Author: bugman
Date: Wed Apr 3 10:58:37 2013
New Revision: 19310
URL: http://svn.gna.org/viewcvs/relax?rev=19310&view=rev
Log:
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.
Modified:
branches/relax_disp/user_functions/relax_disp.py
Modified: branches/relax_disp/user_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/user_functions/relax_disp.py?rev=19310&r1=19309&r2=19310&view=diff
==============================================================================
--- branches/relax_disp/user_functions/relax_disp.py (original)
+++ branches/relax_disp/user_functions/relax_disp.py Wed Apr 3 10:58:37 2013
@@ -29,6 +29,11 @@
from specific_analyses.setup import relax_disp_obj
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
+
+# The model names.
+EXP_FIT = 'exp_fit'
+FAST_2SITE = 'fast 2-site'
+SLOW_2SITE = 'slow 2-site'
# The user function class.
@@ -202,40 +207,48 @@
# The relax_disp.select_model user function.
uf = uf_info.add_uf('relax_disp.select_model')
-uf.title = "Select the relaxation dispersion curve type."
-uf.title_short = "Relaxation dispersion curve type selection."
+uf.title = "Select the relaxation dispersion model."
+uf.title_short = "Relaxation dispersion model setup."
uf.display = True
uf.add_keyarg(
name = "model",
- default = "fast",
- py_type = "str",
- desc_short = "model",
- desc = "The type of relaxation dispersion curve to fit (relating to the
NMR time scale).",
+ default = FAST_2SITE,
+ py_type = "str",
+ desc_short = "dispersion model",
+ desc = "The type of relaxation dispersion model to fit.",
wiz_element_type = "combo",
wiz_combo_choices = [
- "fast: [R2, Rex, kex]",
- "slow: [R2A, kA, dw]"
+ "%s: {R2}" % EXP_FIT,
+ "%s: {R2, Rex, kex}" % FAST_2SITE,
+ "%s: {R2A, kA, dw}" % SLOW_2SITE
],
wiz_combo_data = [
- "fast",
- "slow"
+ EXP_FIT,
+ FAST_2SITE,
+ SLOW_2SITE
],
wiz_read_only = True
)
# Description.
uf.desc.append(Desc_container())
-uf.desc[-1].add_paragraph("The supported equations will include the default
fast-exchange limit as well as the slow-exchange limit.")
-uf.desc.append(Desc_container("The preset experiments"))
-uf.desc[-1].add_paragraph("The parameters of these two models are:")
-uf.desc[-1].add_item_list_element("'fast'", "[R2, Rex, kex],")
-uf.desc[-1].add_item_list_element("'slow'", "[R2A, kA, dw].")
-uf.desc[-1].add_paragraph("The equation for fast exchange is:")
+uf.desc[-1].add_paragraph("A number of different dispersion models will be
supported, from the numerical integration of the Bloch-McConnell equations,
the 2-site fast, intermediate and slow exchange, 3-site exchange, to the most
basic model of simply fitting the exponential curves. The currently
supported models include:")
+uf.desc[-1].add_item_list_element("'%s'" % EXP_FIT, "The simple exponential
curve-fitting with parameters {R2},")
+uf.desc[-1].add_item_list_element("'%s'" % FAST_2SITE, "The 2-site fast
exchange equation with parameters {R2, Rex, kex},")
+uf.desc[-1].add_item_list_element("'%s'" % SLOW_2SITE, "The 2-site slow
exchange equation with parameters {R2A, kA, dw}.")
+uf.desc.append(Desc_container("Simple exponential curve-fitting"))
+uf.desc[-1].add_paragraph("This is the simplest of all models in that the
dispersion part is not modelled. It can be selected by setting the model to
'%s'. Each relaxation curve will be fit to the simple two parameter
exponential as in a R1 or R2 analysis, and the R2eff rates will be
calculated. Monte Carlo simulations can be used to obtain the R2eff errors
independent from the dispersion model." % EXP_FIT)
+uf.desc.append(Desc_container("2-site fast exchange equation"))
+uf.desc[-1].add_paragraph("This is selected by setting the model to '%s'.
The equation for fast exchange is:" % FAST_2SITE)
uf.desc[-1].add_verbatim("""
/ / kex \ 4 * cpmg_frq \
R2eff = R2 + Rex * | 1 - 2 * tanh | ---------------- | * ------------ |
\ \ 2 * 4 * cpmg_frq / kex /
""")
-uf.desc[-1].add_paragraph("and the equation for slow exchange is:")
+uf.desc[-1].add_paragraph("The references for this equation are:")
+uf.desc[-1].add_list_element("Millet et al., JACS, 2000, 122, 2867-2877
(equation 19),")
+uf.desc[-1].add_list_element("Kovrigin et al., J. Mag. Res., 2006, 180,
93-104 (equation 1).")
+uf.desc.append(Desc_container("2-site slow exchange equation"))
+uf.desc[-1].add_paragraph("This is selected by setting the model to '%s'.
The equation for slow exchange is:" % SLOW_2SITE)
uf.desc[-1].add_verbatim("""
/ / dw \ 4 * cpmg_frq \
R2eff = R2A + kA - | sin | ------------ | * ------------ |
@@ -245,14 +258,13 @@
uf.desc[-1].add_verbatim("""
cpmg_frq = 1 / ( 4 * cpmg_tau )
""")
-uf.desc[-1].add_paragraph("The references for these equations are:")
-uf.desc[-1].add_item_list_element("'fast'", "Millet et al., JACS, 2000, 122,
2867-2877 (equation 19), and Kovrigin et al., J. Mag. Res., 2006, 180, 93-104
(equation 1).")
-uf.desc[-1].add_item_list_element("'slow'", "Tollinger et al., JACS, 2001,
123: 11341-11352 (equation 2).")
-# Prompt examples.
-uf.desc.append(Desc_container("Prompt examples"))
-uf.desc[-1].add_paragraph("To pick the model 'fast' for all selected spins,
type one of:")
-uf.desc[-1].add_prompt("relax> relax_disp.select_model('fast')")
-uf.desc[-1].add_prompt("relax> relax_disp.select_model(model='fast')")
+uf.desc[-1].add_paragraph("The reference for this equation is:")
+uf.desc[-1].add_list_element("Tollinger et al., JACS, 2001, 123: 11341-11352
(equation 2).")
+# Prompt examples.
+uf.desc.append(Desc_container("Prompt examples"))
+uf.desc[-1].add_paragraph("To pick the 2-site fast exchange model for all
selected spins, type one of:")
+uf.desc[-1].add_prompt("relax> relax_disp.select_model('%s')" % FAST_2SITE)
+uf.desc[-1].add_prompt("relax> relax_disp.select_model(model='%s')" %
FAST_2SITE)
uf.backend = relax_disp_obj._select_model
uf.menu_text = "&select_model"
uf.gui_icon = "oxygen.actions.list-add"
r19310 - /branches/relax_disp/user_functions/relax_disp.py