-01/msg00028.html.
Corrected the way the scaling matrix is assembled. This is as proposed by Ed in a post at https://mail.gna.org/public/relax-devel/2009-01/msg00079.html. The scaling values are now based on the default values for the different parameters which were slightly modified. The only parameter for which the average is still used (as for intensities in the 'relax_fit.py' code) is 'R_2eff'.
Continued to implement the user function calc_r2eff(). This follows a discussion at https://mail.gna.org/public/relax-devel/2009-01/msg00067.html.
Copied 'test_relax_fit.py' to 'test_relax_disp.py'. This will allow the design of a few unit tests for the relaxation dispersion code.
Added two unit tests for the relaxation dispersion code and fixed errors in the corresponding code. More unit tests will be added soon to help debugging and developing.
Added two more unit tests.
One more unit test.
One more unit test for the relaxation dispersion code.
Added more unit tests and tried to debug what was uncovered by these tests. Still more work is needed for debugging…
A few fixes based on the unit tests problems.
Changed the default value for 'int_cpmg' to avoid an impossible mathematical situation: ln(0).
Fixed a bug where the 'id' argument was not set. This was proposed by Ed in a post at https://mail.gna.org/public/relax-devel/2009-01/msg00127.html.
Started to make changes for multiple field relaxation dispersion analysis. This seems necessary, so maybe we should not support single field analysis of relaxation dispersion at all. -> Kovrigin et al. (2006) JMagRes, 180: 93-104. The changes made here are only a first draft and may not work. In particular, maybe the spectrum.read_intensities(), relax_disp.cpmg_frq(), spectrum.replicated(), spectrum.error_analysis(), and deselect.read() functions will need to know the magnetic field to which the particular dataset is associated… In fact, the different datasets should be input first and their R_2eff calculated independently. In a second step, the actual relaxation dispersion curve fitting should be made with all data.
Fixed a bug which prevented the manual pdf to be compiled. The problem was caused by a ':' character in the references (after the volume number, as usual). This was changed for a '.' character. Equations were fine.. Moreover, a better formatting was done by adding ':' characters after the word 'are' before enumerations.
Fixed the unit tests. This is as proposed by Ed in a post at https://mail.gna.org/public/relax-devel/2009-01/msg00132.html.
Started to implement the reading of 'r2eff' by relax_data.read() by first writing a system test.
Updated a few dosctrings and tried to improve the system test.
Removed the obsolete function 'relax_disp.r2eff_read()'. R_2eff values will be read directly by 'relax_data.read()'.
Reordered a few functions for alphabetical reasons.
A small fix to the system test. However, is this fix the solution or is there something wrong with the reading of data (such as 'R_2eff') by relax_data.read()? Shouldn't the data, for example 'R_2eff', be available in 'cdp.mol[0].res[0].spin[0].R2eff_val[0]' or 'cdp.mol[0].res[0].spin[0].R2eff[0]' for the 1st spin of the 1st residue in the 1st molecule?
Fixed an import (as well as a few comments). This however introduces an error concerning the 'chi2' being undefined in the C module for relaxation dispersion…
Solved an issue created during the merge process concerning the 'return_data_name_doc' call. The solution is based on the code in 'specific_fns/relax_fit.py'.
Brought the relaxation dispersion branch into sync with the 1.3 line. There were many design changes within the 1.3 line that required that the old relaxation dispersion code be updated.
Fixes for the relaxation dispersion system tests. The install path is now in the status object, and not in __main__.
GPLv3 license updates for all files not found in the trunk.
Import fixes for the specific_analyses.relax_disp due to the recent trunk package layout redesign.
Made the non-API methods of the specific_analyses.relax_disp.Relax_disp class private.
Improvements for the GUI representation of the relax_disp user functions.
More import fixes for the new package layout.
Fix for the relax_data.read user function call in the Relax_disp.test_read_r2eff system test. The column numbers must be supplied.
Some more fixes to make the Relax_disp.test_read_r2eff system test pass. These are again changes needed due to the trunk now being very different.
The cpmg_frq argument of the relax_disp.cpmg_frq user function can now be None.
The cpmg_frq argument of the relax_disp.cpmg_frq user function can now be an integer as well as a float.
Updates for the relaxation dispersion system test scripts for the newer design of relax. A number of changes were required as the code was quite old.
Created the lib.dispersion.equations module. This is a translation of Sebastien Morin's C code in the old relax_disp branch.
Created a very basic initial target function class for relaxation dispersion. This code is a translation of Sebastien Morin's C code in the old relax_disp branch.
The relaxation dispersion specific analysis code now uses the Python target function rather than the C.
Fix for the Relax_disp.test_curve_fitting_cpmg_fast system test variable names.
Added the model argument to the dispersion target function class to select between different equations.
The relaxation dispersion target function class now imports the equations from lib.dispersion.equations.
The relaxation dispersion target function class raises a RelaxError when the model is not implemented.
Modified all the relaxation dispersion test data Sparky files at 800 MHz. The last three lines of the files were not properly formatted.
Converted all of the raising of RelaxErrors in the specific_analyses.relax_disp to the new standard. This is for Python 3 support.
Converted all print statements in specific_analyses.relax_disp to function calls. This is for Python 3 compatibility.
Converted the prompt unit tests for relaxation dispersion to the current relax design.
Updated the target_functions package __all__ list for the relax_disp module.
Another fix for the prompt argument unit tests of the relax_disp user functions.
Big changes to the front end of the relax_disp.select_model user function. The model strings have been changed and are now programmatically added to the user function documentation. The main text has also been redesigned. And the new model 'exp_fit' has been added which allows just the exponential curves to be fit.
Python 3 import fix for the specific_analyses.relax_disp module.
Updated the documentation in specific_analyses.relax_disp to use the user_functions package design. The user_functions.objects.Desc_container and user_functions.data.Uf_tables objects are now used to construct the relaxation dispersion documentation.
The relax_disp.select_model backend now handles the 'exp_fit' model.
Removed all aliasing of the current data pipe in specific_analyses.relax_disp as this is in __builtin__.
The specific_analyses.relax_disp module now uses the parameter list object to define parameters. This allows the now unused methods data_names(), default_value(), return_data_name(), and return_grace_string() to be deleted and their contents copied into the parameter definitions in the class __init__() method.
Alphabetical arrangement of methods in the specific_analyses.relax_disp module.
Docstring cleanups for the specific_analyses.relax_disp module.
The relaxation dispersion specific analysis now aliases API base methods for a number of methods.
Import cleanup in the specific_analyses.relax_disp module.
The relaxation dispersion specific analysis module is now using the base _data_init_spin() method. This is aliased to data_init() and replaces the old non-functional method.
Created the relax_disp.spin_lock_field user function. This is used to set the spin-lock field strength of a given R_1ρ spectrum.
Created the relax_disp.relax_time user function. This is almost a direct copy of the relax_fit.relax_time user function, but has been modernised.
Fix for the printout from the relax_disp.relax_time user function - the time is no longer divided by 1k.
Expanded the dispersion model parameters to include the exponential curve parameters.
Clean up of some of the old relax_disp user functions - many argument types are now numbers rather than floats.
Unit test fixes for the prompt relax_disp user function argument checks.
Added the specific_analyses.relax_disp module to the unit test checking of the specific API.
Big cleanup of the relaxation dispersion code to match the analysis specific API. All methods not belonging to the API have been made private. The arguments and keyword arguments for the API methods now match the API.
Completely redesigned the minimisation parts of the specific_analyses.relax_disp module. Instead of dealing with the optimisation of individual spins, groups of spins are now optimised together. This allows for the clustering analysis of relaxation dispersion. The method _block_loop() has been created to loop over spin blocks, but it currently only returns individual spins. However with the rest of the code designed to handle this loop, only this function needs to be modified to enable clustering. The method _param_num() has also been added to determine the total parameter number per spin block. The data structures sent into the Dispersion target function class have also been redesigned to handle spin blocks instead of individual spins.
Modified the relax_disp.cpmg_frq user function to match relax_disp.spin_lock_field. Both the front and back ends now use the same logic as the relax_disp.spin_lock_field user function and will allow some sanity to the analysis specific code.
The relax_disp.cpmg_frq and relax_disp.spin_lock_field user functions now create cdp.curve_count. This is an integer which indicates the number of exponential curves which are to be optimised per spin block.
The relaxation dispersion analysis specific _param_num() method now takes the number of curves into account.
Better setup checking for the relaxation dispersion specific analysis minimise() method.
Renamed cdp.curve_type to cdp.model to better explain the variable.
Fixes for the dispersion specific analysis separating R_2eff from R₂. There is one R_2eff parameter per exponential curve, but only one R₂ per model. The code now better handles this.
The dispersion specific methods now handle one R_2eff and I₀ parameter per exponential curve.
Better management of the global relaxation dispersion data. The user functions relax_disp.cpmg_frq, relax_disp.spin_lock_nu1, and relax_disp.relax_time now maintain data structures in the current data pipe of the unique frequencies, fields, and times (sorted) as well as the number of frequencies, fields, and times. This data is used by the minimise user function back end to set up the target function, and will be required by many other parts of the analysis.
The dispersion specific _assemble_param_vector() method now handles multiple R_2eff and I₀ values. These spin structures are dictionaries holding multiple values.
Created the dispersion specific _exp_curve_loop() method for looping over each exponential curve. This yields the index and key for each curve, simplifying the handling of this data.
Expanded the relax_disp.select_model user function documentation to cover R_2eff and I₀. These parameters and how they are optimised are now better described.
Updated the relaxation dispersion target function class to handle the recent changes.
First attempt at a target function for fitting exponential curves for relaxation dispersion.
Added some synthetic data to test the 'exp_fit' relaxation dispersion model fitting. These are just basic synthetic exponential curves. R_2eff and I₀ should be very easy to find.
The lib.software.sparky.read_list_intensity() function can now handle lowercase in the residue names.
Created the Relax_disp.test_exp_fit system test for checking the relaxation dispersion 'exp_fit' model.
The specific_analyses.relax_disp module is now using minfx correctly. The minfx grid search is no longer part of generic_minimise() and must be called separately.
The relax_disp function _grid_search_setup() now operates in the same way as the relax_fit code. This function originates from the 'relax_fit' specific analysis code, but that code has since evolved. The 'relax_disp' code now mimics the new code, returning lists of grid search increments and upper and lower limits.
The scaling flag is now initialised in the relaxation dispersion target function class.
Created the lib.curve_fit package and associated unit tests. This will be used for holding modules such as for exponential curve-fitting required for the relaxation dispersion analysis.
Created the new lib.curve_fit.exponential module for exponential curve-fitting. This contains the single exponential_2param_neg() function which will be used for the relaxation dispersion target functions. This is based on Sebastien Morin's function exp_2param_neg in maths_fns.exponential.c in his dormant inversion-recovery branch.
Typo fix for the new lib.curve_fit.exponential.exponential_2param_neg() function.
The relaxation dispersion func_exp_fit() target function now uses exponential_2param_neg(). This is from the lib.curve_fit.exponential module.
Fix for the relaxation dispersion specific _assemble_scaling_matrix() method. The values were all inverted - the matrix should hold values on the same order as the parameter values.
Fix for the func_exp_fit() relaxation dispersion target function. The parameter index was not correctly calculated.
The 'exp_fit' relaxation dispersion model now uses the minfx.grid sparseness argument. This is used to skip all parts of the grid search belonging to a different exponential curve or different spin. If the number of curves is N and the number of spins M, the grid size decreases from inc^(2*N*M) to (inc²)*N*M. For lots of spins and curves, this is a huge decrease.
The relaxation dispersion specific _disassemble_param_vector() method is now functional. This should allow the minimise user function to complete.
Fixes for the dispersion specific _assemble_param_vector() method. The R_2eff and I₀ spin dictionary structures are now checked for their keys before pulling the value out.
Fix for the relaxation dispersion grid search. The lower and upper bounds are no longer continually scaled with each optimisation.
Increased the speed of the Relax_disp.test_exp_fit system test by using a smaller grid search.
The relaxation dispersion target function class back_calc variable now matches the values variable. Instead of being a temporary structure which is overwritten for each spin and each exponential curve, the structure now matches the dimensions of the values variable and hence is persistent per function call. This allows external code to access the structure - for example for data back calculation in the relaxation dispersion specific analysis module.
Fixes for the dispersion specific _back_calc() method. This method still has a long way to go before it is of any use.
Created a custom base_data_loop() method for the relaxation dispersion analysis. This defines the base data as the peak intensities of a single exponential curve and yields the spin container and exponential curve key identifying the individual curves.
Activated Monte Carlo simulations for the relaxation dispersion analysis. This required a bit of work. The key parts were renaming _block_loop() to the API method model_loop() as that is exactly what the model_loop() method is supposed to do, converting a bunch of API common spin-based methods to handle dispersion clustering, and to modify existing methods from Seb's original branch to handle the base_data_loop() method. The following methods have been added or modified. _back_calc(): This method has been modified to handle clustering and the returning of peak intensities from only one exponential curve. _exp_curve_index_from_key(): This new method is used to convert exponential curve key into the corresponding index. _intensity_key(): This new method is for converting an exponential curve key and relaxation time into the corresponding intensity key. create_mc_data(): This method is now functional and handles the data from the base_data_loop() method. return_error(): This method now handles the data from the base_data_loop() method. set_selected_sim(): This new method has been modified from the common _set_selected_sim_spin() method but modified for the model_loop() method. sim_pack_data(): This method now handles the data from the base_data_loop() method. sim_return_param(): This new method has been modified from the common _sim_return_param_spin() method to suit the model_loop(). sim_return_selected(): This new method has been modified from the common _sim_return_selected_spin() method again to suit the model_loop().
Modified the Relax_disp.test_exp_fit system test to be faster and not create plots which it cannot.
The Relax_disp.test_exp_fit system test now checks some of the final results.
The relaxation dispersion parameter errors from Monte Carlo simulations are now stored. Previously MC simulations could run, but the errors were not being calculated and stored. The sim_return_param() method was empty. This method is now complete. In addition the set_error() method has been created for setting the parameter errors. And the _exp_curve_key_from_index() and _param_index_to_param_info() auxiliary methods added to facilitate data access.
Expanded the checking in the Relax_disp.test_exp_fit system test.
Converted all relaxation dispersion parameters to lowercase. This is so the variable names match the parameter names identically, avoiding problems with some of the shared methods of the specific analysis API.
The spin parameters are now set up last by the relax_disp.select_model user function back end.
Added 'spin_lock_nu1' as a dictionary type parameter of the relaxation dispersion specific analysis.
Rearrangements of the 2 system tests of Fleming Hansen's CPMG data. The system tests are now called Relax_disp.test_hansen_cpmg_data_fast_2site and Relax_disp.test_hansen_cpmg_data_slow_2site, and the system test scripts are now all in test_suite/system_tests/scripts/relax_disp/.
Created a basic initial auto-analysis script for relaxation dispersion. This currently only supports the optimisation of the 'exp_fit' diffusion model, but has all of the infrastructure set up to make it easy to add other models.
Added the relaxation dispersion module to the auto_analyses package __all__ list.
The relaxation dispersion system test class now imports the auto-analysis. This fixes an import order error.
The Relax_disp.test_exp_fit system test now uses the auto_analyses.relax_disp analysis.
Fix for the relaxation dispersion auto-analysis. The exponential fit model is now selected prior to optimisation.
Removed the relax_disp.select_model user function call from the exp_fit dispersion system test script. This is performed by the auto-analysis and not during setup.
Added testing for spin clustering to the Relax_disp.test_exp_fit system test. This includes calls to the new relax_disp.cluster user function and the checking of pipe variables holding the clustering information.
Fix for the spin ID string for the relax_disp.cluster user function. This is for the exp_fit.py relaxation dispersion system test script.
Implemented the relax_disp.cluster user function. This is for clustering spins together for a dispersion analysis.
Clustering is now enabled for relaxation dispersion. The model_loop() analysis specific API method now loops over the spin clusterings, allowing a cluster of spins to be optimised simultaneously to one set of model parameters.
Fixes for the spin clustering for relaxation dispersion. Both optimisation and Monte Carlo simulations were affected by these bugs.
Speed up of the Relax_disp.test_exp_fit system test by cutting the grid size down to 3 increments.
Expanded the write_results() method of the relaxation dispersion auto-analysis. More Grace graphs are now being produced, and the Rex file creation is now model dependent.
Fix for the relax_disp.cluster user function. The 'free spins' category is now not deleted when empty.
Created an icon set for relaxation dispersion.
Renamed the relaxation dispersion test suite data directory to 'dispersion'.
Changed the relax_disp.cpmg_frq user function id argument to spectrum_id. All the relax_disp user functions now operate with the spectrum IDs instead of experiment IDs.
The relax_disp.cpmg_delayT user function backend now uses the spectrum ID rather than experiment ID.
Expanded the relax_disp.exp_type user function to include the fixed period CPMG experiments.
The relax_disp.cpmg_delayT backend can now handle the 'cpmg fixed' experiment type.
The relax_disp.cpmg_frq user function can now handle values of None. The float function is no longer used if the value of None is encountered.
Updated the dispersion system test script for Flemming Hansen's data. This script should now be close to the final form for a relaxation dispersion analysis of CPMG data with a fixed relaxation time period.
Combined all the system test scripts of Flemming Hansen's fixed time period CPMG data. For details of this data, see http://thread.gmane.org/gmane.science.nmr.relax.devel/3790/focus=3827.
Fixes for the renaming of the relaxation dispersion test suite shared data directory.
Started to redesign how R_2eff is handled in the relaxation dispersion analysis. Instead of being part of the optimisation of the dispersion model, it will itself be the model named R2eff (converted from the 'exp_fit' model). This model will either use the calc user function to determine R_2eff when the fixed relaxation period experiment is selected, or fit exponential curves using the relax_fit C module for the variable relaxation period experiments. The R_2eff values will then be copied over for each dispersion model in the auto-analysis using the value.copy user function.
Created the relax_disp.plot_exp_curves user function. This is to be used to create 2D graphs of the exponential curves (relaxation time verses peak intensity) as the grace.write user function plots are not very nice - the curves from each spectrometer field strength and dispersion point are mixed into one curve.
The relaxation dispersion auto-analysis is now created plots of the exponential curves.
The R2eff model now works for the variable time relaxation period and exponential curve-fitting.
The relax_disp.select_model user function now checks for the compiled C module when required.
Expanded the new analysis wizard in the GUI to accommodate the relaxation dispersion auto-analysis. Now the buttons are a matrix of 4x2 with the NOE, R₁, R₂, and model-free analyses at the top and two new blank buttons have been added to the bottom. One will be used for the dispersion analysis.
Created some basic graphics for the relaxation dispersion analysis fur use in the GUI.
Added the correct sized graphic for the relaxation dispersion button in the new analysis wizard.
Created the relaxation dispersion button in the new analysis wizard.
Created the initial version of the relaxation dispersion auto-analysis GUI frame. This is built from copying lots of code from the NOE, R₁, and R₂ analyses. The dispersion specific parts will be added later.
The relaxation dispersion GUI analysis now has an element for selecting the models to be optimised.
Removed some unneeded checks in the relax_disp.exp_type user function.
Added a GUI element to the relaxation dispersion auto-analysis for selecting the experiment type.
The relax_disp.exp_type user function has been shifted to the new analysis wizard. Instead of being one of the elements on the relaxation dispersion analysis frame, it is now placed between the analysis selection page and the data pipe page of the new analysis wizard. The user function execution is delayed until the set up of the frame, just after the execution of the pipe.create user function. This will allow the frame to be set up differently for each experiment type.
Extended the tooltip for the experiment type GUI element in the relaxation dispersion frame.
Improvements to the tooltips in the relaxation dispersion analysis frame of the GUI.
Changed the peak intensity wizard for the relaxation dispersion frame to match the other analyses.
Unused import removal from the gui.analyses.auto_relax_disp module.
Missing import in the gui.analyses.auto_relax_disp module.
Added support for all the relaxation dispersion user functions in the Peak_intensity_wizard object.
Modified how the fixed time period is specified in the Flemming Hansen data system test. Instead of using relax_disp.cpmg_delayT user function, the relax_disp.relax_time user function will be used. The functionality is duplicated and relax_disp.cpmg_delayT is not needed.
Modified the Spectra_list GUI element to handle relaxation dispersion data.
The relaxation dispersion GUI analysis now uses the dispersion parts of the peak intensity elements. This includes activating the dispersion parts of the Spectra_list GUI element for displaying the spectrum ID with associated metadata and the dispersion parts of the Peak_intensity_wizard for loading the data.
The relaxation dispersion auto-analysis is now correctly executed from the GUI. The GUI data gathering is also now complete in the assemble_data() method.
Added some more module variables to specific_analyses.relax_disp for the experiment types.
The relaxation dispersion auto-analysis now performs the peak intensity error analysis. This is essential for when the GUI is used.
More Unicode characters are now used in the relaxation dispersion GUI analysis frame. The model parameter lists have also been improved.
Removed the spectrum.error_analysis user function call in the exp_fit.py dispersion system test script. This is now performed by the auto-analysis.
Fixed for the error_analysis() method of the relaxation dispersion auto-analysis. The method can now handle missing spectrometer field strength data.
More fixed for the peak intensity error analysis method of the relaxation dispersion auto-analysis. The fixed relaxation time period type experiments can now be handled.
Elimination of the relax_disp.cpmg_delayT user function. This user function is not necessary as the relax_disp.relax_time user function serves the same purpose. The use of relax_disp.relax_time instead allows for code sharing between the fixed and variable time period relaxation dispersion experiment types.
Elimination of the relax_disp.calc_r2eff user function. This user function, which is non-functional anyway, is not needed. The calculation of the R_2eff values will occur with the optimisation of the R2eff model (with a call to the calc user function for the fixed time period experiment types) so direct calculation through a specific user function is not needed.
Improvements to the GUI text subscripting in the relaxation dispersion analysis frame.
Removed the temporary relaxation dispersion SVG graphic for the GUI analysis.
Redesign of the graphic for the relaxation dispersion analysis. This is a modification of the r1.svg graphic to show roughly the graphic as in "Protein NMR Spectroscopy, Principles and Practice" by Cavanagh, Fairbrother, Palmer and Skelton.
Editing of the relaxation dispersion analysis graphic.
Added the relaxation dispersion graphic to all of the dispersion GUI user functions missing a graphic.
Redesign of the relaxation dispersion models in the relax_disp.select_model user function front-end. The models have been renamed and better defined based on the experiment type (CPMG or R_1ρ).
The relaxation dispersion scaling matrix assembly now uses lib.mathematics.round_to_next_order(). This allows the printed out I₀ values for the optimisation of the exponential curves to be easier to scale back to the real value.
The Relax_disp.test_hansen_cpmg_data_fast_2site system test now uses the R2eff model. The equivalent slow exchange system test also uses the model. This model will be used to find the R_2eff values from the fixed relaxation time period data.
Fix for some RelaxError printouts in the relaxation dispersion specific code.
The relaxation dispersion class variables for the experiment types are now used for all comparisons. This should avoid random bugs.
Fix for the calculation part of the relaxation dispersion auto-analysis. This is for the fixed relaxation period data types.
The 2D Grace plots of the exponential curves are now skipped for the fixed relaxation period data types. This is in the relaxation dispersion auto-analysis.
Started to implement the relaxation dispersion analysis specific calculate() method. This will be used to calculate the R_2eff/R_1ρ values for the fixed relaxation time period data types and is equivalent to Sebastien Morin's relax_disp.calc_r2eff user function which was deleted (see http://thread.gmane.org/gmane.science.nmr.relax.scm/17336).
Converted the specific_analyses.relax_disp module into its own package. This is to allow the code to be broken up into separate modules to simplify the analysis.
Shifted out all of the variables and dispersion data specific code into separate modules. The dispersion data private methods have been converted into functions of the specific_analyses.relax_disp.disp_data module. The package variables have also been shifted into the specific_analyses.relax_disp.variables module to avoid circular imports.
Alphabetical ordering of the functions of the specific_analyses.relax_disp.disp_data module.
Created the specific_analyses.relax_disp.disp_data.loop_all_data() function. This is to loop over all possible base relaxation dispersion data (spectrometer frequencies then dispersion points).
Updates for the dispersion user functions for the changes in specific_fns.relax_disp.
Typo fix in the new loop_all_data() function.
Created the lib.dispersion.calc_two_point_r2eff() function. This is for calculating the R_2eff/R_1ρ value for the fixed relaxation time data.
Improvements to the specific_analysis.relax_disp.disp_data module. The function loop_all_data() has been expanded to include the relaxation time period into the loop. The functions return_intensity() and return_key() have been added to return peak intensities and the key corresponding to the data returned by loop_all_data().
Fixes for some latent bugs in the specific_analyses.relax_disp.disp_data module. The checks for the CPMG-data type in a number of functions now uses the CPMG_EXP list instead of fixed strings.
Completed the relaxation dispersion calculate() method. This allows the R_2eff/R_1ρ values to be calculated for the fixed relaxation time period experiments through the calc user function.
Created a script for running a full relaxation dispersion analysis on Flemming Hansen's data. This is located in the shared data directories and is not part of the test suite as a full analysis will take far too long.
Updated the models in the script for the full relaxation dispersion analysis of Hansen's data.
Updated the backend of the relax_disp.select_model to handle the new model names.
Spun out a number of dispersion methods into the new specific_analyses.relax_disp.parameters module. This is a module of functions relating to the parameters of the relaxation dispersion models.
More spacing before the sectioning printouts in the relaxation dispersion auto-analysis.
Modified the printouts of the relax_disp.select_model user function.
Fix for the relaxation dispersion auto-analysis. The data pipes created for each model optimised are now switched to prior to any operations on the pipe.
Changed the φ_ex parameter in the LM63 model back to rex.
Changed the Grace string for the rex parameter to be φ_ex.
Converted all of the specific_analyses.relax_disp.parameters module to handle different models. The R_2eff and I₀ parameters are now only part of the R2eff model and all other standard parameters belong to all of the other models.
Shifted all of the constant relaxation dispersion variables into the specific module. All of the dispersion code now uses the variables of specific_analyses.relax_disp.variables.
Renamed the lib.dispersion.equations.fast_2site() function to r2eff_LM63(). The number of relaxation times has also been replaced by the number of dispersion points.
Added the return_cpmg_frqs() and return_spin_lock_nu1() functions to specific_analyses.relax_disp.disp_data.
Updates to the relaxation dispersion auto-analysis. The Grace plots created are now more dependent on the current model, so that dispersion curves are only created for the R2eff model. The specific_analyses.relax_disp.variables module is now also being used.
Started to redesign the relaxation dispersion target function class. The input data is now expected to be R_2eff/R_1ρ data and all mentions of exponential curves have been eliminated. The func_exp_fit() target function has been deleted as it is not used - as now the _minimise_r2eff() method in the dispersion specific analysis class is used instead. And the func_fast_2site() target function has been renamed to func_LM63().
Redesigned the optimisation code of the dispersion analysis specific class for the new target functions. This includes the assembling of R_2eff/R_1ρ values instead of peak heights, and a number of small fixes.
Shifted the LM63 dispersion model functions into the new lib.dispersion.lm63 module.
The reference spectrum is now not included when counting the number of dispersion points.
Fix for the lib.dispersion.lm63 module and parameters of zero are now gracefully handled.
Fixes for the func_LM63() dispersion target function.
Shifted the R_2eff/R_1ρ value and error assembly into specific_analyses.relax_disp.disp_data. This is in the new return_r2eff_arrays() function. The code has also been debugged and made functional.
Added support for handling missing data in the relaxation dispersion analysis. This support was mentioned in the post http://thread.gmane.org/gmane.science.nmr.relax.devel/3835.
Added a FIXME to a comment about the hardcoded Bootstrap number for relaxation dispersion.
Started to add support for Monte Carlo simulations for the relaxation dispersion models. This is for all models except R2eff. The changes are extensive but incomplete. The new functions disp_point_key_from_index() and disp_point_index_from_key() have been added to the specific_analyses.relax_disp.disp_data module, but the disp_point_index_from_key() function still needs work. The _back_calc() method of the specific_analyses.relax_disp.Relax_disp class has been redesigned, as well as base_data_loop() method and all methods which depend on it.
Updated the relaxation dispersion system tests of the Hansen CPMG data for the new models. The models are now LM63 and CR72, and the tests have been renamed to Relax_disp.test_hansen_cpmg_data_LM63 and Relax_disp.test_hansen_cpmg_data_CR72.
Update of the specific_analyses.relax_disp package docstring.
Fix for the linear constraints setup of the R2eff relaxation dispersion model. There are no constraints, so the specific_analyses.relax_disp.parameters.linear_constraints() function now returns A and b values of None.
Basic fix for the _back_calc_r2eff() relaxation dispersion method. A variable was misnamed.
Major redesign of the relaxation dispersion data model in the relax data store. The data model now revolves around the three concepts of the spectrometer frequency, the dispersion points, and the relaxation times. Peak intensity data is now handled through averaging using the new specific_analyses.relax_disp.disp_data.average_intensity() function. R_2eff/R_1ρ values are now referenced by a key generated from the spectrometer frequency and ν_CPMG frequency or ν₁ spin-lock field strength. All of the specific_analyses.relax_disp package has been standardised around these concepts. This simplifies all of the modules of the package and removes a large number of latent bugs.
A number of fixes to partly enable Monte Carlo simulations for the non R2eff dispersion models.
Finally Monte Carlo simulations for the relaxation dispersion models now work. This was a simple fix for the specific_analyses.relax_disp.parameters.param_index_to_param_info() function.
Created truncated data files of the Hansen CPMG data. This consists of residues 70 and 71 and will be used to massively speed up the system tests.
The truncated Hansen CPMG data is now in the form of Sparky peak lists.
Now all of the Hansen CPMG data is present as truncated Sparky peak lists.
Speedup for the relaxation dispersion system tests which use Flemming Hansen's CPMG data. The system test script now reads the truncated data files (of only residues 70 and 71) to minimise the time required to read the data and store it in the relax data store.
Added a script to the test suite shared data for analysing the truncated Hansen CPMG data.
Fixes for the LM63 dispersion CPMG model. The 'r2' model parameter is now an array as there is one R₂ value per magnetic field strength. And the 'rex' parameter has been renamed to 'φ_ex' and is scaled quadratically with the field strength within the optimisation target function.
Fix for the setup of the relaxation dispersion GUI analysis. The base method add_execute_relax() has been renamed to add_execute_analysis().
Added support for interfacing with Art Palmer's CPMGFit program. The two new user functions relax_disp.cpmgfit_input and relax_disp.cpmgfit_execute have been created to interface with CPMGFit. The first creates the per spin system CPMGFit input files as well as a batch script for executing CPMGFit with all the input files. The second bypasses the batch script and allows CPMGFit to be executed from within relax. This mimics the palmer and dasha user functions. The back end code is in the new specific_analyses.relax_disp.cpmgfit module.
Created the Relax_disp.test_hansen_cpmgfit_input system test. This is for checking the operation of the relax_disp.cpmgfit_input user function conversion of Flemming Hansen's CPMG R_2eff values into input files for CPMGFit. A relax state file containing the results of an analysis of an R2eff model analysis of the truncated data has been added to the test suite data to speed up the test and to check the loading of dispersion state files.
Created a directory for the results of the CPMGFit program using Hansen's truncated CPMG data. The script 'cpmgfit.py' has been added to create the input files for CPMGFit and execute the program. The input and batch files have been added to the repository as well.
Added the results from NESSY of the analysis of Flemming Hansen's truncated CPMG data. This is only for the truncated data of residues 70 and 71. All files, except for the PNG graphics, have been added to the repository. The 'summary' file has been created to hold the data from NESSY's summary tab, as this is not stored in the NESSY saved state and is permanently lost after closing NESSY.
A dispersion saved state from the prompt or script UI can now be associated with a GUI analysis.
Created the Relax_disp.test_hansen_trunc_data GUI test for checking the GUI dispersion auto-analysis. This checks the full operation of the relaxation dispersion GUI analysis, without checking the final results (to be added later).
Fixes for the change to the new spectrometer.frequency user function and associated data structures.
Removed the preview button from the file selection GUI element of the CPMGFit user functions. These are the relax_disp.cpmgfit_execute and relax_disp.cpmgfit_input user functions.
The relaxation dispersion specific code now uses the changes of the spectrometer.frequency user function. This simplifies the handling of magnetic field strength data.
More fixes to the relax_disp branch for the changes of the spectrometer.frequency user function.
Changes to the CPMGFit input files due to the new spectrometer.frequency user function.
The relax_disp.cpmgfit_execute user function now correctly calls CPMGFit. The -grid command line option has been added and the output for each spin is sent to a special output file.
Updated the input files and added the output files for the CPMGFit program with Hansen's CPMG data. This is for the data truncated to residues 70 and 71.
Fixes for the relax_disp branch for the spectrometer.frequency user function changes.
Fix for the Relax_disp.test_hansen_cpmgfit_input system test. This is for the recent spectrometer.frequency user function changes.
The specific_analyses.relax_disp.disp_data.loop_frq() function can now handle missing data. This allows the loop to yield a single value of None when the spectrometer information has not been loaded and enables R_1ρ analyses at a single field strength.
Fix for the LM63 dispersion model target function - the scaled φ_ex value is now used for the R₂.
Fixes for the relaxation dispersion auto-analysis for the LM63 model. The Rex parameter is now the φ_ex parameter.
Added printouts of the optimised parameters to the Relax_disp.test_hansen_cpmg_data_LM63 system test. This includes the conversion to the equivalent CPMGFit parameters.
Massively increased the precision of the R_2eff error analysis. The hard-coded simulation number variable is now set to 100000. This appears to be necessary for reliably reproducing results in the subsequent dispersion models.
Created the specific_analyses.relax_disp.disp_data.spin_has_frq_data() function. This is for determining if a spin has peak intensity for the given spectrometer field strength.
Updates some scripts for the spectrometer.frequency user function change.
Created a script to calculate the R_2eff rate errors extremely precisely for Hansen's CPMG data. This uses 1 million Bootstrap simulations for calculating the errors. The 'r2eff_values.bz2' is saved after deleting the spin specific r2eff_sim structures so that the file drops from 388 Mb in size to 7.3 kb.
The CPMGFit script for Hansen's CPMG data now starts with the high precision error r2eff_values.bz2 file. This ensures consistency between comparisons between relax, NESSY, CPMGFit, etc.
Removed the '_trunc' part of the nessy_results directory from the NESSY final save file.
The relaxation dispersion loop_point() function can now return the reference point. This is enabled via the skip_ref argument.
Created the relax_disp.nessy_input user function front and backends. This user function takes the data in the relax data store and creates a NESSY save file to be opened within NESSY. The backend is the new specific_analyses.relax_disp.nessy module. For the GUI frontend, graphics for icons and the wizard have been taken from the NESSY repository file pics/nessy_new.png@r1088 in the trunk.
A script has been added to create the NESSY input for Flemming Hansen's CPMG data.
Updated the NESSY results for Flemming Hansen's CPMG data for the R_2eff values with high precision errors. A file containing the log or printouts from NESSY has been added for reference.
Updated the NESSY log from the Hansen CPMG data of residue 70 to remove the NESSY errors. These were removed with the commit r1090 to the NESSY trunk.
Split up the r2eff_values.bz2 save file into the results files for each data pipe. This is for Flemming Hansen's CPMG data truncated to residues 70 and 71. This is to simplify the system tests which use this data.
Large simplification of the Relax_disp system tests using Hansen's CPMG data. Instead of calculating the R_2eff values in the test, these are read from the high error precision results files in test_suite/shared_data/dispersion/Hansen. This allows the model parameters to be consistently found and to be identical between different runs of the test.
Added a file which compares the results for the LM63 model with Hansen's CPMG data between all programs. This currently includes relax, NESSY and CPMGFit.
Added a printout to the specific_analyses.relax_disp.cpmgfit.translate_model() function.
The dispersion system test script for Hansen's CPMG data can now run stand-alone.
The log barrier constraint algorithm is now used for the relaxation dispersion optimisation. This is to allow constraints in the absence of gradient target functions. The constraints have been turned on by default in the auto-analysis.
Changed the dispersion GUI tab to use the model names from specific_analyses.relax_disp.variables.
The spectrum wizard now uses the spectrometer.frequency user function rather than frq.set. The frq.set user function is now called spectrometer.frequency.
An upper limit of 200 rad/s has been added to the linear constraints for the R₂ dispersion parameters.
Fixes for the checking in the Relax_disp.test_hansen_cpmgfit_input system test.
The relaxation dispersion auto-analysis now calls the relax_disp.plot_disp_curves user function. This user function is not implemented yet, but will be used to create plots of the dispersion curves.
Implemented a basic graph for the relax_disp.plot_disp_curves user function. This simply plots out the ν_CPMG value or spin-lock field verses the R_2eff/R_1ρ values from the experiment. The graph of the back calculated R_2eff/R_1ρ values from the model fit is still to be added.
Fix for the linear constraints for the R2eff model. The A and b matrices are no longer set to None, as this kills the auto-analysis or any analysis when constraints are turned on. Now the constraints 0 ≤ R_2eff ≤ 200 and I₀ ≥ 0 are used.
Fixes for the peak intensity loading wizard for the frq.set to spectrometer.frequency user function change.
Fixes for the backend of the relax_disp.plot_exp_curves user function. This code needed to be updated for the major changes in the relax_disp branch.
Fixes for the checks in the Relax_disp.test_exp_fit system test. The r2eff and i0 spin data structure keys are now strings.
Two class variables have been added to the dispersion auto-analysis for fast optimisation. This includes variables for the function tolerance and maximum number of iterations, and matches those of the model-free auto-analysis of the dauvergne_protocol module[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b]. These will be used to speed up the test suite.
Speed up of the system tests using Flemming Hansen's CPMG data. The grid search increments, function tolerance and maximum number of iterations have all been made looser.
Added parameter checks to the Relax_disp.test_hansen_cpmg_data_LM63 system test.
Fix for the φ_ex dispersion parameter scaling - the scaling was in the wrong direction.
Added a directory of relax results for the truncated high-precision Hansen CPMG R_2eff values. This uses the base_pipe.bz2 and r2eff_pipe.bz2 files with the high-precision R_2eff errors, and hence can be compared to the NESSY and CPMGFit results.
Added the residue :71 results to the lm63_comparison file. This is a summary of the optimisation results using the high-precision R_2eff error results for the different dispersion softwares.
Changes to the dispersion auto-analysis write_results() method. This is to output more of the dispersion parameters to text files and 2D grace plots.
Created a directory and script in preparation for the relax_disp.sherekhan_input user function.
Created the relax_disp.sherekhan_input user function. This includes an icon for the GUI, and the full front and backends.
Added a wizard graphic for the relax_disp.sherekhan_input user function.
Shifted the core of the model_loop() dispersion method into its own function. The new function specific_analyses.relax_disp.disp_data.loop_cluster() can now be used by other parts of relax. The model_loop() method now yields the data that loop_cluster() yields.
Redesign of the relax_disp.sherekhan_input user function to handle spin clustering.
Added the ShereKhan results for the high-precision R_2eff data for Hansen's CPMG data.
Converted the readme file for Flemming Hansen's CPMG data directory to uppercase.
Updated the LM63 model comparison table.
Modified the dispersion calculate() method for the R_2eff values to use the analytic equation. For the R_2eff/R_1ρ values calculated for the fixed time period dispersion experiments via the calc user function, the very slow and tedious bootstrapping approach has been replaced by the very quick direct error calculation. The two techniques produce the same results as the bootstrap simulation number approaches infinity.
Bug fix for the peak intensity error analysis in the dispersion auto-analysis. Now the error analysis is split based on the magnetic field strength. Previously the analysis was a mess with the split often being individual spectra.
The proper experiment type is now set for the Relax_disp.test_hansen_trunc_data GUI test.
Updated the relax_disp.exp_type user function to be more specific an include more experiment types.
Updated the specific_analyses.relax_disp.variables module for the relax_disp.exp_type changes.
The relax_disp.relax_time page is now always shown in the peak intensity wizard for the dispersion GUI. This number is needed for the fixed time period experiments as well to calculated the R_2eff/R_1ρ values and errors.
Fix for the dispersion auto-analysis write_results() method. The i0 parameter text file and 2D Grace file are now only produced for the R2eff model with the exponential curve base data types.
Simplified the Relax_disp.test_hansen_trunc_data GUI test. The CR72 model is now deactivated and the grid search sized decreased from the default of 21 to 4.
Big speed ups of the Relax_disp.test_hansen_trunc_data GUI test. The optimisation function tolerance and maximum number of iterations are now set to the same low precision as the system tests. This involves adding hidden variables to the dispersion GUI analysis.
Removed the data pipe name check from the Relax_disp.test_hansen_trunc_data GUI test. This makes no sense as this analysis generates a data pipe for each model (similar to the model-free analysis).
Fix for the relax_disp.exp_type call in the Relax_disp.test_exp_fit system test script.
Better formatting of the references for the dispersion analytic model equations.
Updated the relax_disp.select_model user function frontend for the CR72 dispersion model. This includes fixing the parameter list and the equations presented to the user.
Removed the commented out junk model code from the relax_disp.select_model user function frontend.
Added the CR72 model equations to the relax library. This is for the Carver and Richards 1972 2-site exchange model covering all time scales.
Initial implementation of the CR72 target function.
Import fix for the lib.dispersion.cr72 module.
Fixes to the specific_analyses.relax_disp modules to add support for the CR72 dispersion model. The parameters for the CR72 model are now both correct and correctly handled.
Fix for the spin container list of parameters for the CR72 model.
The CR72 dispersion model equations are now more robust against math domain errors. This is for the trigonometric functions which cannot handle certain input values.
Renamed the file for comparing different dispersion software with Flemming Hansen's CPMG data.
Added the initial results of the CR72 model in relax for Flemming Hansen's truncated CPMG data.
Simplified the p_A ≥ p_B constraint in the dispersion linear_constraints() function.
Fixes for the dispersion linear_constraints() function. The indices were being incorrectly handled - the i and k index should be one and the same parameter index.
Added support for the CR72 or 'Full_CPMG' model to the relax_disp.cpmgfit_input user function.
Added the results for the CR72 model optimisation in CPMGFit using Flemming Hansen's truncated CPMG data.
Added the CR72 model results to the software comparison document for Hansen's CPMG data.
Improvements for the φ_ex and δω relaxation dispersion model parameters. These are now stored with the units of ppm² and ppm respectively. The conversion to (rad/s)² and rad/s units respectively now is spin specific, allowing mixed spin types (¹H, ¹³C, ¹⁵N, etc.) to be analysed simultaneously.
Updated the relax results for Hansen's CPMG data for the recent φ_ex and δω changes.
Fixes for the CPMGFit results in the software comparison table for Hansen's CPMG data.
Fix for the grid search setup for the p_A dispersion parameter. As p_A > p_B, then the region from 0.0 to 0.5 does not need to be searched.
The back calculated R_2eff values are now stored for dispersion analysis after minimisation.
Fix for the CR72 model equation in lib.dispersion.cr72.r2eff_CR72(). The eta scaling factor was incorrect.
Updated the relax results for the truncated CPMG data from Flemming Hansen. This is for the recent fixes of the CR72 model equations. Now relax produces identical results to ShereKhan for the LM63 and CR72 models.
Created a directory for holding relaxation dispersion sample scripts.
Added the model for no chemical exchange relaxation to the dispersion analysis.
Updated the NESSY log file for its improved printouts. These printouts allow the R₂⁰ values to be accessed.
Another update of the NESSY log for the improved and more detailed printouts.
And again, another update of the NESSY log.
Added the relax results for the No Rex model.
Updated the software comparison tables for the model of no exchange. This is for Flemming Hansen's truncated CPMG data.
Fix for the Relax_disp system tests using Flemming Hansen's truncated CPMG data. The nuclear isotope is now being set.
Increased the grid size for the hansen_data.py system test script. This is needed to allow the parameters to be reliably found.
Fixes for the checks and printouts of the Relax_disp.test_hansen_cpmg_data_LM63 system test.
Updated some NESSY results in the software comparison document.
Fix for the CPMGFit batch file creation. The command line options are now correct and output is redirected to output files.
Updated the CPMGFit batch file.
Created the Relax_disp.test_hansen_cpmg_data_auto_analysis system test. This is designed to fully test the dispersion auto-analysis for CPMG-type data.
Fix for the Relax_disp.test_hansen_cpmgfit_input system test. This is for the recent CPMGFit batch file changes.
Better checking of optimisation in the Relax_disp system tests. This affects the Relax_disp.test_hansen_cpmg_data_LM63 and Relax_disp.test_hansen_cpmg_data_CR72 system tests. Instead of using the auto-analysis, these tests now set the initial parameters close to the minimum, skip the grid search, and perform a low precision optimisation to reach the minimum. This is important because the low quality grid search and optimisation can not always find the real minimum.
Created the lib.dispersion.equations.calc_two_point_r2eff_err() function. This complements the lib.dispersion.equations.calc_two_point_r2eff() function and is used by the dispersion calculate() method to abstract the mathematics.
Updated the relax_disp.select_model user function docstring for the R_2eff error analysis. This properly describes how the R_2eff/R_1ρ errors are calculated for the fixed relaxation time period experiments.
Docstring fixes for the lib.dispersion.equations module.
Expanded the number of model list variables in specific_analyses.relax_disp.variables. This is to include lists which are specific to CPMG-type and R_1ρ-type experiments.
Added the new M61 model to the specific_analyses.relax_disp.variables module. This is the Meiboom 1961 model for 2-site fast exchange for R_1ρ-type experiments.
Added the M61 model to the relax_disp.select_model user function frontend. This is the Meiboom 1961 model for 2-site fast exchange for R_1ρ-type experiments.
Added the M61 model equations to the relax library. This is for the Meiboom 1961 2-site fast exchange model for R_1ρ-type experiments.
Created the M61 2-site fast exchange dispersion model target function. This is for the Meiboom 1961 model for 2-site fast exchange for R_1ρ-type experiments. The code for the func_M61() method was copied without modification from the func_LM63() method.
Added support for the R_1ρ-type experiments to the relaxation dispersion analysis in the GUI. This involves using a different model list for these experiments compared to the CPMG-type experiments.
Updated the relaxation dispersion GUI to handle the current set of experiment types.
Fix for the Relax_disp.test_hansen_cpmg_data_auto_analysis system test. The correct model list is now being used - the R_1ρ-type experiments should not be included.
Fix for the missing import of the lib.dispersion.equations.calc_two_point_r2eff_err() function.
Added support for the M61 model to the relax_disp.select_model user function back end. This is for the Meiboom 1961 2-site fast exchange model for R_1ρ-type experiments.
Another fix for the Relax_disp.test_hansen_cpmg_data_auto_analysis system test. The correct model list is finally being used.
Fix for the lib.dispersion.equations.calc_two_point_r2eff_err() function. The variables were incorrectly named.
Added support for setting the spin isotope information in the dispersion GUI. A new Text_ctrl element has been added just after the spin system GUI element. This displays a list of all the spin isotopes currently defined and is updated after every GUI user function call. The button of the element launches the spin.isotope user function. The spin isotope information is now checked for prior to executing the GUI analysis and added to the missing list to present to the user when blocking the execution of the analysis. The dispersion GUI test has been updated to use this new element.
Added support for model selection to the relaxation dispersion specific analysis package. This involved redesigning the model_loop() method. Instead of yielding both the spin containers and the spin IDs, now only spin IDs are yielded. This is important as the model loop is used independently of the data pipes. Hence the spin containers cannot be yielded as multiple pipes are compared within the model loop. The auxiliary method _spin_ids_to_containers(spin_ids) has been added to obtain the list of spin containers from the list of spin IDs. To support model selection, the methods duplicate_data(), model_desc() and model_statistics() have been added, and model_type() aliased to the common _model_type_local() method.
Expanded the relaxation dispersion auto-analysis. A final step of model selection has been added to select between the different models for each spin cluster. This is stored in the 'final' data pipe, and its results output via the write_results() method.
The model selection technique can now be changed in the dispersion auto-analysis.
The error when selecting a non-existent model using relax_disp.select_model is now more informative.
Model selection in the dispersion auto-analysis is only performed if 2 or more models are present. Excluding the R2eff model, if only 0 or 1 models are optimised, then model selection is skipped and a warning is given. This avoids tracebacks in the model_selection user function.
Added some synthetic on-resonance R_1ρ data to the test suite. This is in the form of Sparky peak list files containing two spin systems.
Expanded the synthetic on-resonance R_1ρ test suite data. The data now consists of a full set of dispersion curves for the M61 model.
Added a reference to the synthetic on-resonance R_1ρ test suite data. The first ncyc1 data point now has a relaxation time period of zero, hence it can be used as the reference for a fixed time period experiment.
The reference spectra can now be set in the relax_disp.spin_lock_field user function. By setting the field to None, the reference spectrum for a fixed relaxation time period experiment type can now be specified. This mimics the behaviour of the relax_disp.cpmg_frq user function.
Added some error checking to the specific_analyses.relax_disp.disp_data.average_intensity() function. This is for better feedback to the user in case they have not set up their data correctly.
The relax_disp.select_model user function now operates without the spectrometer frequency being set. The special loop_frq() function is now used as this can handle missing spectrometer frequency information.
The find_intensity_keys() function can now handle the reference spectrum. This function in the specific_analyses.relax_disp.disp_data module was failing if the relaxation time period for the reference spectrum was missing. Time information shouldn't be needed for the reference, so is no longer checked.
The dispersion specific optimisation methods can now handle missing spectrometer information.
The return_index_from_frq() now handles missing frequency information. This is in the specific_analyses.relax_disp.disp_data module.
Better support for missing frequency information in the specific_analyses.relax_disp.disp_data module. This is in the return_index_from_frq() function which now returns an index of 0, and in return_r2eff_arrays() which skips calculating the frequency information.
The dispersion disassemble_param_vector() function now handles missing spectrometer information. The loop_frq() function replaces direct looping over cdp.spectrometer_frq_count.
Variable renaming in the lib.dispersion.m61 module. The variable names are now more suited to R_1ρ-type data, rather than CPMG-type data.
Fix for the M61 model target function. The spin-lock fields need to be used, not the CPMG frequencies.
Created the Relax_disp.test_r1rho_on_res_fixed_time_m61 system test. This checks the R_1ρ-type experiment with a fixed relaxation time period using the R2eff and M61 models. It uses the auto-analysis for this, and the 'r1rho_on_res' synthetic relaxation data.
Created the Relax_disp.test_r1rho_on_res_exponential_m61 system test. This is identical to the Relax_disp.test_r1rho_on_res_fixed_time_m61 system test except that the full exponential curves are used rather than the 2-point fixed time approach.
Python 3 fixes for the relaxation dispersion parameter Grace strings.
Python 3 fixes for the modules of the specific_analyses.relax_disp package.
Fix for a bug preventing the optimisation of the dispersion models.
Fixes for the file permission setting on the CMPGFit batch script. The correct file mode is now set for Unix-based systems.
Python 3 fixes for the relax_disp.cpmg_frq and relax_disp.spin_lock_field user functions. The sorting of lists with None is not supported by Python 3, so this has to be carefully handled.
Removed the grid search size check from the dispersion _grid_search_setup() method. This is performed by minfx anyway, and the code was incompatible with Python 3.
Fix for the Relax_disp.test_hansen_cpmgfit_input system test. The frequencies for the CPMGFit input files now are only written to 10 places. This is for Python 2 vs. 3 consistency.
Python 3 fix for the relax_disp.cluster user function.
Fix for the Grace plots created by the relax_disp.plot_disp_curves user function. The data set from each frequency is now a separate set in the G0 graph.
Improvements to the relax_disp.plot_disp_curves user function. The back-calculated R_2eff/R_1ρ values are now included in the plot as separate sets. In addition, the residuals have also been added to allow for a visual statistical comparison.
More improvements to the relax_disp.plot_disp_curves user function. The data sets now have labels, and the residuals have errors set to those of the R_2eff/R_1ρ data.
More improvements to the relax_disp.plot_disp_curves user function. The graph axes maximum is now set to a reasonable value for the given data.
Added the No Rex model to the relax script for optimising Flemming Hansen's CPMG data.
The isotope type is now set in the relax script for optimising Flemming Hansen's CPMG data.
Shifted the _spin_ids_to_containers() method to the disp_data.spin_ids_to_containers() function.
Fix for the relax_disp.sherekhan_input user function. The loop_cluster() function no longer returns spin containers.
Fix for the r2eff_calc.py script for calculating R_2eff values from Flemming Hansen's CPMG data.
Added a check to the dispersion specific minimise() function for the spectrometer field strength. This is essential in all dispersion models to convert between ppm and rad/s units, or ppm² and (rad/s)² for the φ_ex parameter.
The r1rho_on_res_m61.py dispersion system test script now sets the spectrometer frequency information.
Removed cdp.model as this makes no sense - a different model can be used per spin cluster. Now the variable cdp.model_type is used to identify the R2eff model. For all other dispersion models this variable is set to 'Disp'.
Added a log file for the data generation script for the r1rho_on_res dispersion data.
Fixes for the parameter checks in the system tests for the r1rho_on_res synthetic data. This includes both the Relax_disp.test_r1rho_on_res_fixed_time_m61 and Relax_disp.test_r1rho_on_res_exponential_m61 tests.
Fixes for the lib.dispersion.m61.r2eff_M61() function.
Increased the precision of the Sparky peak lists for the r1rho_on_res dispersion test data. All peak intensities are now 1000 bigger. As the values are integers in the Sparky files, the previous values were too truncated for the system tests to properly optimise and find the original parameters.
Speed up of the r1rho_on_res_m61.py system test script. The optimisation precision is now much lower. And the peak intensity errors now have been scaled by 1000 just as the base data was in the previous commit.
Improvements for the parameter checks in the system tests for the r1rho_on_res synthetic data. This includes both the Relax_disp.test_r1rho_on_res_fixed_time_m61 and Relax_disp.test_r1rho_on_res_exponential_m61 tests.
Clustering was accidentally turned off in the r1rho_on_res_m61.py system test script.
Created the specific_analyses.relax_disp.disp_data.count_frq() function. This is for determining the number of spectrometer frequencies present, even if not data has been defined.
Loosened the checks for the Relax_disp.test_hansen_cpmg_data_CR72 system test.
Completely redesigned how parameters are handled in the relaxation dispersion analyses. The key concept is that everything revolves around the new loop_parameter() function. This is a generator function which loops over the parameters of a given cluster, yielding all the information required to access the parameter. The other functions of the parameters module use loop_parameter() to sequentially handle each parameter. This allows for huge simplifications of these functions.
Fixes for the Relax_disp.test_hansen_cpmg_data_auto_analysis system test. One of the models for one spin now optimises completely and the checks have all been loosened.
Fixes for the dispersion specific model_statistics() method. This now handles spin clustering correctly.
Updated the results of relax's analysis of the truncated CPMG data from Flemming Hansen.
Updates for the model variable docstrings.
Added the M61 skew model to the specific_analyses.relax_disp.variables module. This is the Meiboom 1961 model for skewed populations (p_A ≫ p_B). This commit follows step 1 of the relaxation dispersion model addition tutorial.
Added the M61 skew model to the relax_disp.select_model user function frontend. This is the Meiboom 1961 model for skewed populations (p_A ≫ p_B). This commit follows step 2 of the relaxation dispersion model addition tutorial.
Fixes for the spacing after some equations in the relax_disp.select_model docstring.
Simplifications and comment fixes in the lib.dispersion.m61.r2eff_m61() function.
Renamed the lib.dispersion.m61.r2eff_M61() function to r1rho_M61().
Added the M61 skew model equations to the relax library. This is the Meiboom 1961 on-resonance 2-site model for skewed populations (p_A ≫ p_B). This commit follows step 3 of the relaxation dispersion model addition tutorial.
Created the M61 skew model target function. This is the Meiboom 1961 on-resonance 2-site model for skewed populations (p_A ≫ p_B). This commit follows step 4 of the relaxation dispersion model addition tutorial.
Added support for the skewed condition (p_A ≫ p_B) to the specific_analyses.relax_disp.parameters module. This is currently done by constraining p_A to be greater than 0.85.
Added support for the M61 skew model to the relax_disp.select_model user function back end. This is the Meiboom 1961 on-resonance 2-site model for skewed populations (p_A ≫ p_B). This commit follows step 6 of the relaxation dispersion model addition tutorial.
Big speeds ups of the lib.dispersion modules. Many replicated calculations have been shifted outside of the dispersion point loop, as these only need to be calculated once per function call. Some if statements have consequently been simplified.
Renamed the lib.dispersion.equations module to lib.dispersion.two_point.
Renamed the r1rho_on_res dispersion test suite data directory to r1rho_on_res_m61.
Created test data for the M61 skew R_1ρ model. This is the Meiboom 1961 on-resonance 2-site model for skewed populations (p_A ≫ p_B). This commit follows step 7 of the relaxation dispersion model addition tutorial.
Created the Relax_disp.test_r1rho_on_res_fixed_time_m61b system test. This is for the Meiboom 1961 on-resonance 2-site model for skewed populations (p_A ≫ p_B). This commit follows step 7 of the relaxation dispersion model addition tutorial.
Small simplification of the lib.dispersion.m61b module.
Fix for the specific_analyses.relax_disp.disp_data.return_value_from_frq_index() function. This cdp.spectrometer_frq_list list structure rather than the cdp.spectrometer_frq dictionary should be used.
Added a printout at the end of the optimisation of the final dispersion parameter values.
Modified the optimisation printout for better formatting.
Increased the precision of the hansen_data.py relaxation dispersion system test script. This actually speeds up the test, as the Monte Carlo simulations are significantly speed up when the CR72 model optimises to the solution.
Updates for the p_A dispersion parameter optimisation constraints. The parameter is now limited to be between p_B and 1. In the case of the limit p_A ≫ p_B, then instead the constraint is between 0.85 and 1.
Updated the Relax_disp system tests. This is for the recent precision change and constraint changes.
Fixes for the grid search for the M61 skew dispersion model. The p_A parameter search is now between 0.85 and 1.
Fixes for the func_M61b() dispersion target function. This is the Meiboom 1961 on-resonance 2-site model for skewed populations (p_A ≫ p_B).
Small changes to the r1rho_on_res_m61b dispersion test data. One R₂⁰ rate has been increased.
Completed the lib.dispersion.m61.r1rho_M61() function. Now the R₁ relaxation rate and rotating frame tilt angle are correctly handled. This is not used in the target functions as support for the R₁ and offset is not yet implemented.
Added the DPL94 model to the specific_analyses.relax_disp.variables module. This is the David, Perlman and London 1994 R_1ρ 2-site fast exchange model. This commit follows step 1 of the relaxation dispersion model addition tutorial.
Added the DPL94 model to the relax_disp.select_model user function frontend. This is the David, Perlman and London 1994 R_1ρ 2-site fast exchange model. This commit follows step 2 of the relaxation dispersion model addition tutorial.
Updates to the Relax_disp.test_r1rho_on_res_fixed_time_m61b system test.
Added the DPL94 model equations to the relax library. This is the David, Perlman and London 1994 R_1ρ 2-site fast exchange model. This commit follows step 3 of the relaxation dispersion model addition tutorial.
Created the DPL94 model target function. This is the David, Perlman and London 1994 R_1ρ 2-site fast exchange model. This commit follows step 4 of the relaxation dispersion model addition tutorial.
Added support for the DPL94 model to the relax_disp.select_model user function back end. This is the David, Perlman and London 1994 R_1ρ 2-site fast exchange model. This commit follows step 6 of the relaxation dispersion model addition tutorial.
Created the Relax_disp.test_r1rho_on_res_fixed_time_dpl94 system test. This is the David, Perlman and London 1994 R_1ρ 2-site fast exchange model. This commit follows step 7 of the relaxation dispersion model addition tutorial.
Added the IT99 model to the specific_analyses.relax_disp.variables module. This is the Ishima and Torchia 1999 2-site model for all timescales with p_A ≫ p_B. This commit follows step 1 of the relaxation dispersion model addition tutorial.
Added the IT99 model to the relax_disp.select_model user function frontend. This is the Ishima and Torchia 1999 2-site model for all timescales with p_A ≫ p_B. This commit follows step 2 of the relaxation dispersion model addition tutorial.
Updated the model lists of the dispersion analyses GUI element. This adds the IT99 CPMG-type model and the DPL94 and M61b R_1ρ-type models.
Fixes for the IT99 model description in the relax_disp.select_model user function. This is the Ishima and Torchia 1999 2-site model for all timescales with p_A ≫ p_B. This commit follows step 2 of the relaxation dispersion model addition tutorial.
Added the IT99 model equations to the relax library. This is the Ishima and Torchia 1999 2-site model for all timescales with p_A ≫ p_B. This commit follows step 3 of the relaxation dispersion model addition tutorial.
Added the it99 module to the lib.dispersion package __all__ list. This is the Ishima and Torchia 1999 2-site model for all timescales with p_A ≫ p_B. This commit follows step 3 of the relaxation dispersion model addition tutorial.
Created the IT99 model target function. This is the Ishima and Torchia 1999 2-site model for all timescales with p_A ≫ p_B. This commit follows step 4 of the relaxation dispersion model addition tutorial.
Fix for the lib.dispersion.it99 module. This is the Ishima and Torchia 1999 2-site model for all timescales with p_A ≫ p_B. This commit follows step 3 of the relaxation dispersion model addition tutorial.
Added the support for the p_A.δω² parameter 'padw2' to the dispersion specific analysis. This is needed for the Ishima and Torchia 1999 2-site model for all timescales with p_A ≫ p_B. This commit follows step 5 of the relaxation dispersion model addition tutorial.
Added support for the IT99 model to the relax_disp.select_model user function back end. This is the Ishima and Torchia 1999 2-site model for all timescales with p_A ≫ p_B. This commit follows step 6 of the relaxation dispersion model addition tutorial.
Added the support for the t_ex parameter (t_ex = 1/(2k_ex)) to the dispersion specific analysis. This is needed for the Ishima and Torchia 1999 2-site model for all timescales with p_A ≫ p_B. This commit follows step 5 of the relaxation dispersion model addition tutorial.
Added support for the IT99 model to the relax_disp.cpmgfit_input user function. This is the Ishima and Torchia 1999 2-site model for all timescales with p_A ≫ p_B.
Fix for the relax_disp.cpmgfit_input user function for when no directory is given. This was causing tracebacks.
Fix for the LM63 model for the relax_disp.cpmgfit_input user function. The grid search was incorrectly set up - the parameter is Tau, not t_ex.
Fixes for the IT99 model for the relax_disp.cpmgfit_input user function.
Changed the CPMGFit grid search options for the IT99 model in the relax_disp.cpmgfit_input user function.
Fix for the setup of the relaxation dispersion target functions for the IT99 model.
Added the relax optimisation results for the IT99 model applied to Flemming Hansen's CPMG data.
Removed an unnecessary calculation from the lib.dispersion.it99.r2eff_IT99() function.
Added the IT99 model to the software comparison table for Hansen's CPMG data. This includes only the results from relax (and possibly not fully debugged results at that).
Replaced '-' with 'N/A' if the software is missing the model. This is for the software comparison table using Flemming Hansen's CPMG data.
Updated the CPMGFit results for the IT99 model using Flemming Hansen's CPMG data.
Fixed the scaling of the parameter t_ex.
Fixes for the lib.dispersion.it99 module. This is mainly because the omega_1eff parameter was not being correctly converted from the nu_cpmg values.
Updated the relax results for Flemming Hansen's CPMG data for the IT99 model fixes.
Fixes for the relax_disp.cpmgfit_input user function for the IT99 model grid search options.
Updated the CPMGFit results for the IT99 grid search fixes of the last commit.
Basic fix for the checks of the Relax_disp.test_hansen_cpmgfit_input user function. The 't_ex' parameter is now set as 'Tau'.
Disabled the Relax_disp.test_r1rho_on_res_fixed_time_m61b system test as the M61b model is rubbish. The model cannot be properly optimised as the parameters are not independent of each other.
Fixes for the dispersion specific code. The Grace graph code of lib.software.grace no longer accepts the axis min and max arguments.
Created the Relax_disp.test_bug_20889_multi_col_peak_list system test to catch bug #20889.
Fixes for the Relax_disp.test_bug_20889_multi_col_peak_list GUI test.
Fixes for the checks of the Relax_disp.test_bug_20889_multi_col_peak_list GUI test. Intensity errors will not have been calculated yet, and the structure is called baseplane_rmsd anyway.
Fix for the Relax_disp.test_bug_20889_multi_col_peak_list GUI test. The peak intensity wizard _ok() method is now called to terminate the wizard. Otherwise this causes the subsequent GUI test which tries to access the peak intensity wizard to fail.
Created the Relax_disp.test_hansen_cpmg_data_IT99 system test. This is for testing the Ishima and Torchia 1999 2-site model for all timescales with p_A ≫ p_B. This commit follows step 7 of the relaxation dispersion model addition tutorial.
Initialised the relaxation dispersion chapter in the relax manual.
Added 600x600 pixel version of the relaxation dispersion analysis graphic. This is for use in the relax manual.
Fix for the definition of the \Ronerho LaTeX command for the relax manual.
Added EPS versions of the nessy and relax_disp 128x128 icons for the relax manual.
Added icons of all the sizes for ShereKhan.
Updated the relaxation dispersion 128x128 EPS icons to be the correct size and colour.
Updated the relaxation dispersion analysis EPS graphic to be the correct size and colour.
Copied the tutorial for adding dispersion modes to relax into the manual. This was copied from http://article.gmane.org/gmane.science.nmr.relax.devel/3907.
Editing of the tutorial for adding dispersion models in the relax manual.
Edits of the relax_disp.select_model user function docstring.
Added all of the contents of the relax_disp.select_model user function docstring to the manual.
The relaxation dispersion parameters are now defined in the main manual LaTeX file.
Added a couple of sentences about bit rot to the dispersion chapter of the relax manual. This is to the test suite part of the tutorial on adding new dispersion models.
The dispersion auto-analysis now saves the final program state before terminating.
Shifted the dispersion specific Grace plotting code into specific_analyses.relax_disp.disp_data. The private _plot_disp_curves() and _plot_exp_curves() methods of the analysis specific object are now public functions of the specific_analyses.relax_disp.disp_data module.
Removed the state.save user function calls from the relax scripts for Hansen's CPMG data.
Updated the model lists for the relax scripts for Flemming Hansen's CPMG data.
Added a sample script for the relaxation dispersion analysis of CPMG-type data.
Added a preliminary icon set for spin clustering.
The relax_disp.cluster user function GUI menu entry now uses the cluster icon.
Created a very basic GUI element for the dispersion analysis for clustering. This is simply to make this feature more obvious. The button just launches the relax_disp.cluster user function.
Modified the experiment type descriptions in the dispersion GUI.
Shifted the spin cluster GUI element to be just after the spin system GUI element. This is simply a more logical placement.
Modified the title of the dispersion auto-analysis GUI element, removing the 'Setup for' text.
Removed some unused imports from the CPMG dispersion analysis sample script.
Added the CPMG dispersion analysis sample script to the relax manual.
Epydoc docstring fixes for all of the modules of the lib.dispersion package.
Alphabetical ordering of imports.
Shifted the core of the relaxation dispersion API object into its own api module. This is to simplify the relax import cascade - by removing the code from the specific_analyses/relax_disp/__init__.py file, the import of the package no longer results in the imports of other relax modules and packages.
Expanded the modelling of dispersion data section of the relax user manual.
Expansion of the modelling of dispersion data section of the relax user manual.
The relaxation dispersion auto-analysis now outputs text and Grace files for all parameters. This is in response to bug #20917 submitted by Troels Linnet.
The Monte Carlo simulations now generate parameter errors for the relaxation dispersion analysis. The simulation index was being ignored, hence the input data was never the randomised data and all errors were zero.
Removed many decimal points from the MHz value in the Grace plots from relax_disp.plot_disp_curves.
Added support for converting between k_ex and t_ex, and p_A and p_B for the dispersion analysis. This is performed by the new specific_analyses.relax_disp.parameters.param_conversion() function. For this, most of the code from the assemble_param_vector() function has been shifted into get_value(), and most of disassemble_param_vector() into set_value(). The dispersion analysis now also has a custom sim_init_values() method to handle these parameters.
Added support for calculating auxiliary parameter errors for the dispersion analysis. This is via the monte_carlo.error_analysis user function. The errors for the parameter pairs k_ex-t_ex and p_A-p_B for the non-model parameter are now calculated as well.
Fix for the dispersion auto-analysis - p_A and p_B parameters are no longer output for the IT99 model. These are not parameters of this model.
Updated the relax results for Flemming Hansen's truncated CPMG data for all the recent changes.
Fix for bug #2091 - Suggestion for Python script for PNG/EPS/SVG conversion of grace files. Troels Linnet provided this patch, and was discovered during work on a Windows 7 system. This patch will provide a grace2images.py file in each folder where a call to specific_analyses/relax_disp/disp_data.py is called. It is called in plot_disp_curves(dir=None, force=None) and call the function lib.software.grace.script_grace2images(). The conversion script can be executed in Linux and Windows, if the PATH to xmgrace has been specified. It will look in a folder for grace files of ending *.agr and by default convert to PNG. One can also convert to EPS and SVG. Probably more options could be added, as PDF. The conversion depends on xmgrace compilation, and so PNG conversion is for fast inspection of graphs in folder, and EPS for further external conversion to PDF etc. The patch, the output file, and small script to test is attached. I miss to make the file executable in relax, so the script can be executed directly in Linux.
Mac OS X bug fix for the new analysis GUI wizard. The blank button is now using the blank_150x150.png file instead of no image, preventing nasty wxPython bugs from appearing on that system.
Fix for bug #20917. The problem is that the Grace files for each spin system are not created by the relax_disp.plot_disp_curves user function as the ':' character cannot be placed in a file name in MS Windows. All of the file name from the ':' onwards is lost. The solution is to replace each of the characters '#:@' in the spin ID string with '_'.
Another update of the relax results for Flemming Hansen's truncated CPMG data. This includes the grace2images.py script creation contributed by Troels Linnet and the change of the file name of the per-spin dispersion curves.
The value checks in the Relax_disp.test_hansen_cpmg_data_auto_analysis system test are now less precise. This is to allow the tests to pass on certain MS Windows systems.
Fix for the setting of the execute permissions on the grace2images.py scripts. The problem was identified in the post at http://thread.gmane.org/gmane.science.nmr.relax.devel/3953/focus=4000. This is within the relax_disp.plot_disp_curves user function after the grace2images.py script has been created. The commit matches the changes from trunk for the Modelfree4 batch script.
Shifted from argparse to optparse in the grace2images.py scripts from relax_disp.plot_disp_curves. This is associated with bug #20916 and the change suggested in the post http://thread.gmane.org/gmane.science.nmr.relax.devel/3953/focus=4000. The argparse module is only available from for Python 2.7.3 (the version with many Python 3 features backported) and Python ≥ 3.2. The module has been replaced with the similar optparse module as used by relax, and which available in all Python version supported by relax.
Updated the grace2images.py scripts created by the relax_disp.plot_disp_curves user function. This was discussed in bug #20916 and the change suggested in the post http://thread.gmane.org/gmane.science.nmr.relax.devel/3953/focus=4000. Improved that both small and big letters for image types can be used on the command line.
Converted the relaxation dispersion chapter of the user manual to the lstlisting environment. This matches the changes occurring within the trunk.
Added an EPS version of the 128x128 cluster icon for the user manual.
Renamed the LaTeX file for the relaxation dispersion chapter of the user manual.
Completed the script UI section of the relaxation dispersion chapter of the user manual. The sample script is now fully explained.
Added a demonstration of why the Ishima and Torchia 2005 error formula is incorrect. The script test_suite/shared_data/dispersion/error_testing/simulation.py has been added to simulate the fixed relaxation time period error propagation. This produces the test_suite/shared_data/dispersion/error_testing/error_plot.agr Grace graph. The formula, graph and a description has been added to the relax manual explaining everything.
Fix of the two-point dispersion error formula in the docs. This includes the relax_disp.select_model user function docstring and the relax manual.
Loosened a parameter check in the Relax_disp.test_hansen_cpmg_data_IT99 system test to pass on certain Linux systems.
Small edit of the legend of the relaxation dispersion figure showing the Ishima & Torchia 2005 being wrong.
Added Paul Schanda's code for the numerical solution to the Bloch-McConnell equations for 2-sites. This is specifically code which uses complex conjugate matrices. The code was submitted at http://thread.gmane.org/gmane.science.nmr.relax.devel/4132.
Made the lib.dispersion.ns_2site_star module importable in the absence of Scipy.
Polished the lib.dispersion.ns_2site_star module docstring.
Added some code missing from the lib.dispersion.ns_2site_star module. This code was accidentally not copied from http://thread.gmane.org/gmane.science.nmr.relax.devel/4132.
Significant speed ups of the lib.dispersion.ns_2site_star.r2eff_ns_2site_star() function. Replicated calculations have been minimised.
Added the NS 2-site star model to the specific_analyses.relax_disp.variables module. This is the model of the numerical solution for the 2-site Bloch-McConnell equations using complex conjugate matrices. This commit follows step 1 of the relaxation dispersion model addition tutorial.
Added the lib.dispersion.ns_2site_star module name to the package __all__ list.
Updated the lib.dispersion.ns_2site_star module with additional information from Paul Schanda. The details come from http://thread.gmane.org/gmane.science.nmr.relax.devel/4132/focus=4135. The exchange-free R₂ value parameter names have been changed to match the convention of the other lib.dispersion modules.
Added the NS 2-site star model to the relax_disp.select_model user function frontend. This is the model of the numerical solution for the 2-site Bloch-McConnell equations using complex conjugate matrices. This commit follows step 2 of the relaxation dispersion model addition tutorial.
Fix for the non-ASCII character '\xe2' in the lib.dispersion.ns_2site_star module.
Created the NS 2-site star model target function. This is the model of the numerical solution for the 2-site Bloch-McConnell equations using complex conjugate matrices. This commit follows step 4 of the relaxation dispersion model addition tutorial.
Added support for the R_2B⁰ parameter as required by the NS 2-site star model. This is the model of the numerical solution for the 2-site Bloch-McConnell equations using complex conjugate matrices. This commit follows step 5 of the relaxation dispersion model addition tutorial.
Added support for the NS 2-site star model to the relax_disp.select_model user function back end. This is the model of the numerical solution for the 2-site Bloch-McConnell equations using complex conjugate matrices. This commit follows step 6 of the relaxation dispersion model addition tutorial.
Better support for the R_2A⁰ and R_2B⁰ relaxation rate parameters in the relaxation dispersion analysis. This includes a number of fixes to allow these two parameters to be handled correctly.
Added parameter conversions to go from p_A and k_ex to k_ge and k_eg. This is for the NS 2-site star numerical model. The conversions have been added to the start of the target function to minimise mathematical operations to speed up the code.
Added the missing mpower() function as lib.linear_algebra.matrix_power.square_matrix_power(). This is needed by the lib.dispersion.ns_2site_star module. The function comes from the 'fitting_main_kex.py' file attached to comment 3 of task #7712. The mpower() function was copied and modified to suite relax's coding conventions.
Added a module docstring to lib.linear_algebra.matrix_power.
Created the lib.dispersion.ns_matrices module. This module contains a collection of functions for generating the relaxation matrices for the numerical solutions to the Bloch-McConnell equations for relaxation dispersion. The code comes from the 'fitting_main_kex.py' file attached to https://web.archive.org/web/gna.org/task/?7712#comment3.
Docstring fix for the lib.dispersion.ns_matrices.rcpmg_2d() function.
Added the functions for creating the X-axis pi-pulse rotation matrices in lib.dispersion.ns_matrices. The code comes from the 'fitting_main_kex.py' file attached to https://web.archive.org/web/gna.org/task/?7712#comment3.
Huge amounts of documentation added to the lib.dispersion.ns_2site_star module. This comes from Paul Schanda's post at http://thread.gmane.org/gmane.science.nmr.relax.devel/4132/focus=4152
Spacing fixes for the lib.dispersion.ns_2site_star module as determined by the 2to3 program. This is the Python 2 to 3 conversion program.
Docstring fix for the lib.dispersion.ns_2site_star.r2eff_ns_2site_star() function.
Comment updates in the lib.dispersion.ns_2site_star module.
Completed the conversion of the ground and excited states (G, E) to the A and B states. This follows from http://thread.gmane.org/gmane.science.nmr.relax.devel/4132/focus=4154.
Fixes for the construction of the complex conjugate matrix in lib.dispersion.ns_2site_star.
The chemical shift difference is now passed into lib.dispersion.ns_2site_star. This is currently set to the fA parameter, though it is not yet clear if this is correct.
Basic fix for the lib.linear_algebra.matrix_power.square_matrix_power() function.
The fixed relaxation time period is now sent into the NS 2-site star dispersion model.
Fix for the state G+E to A+B conversion in lib.dispersion.ns_2site_star.
The NS 2-site star model is now more robust against math domain failures. This includes the failure of the logarithmic of zero matrices.
Speed ups of the NS 2-site star dispersion model optimisation. The relaxation and magnitisation data structures are now initialised with the target function initialisation, rather than being created at each target function call. The Rex and M0 matrices are now updated at the base of the target function rather than in the lib.dispersion.ns_2site_star module to minimise the number of mathematical operations per target function call. And the M0 matrix has changed shape and a dot product is used in lib.dispersion.ns_2site_star to create Moft instead.
Shifted to using the faster numpy.linalg.matrix_power() function in lib.dispersion.ns_2site_star. This was originally using the lib.linear_algebra.matrix_power.square_matrix_power() function, however the numpy equivalent is faster.
More speed ups of the NS 2-site star dispersion model. A number of calculations have been shifted to the target function initialisation code, avoiding unnecessary repetitive mathematical operations.
Improvement of the error handling in the NS 2-site star model. The fA and p_B parameters are no longer being checked. Instead a Mgx value of 0.0 is being checked for. This catches additional problems. And now instead of the R_2eff value being set to zero, it is set to 1e⁹⁹. This is because log of zero is -inf, and then multiplied by a negative constant gives positive inf.
Docstring completion for lib.dispersion.ns_2site_star.r2eff_ns_2site_star(). Epydoc text was missing for some of the function arguments.
Changed 'numerical integration' to 'numerical solutions' in the dispersion chapter of the manual.
Reworked the dispersion chapter of the manual for the recent support of numerical models. This includes better sectioning and section labelling and referencing, and the addition of the NS 2-site star numerical model. The model and parameter tables have been updated as well.
Added the NS 2-site star red model to the specific_analyses.relax_disp.variables module. This is the model of the numerical solution for the 2-site Bloch-McConnell equations using complex conjugate matrices, whereby the simplification R_2A⁰ = R_2B⁰ is assumed. This commit follows step 1 of the relaxation dispersion model addition tutorial.
Rewrote the relax_disp.select_model user function documentation. All of the detailed model information has been removed as it is now in the relax user manual. The model lists have been modified to match the analytic-numeric sectioning of the manual.
Added the NS 2-site star red model to the relax_disp.select_model user function frontend. This is the model of the numerical solution for the 2-site Bloch-McConnell equations using complex conjugate matrices, whereby the simplification R_2A⁰ = R_2B⁰ is assumed. This commit follows step 2 of the relaxation dispersion model addition tutorial.
Docstring fix for the lib.dispersion.ns_2site_star.r2eff_ns_2site_star() function.
Created the NS 2-site star red model target function. This is the model of the numerical solution for the 2-site Bloch-McConnell equations using complex conjugate matrices, whereby the simplification R_2A⁰ = R_2B⁰ is assumed. The code in common with the NS 2-site star model has been shifted into the new calc_ns_2site_star_chi2() method. This commit follows step 4 of the relaxation dispersion model addition tutorial.
Added support for the NS 2-site star red model to the relax_disp.select_model user function back end. This is the model of the numerical solution for the 2-site Bloch-McConnell equations using complex conjugate matrices, whereby the simplification R_2A⁰ = R_2B⁰ is assumed. This commit follows step 6 of the relaxation dispersion model addition tutorial.
Added the NS 2-site star red model to the relax user manual. This is the model of the numerical solution for the 2-site Bloch-McConnell equations using complex conjugate matrices, whereby the simplification R_2A⁰ = R_2B⁰ is assumed. This commit follows step 2 of the relaxation dispersion model addition tutorial.
Fix for the Monte Carlo simulations for the numeric dispersion models. The back-calculation method was not correctly initialising the target function class.
Added the CR72 red model to the specific_analyses.relax_disp.variables module. This is the Carver and Richards 1972 analytic model with the simplification R_2A⁰ = R_2B⁰. The current CR72 makes the same assumption, but that model will be expanded to support R_2A⁰ and R_2B⁰ later. This commit follows step 1 of the relaxation dispersion model addition tutorial.
Added the CR72 red model to the relax_disp.select_model user function frontend. This is the Carver and Richards 1972 analytic model with the simplification R_2A⁰ = R_2B⁰. The current CR72 makes the same assumption, but that model will be expanded to support R_2A⁰ and R_2B⁰ later. This commit follows step 2 of the relaxation dispersion model addition tutorial.
Created the CR72 red model target function. This is the Carver and Richards 1972 analytic model with the simplification R_2A⁰ = R_2B⁰. The current CR72 makes the same assumption, but that model will be expanded to support R_2A⁰ and R_2B⁰ later. The code in common with the CR72 model has been shifted into the new calc_CR72_chi2() method. This commit follows step 4 of the relaxation dispersion model addition tutorial.
Added support for the CR72 red model to the relax_disp.select_model user function back end. This is the Carver and Richards 1972 analytic model with the simplification R_2A⁰ = R_2B⁰. The current CR72 makes the same assumption, but that model will be expanded to support R_2A⁰ and R_2B⁰ later. This commit follows step 6 of the relaxation dispersion model addition tutorial.
Added the CR72 red model to the relax user manual. This is the Carver and Richards 1972 analytic model with the simplification R_2A⁰ = R_2B⁰. The current CR72 makes the same assumption, but that model will be expanded to support R_2A⁰ and R_2B⁰ later. This commit follows step 2 of the relaxation dispersion model addition tutorial.
LaTeX improvements for the NS 2-site star red model section of the dispersion chapter of the manual.
Expanded the CR72 model to handle both the R_2A⁰ and R_2B⁰ parameters. The CR72 red model now functions as the old CR72 model where R_2A⁰ = R_2B⁰ = R₂⁰. All parts of the code have been modified. The lib.dispersion.cr72.r2eff_CR72() function has been expanded to support the full Carver and Richards 1972 equations, dropping back to the simplified form if R_2A⁰ = R_2B⁰.
Fix for the dispersion specific loop_parameters() method for the R_2A⁰ and R_2B⁰ parameters. The frequency index is now correctly returned for these and the R₂⁰ parameter.
Better printouts of the R_2A⁰ and R_2B⁰ parameters at the end of minimisation.
Documentation fix for the lib.dispersion.cr72 module.
Small speed up for the lib.dispersion.cr72 module for the R_2A⁰ != R_2B⁰ case. Replicated calculations have been minimised.
Added support for model nesting in the relaxation dispersion auto-analysis. This involves copying the parameters from the simpler nested model rather than performing a full grid search. This is currently used to handle all models with R_2A⁰ and R_2B⁰ parameters where a simpler model with the single R₂⁰ parameter is optimised first.
Improvements for the write_results() method of the dispersion auto-analysis. The parameter value and Grace files are now correctly created for all the recent models.
Fix for the Relax_disp.test_hansen_cpmg_data_auto_analysis system test for model name change. This is for the change from the CR72 model to CR72 red model.
Added the NS 2-site model to the specific_analyses.relax_disp.variables module. This is the model of the numerical solution for the 2-site Bloch-McConnell equations. It originates as optimization function number 1 from the fitting_main_kex.py script from Mathilde Lescanne, Paul Schanda, and Dominique Marion (see http://thread.gmane.org/gmane.science.nmr.relax.devel/4138, https://web.archive.org/web/gna.org/task/?7712#comment2 and https://gna.org/support/download.php?file_id=18262). This commit follows step 1 of the relaxation dispersion model addition tutorial.
Added the NS 2-site model to the relax_disp.select_model user function frontend. This is the model of the numerical solution for the 2-site Bloch-McConnell equations. It originates as optimization function number 1 from the fitting_main_kex.py script from Mathilde Lescanne, Paul Schanda, and Dominique Marion (see http://thread.gmane.org/gmane.science.nmr.relax.devel/4138, https://web.archive.org/web/gna.org/task/?7712#comment2 and https://gna.org/support/download.php?file_id=18262). This commit follows step 2 of the relaxation dispersion model addition tutorial.
Added the NS 2-site R_2eff calculating function to the relax library. This is the model of the numerical solution for the 2-site Bloch-McConnell equations. It originates as optimization function number 1 from the fitting_main_kex.py script from Mathilde Lescanne, Paul Schanda, and Dominique Marion (see http://thread.gmane.org/gmane.science.nmr.relax.devel/4138, https://web.archive.org/web/gna.org/task/?7712#comment2 and https://gna.org/support/download.php?file_id=18262). This commit follows step 3 of the relaxation dispersion model addition tutorial.
Updates and fixes for the lib.dispersion.ns_2site module. The function has been renamed, and the R₁ arguments default to 0.0. The flip angle for the from the pulse.
Created the NS 2-site model target function. This is the model of the numerical solution for the 2-site Bloch-McConnell equations. It originates as optimization function number 1 from the fitting_main_kex.py script from Mathilde Lescanne, Paul Schanda, and Dominique Marion (see http://thread.gmane.org/gmane.science.nmr.relax.devel/4138, https://web.archive.org/web/gna.org/task/?7712#comment2 and https://gna.org/support/download.php?file_id=18262). This commit follows step 4 of the relaxation dispersion model addition tutorial.
Converted the NS 2-site model to NS 2-site 3D to be more specific. This might change again in the future.
Added support for the NS 2-site 3D model to the relax_disp.select_model user function back end. This is the model of the numerical solution for the 2-site Bloch-McConnell equations. It originates as optimization function number 1 from the fitting_main_kex.py script from Mathilde Lescanne, Paul Schanda, and Dominique Marion (see http://thread.gmane.org/gmane.science.nmr.relax.devel/4138, https://web.archive.org/web/gna.org/task/?7712#comment2 and https://gna.org/support/download.php?file_id=18262). This commit follows step 6 of the relaxation dispersion model addition tutorial.
Lots of fixes for the relaxation dispersion target function module for the NS 2-site 3D model.
Improvements to the nesting() method of the relaxation dispersion auto-analysis. The use of the parameters of the simpler model in a nested pair now only works if the simpler model is in the model list.
Converted the pi-pulse propagator matrices to numpy array format. This is to enable the use of the much faster numpy.dot() function for performing the dot products.
Speed ups for the NS 2-site 3D model. The pi-pulse propagator is created only once upon target function initialisation rather than for each function call, each spin cluster, each magnetic field strength, each dispersion point, and each CPMG block.
Modified the df, fA, and fB parameters to match the relax omega conventions of δω, wA, and wB. This follows from Paul Schanda's confirmation at http://thread.gmane.org/gmane.science.nmr.relax.devel/4132/focus=4159.
Speed up for the lib.dispersion.ns_matrices.rcpmg_3d() function. The p_A and p_B parameters are now sent into the function rather than being recreated by the function.
More changes to the numerical solution dispersion code to match relax's conventions. This includes the changes of df->δω, fA->wA, fB->wB, and Mgx->Mx.
Added the NS 2-site 3D red model to the specific_analyses.relax_disp.variables module. This is the NS 2-site 3D model with R_2A⁰ = R_2B⁰ = R₂⁰. This commit follows step 1 of the relaxation dispersion model addition tutorial.
Added the NS 2-site 3D red model to the relax_disp.select_model user function frontend. This is the NS 2-site 3D model with R_2A⁰ = R_2B⁰ = R₂⁰. This commit follows step 2 of the relaxation dispersion model addition tutorial.
Created the NS 2-site 3D red model target function. This is the NS 2-site 3D model with R_2A⁰ = R_2B⁰ = R₂⁰. This commit follows step 4 of the relaxation dispersion model addition tutorial.
Added support for the NS 2-site 3D red model to the relax_disp.select_model user function back end. This is the NS 2-site 3D model with R_2A⁰ = R_2B⁰ = R₂⁰. This commit follows step 6 of the relaxation dispersion model addition tutorial.
Updated all of the numerical model sections of the dispersion chapter of the manual. This includes additions for the NS 2-site 3D and NS 2-site 3D red models.
Updated the NS 2-site 3D and NS 2-site 3D red models in the dispersion chapter of the relax manual. The models are now included in the tables and in the introduction.
Added support for nesting to the relaxation dispersion auto-analysis for the 'NS 2-site 3D*' models.
Added the NS 2-site expanded model to the specific_analyses.relax_disp.variables module. This is the numerical model for the 2-site Bloch-McConnell equations expanded using Maple by Nikolai Skrynnikov. This commit follows step 1 of the relaxation dispersion model addition tutorial.
Added the NS 2-site expanded model to the relax_disp.select_model user function frontend. This is the numerical model for the 2-site Bloch-McConnell equations expanded using Maple by Nikolai Skrynnikov. This commit follows step 2 of the relaxation dispersion model addition tutorial.
Added the NS 2-site expanded R_2eff calculating function to the relax library. This is the numerical model for the 2-site Bloch-McConnell equations expanded using Maple by Nikolai Skrynnikov. It originates as optimization function number 5 from the fitting_main_kex.py script from Mathilde Lescanne, Paul Schanda, and Dominique Marion (see http://thread.gmane.org/gmane.science.nmr.relax.devel/4138, https://web.archive.org/web/gna.org/task/?7712#comment2 and https://gna.org/support/download.php?file_id=18262). This commit follows step 3 of the relaxation dispersion model addition tutorial.
Fix for the lib.dispersion.ns_2site_expanded.r2eff_ns_2site_expanded() function. The pg variable should have been p_A and it needs to be sent into the function.
Created the NS 2-site expanded model target function. This is the numerical model for the 2-site Bloch-McConnell equations expanded using Maple by Nikolai Skrynnikov. It originates as optimization function number 5 from the fitting_main_kex.py script from Mathilde Lescanne, Paul Schanda, and Dominique Marion (see http://thread.gmane.org/gmane.science.nmr.relax.devel/4138, https://web.archive.org/web/gna.org/task/?7712#comment2 and https://gna.org/support/download.php?file_id=18262). This commit follows step 4 of the relaxation dispersion model addition tutorial.
Added support for the NS 2-site expanded model to the relax_disp.select_model user function back end. This is the numerical model for the 2-site Bloch-McConnell equations expanded using Maple by Nikolai Skrynnikov. It originates as optimization function number 5 from the fitting_main_kex.py script from Mathilde Lescanne, Paul Schanda, and Dominique Marion (see http://thread.gmane.org/gmane.science.nmr.relax.devel/4138, https://web.archive.org/web/gna.org/task/?7712#comment2 and https://gna.org/support/download.php?file_id=18262). This commit follows step 6 of the relaxation dispersion model addition tutorial.
Fix for the relax_disp.select_model user function for the NS 2-site expanded model. There is only one R₂⁰ parameter as R_2A⁰ = R_2B⁰ in this model.
Added the NS 2-site expanded model to the relax user manual. This is the numerical model for the 2-site Bloch-McConnell equations expanded using Maple by Nikolai Skrynnikov. It originates as optimization function number 5 from the fitting_main_kex.py script from Mathilde Lescanne, Paul Schanda, and Dominique Marion (see http://thread.gmane.org/gmane.science.nmr.relax.devel/4138, https://web.archive.org/web/gna.org/task/?7712#comment2 and https://gna.org/support/download.php?file_id=18262). This commit follows step 2 of the relaxation dispersion model addition tutorial.
Large renaming of the relaxation dispersion models. This includes both the analytic and numerical models. All of the models with separate R_2A⁰ and R_2B⁰ parameters now have ' full' added to the end of the model name. And all of the corresponding reduced models whereby R_2A⁰ = R_2B⁰ = R₂⁰ have had the trailing ' red' removed. All descriptions and variable names have been updated to match.
Updated the dispersion auto-analysis write_results() method for the recent model changes.
Import fix for the NS 2-site expanded dispersion model target function.
Fix for the lib.dispersion.ns_2site_expanded module for the missing sqrt() function import.
Simplified the test_hansen_cpmg_data_*() system tests by shifting most shared code into setup_hansen_cpmg_data().
Created the Relax_disp.test_hansen_cpmg_data_CR72_full system test for checking the CR72 full model.
Expanded the dispersion target function class docstring to include all current dispersion models.
Updated the parameter checks in the Relax_disp.test_hansen_cpmg_data_CR72_full system test.
Fixes for all of the definitions of the k_AB and k_BA exchange parameters. These were inverted in all parts of relax. The changes only affect the numerical dispersion models.
Created the Relax_disp.test_hansen_cpmg_data_ns_2site_3D system test. This checks the NS 2-site 3D numerical dispersion model against some truncated CPMG data from Flemming Hansen.
Created the Relax_disp.test_hansen_cpmg_data_ns_2site_3D_full system test. This checks the NS 2-site 3D full numerical dispersion model against some truncated CPMG data from Flemming Hansen. The parameter checks have not been updated as there appears to be a bug.
Created system tests for the rest of the numerical dispersion models. These include Relax_disp.test_hansen_cpmg_data_ns_2site_expanded, Relax_disp.test_hansen_cpmg_data_ns_2site_star and Relax_disp.test_hansen_cpmg_data_ns_2site_star_full. This checks the NS 2-site expanded, NS 2-site star, and NS 2-site star full numerical dispersion models against some truncated CPMG data from Flemming Hansen. The parameter checks have not been updated for the NS 2-site expanded and NS 2-site star full models as there appears to be bugs.
Fixes for the Relax_disp.test_hansen_cpmg_data_auto_analysis system test. The checks for the CR72 red model are now against the CR72 model. And the models optimised only now include No Rex, LM63, CR72, and IT99, massively speeding up the test.
Fixes for the lib.dispersion.ns_2site_expanded module. These problems were identified using the Relax_disp.test_hansen_cpmg_data_ns_2site_expanded system test. They correspond to the issues with the original fitting_main_kex.py program identified by Mathilde Lescanne in her post at http://thread.gmane.org/gmane.science.nmr.relax.devel/4144.
The Relax_disp.test_hansen_cpmg_data_ns_2site_expanded system test now passes. The test has been set up to match Relax_disp.test_hansen_cpmg_data_CR72. This allows the efficiency of each method to be compared by running the tests with the --time flag.
Fix for the model nesting method of the relaxation dispersion auto-analysis for deselected spins.
Added an upper constraint of 2e⁶ rad/s for the k_ex dispersion parameter. This is to prevent slow optimisation to values in the order of 1e²⁰ for models which fail.
Updated the model lists for the relax scripts for optimising Flemming Hansen's CPMG data. The model lists now include the numeric models and the CR72 full model.
The lib.software.grace.write_xy_header() can now set the legend fill pattern and font size.
The relax_disp.plot_disp_curves user function backend now sets clear legend boxes with smaller text.
Fix for the Grace string for the δω dispersion parameter.
Updated the parameter value checks in the Relax_disp.test_hansen_cpmg_data_CR72 system test. The low precision parameters are slightly different because of the new upper constraint on k_ex, simply because optimisation is terminated early rather than optimisation giving different results.
Updated the rest of the dispersion system tests to check the correct parameter values. It is currently assumed that the 'full' dispersion models are correct as there is currently no way of testing if they are not. So the Relax_disp.test_hansen_cpmg_data_ns_2site_3D_full and Relax_disp.test_hansen_cpmg_data_ns_2site_star_full system tests have been updated to pass.
Modified how the relaxation dispersion auto-analysis handles Monte Carlo simulations. Now there is a flag which allows per-model simulations to be enabled. By default, simulations are now only performed at the end. This is to allow for massive speed ups in the auto-analysis.
Modified the dispersion GUI analysis to not include all dispersion models.
Added Mathilde Lescanne to the copyright notices of the numeric dispersion code in the relax library. The dates must still be checked and updated correctly.
Added support for the mc_sim_all_models flag for the dispersion auto-analysis in the GUI. The new boolean auto-analysis GUI input element is being used for this purpose.
All of the numeric dispersion models are now much more robust. The real part of the magnetization vector for the A state could, for some parameter combinations, be either negative or NaN. These situations are now caught, and the R_2eff value set to a very large number.
Sectioning improvements for the relaxation dispersion chapter of the relax user manual.
Added DOI numbers to a number of bibliography entries for quick links in the relax user manual.
Added the LM63 3-site model to the specific_analyses.relax_disp.variables module. This is the Luz and Meiboom 1963 analytic model for three exchanging sites. This commit follows step 1 of the relaxation dispersion model addition tutorial.
Added the LM63 3-site model to the relax_disp.select_model user function frontend. This is the Luz and Meiboom 1963 analytic model for three exchanging sites. This commit follows step 2 of the relaxation dispersion model addition tutorial.
Added the LM63 3-site model to relaxation dispersion chapter of the relax user manual. This is the Luz and Meiboom 1963 analytic model for three exchanging sites. This commit follows step 2 of the relaxation dispersion model addition tutorial.
Added the LM63 3-site R_2eff calculating function to the relax library. This is the Luz and Meiboom 1963 analytic model for three exchanging sites. This commit follows step 3 of the relaxation dispersion model addition tutorial.
Fixes for the LM63 3-site model equations in the relaxation dispersion chapter of the user manual.
Created the LM63 3-site model target function. This is the Luz and Meiboom 1963 analytic model for three exchanging sites. This commit follows step 4 of the relaxation dispersion model addition tutorial.
Added support to the relaxation dispersion analysis for the LM63 3-site model parameters. This is the Luz and Meiboom 1963 analytic model for three exchanging sites. This commit follows step 3 of the relaxation dispersion model addition tutorial.
Added support for the LM63 3-site model to the relax_disp.select_model user function back end. This is the Luz and Meiboom 1963 analytic model for three exchanging sites. This commit follows step 6 of the relaxation dispersion model addition tutorial.
Added support for the LM63 3-site parameters to the specific_analyses.relax_disp.parameters module. This is the Luz and Meiboom 1963 analytic model for three exchanging sites. This commit follows step 5 of the relaxation dispersion model addition tutorial.
Added the LM63 3-site model to the dispersion scripts for Flemming Hansen's CPMG data.
The relaxation dispersion auto-analysis can now resume if it has been interrupted.
Some fixes for the LM63 3-site dispersion model. The library code was not accepting the correct arguments and it was referencing a non-existent parameter, and the grid search setup was failing.
Added support for optimising the LM63 3-site dispersion model with Art Palmer's CPMGFit. This is for the relax_disp.cpmgfit_input user function. This model in CPMGFit is called '3-site_CPMG'.
Python 3 fixes for the specific_analyses.relax_disp.disp_data module.
Fixes for the relax_disp.cpmgfit_execute user function backend. This would hang if CPMGFit produced error messages. Hopefully this is now fixed.
Updated the CPMGFit results for the LM63 3-site model. This is for the truncated CPMG data from Flemming Hansen.
Speed ups for the LM63 3-site target function. Some mathematical operations have been shifted from the library code into the target function so that is only calculates once per function call.
Updated the relax results for Flemming Hansen's truncated CPMG data for the LM63 3-site model.
The dispersion auto-analysis now outputs files for the k_B, kC, φ_ex,B, and φ_ex,C parameters. This is in the write_results() method and is for creating text files and Grace plots for the LM63 3-site model.
Created some synthetic test data for the LM63 3-site dispersion model. This will be used to test CPMGFit and relax's implementations.
Updated the LM63 3-site dispersion model test data. The CPMG frequencies are now more realistic.
Removed the old Sparky peak lists for the LM63 3-site dispersion model test data.
Added the new Sparky peak lists for the LM63 3-site dispersion model test data.
Updated the reference Sparky peak lists for the LM63 3-site dispersion model test data.
Missing import of the specific_analyses.relax_disp.variables.MODEL_LM63_3SITE variable.
Added scripts for calculating the R_2eff values for the LM63 3-site dispersion model test data.
Created the Relax_disp.test_r2eff_fit_fixed_time system test to show a failure in the auto-analysis. This shows a failure of the R_2eff fitting in the dispersion auto-analysis due to Monte Carlo simulations being run when the calc() function should be called.
Removed some parts of the Relax_disp.test_r2eff_fit_fixed_time system test. The last lines were non-functional.
Fix for the dispersion auto-analysis if not enough models have been input for a final run. The final model selection, Monte Carlo simulation, and results writing stage of the auto-analysis now only occurs when enough models are present for model selection.
Fix for the dispersion auto-analysis for when only the single R2eff model is optimised. This is for the case of exponential curve fitting, and allows Monte Carlo simulations to proceed even when the mc_sim_all_models flag is False.
Removed some unused parts of the r2eff_calc.py script and added the results file.
Made the LM63 3-site dispersion model test data more realistic. Previously all the rates were within a few decimal places of the R₂⁰ values. Now the dispersion is much more significant.
Modified the LM63 3-site dispersion model test data again. This time the data has been changed to be that of two residues rather than two spins.
Another update of the LM63 3-site dispersion model test data. This data now makes CPMGFit happy.
Added the CPMGFit results for the LM63 3-site dispersion model test data.
Added the relax results for the LM63 3-site dispersion model test data.
Added a warning not to use the LM63 3-site model to the dispersion chapter of the user manual.
Added the LM63 3-site dispersion model to the model list in the GUI. It is not selected by default.
Updated the Noe.test_noe_analysis system test. These were the changes to the lib.software.grace.write_xy_header() function.
Fix for the model equivalence setup in the nesting() method of the dispersion auto-analysis. This is the use of the analytic CR72 model parameters for the numeric models to avoid the grid search.
Removed a double full stop in the relax_disp.select_model docstring.
Updates for the test suite data script for optimising Flemming Hansen's CPMG data. The model list has been shorted to the useful models, and the grid search size is now reasonable.
Updated the software_comparison file for the numeric model results from relax. This is the file comparing the results for residues 70 and 71 from Flemming Hansen's CPMG data.
Updated the numeric model results for the software_comparison file.
Updated the relax results for Flemming Hansen's truncated CPMG data. This includes the CR72 full model and all the numeric models (excluding the *full models).
Added Dominique Marion to the copyright notices of all the lib/dispersion/ns_*.py files. This is in response to Paul Schanda's message at http://thread.gmane.org/gmane.science.nmr.relax.devel/4225/focus=4226.
Small fix for the relax_disp.cluster documentation.
Added the new pre_run_dir argument to the relaxation dispersion auto-analysis. This is to enable clustered optimisation. This specifies a directory containing a completed analysis. The parameters from this previous run will be used as the starting point for optimisation of the clustered analysis.
Fix for the Monte Carlo simulations for the dispersion auto-analysis failing under certain conditions. The wrong variable was being checked to see if more than two models were being optimised.
The dispersion minimisation() method now skipped deselected spin clusters. This is defined as all spins of the cluster being deselected.
Implemented the new relax_disp.parameter_copy user function. This is used to copy relaxation dispersion parameters from one data pipe to another, taking cluster averaging into account. It is used by the dispersion auto-analysis to handle clustering.
Added an element to the dispersion GUI analysis for specifying the directory of previous results. This is used for the pre_run_dir argument for the dispersion auto-analysis.
Reactivated Monte Carlo simulations for the R2eff model for exponential data curves. This is within the optimise() method of the dispersion auto-analysis.
Updated the intro chapter of the user manual for the now supported dispersion analysis. This is no longer listed as a future to be implemented feature.
Updated the screenshot of the analysis selection wizard to include the dispersion analysis. This new figure has been updated in the intro chapter of the relax user manual as well.
Renamed an instance of 'numerical simulation' in the dispersion chapter of the manual.
Fix for the final data pipe in the dispersion auto-analysis. The final data pipe is now placed in the data pipe bundle. This is needed to allow the final state file to be opened in the GUI with an associated GUI analysis tab.
Fixes for the clustering display in the GUI. This is for the relaxation dispersion GUI analysis tab.
Updated the README file for Dr. Flemming Hansen's CPMG data in the test suite.
Added Martin Tollinger to the copyright of the lib.dispersion.ns_2site_expanded module. This follows Martin's post at http://article.gmane.org/gmane.science.nmr.relax.devel/4276.
Added links to all of the copyright licensing agreements for the lib.dispersion.ns_2site_expanded module.
Added Nikolai Skrynnikov to the copyright notice of the lib.dispersion.ns_2site_expanded module.
Added the TP02 model to the specific_analyses.relax_disp.variables module. This is the Trott and Palmer 2002 R_1ρ analytic model for 2-site exchange. This commit follows step 1 of the relaxation dispersion model addition tutorial.
Added the TP02 model to the relax_disp.select_model user function frontend. This is the Trott and Palmer 2002 R_1ρ analytic model for 2-site exchange. This commit follows step 2 of the relaxation dispersion model addition tutorial.
Added the TP02 model to relaxation dispersion chapter of the relax user manual. This is the Trott and Palmer 2002 R_1ρ analytic model for 2-site exchange. This commit follows step 2 of the relaxation dispersion model addition tutorial.
Added the TP02 R_1ρ' calculating function to the relax library. This is the Trott and Palmer 2002 R_1ρ analytic model for 2-site exchange. This commit follows step 3 of the relaxation dispersion model addition tutorial. The Matlab code from Skrynnikov and Tollinger has not been converted to Python code yet. This is to allow the Matlab->Python conversion to be followed.
Fix for the M61 skew dispersion model indexing in the user manual.
Added the NS 2-site expanded model to the CPMG dispersion sample script.
Added the NS 2-site expanded and TP02 models to the script in the manual. This is in the script section of the dispersion chapter of the user manual.
Converted the lib.dispersion.tp02 module from Matlab code to Python. The code has also been made fail-safe and repetitive calculations have been shifted outside of the loop to speed things up.
Fixes for the TP02 model section of the dispersion chapter of the manual.
Created the TP02 model target function. This is the Trott and Palmer 2002 R_1ρ analytic model for 2-site exchange. This commit follows step 4 of the relaxation dispersion model addition tutorial.
Added support for the TP02 model to the relax_disp.select_model user function back end. This is the Trott and Palmer 2002 R_1ρ analytic model for 2-site exchange. This commit follows step 6 of the relaxation dispersion model addition tutorial.
The spectrometer frequency information is now checked for the TP02 model.
Started to create a script to create synthetic data for the TP02 dispersion model. This still needs a lot of work.
Added the tp02 module to the lib.dispersion package __all__ list.
Created the synthetic data for the TP02 dispersion model. The Sparky peak lists have been created and added to the repository.
Modified the synthetic data for the TP02 dispersion model. The data is more closely mimics that from the paper, and should now be in the slow exchange regime.
Updated the M61 R_1ρ model conditions in the table in the user manual.
Updated the TP02 R_1ρ model conditions in the table in the manual. This cannot be fast exchange.
Started to create the Relax_disp.test_r1rho_off_res_fixed_time_tp02 system test.
A fix for older numpy versions, as the numpy.add() function argument 'out' is relatively new.
Added the new TSMFK01 model to the specific_analyses\relax_disp\variables.py module. This is the Tollinger/Kay model for the 2-site very-slow exchange model for CPMG-type experiments, which cover the range of microsecond to second time scale. Paper by M. Tollinger, N.R. Skrynnikov, F.A.A. Mulder, J.D.F. Kay and L.E. Kay (2001). Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
lib/dispersion/lm63.py is copied to tsmfk01.py as part of the implementation of the TSMFK01 model equation. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at Tutorial for adding relaxation dispersion models to relax.
Added the TSMFK01 model to the user_functions/relax_disp.py select_model user function frontend. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Created the TSMFK01 model target function for 2-site very-slow exchange model, range of microsecond to second time scale. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Added the TSMFK01 model equations to the relax library lib/dispersion/tsmfk01.py. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
The chemical shift of each spin is now taken into account for the synthetic data for the TP02 dispersion model. The data now properly reflects the spin lock offset.
Updated all of the dispersion system tests for the spectrum.read_intensities user function changes. The arguments heteronuc and proton have been replaced with 'dim'.
Improved the error message for when peak intensity data cannot be found in a dispersion analysis. This is to better aid the user to track down what they did wrong.
More error message improvements for when peak intensity data cannot be found in a dispersion analysis.
Created the relax script for the Relax_disp.test_r1rho_off_res_fixed_time_tp02 system test.
Changed the synthetic data file names for the TP02 dispersion model.
Updated the Relax_disp.test_r1rho_off_res_fixed_time_tp02 system test script for the new file names.
Added a new user function to the Relax_disp.test_r1rho_off_res_fixed_time_tp02 system test. This is the chemical_shift.read user function which currently does not exist. Chemical shifts are needed to interpret off-resonance R_1ρ data.
Copyright of Sebastien Morin and Edward d'Auvergne re-inserted, since tsmfk01 is an alteration of lm63.py and m61.py in same directory. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Fix for converting δω from ppm to rad/s. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Added support for the TSMFK01 model to the relax_disp.select_model user function back end. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Fix for the reading of chemical shifts in the Relax_disp.test_r1rho_off_res_fixed_time_tp02 system test.
Added the Trott and Palmer, 2002 bibtex reference for the user manual.
Added preliminary support for chemical shifts to the dispersion target functions.
Modified the GUI behaviour for a dispersion analysis when the C modules are not compiled. Previously a user was blocked from performing any dispersion analysis in the GUI is the modules were not compiled. Now instead, although an error is still thrown, the analysis will be initialised.
A new check blocking exponential curve fitting in the dispersion analysis when the C modules are not compiled.
Changed how chemical shifts are handled in the dispersion target function class. The chemical shifts in ppm are accepted and they are converted to rad/s inside the __init__() method. A structure for rotating frame tilt angles is now also accepted.
Added a relax_disp.spin_lock_offset user function call to Relax_disp.test_r1rho_off_res_tp02. This is the Relax_disp.test_r1rho_off_res_tp02 system test and the user function does not exist yet.
Implemented the relax_disp.spin_lock_offset user function. This includes both the front end and the back end specific_analyses.relax_disp.disp_data.spin_lock_offset() function.
The offset is now set for all spectra in the Relax_disp.test_r1rho_off_res_fixed_time_tp02 system test. Previously only the reference was set.
Fixed a typo in the dispersion chapter of the user manual. This was identified by Troels Linnet at http://thread.gmane.org/gmane.science.nmr.relax.devel/4410.
Fix for the relax_disp.spin_lock_offset user function. The cdp.dispersion_points structure was being updated when it should not be touched - a remnant of the relax_disp.spin_lock_field backend which this code was copied from.
Added some more arguments to the dispersion target function class for off-resonance R_1ρ models. This is the structure for the spin-lock offsets and the tilt angles for each spin.
Fix for the Relax_disp.test_r1rho_off_res_fixed_time_tp02 system test. The correct spectrum ID is now used for the relax_disp.spin_lock_offset user function calls in the script.
The dispersion specific optimisation code is now assembling chemical shift related data. The specific_analyses.relax_disp.disp_data.return_offset_data() function has been written to return structures for the chemical shifts, offsets, and tilt angles. These are then used by the optimisation functions by passing them into the target function code.
The TP02 model code is now in a semi functional state. The lib.dispersion code has been fixed to properly handle the data it receives and the target function code has been updated to pass in the correct data.
The TP02 model R_1ρ off-resonance test data creation script now creates files of the R₁ relaxation data. These files are needed for the system tests, as R₁ data needs to be read.
The dispersion target function class now handles R₁ relaxation data. This data is essential for the off-resonance R_1ρ models.
The Relax_disp.test_r1rho_off_res_fixed_time_tp02 system test script now reads the R₁ relaxation data. This data is essential for the model optimisation.
The dispersion specific code is now assembling the R₁ data and passing it to the target function. The new specific_analyses.relax_disp.disp_data.return_r1_data() function creates a data structure holding all the R₁ data. This is used in the off-resonance R_1ρ experiments.
Added checks to the specific_analyses.relax_disp.disp_data.return_r1_data() function. This is to help indicate to the user when data is missing.
Fix for the Relax_disp.test_bug_20889_multi_col_peak_list GUI test. The spectrum.read_intensities user function no longer has 'heteronuc' and 'proton' arguments.
Fix to allow R₁ data to be randomised for Monte Carlo simulations for off-resonance R_1ρ data. This is a temporary kludge for the dispersion analysis and needs to be replaced by a cleaner solution via the base_data_loop() method.
Fix for the synthetic data for the TP02 dispersion model. The nitrogen chemical shift was not converted from ppm to rad/s before being used to calculate the offsets.
Fixes for the parameter checks in the Relax_disp.test_r1rho_off_res_fixed_time_tp02 system test. The parameter values had not been updated from when the test was copied from one of the other tests.
Turned off clustering in the Relax_disp.test_r1rho_off_res_fixed_time_tp02 system test. This speeds the test up by more than half.
Fix for the TP02 dispersion model. The rotating frame tilt angle for this model is calculated from the population averaged chemical shift and not the equal weighted average.
Attempt at fixing bug #21080. This was reported by Troels Linnet. The problem is a standard GUI problem. The text from a wxPython GUI is a Unicode string. But relax requires standard strings. Therefore the gui.string_conv.gui_to_str() function needs to be used on the return value of the GUI element GetValue() method, but this call was forgotten.
Fix for the synthetic data for the TP02 dispersion model. The chemical shift is being set to that of state A, the major species, rather than the non-weighted chemical shift average. This could also have been set to the population weighted average.
The TP02 dispersion model now assumes the chemical shift is that of the major population A. Previously the linear chemical shift average was assumed.
Increased the grid search size in the Relax_disp.test_r1rho_off_res_fixed_time_tp02 system test.
The self.field_pre_run_dir GUI element is now deactivated with the execution lock.
Many fixes and improvements for all of the R_1ρ dispersion models in the user manual. The equations are now correct and the parameter table updated with new parameters and equations.
Removed the unused theta and R1 arguments for the lib.dispersion.m61.r1rho_M61() function. These off-resonance parameters are not used in the on-resonance model.
Updated the r1rho_on_res_m61 dispersion on-resonance data for off-resonance models. The chemical shifts are now the same for all spins, to force perfect on-resonance, and the two spins are now different residues.
Added an R₁ data file to r1rho_on_res_m61, by copying from the r1rho_off_res_tp02 test suite data.
Updated the Relax_disp.test_r1rho_on_res_fixed_time_dpl94 system test for off-resonance data. The offsets, R₁ data, and chemical shifts are now setup or read by the script.
Fixes for the DPL94 model to make it truly off-resonance. The tilt angles and R₁ data are now used by the target function.
Fixes for the r1rho_on_res_m61.py system test script. The spins are now different residues. This fixes two system tests.
Renamed all of the current numeric dispersion models in relax to be specific to CPMG-type data. This is in preparation for adding R_1ρ numeric models. It was proposed at http://thread.gmane.org/gmane.science.nmr.relax.devel/4461.
Added the NS R1rho 2-site model to the specific_analyses.relax_disp.variables module. This is the numerical model for the 2-site Bloch-McConnell equations for R_1ρ data. This commit follows step 1 of the relaxation dispersion model addition tutorial.
Added the NS R1rho 2-site model to the relax_disp.select_model user function frontend. This is the numerical model for the 2-site Bloch-McConnell equations for R_1ρ data. This commit follows step 2 of the relaxation dispersion model addition tutorial.
Added the NS R1rho 2-site R_1ρ calculating function to the relax library. This is the numerical model for the 2-site Bloch-McConnell equations for R_1ρ data. This code originates from the Skrynikov & Tollinger code (the sim_all.tar file https://gna.org/support/download.php?file_id=18404 attached to https://web.archive.org/web/gna.org/task/?7712#comment5). Specifically the funNumrho.m file. This commit follows step 3 of the relaxation dispersion model addition tutorial.
Fix for the function name in the lib.dispersion.ns_r1rho_2site module and removed misplaced copyrights.
Created the NS R1rho 2-site model target function. This is the numerical model for the 2-site Bloch-McConnell equations for R_1ρ data. The code originates from the funNumrho.m file from the Skrynikov & Tollinger code (the sim_all.tar file https://gna.org/support/download.php?file_id=18404 attached to https://web.archive.org/web/gna.org/task/?7712#comment5). This commit follows step 4 of the relaxation dispersion model addition tutorial.
Added support for the NS R1rho 2-site model to the relax_disp.select_model user function back end. This is the numerical model for the 2-site Bloch-McConnell equations for R_1ρ data. The code originates from the funNumrho.m file from the Skrynikov & Tollinger code (the sim_all.tar file https://gna.org/support/download.php?file_id=18404 attached to https://web.archive.org/web/gna.org/task/?7712#comment5). This commit follows step 6 of the relaxation dispersion model addition tutorial.
Added the NS R1rho 2-site model to the relax user manual. This is the numerical model for the 2-site Bloch-McConnell equations for R_1ρ data. The code originates from the funNumrho.m file from the Skrynikov & Tollinger code (the sim_all.tar file https://gna.org/support/download.php?file_id=18404 attached to https://web.archive.org/web/gna.org/task/?7712#comment5). This commit follows step 2 of the relaxation dispersion model addition tutorial.
Rearrangement of the model sections in the dispersion chapter of the user manual. These are now better separated into different categories.
Created a save file for the r1rho_off_res_tp02 dispersion data optimised to the R2eff model. This will be used for faster system tests.
Created the Relax_disp.test_r1rho_ns_r1rho_2site_to_tp02 system test for the new NS R1rho 2-site model. This tests the NS R1rho 2-site model against the R_1ρ off-resonance test data from the TP02 model.
A number of fixes for the NS R1rho 2-site dispersion model. The model should now be fully functional. The chemical shift and R₁ related data are now assembled for this model, and the data correctly passed from the target function to the lib.dispersion module.
The Relax_disp.test_r1rho_ns_r1rho_2site_to_tp02 system test now passes. The optimised values have been hard-coded into the system test. They do not match the TP02 results, but are close.
Renamed many of the Relax_disp system tests to bring some order to the naming.
Alphabetical ordering of all of the Relax_disp system tests.
Created a system test to catch bug #21081. This uses a truncated version of Troel Linnet's save state attached to the bug report (the data pipes not used in the model selection have been manually deleted as well as all by the first 3 spins in the remaining 2 data pipes).
Fix for bug #21081 - the failure of a dispersion cluster analysis. The problem was that the specific_analyses.relax_disp.disp_data.loop_cluster() generator method was not taking the spin.select flag into account. Now all deselected spins are excluded from the spin clusters and the free spins.
Better support for off-resonance R_1ρ data in the dispersion GUI. A new row of buttons has been added to the dispersion GUI, just above the Peak list GUI element. The first button is for the spin.isotope user function and replaces the old GUI element. Two new buttons for loading R₁ data and chemical shifts have also been added, as required for off-resonance R_1ρ data.
Changed the chemical shift icon to that of the chemical shift in ppm units - the δ symbol.
The chemical shift icon now has a transparent background.
Small changes to the tooltips of the R₁ and chemical shift buttons.
Used far more Unicode for superscript, subscript and Greek letters for the model parameters. This is for the model list elements in the dispersion GUI tab.
Added the TP02 and NS R1rho 2-site models to the R_1ρ model list in the dispersion GUI. These models were missing from the list.
Fix for the NS R1rho 2-site model description in the relax_disp.select_model user function.
The relax_disp.select_model GUI wizard combo element now uses Unicode for the dispersion parameters. This is for all the models. The LM63 3-site model parameter list has also been fixed to match the current set.
The CPMGFit input and output file names for relaxation dispersion are now MS Windows compatible. This is needed to allow the files in the test suite to exist on Windows systems, as the '#:@'symbols cause problems. The same logic as used for the relax_disp.plot_disp_curves is used to replace these characters with an underscore.
CPMGFit file name fixes for MS Windows. The '#:@' characters have all been replaced by underscores.
Fix for the Relax_disp.test_hansen_cpmgfit_input system test. The '#:@' characters are no longer used in the file names.
Updates to the Relax_disp system tests for the lower precision of MS Windows. These fixes allow the tests to pass on MS Windows.
Renamed ka parameter to kA, to be consistent with naming conventions. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Fix for r20 should be called r20a. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Fix for unpacking the parameters correctly. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Added the k_AB and k_BA parameters to the table of all dispersion parameters.
Proper ordering of all the dispersion models. See the thread at http://thread.gmane.org/gmane.science.nmr.relax.devel/4498 for details.
Added the NS R1rho 2-site model to the dispersion auto-analysis.
Added the TP02 model to the dispersion auto-analysis.
The tutorial for adding dispersion models in the user manual has been simplified. Most of the text from the dispersion model addition tutorial in the dispersion chapter of the manual has been removed. Instead a link to the tutorial on the wiki is given as this is a much better place for such information (Tutorial for adding relaxation dispersion models to relax).
Moved the ordering of the model TSMF. Ordering conventions mentioned in this post http://article.gmane.org/gmane.science.nmr.relax.devel/4500. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Added the relax_disp.spin_lock_offset user function to the peak intensity wizard of the GUI. This is only for R_1ρ-type data and allows off-resonance data to be analysed in the GUI.
Data provided for the implementation of the slow-exchange analytic model of the Tollinger/Kay (2001). This model were used for fitting in the paper http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1458987.
Created the Relax_disp.test_tp02_data_to_tp02 GUI test. This is based on the system test of the same name. This GUI test checks that an off-resonance R_1ρ analysis is functional in the GUI.
Python 3 space fixes for the lib.software.grace.script_grace2images() function. As the script is encoded by strings, the 2to3 program cannot fix this script. Therefore the changes were made by hand.
Unicode strings in the dispersion GUI elements is now set up with the compat.u() function.
Fix for the y-axis in the per spin dispersion curve plots. This fix follows from the thread http://thread.gmane.org/gmane.science.nmr.relax.devel/4512. The test for CPMG-type data was incorrect and should use the CPMG_EXP variable.
Added setup function for the system test of KTeilum_FMPoulsen_MAkke_2006 data. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Fixed a spelling mistake in a number of file names. This is for the test suite data located at test_suite/shared_data/dispersion/KTeilum_FMPoulsen_MAkke_2006.
Fixes for the units in the dispersion parameter table in the user manual. The units for δω are rad.s^-1 when used in the equations, but it is stored internally as ppm.
Truncated the dataset to only one residue L61. The truncated dataset will be expanded later. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Modified the script file for saving of a truncated base_pipe state file. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Added script files for generating a saved state file with R_2eff values. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Added the first system test for model CR72 for the kteilum_fmpoulsen_makke_cpmg_data. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Fix trailing spaces. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Fix epydoc HTML markup code. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Added some MQ dispersion data taken from the GUARDD program.
Modified the Relax_disp.test_dpl94_data_to_dpl94 system test for a relax_disp.exp_type change. This is so that the relax_disp.exp_type user function associates the experiment types with a spectrum ID. This follows from http://thread.gmane.org/gmane.science.nmr.relax.devel/4530.
Clean up and expansion of the dispersion experiment type variables.
Another change to the dispersion experiment type variables.
Fixes for the changes to the dispersion experiment type variables throughout the dispersion code.
Redesigned the relax_disp.exp_type user function to be associated with spectrum IDs. This follows from http://thread.gmane.org/gmane.science.nmr.relax.devel/4530, the thread about supporting multiple data types such as SQ+MQ data simultaneously. The user function backend has been moved from specific_analyses.relax_disp.api to specific_analyses.relax_disp.disp_data. A few temporary code additions have been made to keep the user function functional with the current dispersion code.
Fixes for the relaxation dispersion system tests for the relax_disp.exp_type changes.
The relaxation dispersion system tests requiring the compiled C modules are now skipped when not compiled.
Created the specific_analyses.relax_disp.disp_data.loop_exp*() functions. This follows from http://thread.gmane.org/gmane.science.nmr.relax.devel/4530, the thread about supporting multiple data types such as SQ+MQ data simultaneously. The methods added are loop_exp(), loop_exp_frq(), loop_exp_frq_point() and loop_exp_frq_point_time().
Removed the relax_disp.exp_type user function page from the new analysis wizard.
Modified the dispersion GUI analysis to handle the relax_disp.exp_type user function changes. This follows from http://thread.gmane.org/gmane.science.nmr.relax.devel/4530, the thread about supporting multiple data types such as SQ+MQ data simultaneously. The experiment type GUI element has been removed, the CPMG and R_1ρ model lists merged into one, and much code for the experiment type removed. The peak analysis wizard will need to be heavily modified for the changes.
Added the relax_disp.exp_type user function to the peak intensity loading wizard.
Added the experiment type to the spectrum list GUI element. This is only activated if the exp_type_flag argument is True.
The CPMG frequency and spin-lock field strength columns are merged in the spectrum list GUI element. The column is now for the dispersion point data, and allows different experiment types to be mixed.
The spectra list GUI element in the dispersion auto-analysis now shows all columns.
Removed the temporary FIXMEs from the relax_disp.exp_type user function backend. This is needed to enable the mixed experiment type code to be developed further, but means that the relax_disp branch will be broken for a while.
The specific_analyses.relax_disp.disp_data.loop_point() function now requires the exp_type argument. The exp_type can no longer be determined within the loop_point() function. Therefore it must be specified using a function argument. The rest of the module has been updated for this change.
Updated specific_analyses.relax_disp.parameters.param_num() for the relax_disp.exp_type changes.
Fix for the Relax_disp.test_dpl94_data_to_dpl94 system test. The experiment type is now set for the reference spectrum.
Created the new specific_analyses.relax_disp.checks module. This contains many check_*() functions for raising RelaxErrors to tell the user when something is wrong. This will be used to simplify, make more consistent, and fix cdp.exp_type errors in the dispersion code.
Added a number of auxiliary functions to specific_analyses.relax_disp.disp_data. These are get_curve_type(), has_exponential_exp_type(), and has_fixed_time_exp_type() and will be used to simplify the dispersion code.
Fixes for the specific_analyses.relax_disp.api module for the relax_disp.exp_type change. This follows from http://thread.gmane.org/gmane.science.nmr.relax.devel/4530, the thread about supporting multiple data types such as SQ+MQ data simultaneously. The loop_exp*() functions are now being used throughout the module. The specific_analyses.relax_disp.checks.check_*() functions are also used to simplify the code and fix changes to cdp.exp_type. And some auxiliary functions from specific_analyses.relax_disp.disp_data are being used as well.
Added some functions to specific_analyses.relax_disp.disp_data for checking if certain experiments exist. These are the has_cpmg_exp_type() and has_r1rho_exp_type() functions.
The dispersion auto-analysis no longer references cdp.exp_type. This follows from http://thread.gmane.org/gmane.science.nmr.relax.devel/4530, the thread about supporting multiple data types such as SQ+MQ data simultaneously.
Fix for the new loop_exp_frq() dispersion function.
A few fixes for the relax_disp.exp_type user function changes. This follows from http://thread.gmane.org/gmane.science.nmr.relax.devel/4530, the thread about supporting multiple data types such as SQ+MQ data simultaneously.
Fixes for the specific_analyses.relax_disp.disp_data.find_intensity_keys() function. This is for the cdp.exp_type changes.
Fixes for the relax_disp.plot_disp_curves user function backend for the cdp.exp_type changes.
A number of fixes for the relax_disp.exp_type user function changes. This follows from http://thread.gmane.org/gmane.science.nmr.relax.devel/4530, the thread about supporting multiple data types such as SQ+MQ data simultaneously.
Updated the Hansen CPMG data relax save files for the cdp.exp_type changes.
Fix for the Relax_disp.test_hansen_cpmgfit_input system test for a new set of errors. The Hansen R_2eff values have been recalculated and the errors are now slightly different.
More fixes due to the cdp.exp_type change. This follows from http://thread.gmane.org/gmane.science.nmr.relax.devel/4530, the thread about supporting multiple data types such as SQ+MQ data simultaneously.
Updated the r1rho_off_res_tp02 dispersion system test data for the cdp.exp_type changes.
Some more fixes for the cdp.exp_type now being dependent on the spectrum ID. This follows from http://thread.gmane.org/gmane.science.nmr.relax.devel/4530, the thread about supporting multiple data types such as SQ+MQ data simultaneously.
Changes so that the target function will handle multiple experiment types. This follows from http://thread.gmane.org/gmane.science.nmr.relax.devel/4530, the thread about supporting multiple data types such as SQ+MQ data simultaneously. The data structures from return_r2eff_arrays() now have an additional dimension. The new first dimension is that of the experiment type. This affects the values, errors, and missing data structures. This dimension is stripped in the dispersion target function class for the single experiment type models, but will be preserved for the combined models to be added in the future.
The spectrum list GUI element is now more robust to missing data. The cdp.spectrum_ids data structure no longer needs to exist.
The peak intensity wizard requires more than 10 pages. The hardcoded limit of a maximum of 10 wizard pages has been increased to 15. Due to the non-linearity for the wizard pages, not all are seen, but many pages are required.
The spectrum list GUI element can now handle the cdp.exp_type data structure not existing.
Fixes for all of the specific_analyses.relax_disp.disp_data.has_*_exp_type() functions. They now operate when no experiment types have been specified.
Redesigned the peak intensity loading GUI wizard for handling multiple experiment types. This follows from http://thread.gmane.org/gmane.science.nmr.relax.devel/4530, the thread about supporting multiple data types such as SQ+MQ data simultaneously. The logic for the page ordering needed to be changed to be more dynamic. The CPMG and R_1ρ pages need to be shown only if the corresponding experiment type exists in the current data pipe. Hence the has_cpmg_exp_type() and has_r1rho_exp_type() dispersion functions are now used by the new methods wizard_page_after_relax_time() and wizard_page_after_cpmg_frq(). A number of now useless flags have also been removed.
Added some sanity checks to the dispersion target function class. R_1ρ models cannot be used with CPMG-type experiments, and CPMG models cannot be used with R_1ρ-type experiments.
Fixes for all of the GUI dispersion tests for the changes to cdp.exp_type. This follows from http://thread.gmane.org/gmane.science.nmr.relax.devel/4530, the thread about supporting multiple data types such as SQ+MQ data simultaneously.
Large speed up of the Relax_disp.test_tp02_data_to_tp02 GUI test. By minimising the number of times the peak intensity wizard pages are regenerated, the test time decreased on one system from ~32s to ~12s.
Simplified the code of the Relax_disp.test_hansen_trunc_data GUI test.
The GUI now warns if the user choses inappropriate models. When clicking on 'Execute', an error message appears if R_1ρ models are selected for CPMG data and vice versa. This is simply for more intuitive user feedback.
Fix for the relax_disp.exp_type pop up menu entry in the spectrum list GUI element. This was calling relax_fit.exp_type rather than relax_disp.exp_type.
Fix for the relax_disp.cpmg_frq pop up menu entry in the spectrum list GUI element. The method associated with the menu entry action_relax_disp_cpmg_frq() was buggy.
Fix for the relax_disp.spin_lock_field pop up menu entry in the spectrum list GUI element. Another action method bug - the same as in the last commit.
Added two functions for determining if a spectrum ID corresponds to a CPMG or R_1ρ experiment. These are functions in specific_analyses.relax_disp.disp_data and they are called is_cpmg_exp_type() and is_r1rho_exp_type().
Big redesign of the spectrum list GUI element for the dispersion analysis. This follows from http://thread.gmane.org/gmane.science.nmr.relax.devel/4530, the thread about supporting multiple data types such as SQ+MQ data simultaneously. The popup menu must be generated on the fly, as the CPMG frequency and spin-lock field strength menu entries should only be shown for the appropriate experiment type. Therefore the new generate_popup_menu() method has been added to the gui.components.base_list GUI element. The flags sent into the spectrum list GUI element have also been completely changed to now indicate the analysis type directly.
Expanded the Relax_disp.test_hansen_trunc_data GUI test to check the spectrum list GUI element. The popup menu is now tested with the Fake_right_click() trick. And the actions of a number of the menu items, the action*() methods, are tested to see if the user functions are correctly called.
Modified many of the spectrum list GUI element action_*() methods for the GUI tests. These now take the 'item' keyword argument which overrides the ListCtrl.GetFirstSelected() call. This ListCtrl call cannot be reliably simulated on all operating systems, so the item keyword argument can be used to explicitly select list items.
Fix for setting the relaxation time in the spectrum list GUI element for the dispersion analysis. The popup menu item was calling the relax_fit.relax_time user function and not relax_disp.relax_time.
Fix for the action_relax_disp_cpmg_frq() method of the spectrum list GUI element. The relax_disp.cpmg_frq user function was being incorrectly called. This was identified via the Relax_disp.test_hansen_trunc_data system test.
Modified the Relax_disp.test_tp02_data_to_tp02 GUI test to check the spectrum list GUI element. The popup menu is now tested in the same way as in the Relax_disp.test_hansen_trunc_data GUI test.
Modified the spectrum list GUI element action_relax_disp_spin_lock_field() method for the GUI tests. This now accepts the optional 'item' keyword argument like the other action_*() methods.
Bug fix for the spectrum list GUI element popup menu relax_disp.spin_lock_field entry. This was calling the relax_disp.spin_lock_field user function incorrectly. The bug was identified by the Relax_disp.test_tp02_data_to_tp02 system test.
Fix for the Mf.test_auto_analysis GUI test due to the spectrum list GUI element changes. The Fake_right_click() class now needs a GetPosition() method.
Moved the experiment type setting into per spectra settings. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Fixed typo. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Added the truncated test data for system test: relax -s Relax_disp.test_kteilum_fmpoulsen_makke_cpmg_data_to_cr72. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Created a relax save file with just R_2eff values for the r1rho_on_res_m61 dispersion system tests data.
Created 3 new dispersion system tests. These are for checking a new function that doesn't exist yet. The get_curve_type() function will be used to determine if the experiment corresponding to the given ID consists of exponential curves or of fixed time data.
Fixed values for system test: relax -s Relax_disp.test_kteilum_fmpoulsen_makke_cpmg_data_to_cr72. The test now passes. The values are compared to a relax run with 500 Monte Carlo simulations. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Added "CR72 full" test suite for kteilum_fmpoulsen_makke_cpmg_data. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Added file which setup a truncated spin system. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Changed the initialization script to use the truncated spin system. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Changed the saved states to the truncated spin system. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Fix for the residue index in the test suite when using the truncated spin system. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
The R_2eff result save file for the r1rho_on_res_m61 dispersion data now contains the full data set. The previous file did not contain the full exponential curves.
The get_curve_type() function now works with the spectrum ID. This specific_analyses.relax_disp.disp_data.get_curve_type() function already existed but it operated on all the loaded data. Now it can handle a single spectrum ID. The count_relax_times() function has been added to aid get_curve_type().
The get_curve_type() function is now imported into the dispersion system test module.
Modified the Relax_disp.test_dpl94_data_to_dpl94 system test. This is in preparation for another relax_disp.exp_type change - the fixed and exponential parts will be dropped as this can be determined automatically by relax.
Changed the relax_disp.exp_type user function front end. The supported types will now be 'CPMG' and 'R1rho', as the fixed time verses full exponential curve can be automatically determined by relax from what the user inputs.
Started a system test for model TSMFK01. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Modified the script for the full analysis of all models of CPMG type. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Simplified the dispersion experiment type classes. The supported types will now be 'CPMG' and 'R1rho', as the fixed time verses full exponential curve can be automatically determined by relax from what the user inputs. The EXP_TYPE_* dispersion variables have all changed and many have now been lost. To support the changes, the new specific_analyses.relax_disp.disp_data.loop_spectrum_ids() function has been created. This is a loop over all spectrum IDs whereby the experiment type, magnetic field strength, dispersion point, or relaxation time can be specified to isolate ID subsets. Many of the specific_analyses.relax_disp.checks.check_*() has also been modified as their logic no longer works. The auxiliary get_times() function has been added to create a per-experiment dictionary of relaxation times so that the checks can be independent of the other dispersion modules.
Updated much of the dispersion test data. The experiment type has been changed in all the scripts and the relax save files updated.
Fixed expydoc formatting. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Created some more specific_analyses.relax_disp.checks.check_*() functions. This is for better checking of the dispersion data. The check_spectra_id_setup() is useful for checking that all of the spectrum information is set up.
The checks prior to minimisation of the dispersion models is now more comprehensive.
Bug fixes for the specific_analyses.relax_disp.checks.get_times() function. The function is now more tolerant if certain data has now been set up yet.
Fixes for some of the R_1ρ dispersion system test scripts. The relaxation time must be set for the reference spectrum.
Fixes for the Relax_disp.test_exp_fit system test - the spectrometer frequency is now set. This information is now compulsory.
Converted references of ka and kA to k_AB. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Updated the CPMG dispersion analysis sample script for the relax_disp.exp_type user function changes.
Updated the user manual for the relax_disp.exp_type user function changes. The script in the prompt/script UI section of the dispersion chapter needed to be updated.
Referencing fixes for the dispersion chapter of the user manual.
Updated the scripts and save files for the KTeilum_FMPoulsen_MAkke_2006 dispersion data. This is for the recent relax_disp.exp_type user function changes and this allows the tests to pass. Information on how to run the scripts and tee the output to logs has been added, and the logs added to the repository.
Added k_AB to parameters. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
More fixes for the relax_disp.exp_type user function changes.
The relaxation dispersion GUI elements now use the lib.text.gui module for Unicode strings.
Some Unicode text fixes in the dispersion GUI analysis for older MS Windows versions.
Updated the Grace string for the k_AB parameter - it was being shown as kA.
Fix for the model list in the GUI - the TSMFK01 model entry was broken.
Increased the size of the dispersion model list GUI window so that all models fit without scrolling.
Refinement of the dispersion model list in the GUI. Descriptions have been added and the fixed window size adjusted to the best fit.
Modified system test after inclusion of 1M GuHCl dataset. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Moved files into folder which is specific for the experiment. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Changed scripts after moving data. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Re-run of data after movement of scripts. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Added dataset experiment in 1.01 M GuHCl (guanidine hydrochloride). Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Added to the README file for the 1.01 M GuHCL experiment. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Modified doc string for the script analysing all models for residue L61. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Added the output from relax after analysis of all models. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Removed the size variable from the dispersion model list GUI window as it is no longer used.
Added the k_AB and k_BA conversion equations to the dispersion parameter table in the user manual.
Changed reference to Tollinger et al. instead of Tollinger/Kay. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Fixes for the dispersion GUI tests for the changes to the model list GUI element.
Added the button for the interatom.define user function in preparation for the MQ dispersion data. This is in the dispersion tab of the GUI.
The return_cpmg_frqs() and return_spin_lock_nu1() functions now return numpy arrays. These are functions from specific_analyses.relax_disp.disp_data.
Speed ups for the optimisation of all of the R_1ρ dispersion models. The spin-lock field strength data structure is now converted from Hz to rad.s^-1 in the dispersion target function initialisation. Previously the conversion was happening multiple times per target function call. This has a noticeable effect on the test suite timings.
Some small speed ups for the TP02 R_1ρ dispersion model optimisation. Some unneeded calculations and aliases were removed.
Added the write-out of 'δω' and 'k_AB' for model TSMFK01, when performing auto-analysis. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Added to calculate the tau_cpmg times when model is TSMFK01. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Optimized the target function for model TSMFK. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Added the conversion to k_AB from k_ex and p_A. k_AB = k_ex * (1.0 - p_A). Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Some more speed ups for the R_1ρ dispersion models. For many models, the square of the spin-lock field strength is a part of the equations. Therefore this is now pre-calculated when the target function is initialised.
Added the relaxation dispersion documentation to all of the value user function documentation.
Fix for the CPMG dispersion sample script - the numeric solution model name was not correct.
Fix for the dispersion model list in the GUI - the R_1ρ models were mixed up.
Added a sample script for an off-resonance R_1ρ dispersion analysis.
Created the empty specific_analyses.relax_disp.optimisation module. This will contain functions and other objects relating to the optimisation of the dispersion models.
Fixed bug, where k_ex to k_AB where not possible if the model does not contain parameter p_A. The conversion is now skipped. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Added the conversion to k_BA from k_ex and p_A. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Added system test for testing conversion to k_BA from k_ex and p_A. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Fix for passing system test on Windows with Python 32. Precision lowered by 2 decimals. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Added system tests for conversion of k_ex to k_AB/k_BA for models where k_ex and p_A is present. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Modified headers for scripts producing analysis for data which is full or truncated. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Created the dispersion default_value_doc object. This table is needed for the value.set user function.
Huge speed win for the relaxation dispersion analysis - optimisation now uses the multi-processor. The relaxation dispersion optimisation has been parallelised at the level of the spin clustering. It uses Gary Thompson's multi-processor framework. This allows the code to run on multi-core, multi-processor systems, clusters, grids, and anywhere the OpenMPI protocol is available. Because the parallelisation is at the cluster level there are some situations, whereby instead of optimisation being faster when running on multiple slaves, the optimisation will be slower. This is the case when all spins being studied in clustered into a small number of clusters. It is also likely to be slower for the minimise user function when no clustering is defined, due to the overhead costs of data transfer (but for the numeric models, in this case there will be a clear win). The two situations where there will be a huge performance win is the grid_search user function when no clustering is defined and the Monte Carlo simulations for error analysis.
Decreased the number of grid increments in the dispersion sample scripts from 21 to 11. This is a much easier optimisation problem than the other analyses in relax, so 21 increments is an overkill. It also takes far too long for some of the models due to the high number of parameters.
Removed a tonne of unused imports from the modules of the specific_analyses.relax_disp package.
Deselected most of the default dispersion models from the dispersion GUI model list. Now only one analytic and numeric model is selected per experiment type. This is to hint to the user that maybe they shouldn't just use all models.
Added desc. item for model TSMFK01. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Added TSMFK01 to model overview table. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Added subsection with TSMFK01 model. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Fix for adding TSMFK01 to sample scripts. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Updated the relax_disp_trunc.py script for Flemming Hansen's CMPG test data.
Started to create the relax_disp.catia_input user function. The frontend has been written and a stub of a function for the backend. The new specific_analyses.relax_disp.catia module has been created for this.
Created the Relax_disp.test_hansen_catia_input system test. This is to check the output of the relax_disp.catia_input user function.
The relax_disp.catia_input user function now creates the main CATIA input file and all R_2eff data files.
Created a script for converting Flemming Hansen's data into CATIA input files. This is for checking the relax_disp.catia_input and relax_disp.catia_execute user functions.
Fix for the CATIA main execution file created by relax_disp.catia_input. The CATIA DataDirectory needs a '/' at the end.
Improvements to the relax_disp.catia_input user function. On top of general improvements, the global parameter and parameter set files are now created.
More improvements for the relax_disp.catia_input user function. The output directory for CATIA results is now an argument for the main backend function. This directory is now also created, as required by CATIA.
Implemented the relax_disp.catia_execute user function. This is modelled on the palmer.execute user function.
The relax_disp.catia_input user function now has a GUI icon associated with it.
Added the CATIA input files generated by relax for Flemming Hansen's truncated CPMG data set.
Rearranged the numeric CPMG models in the dispersion model list in the GUI.
The main CATIA input file requires the chemical shifts and R₁ values to be fixed, even when missing. This is for the relax_disp.catia_input user function.
Added Tollinger reference. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Added Tollinger model TSMFK01 to sample scripts. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Fixed several typo errors of "Is it selected"->"It is selected". A copy-paste error which has spread. Progress sr #3071 - Implementation of Tollinger/Kay dispersion model (2001). Following the guide at: Tutorial for adding relaxation dispersion models to relax.
Spacing fixes for the Tollinger01 Bibtex entry for the author initials.
Removed some strange characters from the Tollinger01 Bibtex abstract.
Fix for some inline references in the dispersion chapter of the user manual.
Enabled the parallelisation of Monte Carlo simulations for the relaxation dispersion analysis.
Created a set of scripts for testing out the multi-processor abilities of the dispersion analysis.
Added Remco Sprangers' truncated ClpP data to test_suite/shared_data/dispersion/Spranger_ClpP. This is the data attached to https://web.archive.org/web/gna.org/task/?7712#comment6, and it will be used for testing the implementation of the MQ NS 2-site model, when added to relax.
Concatenated the peak intensity files.
Created a relax script for analysing Remco Sprangers' ClpP data with the MQ NS 2-site model. This currently does not work, as the model is absent.
Modified the dispersion auto-analysis to check if peak intensity errors have been pre-calculated. This allows the user to perform custom analyses and the auto-analysis will then not overwrite these values.
Bug fixes for the averaging of peak intensity errors in the dispersion analysis. This is in the specific_analysis.relax_disp.disp_data.average_intensity() function.
Fix for the docstring formula in lib.dispersion.two_point.calc_two_point_r2eff_err().
Updated the relax script for analysing Remco Sprangers' ClpP data with the MQ NS 2-site model. The error analysis has been removed as it is identical to what the auto-analysis does.
Renamed the directory of Remco Sprangers' CPMG dispersion data to correctly spell his name.
Updated the script for Remco Sprangers' MQ CPMG data.
Created the Relax_disp.test_sprangers_cpmg_data_auto_analysis system test. This checks the MQ NS 2-site model against Remco Sprangers' MQ CPMG data using the auto-analysis.
Fixes for the checks of the new Relax_disp.test_sprangers_cpmg_data_auto_analysis system test. The MQ NS 2-site model checks were still set up to those of the Relax_disp.test_hansen_cpmg_data_auto_analysis system test.
Added the MQ NS CPMG 2-site model to the dispersion variables. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax The new dispersion variable MODEL_MQ_NS_CPMG_2SITE has been added. As this is a new data type, multi-quantum CPMG, the new MODEL_LIST_MQ_CPMG and MODEL_LIST_MQ_CPMG_FULL lists have been created.
Rearranged the documentation for the relax_disp.select_model user function to simplify the text.
Created the lib.text.gui.dwH Unicode string for use with the MQ NS 2-site dispersion model.
Added the MQ NS CPMG 2-site model to the relax_disp.select_model user function frontend. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#The relax disp.select model user function front end Two new sections were added to the user function docstring for the MQ CPMG and MQ R_1ρ experiment types.
Added support for the MQ NS CPMG 2-site model to the relax_disp.select_model user function back end. This is the numeric solution for 2-site exchange for multi-quantum CPMG-type data. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#The relax disp.select model user function back end.
Added support for the new 'δω_H' dispersion parameter. This is needed for the MQ NS CPMG 2-site model support. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#Adding support for the parameters.
Improved the RelaxError from the relax_disp.exp_type user function when an invalid experiment type is set.
Added the multi-quantum CPMG and R_1ρ experiment types to the dispersion variables. This is needed for the MQ NS CPMG 2-site model. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#Creating a new experiment type.
Added relaxation dispersion model lists for the MQ R_1ρ models. These are stubs as no MQ R_1ρ models are yet supported by relax.
Added support for the MQ dispersion data type to the specific_analyses.relax_disp.disp_data module. This is needed for the MQ NS CPMG 2-site model. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#Creating a new experiment type.
Added support for the MQ dispersion data types to the rest of relax. This is needed for the MQ NS CPMG 2-site model, and the changes affect the dispersion data checks and the dispersion target functions. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#Creating a new experiment type.
Updated the Relax_disp.test_sprangers_cpmg_data_auto_analysis system test for 'MQ CPMG' data. This also affects the script in the shared_data test suite directory. The relax_disp.exp_type user function exp_type argument has been changed from 'CPMG' to 'MQ CPMG'.
Updated the relax_disp.exp_type user function for the new 'MQ CPMG' and 'MQ R1rho' experiment types. This is needed for the MQ NS CPMG 2-site model. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#Creating a new experiment type.
Created the MQ NS CPMG 2-site model target function. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#The target function.
Added the MQ NS CPMG 2-site R_1ρ calculating function to the relax library. This is the 2-site numeric solution for multi-quantum CPMG-type data. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#The relax library.
Updated the MQ NS CPMG 2-site model target function to match the function in the relax library.
Decreased the grid increments in the Relax_disp.test_sprangers_cpmg_data_auto_analysis system test. This is to speed up this test.
Some small changes for the script for optimising Sprangers' ClpP MQ CPMG data.
Added the MQ NS CPMG 2-site model to the dispersion auto-analysis. This is the 2-site numeric solution for multi-quantum CPMG-type data. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#The auto-analysis.
Added the MQ NS CPMG 2-site model to the GUI model list. This is the 2-site numeric solution for multi-quantum CPMG-type data. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#The GUI.
Rearranged the 'Implemented models' subsection of the dispersion chapter of the manual.
Fixed the MQ NS CPMG 2-site model description in the relax_disp.select_model user function. The magnitisation vector is 2D, not 3D.
Added a latex definition for the δω_H dispersion parameter and added the 'MQ' abbreviation.
Added the MQ NS CPMG 2-site model to the relax user manual. This is the 2-site numeric solution for multi-quantum CPMG-type data. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#The relax manual.
Simplified the MQ NS CPMG 2-site model code in lib.dispersion.
Fixes for the MQ NS CPMG 2-site model equations in the user manual.
Rearrangements of the tables in the dispersion chapter of the user manual. The tables have been shifted out into their own LaTeX files, and all dispersion model tables have been concatenated into one.
Edited the MQ abbreviation in the user manual.
Fixed some bad referencing in the dispersion chapter of the manual.
Docstring fix for the lib.dispersion.mq_ns_cpmg_2site.populate_matrix() function.
Fix for a bug in the specific_analyses.relax_disp.disp_data.loop_point() function introduced at r21060.
Speed ups for the Relax_disp.test_sprangers_cpmg_data_auto_analysis system test. This test does not pass yet, but this should allow the test to complete in under an hour.
Added some value.set user function calls to the script for Sprangers' ClpP data.
Added some value.set calls to the Relax_disp.test_sprangers_cpmg_data_auto_analysis system test. These user function calls will be used to test a new concept of fixing parameters in the grid search. The δω and δω_H parameters are fixed to the experimental values, as described in the README file from Remco Sprangers (in test_suite/shared_data/dispersion/Sprangers_ClpP).
Changed the operation of the grid search for the relaxation dispersion analysis. If a parameter is a simple floating number type and it already has a value, then the grid search over that dimension is fixed. The grid increments are set to 1, and the upper and lower bounds set to the parameter value. This allows parameters to be pre-set, if known from experiment. They will nevertheless be optimised via the minimise user function.
Added a printout for the pre-set dispersion parameter skipping in grid search.
Updated the dispersion grid search function to user the loop_parameters() function. This is an important fix as the specific_analyses.relax_disp.optimisation.grid_search_setup() function was not matching the rest of the dispersion code, hence the parameters of the grid increments and bounds were not matching the parameter vector, scaling matrix, target function parameter depacking, etc.
A bit of help for some of the R_1ρ dispersion model system tests. These now fail after a fundamental fix. The problem is only due to the very coarse grid search size - a finer grid search allows the solution to be correctly found. However as this is far too slow, instead the k_ex parameter is set to be close to the solution to skip a grid search dimension.
Some basic fixes for the Relax_disp.test_hansen_catia_input system test. The relax_disp.catia_input user function is not complete, but this allows the Relax_disp system tests to pass.
The dispersion multi-processor optimisation code now prints out its own simulation messages. This is to fix bug #21190. The memo object now is feed in the spin IDs of the cluster and stores this as the cluster_name variable. This is used by the results object run() method, which is run on the master at the end, to print out a message along the lines of "Simulation X, cluster yyy". Therefore the message is only printed out once the calculation of that slave command is complete and returned to the master.
Replaced all usage of scipy.linalg.expm() with lib.linear_algebra.matrix_exponential.matrix_exponential(). This is for the functions of the lib.dispersion package used for the relaxation dispersion numeric solution models. The change eliminates a bug in the scipy function which uses the Pade approximation which fails horribly for the complex part of the matrix. The real part looks good, but the complex part looks to have nasty truncation artefacts which is propagated and amplified through the Bloch-McConnell equations.
Modified the Relax_disp.test_sprangers_cpmg_data_auto_analysis system test so the models are programatically changed.
Changes to the Sprangers ClpP data analysis script.
Simplified the Relax_disp.test_sprangers_cpmg_data_auto_analysis system test script. The p_A and k_ex parameters are now also pre-set to speed things up.
Added a script and results files for the base R2eff model for Remco Sprangers' ClpP data.
Fixes for the R_2eff data files for Sprangers ClpP data.
Artificially increased the errors in Sprangers ClpP data to match the publication. The R_2eff errors are simply multiplied by 5, as the errors from the paper cannot be replicated.
Converted the Relax_disp.test_sprangers_cpmg_data_auto_analysis system test to not use the auto-analysis. The test has been renamed to Relax_disp.test_sprangers_data_to_mq_ns_cpmg_2site. The optimisation is now for the cluster and has been severely cut back. The MQ NS CPMG 2-site model appears to be rubbish anyway - it looks to be indeterminate with multiple solutions, and possibly infinite lines of solutions. The test now passes, and quickly.
Created the Relax_disp.test_sprangers_data_to_mq_cr72 system test. This was copied from the Relax_disp.test_sprangers_data_to_mq_ns_cpmg_2site system test and the model changed to MQ CR72. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#The test suite.
Added the MQ CR72 model to the dispersion variables. This is the Carver and Richards (1972) 2-site model expanded for MQ CPMG data by Korzhnev et al., 2004. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#Adding the model to the list.
Added the MQ CR72 model to the relax_disp.select_model user function frontend. This is the Carver and Richards (1972) 2-site model expanded for MQ CPMG data by Korzhnev et al., 2004. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#The relax disp.select model user function front end.
Added support for the MQ CR72 model to the relax_disp.select_model user function back end. This is the Carver and Richards (1972) 2-site model expanded for MQ CPMG data by Korzhnev et al., 2004. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#The relax disp.select model user function back end.
Created the MQ NS CPMG 2-site model target function. This is the Carver and Richards (1972) 2-site model expanded for MQ CPMG data by Korzhnev et al., 2004. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#The target function.
Added the MQ CR72 R_2eff calculating function to the relax library. This is the Carver and Richards (1972) 2-site model expanded for MQ CPMG data by Korzhnev et al., 2004. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#The relax library. The corresponding target function was updated to input the correct arguments.
Added the MQ CR72 model to the dispersion auto-analysis. This is the Carver and Richards (1972) 2-site model expanded for MQ CPMG data by Korzhnev et al., 2004. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#The auto-analysis.
Added the MQ CR72 model to the GUI model list. This is the Carver and Richards (1972) 2-site model expanded for MQ CPMG data by Korzhnev et al., 2004. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#The GUI.
A number of fixes for the lib.dispersion.mq_cr72 module.
The lib.dispersion.mq_cr72 module now more closely resembles the cr72 module in syntax.
Added a relax script for the MQ CR72 model optimised using Flemming Hansen's CPMG data. This is to demonstrate, though not exactly successfully, that the MQ CR72 model can collapse to the CR72 model. The imperfection might be due to truncation artefacts in the sin ratio in the mD and mZ factors. The results files and output log file from the script have been added to the repository as well.
Updates for the script and results for the MQ CR72 model optimised using Flemming Hansen's CPMG data.
Added a script and results files for optimising Sprangers' ClpP MQ CPMG data to the MQ CR72 model.
Bug fix for the dispersion specific loop_parameters() function for the multiple quantum models. The δω and δω_H parameters were being interleaved rather than all δω for all spins first and then all δω_H. The result was that these parameters were being mixed up in the MQ model target functions when clustering was activated, causing total failure of the MQ models.
Added a script and results files for optimising Sprangers' ClpP MQ CPMG data to the MQ CR72 model. This is with all spins clustered. It complements the files which are used for the pre-run results of the auto-analysis.
Better spacing in the model table of the relaxation dispersion chapter of the relax manual.
Added the Tollinger et al., 2001 reference for the NS CPMG 2-site expanded model. This reference was communicated in a private email.
Improvements for the LaTeX maths commands used in the dispersion chapter of the user manual.
Added Skrynnikov and Tollinger to the copyright notice in lib/dispersion/ns_cpmg_2site_star.py. I can now see that the code derives from the funNumcpmg.m of the sim_all.tar file (https://gna.org/support/download.php?file_id=18404) attached to https://web.archive.org/web/gna.org/task/?7712#comment5. This sim_all.tar file is the original code of Nikolai and Martin.
Modified the relaxation dispersion auto-analysis to take nesting of MQ models. This is specifically the nesting of the analytic MQ CR72 model and the MQ NS CPMG 2-site models. The analytic solution is now used as the optimisation starting point for the numeric model.
Used the \imath LaTeX symbol for complex numbers in the dispersion chapter of the manual.
Added scripts and results for optimising Sprangers' ClpP MQ CPMG data to the MQ NS CPMG 2-site model. This includes two scripts for non-clustered followed by clustered analysis using the MQ CR72 model in the auto-analysis so its parameters will be used as the optimisation starting point for the MQ NS CPMG 2-site model. The results files for both scripts have been added to the repository.
Added the MQ CR72 model to the relax user manual. This is the Carver and Richards (1972) 2-site model expanded for MQ CPMG data by Korzhnev et al., 2004. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#The relax manual.
Modified the δω_H symbol in the relax user manual.
Created a 'TODO' section in the dispersion chapter of the relax user manual. This lists all of the features and models currently missing from the dispersion analysis in relax.
Added the original Maple script to the lib.dispersionns_cpmg_2site_expanded module docstring for reference. This was sent by Nikolai in a private communication.
More expansion of the lib.dispersionns_cpmg_2site_expanded module docstring for reference. The link https://web.archive.org/web/gna.org/task/?7712#comment8 to the p3.analytical script in the Gna! tasks has been added and the contents of the sim_all.tar file funNikolai.m has been copied into the docstring as well.
Epydoc docstring fixes to allow the API documentation to be properly compiled.
Python 3 fix for the lib.dispersion.mq_ns_cpmg_2site module. The numpy.linalg.matrix_power requires an integer power, but Python 3 was creating a floating point number for the 'fact' variable.
Updated the Relax_disp.test_sprangers_data_to_mq_cr72 system test so it passes. The parameters found in the analysis located in the directory test_suite/shared_data/dispersion/Sprangers_ClpP/mq_cr72_analysis_clustered have been used as the starting point.
A number of Python 3 fixes.
Python 3 fixes for the dispersion data key generation and the data assembly. The specific_analyses.relax_disp.disp_data.return_param_key_from_data() function was generating different keys for Python 2 and 3. This has been fixed. The return_r2eff_arrays() function has also been modified to correctly check for these keys.
Removed an insanely large log file from the Flemming Hansen dispersion data directories. This is the log file for the CPMGFit analysis.
A large number of fixes for the relaxation dispersion system tested needed for the fix which changed the format of the keys by which the R_2eff/R_1ρ data is accessed.
Updated the Relax_disp.test_sprangers_data_to_mq_ns_cpmg_2site system test to allow it to pass.
Created the new Relax_disp.test_hansen_cpmg_data_auto_analysis_numeric system test. This will be used to test a new feature whereby pure numeric models will be used in the auto-analysis.
Added the model_class variable to the relaxation dispersion auto-analysis class.
Changed the new dispersion auto-analysis class variable model_class to the numeric_only flag.
Created list variables of all analytic and numeric dispersion models. These are the MODEL_LIST_ANALYTIC and MODEL_LIST_NUMERIC lists in the module specific_analyses.relax_disp.variables.
Fix for the hansen_data.py dispersion auto-analysis script used for a number of system tests. The numeric_only flag was not being handled correctly.
Implemented the numeric only option for the dispersion auto-analysis. If the numeric_only flag is set to True, then no analytic models will be used in the final model selection.
Completed the Relax_disp.test_hansen_cpmg_data_auto_analysis_numeric system test. This now checks all the optimised parameter values and makes sure that no CR72 model was selected.
Added a new button to the button bar in the relaxation dispersion GUI analysis tab. This is a button used to launch the value.set user function to allow the user to pre-set certain parameters so that they are not used in the grid search.
Created a GUI element for the numeric_only flag of the auto-analysis for the dispersion GUI tab. This defaults to false to allow all model types to be used.
Loosened the Relax_disp.test_sprangers_data_to_mq_ns_cpmg_2site system test to allow it to pass on Mac OS X.
Fixes to allow the Mf.test_mf_auto_analysis system test to pass on Mac OS X. The simulated event.GetPosition() method in the Fake_right_click class the file test_suite/gui_tests/model_free.py must return a wx.Point object and not a Python tuple. The gui.components.base_list.Base_list.on_right_click() method has also been modified with a wx.Yield() call to allow the test to pass.
Loosened some of the relaxation dispersion system tests to allow them to pass on MS Windows.
Commented out some checks of the Relax_disp.test_hansen_cpmg_data_auto_analysis_numeric system test. This is to allow this test to pass on 32-bit GNU/Linux systems. The numeric model optimisation is incomplete but different between the 32-bit and 64-bit systems.
Fix for the relaxation dispersion system test tearDown() method. The rmtree function is no longer user, rather the test_suite.clean_up.deletion() function is being used to handle the issue of MS Windows not releasing the file in time.
Fix for the test_suite.clean_up.deletion() method for another MS Windows problem. Sometimes the failed rmtree() call actually deletes the files and throws the WindowsError error. Therefore the second rmtree() call will throw another WindowsError for the missing files. This is now caught.
Elimination of the relaxation dispersion system test tearDown() method. The functionality is fully covered by the base system test method.
Shifted all of the numerical dispersion code to use the internal matrix power function. Instead of using the numpy.linalg.matrix_power() function, the relax lib.linear_algebra.square_matrix_power() function is being used instead. This allows the code to run on many older systems, as the numpy function is relatively new.
Updated the Relax_disp.test_hansen_cpmg_data_to_ns_cpmg_2site_star_full system test.
Fix for the lib.dispersion.cr72 module for early Python versions. For Python 2.5 and earlier, the math.acosh() function does not exist. Therefore the numpy equivalents are now being used.
Loosened the checks for the Relax_disp.test_hansen_cpmg_data_to_ns_cpmg_2site_star_full system test. This is to allow the test to pass on 32-bit Linux systems.
Caught a divide by zero in the specific_analyses.relax_disp.disp_data.return_offset_data() function. This was identified by turning all numpy warnings to errors.
More loosening of the Relax_disp.test_hansen_cpmg_data_to_ns_cpmg_2site_star_full system test. This is now for 64-bit Mac OS X to pass.
The dispersion GUI analysis cluster_update() method is now thread safe. This removes many error messages when running the dispersion analysis in the GUI, especially for Mac OS X systems.
The dispersion data return_cpmg_frqs() and return_spin_lock_nu1() functions are now safer. These specific_analyses.relax_disp.disp_data module functions can now be called when no data is present.
Fixes for the calc user function for the dispersion analysis. This now does something logical for the non-R2eff models. The chi-squared value is now being calculated and stored. Previously this was only calculating the R_2eff/R_1ρ values for fixed relaxation time period data for the R2eff model and failing for all others. Now the pre-existing _back_calc_r2eff() method is used to back-calculate and store the chi-squared value.
Redesigned the Relax_disp.test_hansen_cpmg_data_to_ns_cpmg_2site_star_full system test. The R_2A⁰ and R_2B⁰ rates cannot be distinguished for this data, therefore there was no unique solution. This resulted in too much variability between 32 and 64-bit systems as well as different operating systems. Instead a single calc user function call is used to determine the chi-squared value for a fixed set of parameters.
Loosened the test_hansen_cpmg_data_to_ns_cpmg_2site_star_full system test for Mac OS X. Even the calc user function does not help, the results are quite different between different systems.
The specific API calculate_r2eff() method for the dispersion analysis is now private. This is not part of the API, so it must be made private for the test suite to pass.
Fix for the Mf.test_mf_auto_analysis system test on MS Windows. The Fake_right_click.GetPosition() method now returns a valid position. This is the original (10, 10) position.
Fix for a bug introduced earlier - the call to the calculate_r2eff() must also be made private.
Fixes for 2 Relax_disp GUI tests to match the previous model-free fixes. The Fake_right_click.GetPosition() method now returns a wx.Point object.
Added test data where both the spin-lock time, the spin lock offset and the spin lock field is varied. The data is published in "Kjaergaard, M., Andersen, L., Nielsen, L.D. & Teilum, K. (2013). A Folded Excited State of Ligand-Free Nuclear Coactivator Binding Domain (NCBD) Underlies Plasticity in Ligand Recognition. Biochemistry, 52, 1686-1693" with experimental conditions that "off-resonance R_1ρ relaxation dispersion experiments on ¹⁵N were recorded at 18.8 T and 31 C." and "using the pulse sequence of Mulder et al. with spin-lock field strengths from 431 to 1649 Hz and offsets ranging from 0 to 10000 Hz."
Shifted the NS CPMG 2-site expanded model to the top of the CPMG numerical solutions in the manual. This is because this is the default model which should be used in most cases.
A 20-25% speed increase for the NS CPMG 2-site expanded dispersion model. Many repetitive mathematical operations have been eliminated and the equations have been changed to optimise the calculation speed.
Modified settings script for R_1ρ test dataset.
Fix for the amsmath LaTeX package in the user manual. It needs to be after the hyperref package, as hyperref clobbers a number of amsmath features.
Added all of the equations for the NS CPMG 2-site expanded dispersion model to the relax manual. These are essentially the source code modified to look good in LaTeX.
Fix for the NS CPMG 2-site expanded model equations in the manual.
Better section spacing in the dispersion chapter of the manual. Each model section is now on a new page.
Fix for the display of the spin-lock ν₁ values in the dispersion GUI tab. This was reported by Troels at http://thread.gmane.org/gmane.science.nmr.relax.devel/4708. The GUI spectrum element at gui.components.spectrum was at fault, the add_disp_point() method was buggy.
Fix for the right click pop up menu entry "Set the spin-lock field" in the dispersion GUI tab. This is for the spectra list relax_disp.spin_lock_field user function call. The reference spectra are now detected and the field value set to None. This fix has been propagated to the relax_disp.cpmg_frq user function menu entry as well.
Correcting the R_1ρ settings script for the right calculation of the spin-lock offset, omega_rf, in ppm when offset values are provided in Hz.
Added ZQ and DQ data to the TODO list in the dispersion chapter of the manual.
Fix for the relaxation dispersion specific private _cluster_ids() method. This was identified at http://thread.gmane.org/gmane.science.nmr.relax.devel/4716. The cluster data structure was not being referenced correctly.
Added some lines to the end of the script UI section of the dispersion chapter about custom protocols.
Added a new section to the dispersion chapter of the manual for comparing different dispersion software. This is an expansion of the table in the paper draft.
Updates for the dispersion software comparison section of the user manual.
Bug fix for the MQ NS CPMG 2-site model. This was found with the aid of private feedback from Dmitry Korzhnev and him emailing his cpmg_fitd9 program. The problem is that he defines the 'n' parameter as half of a CPMG block. The code was however assuming that 'n' is a full CPMG block.
Added ZZ exchange as a missing feature to the dispersion chapter of the manual.
Added Dmitry Korzhnev's Fyn SH3 domain data for Asp 9 to the repository. This is from 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. 127, 15602-15611 (doi: http://dx.doi.org/10.1021/ja054550e). It consists of the ¹H SQ, ¹⁵N SQ, ZQ, DQ, ¹H MQ and ¹⁵N MQ data for residue Asp 9 of the Fyn SH3 domain mutant.
Added the results from Korzhnev's cpmg_fit program for the Asp9 Fyn SH3 dispersion data.
Created a relax state for the R_2eff SQ data of Korzhnev et al., 2005.
Added printouts for the overfit_deselect() specific API method for the dispersion analysis. This is to inform the user whenever spins are deselected and why. This is to help avoid user confusion.
Started to add some preliminary dispersion results for the Korzhnev data.
Started the conversion of the MQ NS CPMG 2-site model to MMQ 2-site. This follows from the post at http://article.gmane.org/gmane.science.nmr.relax.devel/4734.
Renamed all of the MQ NS CPMG 2-site modules and functions for the change to MMQ 2-site. This follows from the post at http://article.gmane.org/gmane.science.nmr.relax.devel/4734.
Added the ZQ and DQ CPMG experiment types to the dispersion variables. This is needed for the MQ NS CPMG 2-site model change to MMQ 2-site and follows from the post at http://article.gmane.org/gmane.science.nmr.relax.devel/4734. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#Creating a new experiment type.
Created two new dispersion variables - EXP_TYPE_LIST_CPMG and EXP_TYPE_LIST_R1RHO. This will be used to simplify identifying CPMG vs. R_1ρ data types.
Added support for the ZQ and DQ CPMG data type to the specific_analyses.relax_disp.disp_data module. This is needed for the MQ NS CPMG 2-site model change to MMQ 2-site and follows from the post at http://article.gmane.org/gmane.science.nmr.relax.devel/4734. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#Creating a new experiment type.
Completed the support for ZQ and DQ CPMG experiment types in relax. This is needed for the MQ NS CPMG 2-site model change to MMQ 2-site and follows from the post at http://article.gmane.org/gmane.science.nmr.relax.devel/4734. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#Creating a new experiment type.
The MMQ 2-site model target function can now handle multiple CPMG data types.
Added dispersion curve plotting to the relax script for Korzhnev et al., 2005 MMQ data.
Turned off the δω, δω_H > 0 constraint for the MMQ 2-site model.
Added a page reference back to the intro chapter in the scripting section of the dispersion chapter. This is to help the user work out how to run a relax script.
Fix for the sqrt() function in the dispersion parameter table.
Added a section to the dispersion chapter about spin clustering.
Removed most of the \clearpage commands in the dispersion chapter of the manual. There was far too much whitespace.
Added a 600x600 pixel graphic for the spin cluster for use in the user manual.
Added the cluster graphic to the cluster section of the dispersion chapter and improved the text.
Proper handling of the back-calculated dispersion data for the new MMQ 2-site model.
Shifted the optimisation printouts for the dispersion analysis out of the memo. This improved the ordering of the printed out messages when running on a cluster. Instead of having multiple optimisation printouts followed by a list of the corresponding optimised values, now they are interleaved as they should be.
Changed the definition of t_ex thanks to feedback from Nikolai Skrynnikov. This was previously defined as t_ex = 1/(2k_ex) to be compatible with CPMGFit, but has now been changed to t_ex = 1/k_ex.
Converted the IT99 dispersion model parameters to p_A and δω. This is thanks to feedback from Nikolai Skrynnikov. I have no idea why the φ_ex and p_A.δω² parameters were being used in the first place. The model results after the change are identical.
Fix for the optimised parameter printout - the parameters are now scaled. This problem was only recently introduced.
The dispersion sample scripts now have the NUMERIC_ONLY boolean variable defined.
Decreased the number of models presented to the user in the dispersion sample scripts.
The model type is now being written to file for the final run of the dispersion auto-analysis.
Added the model_type spin variable to the dispersion analysis specific PARAMS data object.
Updated the text and Grace files output for the IT99 model in the dispersion auto-analysis.
Fixes for the output of the selected mode in the dispersion auto-analysis. The correct variable is now used.
Proper fix for the printout of the optimised dispersion parameters. The loop_parameters() dispersion function is no longer used, avoiding all requirements on the current data pipe existing. This allows for proper printouts on a MPI cluster.
Added a page reference to the multi-processor section in the script section of the dispersion chapter.
Added residue 4 to the truncated CPMG data from Flemming Hansen for another test system.
Updated the CPMGFit results for Flemming Hansen's CPMG data truncated to 3 spins.
Updated the README file explaining how to convert the CPMGFit parameters to those of other software.
Updated the relax results for Flemming Hansen's CPMG data for the recent changes.
Updated the NESSY results for Flemming Hansen's data. A number of improvements have been added to NESSY including being able top optimise residues with missing data sets. A number of bugs have also been eliminated.
Updated the NESSY log for the bug fix of r1105 (in the NESSY repository).
Updated the ShereKhan results to include residue :4 and the ShereKhan numeric results. The numeric model in ShereKhan was previously buggy and did not return results. This has been fixed after I sent feedback to the authors.
Updated the software comparison document for a subset of Flemming Hansen's CPMG data. This now includes residue 4, the changes in results for all software, new NESSY results due to fixes I made in NESSY, and the new results for numeric model in ShereKhan.
Added all of the new NESSY plots for the truncated Hansen CPMG data.
Fixes for all of the system tests using Flemming Hansen's CPMG data subset. The errors are now different and the new residue 4 has to be deselected and ignored.
Created the new relax_disp.insignificance user function. This will be used to deselect all spins whereby the maximum difference in all its dispersion curves is below a certain cutoff.
Improvements for the relax_disp.insignificance user function. Text is now printed out when a spin is deselected. And all spins set to the R2eff model are skipped.
The relaxation dispersion auto-analysis now accepts the 'insignificance' argument. This is then used in the relax_disp.insignificance user function prior to the optimisation of each model, so that spins with insignificant dispersion curves are not optimised. The R2eff and No Rex models are skipped for obvious reasons.
Created an INSIGNIFICANCE variable for the relaxation dispersion sample scripts. This is to allow the user to eliminate insignificant models.
Added the insignificance dispersion auto-analysis argument to the Hansen CPMG data optimisation script.
Updated script UI section of the dispersion chapter of the user manual. This is for the recent changes to the sample scripts including the addition of the RESULTS_DIR and INSIGNIFICANCE variables.
Added the No Rex model to the R1rho_analysis.py sample script.
A number of fixes for the script UI section of the dispersion chapter of the manual. The NUMERIC_ONLY variable is now explained and the R_1ρ MODEL list has been changed to a set of reasonable models.
A GUI element for the insignificance level for the dispersion auto-analysis has been added. This defaults to 1.0. The user can input any number they wish. Checks were added for non-numerical input.
Updated the insignificance argument docstring for the dispersion auto-analysis.
The dispersion analysis GUI element now uses the float GUI element for the insignificance level. This makes sure that the user can only enter a number.
Created the Relax_disp.test_r2eff_read and Relax_disp.test_r2eff_read_spin system tests. These check the operation of the currently non-existent relax_disp.r2eff_read and relax_disp.r2eff_read_spin user functions.
Modified the Relax_disp.test_r2eff_read system test. A new disp_frq argument has been added for the relax_disp.r2eff_read user function.
Renamed specific_analyses.relax_disp.disp_data.exp_type() to set_exp_type(). This is to avoid classes with the 'exp_type' function arguments.
Small fix for the printout from specific_analyses.relax_disp.disp_data.set_exp_type().
Improved printout from the specific_analyses.relax_disp.disp_data.set_exp_type() function.
Improved printout for the relax_disp.cpmg_frq user function.
Improved printout for the relax_disp.spin_lock_field user function.
Implemented the relax_disp.r2eff_read user function. Bot the frontend and backend have been implemented and are functional.
Created the Relax_disp.test_hansen_cpmg_data_auto_analysis_r2eff system test. This is to test the full dispersion auto-analysis on Flemming Hansen's CPMG data using the original R_2eff data rather than the derived peak heights.
Changes for the Relax_disp.test_hansen_cpmg_data_auto_analysis_r2eff system test. The file paths have been changed.
Created files of R_2eff values and errors for Flemming Hansen's CPMG data.
File path fixes for the script of the Relax_disp.test_hansen_cpmg_data_auto_analysis_r2eff system test.
The error analysis is now skipped in the dispersion auto-analysis if the R2eff model is not given. It is then assumed that R_2eff/R_1ρ data has already been loaded into the base data pipe and hence the error analysis is not needed. This avoids fatal errors.
The specific_analyses.relax_disp.disp_data.loop_time() function can now handle no relaxation times being set.
The relax_disp.r2eff_read user function now prints out all the data which has been read. This feedback is useful for the user to know what has or has not been read into relax.
Fix for the dispersion auto-analysis if R_2eff data already exists. The data is no longer copied from the non-existent 'R2eff' data pipe.
Fixes for the dispersion specific overfit_deselect() method for when R_2eff data is read. This now no longer checks for intensity data but rather R_2eff data, as intensity data will not be present if R_2eff data is directly read rather than peak intensities.
Fixes for the Relax_disp.test_hansen_cpmg_data_auto_analysis system test. The setup of the auto-analysis could be simplified as the base data pipe can now contain R_2eff data. The R_2eff data in the 'R2eff' data pipe was no longer being read.
Some small fixes to allow the optimisation of dispersion models when no peak intensity data has been read. This is for when R_2eff data has been read instead.
The relax_disp.insignificance user function can now handle selected spins with no R_2eff/R_1ρ data.
Fixes for the Monte Carlo simulations in the dispersion analysis when R_2eff data has been read. As peak intensity data has not been read, the relaxation time period will not have been set. The _back_calc_r2eff() method can now handle this.
Improved the R_2eff errors for Flemming Hansen's CPMG data. The errors are now calculated using the data from all spins rather than a truncated subset. The errors will therefore be much more accurate.
Fix for return_index_from_disp_point() for when R_2eff/R_1ρ data is loaded rather than intensities. This specific_analyses.relax_disp.disp_data.return_index_from_disp_point() function was always subtracting 1 from the dispersion point index to take the reference spectrum into account. This however fails if R_2eff/R_1ρ data is loaded instead.
Fixes for the Relax_disp.test_hansen_cpmg_data_auto_analysis* system tests. The Relax_disp.test_hansen_cpmg_data_auto_analysis system test needed updating due to the more accurate R_2eff errors. The Relax_disp.test_hansen_cpmg_data_auto_analysis_r2eff system test also needed this change. It also no longer has a spin system for residue 4.
Fixes for all of the Relax_disp system tests which use Flemming Hansen's CPMG data. These are needed due to the improved error estimates in the data files.
Fix for a duplicated line typo in the Relax_disp.test_hansen_cpmgfit_input system test.
Fixed a typo in the user function name in the Relax_disp.test_r2eff_read_spin system test.
Fixes for the Relax_disp.test_r2eff_read_spin system test.
Implemented the relax_disp.r2eff_read_spin user function. This allows R_2eff/R_1ρ files for each spin to be read.
Fixed a docstring talking about RDC data in the dispersion analysis.
Fix for the Relax_disp.test_hansen_cpmg_data_auto_analysis_numeric system test for 32-bit Linux. The NS CPMG 2-site expanded model checks have been turned off again for residue 71 as these results are far to variable.
Another fix for the Relax_disp.test_hansen_cpmg_data_auto_analysis_numeric system test. The selected model is no longer checked for residue 71.
Loosened the checks for a number of Relax_disp system tests to allow them to pass on 32-bit Linux.
Loosened a check for the Relax_disp.test_hansen_cpmg_data_to_ns_cpmg_2site_star system test for Mac OS X.
Loosened a check for the test_hansen_cpmg_data_to_ns_cpmg_2site_star system test for MS Windows.
Added some polish to the relax_disp.exp_type user function frontend.
Created the MODEL_LIST_CPMG_NUM dispersion list variable. This is for defining in one place the list of models which require the number of CPMG blocks.
The dispersion optimisation code now checks for the relaxation time period being set for certain models. This is for the models which require the number of CPMG blocks, calculated via the relaxation time and ν_CPMG.
The dispersion target function setup now uses the new MODEL_LIST_CPMG_NUM variable.
The dispersion specific check_exp_type() function now accepts the id argument to check individual IDs.
Redesigned the relax_disp.r2eff_read and relax_disp.r2eff_read_spin user functions. These now no longer set the metadata (spectrometer frequency and experiment type) themselves. Instead an experiment ID string must be supplied. The spectrometer.frequency and relax_disp.exp_type user functions will therefore need to be called before these R_2eff functions.
Fixes for the Relax_disp.test_hansen_cpmg_data_auto_analysis_r2eff system test. This is for the changes in the relax_disp.r2eff_read user function.
Fixes and completion of the Relax_disp.test_r2eff_read and Relax_disp.test_r2eff_read_spin system tests. These now handle the new user function design and now also check all of the global and spin data.
A number of fixes for the dispersion analysis for all the recent changes.
Better MMQ data support for the dispersion specific loop_cluster() function. For the models using proton-heteronuclear multi-multiple quantum data, proton spin containers are now skipped as all the data will be analysed from the perspective of the heteronucleus.
Conversion of the format of the relaxation dispersion R_2eff/R_1ρ data structures. These are now lists of lists of lists of numpy arrays instead of pure numpy rank-4 arrays. This only affects a number of related data structures in the dispersion target function class. The main purpose is to prepare to have a different number of dispersion points per experiment, per spin, and per spectrometer frequency.
The return_cpmg_frqs() and return_spin_lock_nu1() dispersion functions now return lists of lists of arrays. The dispersion data structures are now experiment and spectrometer frequency dependent. Therefore the number of dispersion points can now be different for each.
The dispersion target function num_disp_points structure is now variable. The number of points can now be different for each experiment type and each magnetic field strength.
Added a header comment to the grace2images.py script to explain its dependence on Grace. This is thanks to feedback from Nikolai Skrynnikov.
Better organisation of the models by data type in the dispersion software comparison table in the manual.
Added Dmitry Korzhnev's cpmg_fit software to the dispersion chapter of the manual. This is in the last section of that chapter and in the software comparison table.
Added the chemex software to the dispersion chapter of the user manual.
Updated the GLOVE details in the dispersion software comparison table in the manual.
Updates for the TODO section of the dispersion chapter of the user manual. Some of the entries were rubbish.
Readded the accidentally deleted \clearpage command to keep the dispersion software table nicely formatted.
Added the scripting interface for cpmg_fit to the dispersion software comparison table in the manual.
Added constrained optimisation and Monte Carlo simulations to the dispersion software comparison table. This is for the user manual.
Added a section on open source licencing to the dispersion software comparison table. This is for the dispersion chapter of the user manual.
Updated the GUARDD details in the dispersion software comparison table of the manual.
Added a section about programming language to the dispersion software comparison table of the manual.
Added a page break for better formatting of the dispersion software comparison table of the manual.
Removed a now unneeded midrule from the dispersion software comparison table.
Editing and expansion of the dispersion software comparison table in the manual. The optimisation algorithms are now listed, where known. A number of entries and sections have also been rearranged.
More updates for the dispersion software comparison in the manual.
Updates for the grid search and GLOVE in the dispersion software comparison table in the manual.
More updates for the dispersion software comparison table in the manual.
Updated the dispersion software comparison table in the manual for GUARDD. This is based on feedback from Ian Kleckner.
A bit more editing of the dispersion software comparison table of the manual.
Expanded the abbreviations of the user manual for many relaxation dispersion terms.
Update for NESSY in the dispersion software comparison table of the manual.
Added more R_1ρ model references to the bibliography file for the manual. This includes the Trott and Palmer 2004 N-site and the Miloushev and Palmer 2005 2-site models. The Trott and Palmer 2002 R_1ρ model reference has been expanded to include all details.
Added the TP02 and MP05 R_1ρ dispersion models to the manual. These are not implemented in relax, or any of the software in the software comparison section, but are included for completeness. This was pointed out by Art Palmer.
Added the Korzhnev et al., 2005 reference to the bibliography file for the manual.
Fixes for a number of page numbers in the bibtex file for the user manual.
Expanded the numeric dispersion models to include the linear and branched 3-site models in the manual.
Removed a typo from the dispersion model table.
Rearranged the sections of the dispersion chapter of the manual.
Improvements for the supported dispersion model table in the manual. Footnotes have been added to indicate which models are not implemented yet.
Updated the TODO section of the dispersion chapter of the manual for the newly listed models.
Fix for the figure labelling in the dispersion chapter of the manual.
Small LaTeX layout changes to the dispersion chapter file.
Updated the dispersion software comparison table for the optimisation in GUARDD. I have added the 'MATLAB interior-point black magic' algorithm as MATLAB is not kind enough to explain what algorithm it is really using.
The Arrhenius analysis is also performed by cpmg_fit. This is for the dispersion software comparison table in the manual.
Added the TAP03 model to the dispersion chapter of the user manual.
Updated some ShereKhan language details in the dispersion software comparison table of the manual.
The dispersion GUI analysis now uses graphics.fetch_icon() for all icons. The gui.paths module no longer exists.
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 [[Tutorial for adding relaxation dispersion models to relax#The test suite].
Added the MP05 model to the dispersion variables. This is the Miloushev and Palmer 2005 R_1ρ analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#Adding the model to the list.
Added the MP05 model to the relax_disp.select_model user function frontend. This is the Miloushev and Palmer 2005 R_1ρ analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#The relax disp.select model user function front end.
Added support for the MP05 model to the relax_disp.select_model user function back end. This is the Miloushev and Palmer 2005 R_1ρ analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#The relax disp.select model user function back end.
Created the MP05 model target function. This is the Miloushev and Palmer 2005 R_1ρ analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#The target function.
Added the MP05 R_2eff calculating function to the relax library. This is the Miloushev and Palmer 2005 R_1ρ analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at 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.
Debugging of the MP05 dispersion model - optimisation is now setup correctly. This is the Miloushev and Palmer 2005 R_1ρ analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#Debugging.
Fixes and improvements to the Relax_disp.test_tp02_data_to_mp05 system test. The MP05 model values, which are almost the same as the TP02 model parameters, are now being checked. The optimised parameters are now being printed out to aid in debugging. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#Debugging.
Speed ups of the Relax_disp.test_tp02_data_to_tp02 and Relax_disp.test_tp02_data_to_mp05 system tests. The optimisation precision and number of Monte Carlo simulations have both been dropped.
Added the MP05 model to the GUI model list. This is the Miloushev and Palmer 2005 R_1ρ analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#The GUI.
Added the MP05 model to the dispersion auto-analysis. This is the Miloushev and Palmer 2005 R_1ρ analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#The auto-analysis.
Added the MP05 model to the relax user manual. This is the Miloushev and Palmer 2005 R_1ρ analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#The relax manual. The MP05 model was already partly in the manual, however it was listed as unimplemented. All of the tables and the dispersion chapter text has been updated for the model.
Modified the R1rho_analysis.py sample script to use the MP05 model. This is the Miloushev and Palmer 2005 R_1ρ analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#The sample scripts.
The limitations of the 'TP03' dispersion model are now listed in the user manual.
The MP05 and NS R1rho 2-site are now nested in the dispersion auto-analysis. As the MP05 model is valid across all times scales and does not require skewed populations, its optimised parameters can be used as the starting point of optimisation of the NS R1rho 2-site numeric model. This results in huge speed ups of the numeric model as previously a grid search was being performed.
Removed all remnants of the MQ R_1ρ data type. This data type does not exist and was mostly removed, but some small bits remained.
Created the Relax_disp.test_tp02_data_to_tap03 system test. This is the Trott et al, 2003 R_1ρ analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at [[Tutorial for adding relaxation dispersion models to relax#The test suite] This was copied from the Relax_disp.test_tp02_data_to_mp05 system test.
Added the TAP03 model to the dispersion variables. This is the Trott, Abergel and Palmer 2003 R_1ρ analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#Adding the model to the list.
Added the TAP03 model to the relax_disp.select_model user function frontend. This is the Trott, Abergel and Palmer 2003 R_1ρ analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#The relax disp.select model user function front end.
Added support for the TAP03 model to the relax_disp.select_model user function back end. This is the Trott, Abergel and Palmer 2003 R_1ρ analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#The relax disp.select model user function back end.
Created the TAP03 model target function. This is the Trott, Abergel and Palmer 2003 R_1ρ analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#The target function.
Added the TAP03 R_2eff calculating function to the relax library. This is the Trott, Abergel and Palmer 2003 R_1ρ analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#The relax library.
Debugging of the TAP03 dispersion model - optimisation is now setup correctly. This is the Trott, Abergel and Palmer 2003 R_1ρ analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#Debugging.
Debugging of the TAP03 dispersion model. Removed a Unicode character from the lib.dispersion.tap03 module docstring to allow it to be used in Python 2. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#Debugging.
The lib.dispersion.tap03 module can now handle negative γ values. This avoids fatal errors during optimisation.
Many fixes for the lib.dispersion.tap03 module to match the original equations. The TAP03 model solution is now similar to those of TP02 and MP05.
Updated the Relax_disp.test_tp02_data_to_tap03 system test numbers to match the optimised values. These were so close to the MP05 model values that the test was passing anyway.
Added the TAP03 model to the GUI model list. This is the Trott, Abergel and Palmer 2003 R_1ρ analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#The GUI.
Added the TAP03 model to the dispersion auto-analysis. This is the Trott, Abergel and Palmer 2003 R_1ρ analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#The auto-analysis.
Added the TAP03 model to the relax user manual. This is the Trott, Abergel and Palmer 2003 R_1ρ analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at Tutorial for adding relaxation dispersion models to relax#The relax manual. The TAP03 model was already partly in the manual, however it was listed as unimplemented. All of the tables and the dispersion chapter text has been updated for the model.
Added the TAP03 and MP05 models to the abbreviations in the user manual.
Improvements to all of the R_1ρ model descriptions in the dispersion chapter of the manual.
Added a placeholder for the relaxation dispersion citation to the citation chapter of the manual. The bibtex entry for this will need to be updated later once the citation is published.
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.
Updated the relaxation dispersion target functions. The input data structures have changed type.
Implemented the MMQ 2-site CPMG model equations [Korzhnev et al., 2005a]. 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 R_2eff 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 R_2A⁰ and R_2B⁰, though the mmq_2site module defaults to R_2A⁰=R_2B⁰.
The r2eff_mmq_*() functions of lib.dispersion.mmq_2site now accept different R_2A⁰ and R_2B⁰ arguments. These are set to the same thing within the dispersion target function.
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 R₂⁰key rather than frequency index is returned for the R₂⁰ parameters. Many other code changes were required.
The R₂⁰ values are now correctly handled in the dispersion target function for MMQ-type data.
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.
Change of the base relaxation dispersion experiment types. The base CPMG-type experiment has been changed from "CPMG" to "SQ CPMG". This is for better combined proton-heteronuclear SQ, ZQ, DQ, and MQ (MMQ) data support. The relax_disp.exp_type user function now also as the proton SQ and MQ CPMG-types available to select from rather than the previous behaviour of relax automatically determining the type from the spin type. All of the CPMG experiment type variables in specific_analyses.relax_disp.variables have been renamed for better ordering. Many changes were therefore required.
Fix for the specific_analyses.relax_disp.disp_data.num_exp_types() function. This needed updating after the change in the relaxation dispersion experiment type variables.
Different relaxation time periods for each experiment is now taken into account in the dispersion code. Previously only the first relaxation time period was being used. This was fine for single data type models, but was preventing the MMQ-type models from working. Now the return_r2eff_data() function of the specific_analyses.relax_disp.disp_data module assembles and returns the relax_times data structure which has two dimensions - the experiment type and the magnetic field strength.
Added a relax script to optimise just the ¹⁵N SQ CPMG data from Korzhnev et al., 2005. The corresponding log file has also been added to the repository.
Created the Relax_disp.test_korzhnev_2005_15N_sq_data system test. This is used to check the optimisation of the ¹⁵N SQ CPMG data using the MMQ 2-site model.
Fixes for the dispersion optimisation Disp_result_command.run() method. The dispersion point loop is fixed over all dispersion points, but the 'missing' data structure has a variable length.
Big redesign of the dispersion point returning and loop_*() functions. These are the functions in the specific_analyses.relax_disp.disp_data module. The return_cpmg_frqs() and return_spin_lock_nu1() functions now no longer take the spins and spin_ids arguments. Instead they determine if a dispersion point exists for the given experiment and spectrometer frequency using the intensity keys and data in the base of the data pipe. The specific_analyses.relax_disp.disp_data.loop_*() functions now accept the return_indices argument which if True will cause all of the relevant experiment type, spectrometer frequency, dispersion point, and relaxation time indices to be returned. The behaviour of the loop_point() method is now different. Instead of looping over all possible dispersion points, it only loops over those points present for the given experiment and spectrometer frequency. This change allows for many simplifications and latent bug fixes in the dispersion analysis.
Added cmpg_fit input and results files for the ¹⁵N SQ CPMG data from Korzhnev et al., 2005.
Added cmpg_fit input and results files for all single CPMG data combinations from Korzhnev et al., 2005.
Updated the cpmg_fit results for the Korzhnev et al., 2005 single data sets. The starting point for optimisation is now the solution for using all data together. This allows a much better solution to be found for each script.
Created 5 more system tests for checking the optimisation of single sets of Korzhnev et al., 2005 data. These are Relax_disp.test_korzhnev_2005_15n_dq_data, Relax_disp.test_korzhnev_2005_15n_mq_data, Relax_disp.test_korzhnev_2005_15n_zq_data, Relax_disp.test_korzhnev_2005_1h_mq_data, and Relax_disp.test_korzhnev_2005_1h_sq_data. These should individually test out all parts of the MMQ 2-site dispersion model.
The cpmg_fit script for the Korzhnev et al., 2005 ¹⁵N ZQ CPMG data now starts at the relax solution. This is to try to find better solutions for δω and δω_H, thought it was not so successful.
Updated the Relax_disp.test_korzhnev_2005_15n_zq_data system test. It now starts at the relax solution and the test passes as it seems to reasonably match the cpmg_fit results.
Reintroduced the F vector into r2eff_mmq_2site_mq() to calculate the magnetisation.
Added the cpmg_fit results for optimisation all of the Korzhnev et al., 2005 CPMG data. This is for the 2-site model. It includes all proton-nitrogen SQ, ZQ, DQ, and MQ data.
Updated the cpmg_fit results for all Korzhnev et al., 2005 data.
Shifted the relax results for the ¹⁵N SQ Korzhnev 2005 CPMG data to its own directory. The relax save state and grace curve have been added to the repository as well.
Created a Grace plot of the failed cpmg_fit results. This is for the Korzhnev et al., 2005 data, using all data sets.
Fixes for the cpmg_fit results for all of the data from Korzhnev et al., 2005. The δω_H value must start negative, otherwise optimisation will fail to find the correct minimum.
Created a Grace graph for the ¹H SQ data fitting of cpmg_fit.
The dispersion specific overfit_deselect() method now handles the MMQ-type models better.
The MMQ 2-site dispersion model can now be optimised if no heteronuclear R_2eff data is loaded.
Many more fixes for the MMQ-type dispersion models for the proton spin data.
Added many new relax results for the CPMG data form Korzhnev et al., 2005.
The R_2eff data key has been changed in the dispersion analysis. The experiment type has been added to the key so that R_2eff data is not mixed up when data from multiple experiments is present.
Updated the synthetic TP02 model data for the recent changes.
Fix for the dispersion base_data_loop() method for deselected spins. A recent change broke this function when spins were deselected.
Updated the truncated CPMG data set from Flemming Hansen to include residue :4. This is deselected in the test suite, but allows the comparison in the shared_data directory to use all four spins (:4, :70, :71).
Changed the current data pipe in the relax saved states for Flemming Hansen's truncated CPMG data.
Another change of the base relax files of the truncated CPMG data.
Bug fix for the relax_disp.cpmgfit_input user function. The ν_CPMG values need to be doubled and then divided by 1e³ to obtain the 1/τ_CPMG values in ms.
Fix for the relax_disp.sherekhan_input user function for the recent changes.
Updated all of the results for the truncated CPMG data from Flemming Hansen in the test suite. The results are now different as the errors are now much more precise as they come from all spin systems rather than just the truncated set of :4, :70, and :71.
Bug fix for the Ishima and Torchia 1999 dispersion model. Their value of omega_1eff is defined in terms of ν_CPMG, hence it is missing the radian unit. This is clearly a mistake, but is probably compensated by their stated rather than derived definitions.
Updated all of the relax results for the IT99 model fix.
Added the new relax IT99 model results to the software_comparison file. This is for the truncated CPMG data from Flemming Hansen.
Fix for the LM63 dispersion model equation in the manual.
The CR72 dispersion model descriptions now emphasise the fact that it is not accurate on all time scales. This is for the dispersion chapter of the user manual.
Modified the relax_disp.select_model user function CR72 model descriptions. Instead of saying all time scales, the CR72, CR72 full, and MQ CR72 model descriptions instead now say most time scales.
Minor equation improvement in the dispersion chapter of the manual.
Fix for the relax_disp.plot_disp_curves user function in the GUI. The directory argument was incorrectly set to the 'dir' type rather than 'dir sel' type so it was not shown in the GUI.
Created the relax_disp.write_disp_curves user function. This is based on feedback from Nikolai Skrynnikov. The user function will generate one file per spin system and dump all of the R_2eff values (measured, back calculated, and errors) into the file.
The relax_disp.write_disp_curves user function is now called from the dispersion auto-analysis.
Another bug fix for the IT99 model. This was pointed out by Nikolai Skrynnikov that the omega_1eff definition is incorrect and instead it should be omega_1eff = 4 * sqrt(3) * ν_CPMG.
Updated the Relax_disp.test_hansen_cpmg_data_to_it99 system test for the IT99 model fixes.
Updated the relax results for the truncated CPMG data from Flemming Hansen. This is needed as the IT99 model has been fixed and the new relax_disp.write_disp_curves user function introduced.
Fix for the relax_disp.write_disp_data user function. The spectrometer frequency in the output files is now in MHz.
A small output formatting change for the relax_disp.write_disp_curves user function.
The relax_disp.write_disp_curves user function is now more robust for when data is missing.
Fix for the setup of the Relax_disp.test_korzhnev_2005_1h_mq_data system test.
Fixes for the Relax_disp.test_hansen_cpmgfit_input system test. These are needed as the relax_disp.cpmgfit_input user function has been fixed resulting in different files being produced.
Bug fix for the relaxation dispersion model selection. Deselected spins in the current pipe were being skipped, so for model selection between different data pipes that results in spins not being used when they should be.
Bug fix for the dispersion specific model_information() method. This can now handle deselected spins with no data.
Bug fixes for the model_loop() method no longer skipping deselected spins. This is needed for model selection when the spins from all data pipes are deselected.
One last fix for the dispersion analysis for the changes of the model_loop() method.
Updated the relax script for optimising Flemming Hansen's CPMG data.
Better support for the MMQ-type data dispersion models for the end of the optimisation. The back calculated R_2eff values are now handled correctly for the attached proton in the spin system.
Updated the Relax_disp.test_korzhnev_2005_15n_dq_data system test so it passes. The optimised values are very similar to that from cpmg_fit, so the code must be functioning correctly.
Improvement for the file names in the relax_disp.plot_disp_curves user function. The '_' character is now used between the experiment name and the rest of the file name.
Bug fix for the specific_analyses.relax_disp.disp_data.find_intensity_keys() function. This function was not handling multiple experiment types correctly.
Created the Relax_disp.test_korzhnev_2005_all_data system test for checking the MMQ 2-site model. This checks against all six data types, ¹H SQ, ¹⁵N SQ, DQ, ZQ, ¹H MQ, and ¹⁵N MQ. This is currently set to the values found by cpmg_fit. As this is the true solution, relax should find similar parameter values.
Created a Grace plot of the ¹⁵N MQ CPMG data fitting from cpmg_fit.
Bug fix for the multiple quantum relaxation dispersion models. These require both the heteronuclear and proton chemical shift differences. But the proton difference was being scaled by the heteronuclear Larmor frequency and not the proton frequency.
The relaxation dispersion calculate user function now stores the back calculated R_2eff values. A number of changes were required for this. The code from the end of the Disp_result_command.run() method was converted to the function specific_analyses.relax_disp.disp_data.pack_back_calc_r2eff(). This allows the back calculation R_2eff unpacking code to be shared. The new has_proton_mmq_cpmg() function has also been created to simplify the code.
Bug fix for the dispersion calculate user function.
Created a script to compare the cpmg_fit and relax solutions for the MMQ 2-site dispersion model.
Clean ups and speed ups of the ¹H MMQ flag calls.
Large improvements to the relax_disp.plot_disp_curves user function including :Category:MMQ CPMG data|MMQ]] model support. This user function now handles multiple dispersion data sets better by placing each into a new graph. All graphs have also been improved by matching the colours of the sets for each field strength and using different symbols and line styles to emphasize the data.
Fixes for the relax_disp.plot_exp_curves user function for the lib.software.grace changes.
The relax_disp.plot_disp_curves now shows the experiment type as part of the Y-axis label. This is to allow for easy identification of the experiment when more than one is present.
Bug fix for the MMQ 2-site dispersion model target function. The relaxation time was being taken as that of the first experiment for all experiments. This is a relic from the code being copied from a single experiment type model.
Converted the MQ CR72 dispersion model to handle MMQ data. This model can now handle proton-heteronuclear SQ, ZQ, DQ, and MQ CPMG-type data. Some debugging might still be required.
Fix for the MQ CR72 model for MQ-type data. The check to prevent acos of a number less than 1 has been changed to switch the sign rather than to set the back calculated R_2eff to 1e⁹⁹.
Another bug fix for the MQ CR72 dispersion model. The ν_CPMG value rather than the relaxation time was being used to calculate the R_2eff values as the division by 'n' was missing.
The relax_disp.plot_disp_curves user function can now handle values of NaN. These are simply replaced by 0.0 to allow Grace to open the file.
Fixes for the MQ CR72 dispersion model target function.
Removed a latent bug in the MMQ 2-site dispersion model. This was not being seen but might have caused problems in the future.
Fix for the MQ CR72 dispersion model target function. The correct R₂⁰ values are now extracted from the parameter vector.
Improvements for the CR72 and MQ CR72 dispersion model R_2eff calculating functions. The numpy.arccosh() function can handle all input values when complex, therefore the checks for the real part being above 1 are not necessary.
General improvement for the optimisation of many target functions. For those models which use the τ_CPMG value, this is now recalculated. This means that if a user inputs truncated ν_CPMG values, these are corrected when calculating τ_CPMG so that full precision values will be used for the optimisation.
Changed the sign of the δω frequency for the ZQ data in the CR72 and MQ CR72 models.
Last fix for the MQ CR72 dispersion model. The wrong value was being subtracted from the first eigenvalue - the value of log(Q)/relax_T should not be divided by the number of CPMG blocks.
Simplified the first MQ CR72 dispersion model formula in the manual.
Created a relax script to compare the MQ CR72 dispersion model results to cpmg_fit. The cpmg_fit solution is used as the input parameters for relax, and then a calc user function call is used to back calculate the R_2eff values. These values are then plotted to show the perfect match.
Bug fixes for the MMQ 2-site dispersion model. The matrix power factor must be found with the Python math.floor() function and not int() as the later will sometimes round up.
Updated all of the relax vs. cpmg_fit comparison files in the shared data directory. These now show the perfect match between the programs. The cpmg_fit source code was modified to improve the accuracy of the gyromagnetic ratio values.
Updated the cpmg_fit results for the CPMG data of Korzhnev et al., 2005. This is using a modified binary wherein the gyromagnetic ratio and optimisation tolerances and maximum number of iterations are far more accurate (to the same level as relax). The cpmg_fit output has also been made more accurate by writing out the values to much higher precision.
Fixes for the relaxation dispersion system tests for the changed behaviour of the CR72 model. The optimisation is slightly different as values are now always passed into the numpy.arccosh() function.
Eliminated the MODEL_LIST_CPMG_NUM variable. This was far too specific and its misuse caused a bug in the target function of a number of dispersion models.
Fixes for a number of dispersion system tests due to the higher accuracy of the τ_CPMG values. This is required as the τ_CPMG values have been corrected to eliminate user input truncation artifacts.
The Relax_disp.test_korzhnev_2005_all_data system test no longer dumps files in the current directory.
Updated all of the cpmg_fit results to use the numeric 2-site CPMG model. This also uses the modified cpmg_fit binary with higher accuracy.
Updated the Relax_disp.test_sprangers_data_to_mq_cr72 system test to pass. The MQ CR72 model is now much more accurate due to a number of recent bug fixes.
Fixes for all of the Relax_disp.test_korzhnev_2005_*_data system tests. These now start optimising at the solution found by cpmg_fit. All tests now pass.
Fix for the legends in the Grace graphs produced by the relax_disp.plot_disp_curves user function.
The grid search for the MMQ-type models now looks for negative chemical shift differences.
Converted the dispersion api method _back_calc_r2eff() into a function of the optimisation module.
Updated the spin-lock field strength data structures to be experiment and field specific. This allows different spin-locks to be used as different field strengths, or different experiments. It brings the structures in line with those for CPMG-type experiments.
Updates for the dispersion auto-analysis system tests using Flemming Hansen's data. The grid search increments have been increased by one to make sure the solution is always found.
Increased the range of chemical shift differences in the grid search for the dispersion models. The range was too narrow.
Fix for the Relax_disp.test_hansen_cpmg_data_auto_analysis system test. The k_ex value check needed to be scaled back.
The relax_disp.plot_disp_curves user function now produces interpolated dispersion curves. For this the new 'num_points' and 'extend' arguments have been added to the user function to give the user better control of this plotting. The interpolated curve is disabled from the numeric CPMG models as these do not support interpolation, and the R2eff model as interpolation is not needed. To support this, the specific_analyses.relax_disp.optimisation.back_calc_r2eff() function has been extended to support the CPMG frequencies or spin-lock field strengths been supplied instead of retrieved. This allows a set of custom dispersion points to be used in the back calculation. The dispersion target function setup was modified to prevent the recalculation of τ_CPMG values when asked, as interpolation is not compatible with this.
The relax_disp.plot_disp_curves user function now places the X-axis at zero. This is for better visualisation of the residuals.
Interpolated curves are now produced for the numeric CPMG-type models. This if for the relax_disp.plot_disp_curves user function. The resolution of these are limited to the frequency of a single CPMG block in the relaxation time period. Therefore the plots are produced slightly differently. To enable this functionality, the new count_exp() and return_relax_times() functions have been added to the specific_analyses.relax_disp.disp_data module.
Improved the text for the relax_disp.plot_disp_curves user function.
Fix for the interpolation for the numeric CPMG-type models in relax_disp.plot_disp_curves.
Updated the relax results files for the CPMG data from Korzhnev et al., 2005.
Improvements to the data-type labelling in the dispersion chapter of the user manual.
The dispersion model GUI window is now set to a reasonable size for most screens. The scrolled panel now allows all contents to be shown while having the window smaller than its contents. The height of 750 pixels should be visible on the majority of computer monitors. According to Google Analytics, ~13% of visits to http://www.nmr-relax.com have screen resolutions of 1366x768, therefore the dispersion model list window should now not be bigger than their screens.
Merged the MQ CR72 dispersion model into the MMQ data type sections in the tables of the manual.
Implemented model elimination for the relaxation dispersion analysis. This currently uses the p_A limits of 0.501 < p_A < 0.999 to determine if a model has failed. To implement this, the dispersion API methods deselect(), eliminate(), get_param_names() and get_param_values() were written. These were copied from the model-free analysis and modified as needed.
Model elimination is now activated in the dispersion auto-analysis.
The relaxation dispersion target function class can now handle cpmg_frqs arguments of None. This is useful for R_1ρ models.
Bug fix for the recently added dispersion API eliminate method. This was accidentally always eliminating the model.
Created a new section in the dispersion chapter of the manual covering optimisation. This describes the auto-analysis, the chi-squared function, the grid search values, how optimisation is implemented, the linear constraints used, the diagonal scaling, model elimination, and the use of OpenMPI. It absorbs the clustering section.
Improvements for the dispersion API eliminate() method.
Added text about the relax_disp.insignificance user function to the dispersion chapter of the manual.
Updates for the MMQ 2-site model equations in the manual.
Added the t_ex > 1.0 model elimination rule for the dispersion analysis.
Updated the description of the dispersion auto-analysis in the manual.
Added a MC simulation elimination section to the dispersion chapter of the manual.
Fix for the new analysis GUI wizard - two model-free analysis buttons were present. This is due to an imperfect merge of the relax_disp branch back to trunk.
Fixes for the lib.software.grace for an imperfect merger of the relax_disp branch.
Fix for the Noe.test_noe_analysis system test. The old Grace file was turning the legend first off and then on, but now this is fixed.
Fixes for the Relax_disp.test_tp02_data_to_tp02 GUI test. This should have been fixed in the relax_disp branch.
Fix for the Wiz_window.setup_page() method. The user function SetValue() methods are no longer called but instead the Uf_page.SetValue() method is used to set up user function arguments. This is important as this later method can properly handle the free file format arguments and other special arguments whereas the former cannot.
Attempts at fixing and improving the Relax_disp.test_hansen_trunc_data GUI test. These changes have uncovered a spin ID updating problem in the relax data store after calling the residue.delete user function.
Fix for two system tests to prevent relax save files from being dumped in the installation directory. This would have been fatal for the tests suite on systems with relax installed as root.
Fix for the GUI tests for a wxPython 2.9 ListCtrl.HitTest() bug. This only affects the relax test suite. The suite should now pass on all systems.
Shifted the dispersion chapter of the user manual to its correct position. Somehow during the relax_disp branch merger, this chapter was shifted into the "Advanced Topics" partition of the manual.
API documentation fix for test_suite.system_tests.relax_disp.Relax_disp.setup_korzhnev_2005_data().
Limited the optimisation time in the N_state_model.test_populations system test. This test can take a huge amount of time on Mac OS X and MS Windows (~6 seconds on Linux, ~360 seconds on Mac OS X, and ~120 seconds on MS Windows, all on similar hardware). Now the minimise user function max_iter argument is set to 2000 to speed the test up.
Increased the speed of the N_state_model.test_populations system test again. The maximum number of iterations for the minimise user function is now set to 500.
Fix for the N_state_model.test_populations system test on Mac OS X. The optimisation on Macs is not as precise as on Linux, so the test was loosened.
Fix for the Relax_disp.test_m61_exp_data_to_m61 system test on 32-bit Mac OS X. The optimisation precision was not great enough to find the minimum, so the grid search increments have been increased from 3 to 4.
Loosened all of the Relax_disp.test_korzhnev_2005_*_data system tests to pass on Mac OS X. This should hopefully fix the tests for MS Windows as well.
More loosening of the Relax_disp.test_korzhnev_2005_*_data system tests to pass on Mac OS X. These problems were identified on a different test machine.
Loosened all checks of the N_state_model.test_populations system test. This is needed for the woeful optimisation capabilities of Mac OS X (and partly MS Windows as well).
Avoided some wxPython 2.9.4.1 in the Relax_disp GUI tests. wxPython is quite buggy, so certain checks and tests cannot be performed.
Fix for the specific_analyses.relax_disp.optimisation.back_calc_r2eff() function. The R_2eff error data structure when the cpmg_frqs or spin_lock_nu1 argument is supplied was all zeros, whereas it should all be ones. This was causing many divide by zero numpy warnings to appear on certain operating systems (Mac OS X).
The relax system test base tearDown() method should now be fail proof. Most code is now warped in a 'try: except: pass' block to catch all failures.
Improvements in the test_suite.clean_up.deletion() function. It is now more fail safe on Python 3 by completely avoiding the WindowsError checking.

Bugfixes

Bug fixes for a number of broken Oxygen icon lookups in the GUI.
Bug fixes for the molecule.delete, residue.delete and spin.delete user functions. The molecule, residue, and spin metadata in the relax data store was not being updated correctly after these user function calls so that any subsequent operations on this data was failing. This metadata problem was not noticed before as it disappears if the state is saved and reloaded into relax after a restart.

Links

For reference, the following links are also part of the announcement for this release:

Announcements

If you would like to receive announcements about new relax versions, please subscribe to the relax announcement mailing list. This list only receives ~10 emails per year. It is archived at the SourceForge archives and in The Mail Archive.

References

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