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,
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Re: r24965 - /branches/R1_fitting/specific_analyses/relax_disp/variables.py