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Relax 3.1.0

27 bytes added, 14:13, 8 September 2014
Hex code fixes.
 
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* The [[CR72]] SQ CPMG-type analytic model - the reduced Carver and Richards 1972 2-site equation for most time scales whereby the simplification R20A = R20B is assumed with the parameters {R20, ..., pA, dw, kex} [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 {R20A, R20B, ..., pA, dw, kex} [Carver and Richards 1972].
* The [[IT99]] SQ CPMG-type analytic model - the Ishima and Torchia 1999 2-site model for all time scales with pA &#226Bx226B; pB and with parameters {R20, ..., phi_ex, pA.dw^2, kex} [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 {R20A, ..., dw, 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, ..., pA, dw, kex}.
* 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 {R20A, R20B, ..., pA, dw, kex}.
* The [[M61]] R1rho-type analytic model - the Meiboom 1961 2-site fast exchange equation for on-resonance data with parameters {R1rho', ..., phi_ex, kex} [Meiboom 1961].
* The [[M61 skew]] R1rho-type analytic model - the Meiboom 1961 2-site equation for all time scales with pA &#226Bx226B; pB and with parameters {R1rho', ..., pA, dw, kex} [Meiboom 1961].
* The [[DPL94]] R1rho-type analytic model - the Davis et al., 1994 2-site fast exchange equation extending the 'M61' model for off-resonance data with parameters {R1rho', ..., phi_ex, kex} [Davis et al., 1994].
* The [[TP02]] R1rho-type analytic model - the Trott and Palmer 2002 2-site equation for all time scales with pA &#226Bx226B; pB and with parameters {R1rho', ..., pA, dw, kex} [Trott and Palmer 2002].* The [[TAP03]] R1rho-type analytic model - the Trott et al., 2003 off-resonance 2-site equation for all time scales with the weak condition pA &#226Bx226B; pB and with parameters {R1rho', ..., pA, dw, kex} [Trott et al., 2003].
* The [[MP05]] R1rho-type analytic model - the Miloushev and Palmer 2005 off-resonance 2-site equation for all time scales with parameters {R1rho', ..., pA, dw, kex} [Miloushev and Palmer 2005].
* The [[NS R1rho 2-site]] R1rho numeric model - the model for 2-site exchange using 3D magnetisation vectors with the parameters {R1rho', ..., pA, dw, kex}.
* 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 (pA &#226Bx226B; pB). This commit follows step 1 of the relaxation dispersion model addition tutorial (http://thread.gmane.org/gmane.science.nmr.relax.devel/3907).* Added the 'M61 skew' model to the relax_disp.select_model user function frontend. This is the Meiboom 1961 model for skewed populations (pA &#226Bx226B; pB). This commit follows step 2 of the relaxation dispersion model addition tutorial (http://thread.gmane.org/gmane.science.nmr.relax.devel/3907).
* 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 (pA &#226Bx226B; pB). This commit follows step 3 of the relaxation dispersion model addition tutorial (http://thread.gmane.org/gmane.science.nmr.relax.devel/3907).* Created the M61 skew model target function. This is the Meiboom 1961 on-resonance 2-site model for skewed populations (pA &#226Bx226B; pB). This commit follows step 4 of the relaxation dispersion model addition tutorial (http://thread.gmane.org/gmane.science.nmr.relax.devel/3907).* Added support for the skewed condition (pA &#226Bx226B; pB) to the specific_analyses.relax_disp.parameters module. This is currently done by constraining pA 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 (pA &#226Bx226B; pB). This commit follows step 6 of the relaxation dispersion model addition tutorial (http://thread.gmane.org/gmane.science.nmr.relax.devel/3907).
* 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' R1rho model. This is the Meiboom 1961 on-resonance 2-site model for skewed populations (pA &#226Bx226B; pB). This commit follows step 7 of the relaxation dispersion model addition tutorial (http://thread.gmane.org/gmane.science.nmr.relax.devel/3907).* 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 (pA &#226Bx226B; pB). This commit follows step 7 of the relaxation dispersion model addition tutorial (http://thread.gmane.org/gmane.science.nmr.relax.devel/3907).
* 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.
* 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 pA dispersion parameter optimisation constraints. The parameter is now limited to be between pB and 1. In the case of the limit pA &#226Bx226B; pB, 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 pA 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 (pA &#226Bx226B; pB).
* 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 support for the DPL94 model to the relax_disp.select_model user function back end. This is the David, Perlman and London 1994 R1rho 2-site fast exchange model. This commit follows step 6 of the relaxation dispersion model addition tutorial (http://thread.gmane.org/gmane.science.nmr.relax.devel/3907).
* Created the Relax_disp.test_r1rho_on_res_fixed_time_dpl94 system test. This is the David, Perlman and London 1994 R1rho 2-site fast exchange model. This commit follows step 7 of the relaxation dispersion model addition tutorial (http://thread.gmane.org/gmane.science.nmr.relax.devel/3907).
* 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 pA &#226Bx226B; pB. This commit follows step 1 of the relaxation dispersion model addition tutorial (http://thread.gmane.org/gmane.science.nmr.relax.devel/3907).* 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 pA &#226Bx226B; pB. This commit follows step 2 of the relaxation dispersion model addition tutorial (http://thread.gmane.org/gmane.science.nmr.relax.devel/3907).
* Updated the model lists of the dispersion analyses GUI element. This adds the IT99 CPMG-type model and the DPL94 and M61B R1rho-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 pA &#226Bx226B; pB. This commit follows step 2 of the relaxation dispersion model addition tutorial (http://thread.gmane.org/gmane.science.nmr.relax.devel/3907).* Added the IT99 model equations to the relax library. This is the Ishima and Torchia 1999 2-site model for all timescales with pA &#226Bx226B; pB. This commit follows step 3 of the relaxation dispersion model addition tutorial (http://thread.gmane.org/gmane.science.nmr.relax.devel/3907).* 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 pA &#226Bx226B; pB. This commit follows step 3 of the relaxation dispersion model addition tutorial (http://thread.gmane.org/gmane.science.nmr.relax.devel/3907).* Created the IT99 model target function. This is the Ishima and Torchia 1999 2-site model for all timescales with pA &#226Bx226B; pB. This commit follows step 4 of the relaxation dispersion model addition tutorial (http://thread.gmane.org/gmane.science.nmr.relax.devel/3907).* Fix for the lib.dispersion.it99 module. This is the Ishima and Torchia 1999 2-site model for all timescales with pA &#226Bx226B; pB. This commit follows step 3 of the relaxation dispersion model addition tutorial (http://thread.gmane.org/gmane.science.nmr.relax.devel/3907).* Added the support for the pA.dw^2 parameter 'padw2' to the dispersion specific analysis. This is needed for the Ishima and Torchia 1999 2-site model for all timescales with pA &#226Bx226B; pB. This commit follows step 5 of the relaxation dispersion model addition tutorial (http://thread.gmane.org/gmane.science.nmr.relax.devel/3907).* 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 pA &#226Bx226B; pB. This commit follows step 6 of the relaxation dispersion model addition tutorial (http://thread.gmane.org/gmane.science.nmr.relax.devel/3907).* Added the support for the tex parameter (tex = 1/(2kex)) to the dispersion specific analysis. This is needed for the Ishima and Torchia 1999 2-site model for all timescales with pA &#226Bx226B; pB. This commit follows step 5 of the relaxation dispersion model addition tutorial (http://thread.gmane.org/gmane.science.nmr.relax.devel/3907).* 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 pA &#226Bx226B; pB.
* 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 tex.
* 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 pA &#226Bx226B; pB. This commit follows step 7 of the relaxation dispersion model addition tutorial (http://thread.gmane.org/gmane.science.nmr.relax.devel/3907).
* 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.
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