Author: tlinnet Date: Tue Aug 5 13:52:51 2014 New Revision: 24965 URL: http://svn.gna.org/viewcvs/relax?rev=24965&view=rev Log: Added the equivalend R1 fit models for: TP02, TAP03, MP05 and NS_R1RHO_2SITE. The R1 fit modeÃls will no be implemented for 3 site models, because there will be to many variables. sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models. Modified: branches/R1_fitting/specific_analyses/relax_disp/variables.py Modified: branches/R1_fitting/specific_analyses/relax_disp/variables.py URL: http://svn.gna.org/viewcvs/relax/branches/R1_fitting/specific_analyses/relax_disp/variables.py?rev=24965&r1=24964&r2=24965&view=diff ============================================================================== --- branches/R1_fitting/specific_analyses/relax_disp/variables.py (original) +++ branches/R1_fitting/specific_analyses/relax_disp/variables.py Tue Aug 5 13:52:51 2014 @@ -126,15 +126,28 @@ MODEL_DESC_TP02 = "The Trott and Palmer (2002) off-resonance 2-site model for R1rho-type experiments." MODEL_PARAMS_TP02 = ['r2', 'pA', 'dw', 'kex'] +MODEL_TP02_FIT_R1 = "%s_fit_r1"%MODEL_TP02 +MODEL_DESC_TP02_FIT_R1 = "The Trott and Palmer (2002) off-resonance 2-site model for R1rho-type experiments, where R1 is fitted." +MODEL_PARAMS_TP02_FIT_R1 = ['r1_fit', 'r2', 'pA', 'dw', 'kex'] + MODEL_TAP03 = 'TAP03' MODEL_DESC_TAP03 = "The Trott, Abergel and Palmer (2003) off-resonance 2-site model for R1rho-type experiments." MODEL_PARAMS_TAP03 = ['r2', 'pA', 'dw', 'kex'] + +MODEL_TAP03_FIT_R1 = "%s_fit_r1"%MODEL_TAP03 +MODEL_DESC_TAP03_FIT_R1 = "The Trott, Abergel and Palmer (2003) off-resonance 2-site model for R1rho-type experiments, where R1 is fitted." +MODEL_PARAMS_TAP03_FIT_R1 = ['r1_fit', 'r2', 'pA', 'dw', 'kex'] MODEL_MP05 = 'MP05' """The R1rho 2-site off-resonance exchange model of Miloushev and Palmer (2005).""" MODEL_DESC_MP05 = "The Miloushev and Palmer (2005) off-resonance 2-site model for R1rho-type experiments." MODEL_PARAMS_MP05 = ['r2', 'pA', 'dw', 'kex'] +MODEL_MP05_FIT_R1 = "%s_fit_r1"%MODEL_MP05 +"""The R1rho 2-site off-resonance exchange model of Miloushev and Palmer (2005).""" +MODEL_DESC_MP05_FIT_R1 = "The Miloushev and Palmer (2005) off-resonance 2-site model for R1rho-type experiments, where R1 is fitted." +MODEL_PARAMS_MP05_FIT_R1 = ['r1_fit', 'r2', 'pA', 'dw', 'kex'] + # The Numerical model names. MODEL_NS_CPMG_2SITE_3D = 'NS CPMG 2-site 3D' @@ -160,6 +173,10 @@ MODEL_NS_R1RHO_2SITE = 'NS R1rho 2-site' MODEL_DESC_NS_R1RHO_2SITE = "The reduced numerical solution for the 2-site Bloch-McConnell equations using 3D magnetisation vectors for R1rho-type experiments, whereby the simplification R20A = R20B is assumed." MODEL_PARAMS_NS_R1RHO_2SITE = ['r2', 'pA', 'dw', 'kex'] + +MODEL_NS_R1RHO_2SITE_FIT_R1 = "%s_fit_r1"%MODEL_NS_R1RHO_2SITE +MODEL_DESC_NS_R1RHO_2SITE_FIT_R1 = "The reduced numerical solution for the 2-site Bloch-McConnell equations using 3D magnetisation vectors for R1rho-type experiments, whereby the simplification R20A = R20B is assumed, and where R1 is fitted." +MODEL_PARAMS_NS_R1RHO_2SITE_FIT_R1 = ['r1_fit', 'r2', 'pA', 'dw', 'kex'] MODEL_NS_R1RHO_3SITE = 'NS R1rho 3-site' MODEL_DESC_NS_R1RHO_3SITE = "The numerical solution for the 3-site Bloch-McConnell equations using 3D magnetisation vectors for R1rho-type experiments, whereby the simplification R20A = R20B = R20C is assumed." @@ -251,7 +268,7 @@ """The list of all dispersion models specifically for analytical R1rho-type experiments which use R1 in their equations (excluding the R2eff model and model 'No Rex').""" #### Off-resonance R1rho models, where R1 will be fitted. -MODEL_LIST_ANALYTIC_R1RHO_FIT_R1 = [MODEL_DPL94_FIT_R1] +MODEL_LIST_ANALYTIC_R1RHO_FIT_R1 = [MODEL_DPL94_FIT_R1, MODEL_TP02_FIT_R1, MODEL_TAP03_FIT_R1, MODEL_MP05_FIT_R1] """The list of all dispersion models specifically for R1rho-type experiments which fit R1 in their equations (excluding the R2eff model and model 'No Rex').""" ### The numerical models. @@ -260,7 +277,7 @@ """The list of all dispersion models specifically for numeric R1rho-type experiments which use R1 in their equations (excluding the R2eff model and model 'No Rex').""" #### Off-resonance R1rho models, where R1 will be fitted. -MODEL_LIST_NUMERIC_R1RHO_FIT_R1 = [] +MODEL_LIST_NUMERIC_R1RHO_FIT_R1 = [MODEL_NS_R1RHO_2SITE_FIT_R1] """The list of all dispersion models specifically for numeric R1rho-type experiments which fit R1 in their equations (excluding the R2eff model and model 'No Rex').""" ### All R1rho models. @@ -314,7 +331,7 @@ """The list of the R2eff model together with all dispersion models.""" # The model lists dependent on parameter. -MODEL_PARAM_INV_RELAX_TIMES = [MODEL_B14, MODEL_B14_FULL, MODEL_MMQ_CR72, MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_MMQ_2SITE, MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR, MODEL_NS_R1RHO_2SITE, MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR] +MODEL_PARAM_INV_RELAX_TIMES = [MODEL_B14, MODEL_B14_FULL, MODEL_MMQ_CR72, MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_MMQ_2SITE, MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR, MODEL_NS_R1RHO_2SITE, MODEL_NS_R1RHO_2SITE_FIT_R1, MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR] """The inverted relaxation delay""" MODEL_PARAM_R20B = [MODEL_B14_FULL, MODEL_CR72_FULL, MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_STAR_FULL] @@ -347,14 +364,18 @@ MODEL_DPL94: MODEL_DESC_DPL94, MODEL_DPL94_FIT_R1: MODEL_DESC_DPL94_FIT_R1, MODEL_TP02: MODEL_DESC_TP02, + MODEL_TP02_FIT_R1: MODEL_DESC_TP02_FIT_R1, MODEL_TAP03: MODEL_DESC_TAP03, + MODEL_TAP03_FIT_R1: MODEL_DESC_TAP03_FIT_R1, MODEL_MP05: MODEL_DESC_MP05, + MODEL_MP05_FIT_R1: MODEL_DESC_MP05_FIT_R1, MODEL_NS_CPMG_2SITE_3D: MODEL_DESC_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL: MODEL_DESC_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_STAR: MODEL_DESC_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL: MODEL_DESC_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_CPMG_2SITE_EXPANDED: MODEL_DESC_NS_CPMG_2SITE_EXPANDED, MODEL_NS_R1RHO_2SITE: MODEL_DESC_NS_R1RHO_2SITE, + MODEL_NS_R1RHO_2SITE_FIT_R1: MODEL_DESC_NS_R1RHO_2SITE_FIT_R1, MODEL_NS_R1RHO_3SITE: MODEL_DESC_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR: MODEL_DESC_NS_R1RHO_3SITE_LINEAR, MODEL_MMQ_CR72: MODEL_DESC_MMQ_CR72, @@ -382,14 +403,18 @@ MODEL_DPL94: MODEL_PARAMS_DPL94, MODEL_DPL94_FIT_R1: MODEL_PARAMS_DPL94_FIT_R1, MODEL_TP02: MODEL_PARAMS_TP02, + MODEL_TP02_FIT_R1: MODEL_PARAMS_TP02_FIT_R1, MODEL_TAP03: MODEL_PARAMS_TAP03, + MODEL_TAP03_FIT_R1: MODEL_PARAMS_TAP03_FIT_R1, MODEL_MP05: MODEL_PARAMS_MP05, + MODEL_MP05_FIT_R1: MODEL_PARAMS_MP05_FIT_R1, MODEL_NS_CPMG_2SITE_3D: MODEL_PARAMS_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL: MODEL_PARAMS_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_STAR: MODEL_PARAMS_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL: MODEL_PARAMS_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_CPMG_2SITE_EXPANDED: MODEL_PARAMS_NS_CPMG_2SITE_EXPANDED, MODEL_NS_R1RHO_2SITE: MODEL_PARAMS_NS_R1RHO_2SITE, + MODEL_NS_R1RHO_2SITE_FIT_R1: MODEL_PARAMS_NS_R1RHO_2SITE_FIT_R1, MODEL_NS_R1RHO_3SITE: MODEL_PARAMS_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR: MODEL_PARAMS_NS_R1RHO_3SITE_LINEAR, MODEL_MMQ_CR72: MODEL_PARAMS_MMQ_CR72,