Author: tlinnet
Date: Wed Aug 13 10:46:58 2014
New Revision: 25008
URL: http://svn.gna.org/viewcvs/relax?rev=25008&view=rev
Log:
Added front-end description of the 6 new R1 fit R1rho models for
relax_disp.select_model.
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/user_functions/relax_disp.py
Modified: branches/R1_fitting/user_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/R1_fitting/user_functions/relax_disp.py?rev=25008&r1=25007&r2=25008&view=diff
==============================================================================
--- branches/R1_fitting/user_functions/relax_disp.py (original)
+++ branches/R1_fitting/user_functions/relax_disp.py Wed Aug 13 10:46:58
2014
@@ -33,7 +33,7 @@
FD_SAVE = -1
# relax module imports.
-from lib.text.gui import dw, dw_AB, dw_BC, dwH, dwH_AB, dwH_BC, i0, kex,
kAB, kBC, kAC, phi_ex, phi_exB, phi_exC, nu_1, nu_cpmg, r1rho, r1rho_prime,
r2, r2a, r2b, r2eff, tex, theta, w_eff, w_rf
+from lib.text.gui import dw, dw_AB, dw_BC, dwH, dwH_AB, dwH_BC, i0, kex,
kAB, kBC, kAC, phi_ex, phi_exB, phi_exC, nu_1, nu_cpmg, r1rho, r1rho_prime,
r1_fit, r2, r2a, r2b, r2eff, tex, theta, w_eff, w_rf
from graphics import ANALYSIS_IMAGE_PATH, WIZARD_IMAGE_PATH
from pipe_control import pipes, spectrum
from pipe_control.mol_res_spin import get_spin_ids
@@ -44,7 +44,7 @@
from specific_analyses.relax_disp.nessy import nessy_input
from specific_analyses.relax_disp.parameters import copy
from specific_analyses.relax_disp.sherekhan import sherekhan_input
-from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_DQ,
EXP_TYPE_CPMG_MQ, EXP_TYPE_CPMG_SQ, EXP_TYPE_CPMG_ZQ,
EXP_TYPE_CPMG_PROTON_MQ, EXP_TYPE_CPMG_PROTON_SQ, EXP_TYPE_R1RHO, MODEL_B14,
MODEL_B14_FULL, MODEL_CR72, MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99,
MODEL_LM63, MODEL_LM63_3SITE, MODEL_M61, MODEL_M61B, MODEL_MMQ_CR72,
MODEL_MP05, MODEL_NOREX, 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_R2EFF, MODEL_TAP03, MODEL_TP02,
MODEL_TSMFK01
+from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_DQ,
EXP_TYPE_CPMG_MQ, EXP_TYPE_CPMG_SQ, EXP_TYPE_CPMG_ZQ,
EXP_TYPE_CPMG_PROTON_MQ, EXP_TYPE_CPMG_PROTON_SQ, EXP_TYPE_R1RHO, MODEL_B14,
MODEL_B14_FULL, MODEL_CR72, MODEL_CR72_FULL, MODEL_DPL94, MODEL_DPL94_FIT_R1,
MODEL_IT99, MODEL_LM63, MODEL_LM63_3SITE, MODEL_M61, MODEL_M61B,
MODEL_MMQ_CR72, MODEL_MP05, MODEL_MP05_FIT_R1, MODEL_NOREX,
MODEL_NOREX_R1RHO, MODEL_NOREX_R1RHO_FIT_R1, 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, MODEL_R2EFF, MODEL_TAP03, MODEL_TAP03_FIT_R1,
MODEL_TP02, MODEL_TP02_FIT_R1, MODEL_TSMFK01
from specific_analyses.relax_disp import uf as relax_disp_uf
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
@@ -862,6 +862,8 @@
wiz_combo_choices = [
"%s: {%s/%s, %s}" % (MODEL_R2EFF, r2eff, r1rho, i0),
"%s: {%s, ...}" % (MODEL_NOREX, r2),
+ "%s: {%s, ...}" % (MODEL_NOREX_R1RHO, r2),
+ "%s: {%s, %s, ...}" % (MODEL_NOREX_R1RHO_FIT_R1, r1_fit, r2),
"%s: {%s, ..., %s, %s}" % (MODEL_LM63, r2, phi_ex, kex),
"%s: {%s, ..., %s, kB, %s, kC}" % (MODEL_LM63_3SITE, r2, phi_exB,
phi_exC),
"%s: {%s, ..., pA, %s, %s}" % (MODEL_CR72, r2, dw, kex),
@@ -882,16 +884,23 @@
"%s: {%s, ..., %s, %s}" % (MODEL_M61, r1rho_prime, phi_ex, kex),
"%s: {%s, ..., pA, %s, %s}" % (MODEL_M61B, r1rho_prime, dw, kex),
"%s: {%s, ..., %s, %s}" % (MODEL_DPL94, r1rho_prime, phi_ex, kex),
+ "%s: {%s, %s, ..., %s, %s}" % (MODEL_DPL94_FIT_R1, r1_fit,
r1rho_prime, phi_ex, kex),
"%s: {%s, ..., pA, %s, %s}" % (MODEL_TP02, r1rho_prime, dw, kex),
+ "%s: {%s, %s, ..., pA, %s, %s}" % (MODEL_TP02_FIT_R1, r1_fit,
r1rho_prime, dw, kex),
"%s: {%s, ..., pA, %s, %s}" % (MODEL_TAP03, r1rho_prime, dw, kex),
+ "%s: {%s, %s, ..., pA, %s, %s}" % (MODEL_TAP03_FIT_R1, r1_fit,
r1rho_prime, dw, kex),
"%s: {%s, ..., pA, %s, %s}" % (MODEL_MP05, r1rho_prime, dw, kex),
+ "%s: {%s, %s, ..., pA, %s, %s}" % (MODEL_MP05_FIT_R1, r1_fit,
r1rho_prime, dw, kex),
"%s: {%s, ..., pA, %s, %s}" % (MODEL_NS_R1RHO_2SITE, r1rho_prime,
dw, kex),
+ "%s: {%s, %s, ..., pA, %s, %s}" % (MODEL_NS_R1RHO_2SITE_FIT_R1,
r1_fit, r1rho_prime, dw, kex),
"%s: {%s, ..., pA, %s, %s, pB, %s, %s}" %
(MODEL_NS_R1RHO_3SITE_LINEAR, r2, dw_AB, kAB, dw_BC, kBC),
"%s: {%s, ..., pA, %s, %s, pB, %s, %s, %s}" % (MODEL_NS_R1RHO_3SITE,
r2, dw_AB, kAB, dw_BC, kBC, kAC)
],
wiz_combo_data = [
MODEL_R2EFF,
MODEL_NOREX,
+ MODEL_NOREX_R1RHO,
+ MODEL_NOREX_R1RHO_FIT_R1,
MODEL_LM63,
MODEL_LM63_3SITE,
MODEL_CR72,
@@ -912,10 +921,15 @@
MODEL_M61,
MODEL_M61B,
MODEL_DPL94,
+ MODEL_DPL94_FIT_R1,
MODEL_TP02,
+ MODEL_TP02_FIT_R1,
MODEL_TAP03,
+ MODEL_TAP03_FIT_R1,
MODEL_MP05,
+ MODEL_MP05_FIT_R1,
MODEL_NS_R1RHO_2SITE,
+ MODEL_NS_R1RHO_2SITE_FIT_R1,
MODEL_NS_R1RHO_3SITE_LINEAR,
MODEL_NS_R1RHO_3SITE
],
@@ -926,6 +940,8 @@
uf.desc[-1].add_paragraph("A number of different dispersion models are
supported. This includes both analytic models and numerical models. Models
which are independent of the experimental data type are:")
uf.desc[-1].add_item_list_element("'%s'" % MODEL_R2EFF, "This is the model
used to determine the R2eff/R1rho values and errors required as the base data
for all other models,")
uf.desc[-1].add_item_list_element("'%s'" % MODEL_NOREX, "This is the model
for no chemical exchange being present.")
+uf.desc[-1].add_item_list_element("'%s'" % MODEL_NOREX_R1RHO, "This is the
model for no chemical exchange being present, for off-resonance R1rho-type
experiments. R1rho = R1 * cos(theta)^2 + r1rho_prime * sin(theta)^2")
+uf.desc[-1].add_item_list_element("'%s'" % MODEL_NOREX_R1RHO_FIT_R1, "This
is the model for no chemical exchange being present, for off-resonance
R1rho-type experiments where R1 is fitted. R1rho = R1 * cos(theta)^2 +
r1rho_prime * sin(theta)^2")
# CPMG-type data.
uf.desc.append(Desc_container('The SQ CPMG-type experiments'))
uf.desc[-1].add_paragraph("The currently supported analytic models are:")
@@ -953,15 +969,22 @@
# R1rho-type data.
uf.desc.append(Desc_container('The R1rho-type experiments'))
uf.desc[-1].add_paragraph("The currently supported analytic models are:")
+uf.desc[-1].add_paragraph("On-resonance models are:")
uf.desc[-1].add_item_list_element("'%s'" % MODEL_M61, "The Meiboom (1961)
2-site fast exchange equation with parameters {R1rho', ..., phi_ex, kex},")
uf.desc[-1].add_item_list_element("'%s'" % MODEL_M61B, "The Meiboom (1961)
2-site equation for all time scales with pA >> pB and with parameters
{R1rho', ..., pA, dw, kex},")
+uf.desc[-1].add_paragraph("Off-resonance models are:")
uf.desc[-1].add_item_list_element("'%s'" % MODEL_DPL94, "The Davis, Perlman
and London (1994) 2-site fast exchange equation with parameters {R1rho', ...,
phi_ex, kex},")
+uf.desc[-1].add_item_list_element("'%s'" % MODEL_DPL94_FIT_R1, "The Davis,
Perlman and London (1994) 2-site fast exchange equation, where R1 is fitted,
with parameters {R1rho', r1_fit, ..., phi_ex, kex},")
uf.desc[-1].add_item_list_element("'%s'" % MODEL_TP02, "The Trott and Palmer
(2002) 2-site equation for all time scales with parameters {R1rho', ..., pA,
dw, kex}.")
+uf.desc[-1].add_item_list_element("'%s'" % MODEL_TP02_FIT_R1, "The Trott and
Palmer (2002) 2-site equation for all time scales, where R1 is fitted, with
parameters {R1rho', r1_fit, ..., pA, dw, kex}.")
uf.desc[-1].add_item_list_element("'%s'" % MODEL_TAP03, "The Trott, Abergel
and Palmer (2003) off-resonance 2-site equation for all time scales with
parameters {R1rho', ..., pA, dw, kex}.")
+uf.desc[-1].add_item_list_element("'%s'" % MODEL_TAP03_FIT_R1, "The Trott,
Abergel and Palmer (2003) off-resonance 2-site equation for all time scales,
where R1 is fitted, with parameters {R1rho', r1_fit, ..., pA, dw, kex}.")
uf.desc[-1].add_item_list_element("'%s'" % MODEL_MP05, "The Miloushev and
Palmer (2005) 2-site off-resonance equation for all time scales with
parameters {R1rho', ..., pA, dw, kex}.")
+uf.desc[-1].add_item_list_element("'%s'" % MODEL_MP05_FIT_R1, "The Miloushev
and Palmer (2005) 2-site off-resonance equation for all time scales, where R1
is fitted, with parameters {R1rho', r1_fit, ..., pA, dw, kex}.")
uf.desc[-1].add_paragraph("The currently supported numeric models are:")
-uf.desc[-1].add_item_list_element("'%s'" % MODEL_NS_R1RHO_2SITE, "The
numerical solution for the 2-site Bloch-McConnell equations using 3D
magnetisation vectors whereby the simplification R20A = R20B = R20C is
assumed and linearised with kAC = kCA = 0. Its parameters are {R1rho', ...,
pA, dw(AB), kex(AB), pB, dw(BC), kex(BC)}.")
-uf.desc[-1].add_item_list_element("'%s'" % MODEL_NS_R1RHO_3SITE_LINEAR, "The
numerical solution for the 3-site Bloch-McConnell equations using 3D
magnetisation vectors whereby the simplification R20A = R20B = R20C is
assumed. Its parameters are {R1rho', ..., pA, dw, kex}.")
+uf.desc[-1].add_item_list_element("'%s'" % MODEL_NS_R1RHO_2SITE, "The
numerical solution for the 2-site Bloch-McConnell equations using 3D
magnetisation vectors whereby the simplification R20A = R20B. Its parameters
are {R1rho', ..., pA, dw, kex}.")
+uf.desc[-1].add_item_list_element("'%s'" % MODEL_NS_R1RHO_2SITE_FIT_R1, "The
numerical solution for the 2-site Bloch-McConnell equations using 3D
magnetisation vectors whereby the simplification R20A = R20B and where R1 is
fitted. Its parameters are {R1rho', r1_fit, ..., pA, dw, kex}.")
+uf.desc[-1].add_item_list_element("'%s'" % MODEL_NS_R1RHO_3SITE_LINEAR, "The
numerical solution for the 3-site Bloch-McConnell equations using 3D
magnetisation vectors whereby the simplification R20A = R20B = R20C is
assumed and linearised with kAC = kCA = 0. Its parameters are {R1rho', ...,
pA, dw(AB), kex(AB), pB, dw(BC), kex(BC)}.")
uf.desc[-1].add_item_list_element("'%s'" % MODEL_NS_R1RHO_3SITE, "The
numerical solution for the 3-site Bloch-McConnell equations using 3D
magnetisation vectors. Its parameters are {R1rho', ..., pA, dw(AB), kex(AB),
pB, dw(BC), kex(BC), kex(AC)}.")
# Prompt examples.
uf.desc.append(Desc_container("Prompt examples"))
r25008 - /branches/R1_fitting/user_functions/relax_disp.py