Author: bugman
Date: Wed Oct 9 19:22:06 2013
New Revision: 21033
URL: http://svn.gna.org/viewcvs/relax?rev=21033&view=rev
Log:
Rearranged the documentation for the relax_disp.select_model user function to
simplify the text.
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=21033&r1=21032&r2=21033&view=diff
==============================================================================
--- branches/relax_disp/user_functions/relax_disp.py (original)
+++ branches/relax_disp/user_functions/relax_disp.py Wed Oct 9 19:22:06 2013
@@ -572,41 +572,33 @@
)
# Description.
uf.desc.append(Desc_container())
-uf.desc[-1].add_paragraph("A number of different dispersion models are
supported. This includes both analytic models and numerical models.")
-# Analytic models.
-uf.desc.append(Desc_container('Analytic models'))
-uf.desc[-1].add_paragraph("The analytic models are closed solutions to the
Bloch-McConnell equations under specific conditions. The analytic models are
dependent upon whether the data originates from a CPMG-type or R1rho-type
experiment. For the CPMG-type experiments, the currently supported models
are:")
-uf.desc[-1].add_item_list_element("'%s'" % MODEL_R2EFF, "This is the model
used to determine the R2eff 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_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.")
+# CPMG-type data.
+uf.desc.append(Desc_container('The CPMG-type experiments'))
+uf.desc[-1].add_paragraph("The currently supported analytic models are:")
uf.desc[-1].add_item_list_element("'%s'" % MODEL_LM63, "The original Luz and
Meiboom (1963) 2-site fast exchange equation with parameters {R20, ...,
phi_ex, kex},")
uf.desc[-1].add_item_list_element("'%s'" % MODEL_LM63_3SITE, "The original
Luz and Meiboom (1963) 3-site fast exchange equation with parameters {R20,
..., phi_ex, kex, phi_ex2, kex2},")
-uf.desc[-1].add_item_list_element("'%s'" % MODEL_CR72, "The reduced Carver
and Richards (1972) 2-site equation for all time scales whereby the
simplification R20A = R20B is assumed. The parameters are {R20, ..., pA, dw,
kex}.")
-uf.desc[-1].add_item_list_element("'%s'" % MODEL_CR72_FULL, "The full Carver
and Richards (1972) 2-site equation for all time scales with parameters
{R20A, R20B, ..., pA, dw, kex}.")
-uf.desc[-1].add_item_list_element("'%s'" % MODEL_IT99, "The Ishima and
Torchia (1999) 2-site model for all time scales with pA >> pB and with
parameters {R20, ..., phi_ex, padw2, kex}.")
+uf.desc[-1].add_item_list_element("'%s'" % MODEL_CR72, "The reduced Carver
and Richards (1972) 2-site equation for all time scales whereby the
simplification R20A = R20B is assumed. The parameters are {R20, ..., pA, dw,
kex},")
+uf.desc[-1].add_item_list_element("'%s'" % MODEL_CR72_FULL, "The full Carver
and Richards (1972) 2-site equation for all time scales with parameters
{R20A, R20B, ..., pA, dw, kex},")
+uf.desc[-1].add_item_list_element("'%s'" % MODEL_IT99, "The Ishima and
Torchia (1999) 2-site model for all time scales with pA >> pB and with
parameters {R20, ..., phi_ex, padw2, kex},")
uf.desc[-1].add_item_list_element("'%s'" % MODEL_TSMFK01, "The Tollinger,
Kay et al. (2001) 2-site very-slow exchange model, range of microsecond to
second time scale. Applicable in the limit of slow exchange, when
|R20A-R20B| << k_AB,kB << 1/tau_CP. R20A is the transverse relaxation rate
of site A in the absence of exchange. 2*tau_CP is is the time between
successive 180 deg. pulses. The parameters are {R20A, ..., dw, k_AB}.")
-uf.desc[-1].add_paragraph("For the R1rho-type experiment, the currently
supported models are:")
-uf.desc[-1].add_item_list_element("'%s'" % MODEL_R2EFF, "This is the same
model model as for the CPMG-type experiments except that the R1rho and not
R2eff values are determined.")
-uf.desc[-1].add_item_list_element("'%s'" % MODEL_NOREX, "This is the model
for no chemical exchange being present,")
+uf.desc[-1].add_paragraph("The currently supported numeric models are:")
+uf.desc[-1].add_item_list_element("'%s'" % MODEL_NS_CPMG_2SITE_3D, "The
reduced numerical solution for the 2-site Bloch-McConnell equations using 3D
magnetisation vectors whereby the simplification R20A = R20B is assumed. Its
parameters are {R20, ..., pA, dw, kex},")
+uf.desc[-1].add_item_list_element("'%s'" % MODEL_NS_CPMG_2SITE_3D_FULL, "The
full numerical solution for the 2-site Bloch-McConnell equations using 3D
magnetisation vectors. Its parameters are {R20A, R20B, ..., pA, dw, kex},")
+uf.desc[-1].add_item_list_element("'%s'" % MODEL_NS_CPMG_2SITE_STAR, "The
reduced numerical solution for the 2-site Bloch-McConnell equations using
complex conjugate matrices whereby the simplification R20A = R20B is assumed.
It has the parameters {R20, ..., pA, dw, kex},")
+uf.desc[-1].add_item_list_element("'%s'" % MODEL_NS_CPMG_2SITE_STAR_FULL,
"The full numerical solution for the 2-site Bloch-McConnell equations using
complex conjugate matrices with parameters {R20A, R20B, ..., pA, dw, kex},")
+uf.desc[-1].add_item_list_element("'%s'" % MODEL_NS_CPMG_2SITE_EXPANDED,
"The numerical solution for the 2-site Bloch-McConnell equations expanded
using Maple by Nikolai Skrynnikov. It has the parameters {R20, ..., pA, dw,
kex}.")
+# 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_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_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_TP02, "The Trott and Palmer
(2002) 2-site equation for all time scales with parameters {R1rho', ..., pA,
dw, kex},")
-uf.desc[-1].add_paragraph("Except for '%s' and '%s', these CPMG and R1rho
models are fit to clusterings of spins, or spin blocks." % (MODEL_R2EFF,
MODEL_NOREX))
-# Numerical models.
-uf.desc.append(Desc_container('Numerical models'))
-uf.desc[-1].add_paragraph("The Bloch-McConnell equations can also be solved
numerically. The numeric models are also dependent upon whether the data
originates from a CPMG-type or R1rho-type experiment. For the CPMG-type
experiments, the currently supported models are:")
-uf.desc[-1].add_item_list_element("'%s'" % MODEL_R2EFF, "This is the model
used to determine the R2eff 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_NS_CPMG_2SITE_3D, "The
reduced numerical solution for the 2-site Bloch-McConnell equations using 3D
magnetisation vectors whereby the simplification R20A = R20B is assumed. Its
parameters are {R20, ..., pA, dw, kex}.")
-uf.desc[-1].add_item_list_element("'%s'" % MODEL_NS_CPMG_2SITE_3D_FULL, "The
full numerical solution for the 2-site Bloch-McConnell equations using 3D
magnetisation vectors. Its parameters are {R20A, R20B, ..., pA, dw, kex}.")
-uf.desc[-1].add_item_list_element("'%s'" % MODEL_NS_CPMG_2SITE_STAR, "The
reduced numerical solution for the 2-site Bloch-McConnell equations using
complex conjugate matrices whereby the simplification R20A = R20B is assumed.
It has the parameters {R20, ..., pA, dw, kex}.")
-uf.desc[-1].add_item_list_element("'%s'" % MODEL_NS_CPMG_2SITE_STAR_FULL,
"The full numerical solution for the 2-site Bloch-McConnell equations using
complex conjugate matrices with parameters {R20A, R20B, ..., pA, dw, kex}.")
-uf.desc[-1].add_item_list_element("'%s'" % MODEL_NS_CPMG_2SITE_EXPANDED,
"The numerical solution for the 2-site Bloch-McConnell equations expanded
using Maple by Nikolai Skrynnikov. It has the parameters {R20, ..., pA, dw,
kex}.")
-uf.desc[-1].add_paragraph("For the R1rho-type experiment, the currently
supported models are:")
-uf.desc[-1].add_item_list_element("'%s'" % MODEL_R2EFF, "This is the same
model model as for the CPMG-type experiments except that the R1rho and not
R2eff values are determined.")
-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_TP02, "The Trott and Palmer
(2002) 2-site equation for all time scales with parameters {R1rho', ..., 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. Its parameters are {R1rho', ..., pA, dw, kex}.")
-uf.desc[-1].add_paragraph("Again as for the analytic models, except for '%s'
and '%s', these CPMG and R1rho models are fit to clusterings of spins, or
spin blocks. All models are described in full detail in the relax user
manual." % (MODEL_R2EFF, MODEL_NOREX))
# 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:")
r21033 - /branches/relax_disp/user_functions/relax_disp.py