Author: bugman
Date: Tue Sep 3 13:47:19 2013
New Revision: 20769
URL: http://svn.gna.org/viewcvs/relax?rev=20769&view=rev
Log:
Proper ordering of all the dispersion models.
See the thread at http://thread.gmane.org/gmane.science.nmr.relax.devel/4498
for details.
Modified:
branches/relax_disp/specific_analyses/relax_disp/api.py
branches/relax_disp/specific_analyses/relax_disp/variables.py
branches/relax_disp/target_functions/relax_disp.py
branches/relax_disp/user_functions/relax_disp.py
Modified: branches/relax_disp/specific_analyses/relax_disp/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/api.py?rev=20769&r1=20768&r2=20769&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/api.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/api.py Tue Sep 3
13:47:19 2013
@@ -709,6 +709,50 @@
params.append('r2')
params += ['phi_ex', 'padw2', 'tex']
+ # Full NS CPMG 2-site 3D model.
+ elif model == MODEL_NS_CPMG_2SITE_3D_FULL:
+ print("The full numerical solution for the 2-site
Bloch-McConnell equations for CPMG data using 3D magnetisation vectors.")
+ params = []
+ for frq in loop_frq():
+ params.append('r2a')
+ for frq in loop_frq():
+ params.append('r2b')
+ params += ['pA', 'dw', 'kex']
+
+ # Reduced NS CPMG 2-site 3D model.
+ elif model == MODEL_NS_CPMG_2SITE_3D:
+ print("The reduced numerical solution for the 2-site
Bloch-McConnell equations for CPMG data using 3D magnetisation vectors,
whereby the simplification R20A = R20B is assumed.")
+ params = []
+ for frq in loop_frq():
+ params.append('r2')
+ params += ['pA', 'dw', 'kex']
+
+ # NS CPMG 2-site expanded model.
+ elif model == MODEL_NS_CPMG_2SITE_EXPANDED:
+ print("The numerical solution for the 2-site Bloch-McConnell
equations for CPMG data expanded using Maple by Nikolai Skrynnikov.")
+ params = []
+ for frq in loop_frq():
+ params.append('r2')
+ params += ['pA', 'dw', 'kex']
+
+ # Full NS CPMG 2-site star model.
+ elif model == MODEL_NS_CPMG_2SITE_STAR_FULL:
+ print("The full numerical solution for the 2-site
Bloch-McConnell equations for CPMG data using complex conjugate matrices.")
+ params = []
+ for frq in loop_frq():
+ params.append('r2a')
+ for frq in loop_frq():
+ params.append('r2b')
+ params += ['pA', 'dw', 'kex']
+
+ # Reduced NS CPMG 2-site star model.
+ elif model == MODEL_NS_CPMG_2SITE_STAR:
+ print("The numerical reduced solution for the 2-site
Bloch-McConnell equations for CPMG data using complex conjugate matrices,
whereby the simplification R20A = R20B is assumed.")
+ params = []
+ for frq in loop_frq():
+ params.append('r2')
+ params += ['pA', 'dw', 'kex']
+
# M61 model.
elif model == MODEL_M61:
print("The Meiboom (1961) 2-site fast exchange model for
R1rho-type experiments.")
@@ -717,6 +761,14 @@
params.append('r2')
params += ['phi_ex', 'kex']
+ # M61 skew model.
+ elif model == MODEL_M61B:
+ print("The Meiboom (1961) on-resonance 2-site model with skewed
populations (pA >> pB) for R1rho-type experiments.")
+ params = []
+ for frq in loop_frq():
+ params.append('r2')
+ params += ['pA', 'dw', 'kex']
+
# DPL94 model.
elif model == MODEL_DPL94:
print("The Davis, Perlman and London (1994) 2-site fast exchange
model for R1rho-type experiments.")
@@ -724,58 +776,6 @@
for frq in loop_frq():
params.append('r2')
params += ['phi_ex', 'kex']
-
- # M61 skew model.
- elif model == MODEL_M61B:
- print("The Meiboom (1961) on-resonance 2-site model with skewed
populations (pA >> pB) for R1rho-type experiments.")
- params = []
- for frq in loop_frq():
- params.append('r2')
- params += ['pA', 'dw', 'kex']
-
- # Full NS CPMG 2-site 3D model.
- elif model == MODEL_NS_CPMG_2SITE_3D_FULL:
- print("The full numerical solution for the 2-site
Bloch-McConnell equations for CPMG data using 3D magnetisation vectors.")
- params = []
- for frq in loop_frq():
- params.append('r2a')
- for frq in loop_frq():
- params.append('r2b')
- params += ['pA', 'dw', 'kex']
-
- # Reduced NS CPMG 2-site 3D model.
- elif model == MODEL_NS_CPMG_2SITE_3D:
- print("The reduced numerical solution for the 2-site
Bloch-McConnell equations for CPMG data using 3D magnetisation vectors,
whereby the simplification R20A = R20B is assumed.")
- params = []
- for frq in loop_frq():
- params.append('r2')
- params += ['pA', 'dw', 'kex']
-
- # NS CPMG 2-site expanded model.
- elif model == MODEL_NS_CPMG_2SITE_EXPANDED:
- print("The numerical solution for the 2-site Bloch-McConnell
equations for CPMG data expanded using Maple by Nikolai Skrynnikov.")
- params = []
- for frq in loop_frq():
- params.append('r2')
- params += ['pA', 'dw', 'kex']
-
- # Full NS CPMG 2-site star model.
- elif model == MODEL_NS_CPMG_2SITE_STAR_FULL:
- print("The full numerical solution for the 2-site
Bloch-McConnell equations for CPMG data using complex conjugate matrices.")
- params = []
- for frq in loop_frq():
- params.append('r2a')
- for frq in loop_frq():
- params.append('r2b')
- params += ['pA', 'dw', 'kex']
-
- # Reduced NS CPMG 2-site star model.
- elif model == MODEL_NS_CPMG_2SITE_STAR:
- print("The numerical reduced solution for the 2-site
Bloch-McConnell equations for CPMG data using complex conjugate matrices,
whereby the simplification R20A = R20B is assumed.")
- params = []
- for frq in loop_frq():
- params.append('r2')
- params += ['pA', 'dw', 'kex']
# TP02 model.
elif model == MODEL_TP02:
Modified: branches/relax_disp/specific_analyses/relax_disp/variables.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/variables.py?rev=20769&r1=20768&r2=20769&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/variables.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/variables.py Tue Sep 3
13:47:19 2013
@@ -62,14 +62,14 @@
MODEL_IT99 = 'IT99'
"""The CPMG 2-site model for all time scales with pA >> pB of Ishima and
Torchia (1999)."""
-MODEL_DPL94 = 'DPL94'
-"""The R1rho 2-site fast exchange model of Davis, Perlman and London
(1994)."""
-
MODEL_M61 = 'M61'
"""The R1rho 2-site fast exchange model of Meiboom (1961)."""
MODEL_M61B = 'M61 skew'
"""The R1rho 2-site model for all time scales with pA >> pB of Meiboom
(1961)."""
+
+MODEL_DPL94 = 'DPL94'
+"""The R1rho 2-site fast exchange model of Davis, Perlman and London
(1994)."""
MODEL_TP02 = 'TP02'
"""The R1rho 2-site exchange model of Trott and Palmer (2002)."""
@@ -96,10 +96,10 @@
# The model lists.
-MODEL_LIST_DISP = [MODEL_NOREX, MODEL_LM63, MODEL_TSMFK01, MODEL_LM63_3SITE,
MODEL_CR72, MODEL_CR72_FULL, MODEL_IT99, MODEL_M61, MODEL_DPL94, MODEL_M61B,
MODEL_TP02, MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL,
MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL,
MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_R1RHO_2SITE]
+MODEL_LIST_DISP = [MODEL_NOREX, MODEL_LM63, MODEL_TSMFK01, MODEL_LM63_3SITE,
MODEL_CR72, MODEL_CR72_FULL, MODEL_IT99, MODEL_M61, MODEL_M61B, MODEL_DPL94,
MODEL_TP02, MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL,
MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL,
MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_R1RHO_2SITE]
"""The list of all dispersion models (excluding the R2eff model)."""
-MODEL_LIST_FULL = [MODEL_R2EFF, MODEL_NOREX, MODEL_LM63, MODEL_TSMFK01,
MODEL_LM63_3SITE, MODEL_CR72, MODEL_CR72_FULL, MODEL_IT99, MODEL_M61,
MODEL_DPL94, MODEL_M61B, MODEL_TP02, MODEL_NS_CPMG_2SITE_3D,
MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_STAR,
MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_CPMG_2SITE_EXPANDED,
MODEL_NS_R1RHO_2SITE]
+MODEL_LIST_FULL = [MODEL_R2EFF, MODEL_NOREX, MODEL_LM63, MODEL_TSMFK01,
MODEL_LM63_3SITE, MODEL_CR72, MODEL_CR72_FULL, MODEL_IT99, MODEL_M61,
MODEL_M61B, MODEL_DPL94, MODEL_TP02, MODEL_NS_CPMG_2SITE_3D,
MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_STAR,
MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_CPMG_2SITE_EXPANDED,
MODEL_NS_R1RHO_2SITE]
"""The list of the R2eff model together with all dispersion models."""
MODEL_LIST_CPMG = [MODEL_NOREX, MODEL_LM63, MODEL_TSMFK01, MODEL_LM63_3SITE,
MODEL_CR72, MODEL_CR72_FULL, MODEL_IT99, MODEL_NS_CPMG_2SITE_3D,
MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_STAR,
MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_CPMG_2SITE_EXPANDED]
@@ -108,8 +108,8 @@
MODEL_LIST_CPMG_FULL = [MODEL_R2EFF, MODEL_NOREX, MODEL_LM63, MODEL_TSMFK01,
MODEL_LM63_3SITE, MODEL_CR72, MODEL_CR72_FULL, MODEL_IT99,
MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL,
MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL,
MODEL_NS_CPMG_2SITE_EXPANDED]
"""The list of the R2eff model together with all dispersion models
specifically for CPMG-type experiments."""
-MODEL_LIST_R1RHO = [MODEL_NOREX, MODEL_M61, MODEL_DPL94, MODEL_M61B,
MODEL_TP02, MODEL_NS_R1RHO_2SITE]
+MODEL_LIST_R1RHO = [MODEL_NOREX, MODEL_M61, MODEL_M61B, MODEL_DPL94,
MODEL_TP02, MODEL_NS_R1RHO_2SITE]
"""The list of all dispersion models specifically for R1rho-type experiments
(excluding the R2eff model)."""
-MODEL_LIST_R1RHO_FULL = [MODEL_R2EFF, MODEL_NOREX, MODEL_M61, MODEL_DPL94,
MODEL_M61B, MODEL_TP02, MODEL_NS_R1RHO_2SITE]
+MODEL_LIST_R1RHO_FULL = [MODEL_R2EFF, MODEL_NOREX, MODEL_M61, MODEL_M61B,
MODEL_DPL94, MODEL_TP02, MODEL_NS_R1RHO_2SITE]
"""The list of the R2eff model together with all dispersion models
specifically for R1rho-type experiments."""
Modified: branches/relax_disp/target_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/target_functions/relax_disp.py?rev=20769&r1=20768&r2=20769&view=diff
==============================================================================
--- branches/relax_disp/target_functions/relax_disp.py (original)
+++ branches/relax_disp/target_functions/relax_disp.py Tue Sep 3 13:47:19
2013
@@ -221,12 +221,6 @@
self.func = self.func_CR72
if model == MODEL_IT99:
self.func = self.func_IT99
- if model == MODEL_M61:
- self.func = self.func_M61
- if model == MODEL_DPL94:
- self.func = self.func_DPL94
- if model == MODEL_M61B:
- self.func = self.func_M61b
if model == MODEL_NS_CPMG_2SITE_3D_FULL:
self.func = self.func_ns_cpmg_2site_3D_full
if model == MODEL_NS_CPMG_2SITE_3D:
@@ -237,6 +231,12 @@
self.func = self.func_ns_cpmg_2site_star_full
if model == MODEL_NS_CPMG_2SITE_STAR:
self.func = self.func_ns_cpmg_2site_star
+ if model == MODEL_M61:
+ self.func = self.func_M61
+ if model == MODEL_M61B:
+ self.func = self.func_M61b
+ if model == MODEL_DPL94:
+ self.func = self.func_DPL94
if model == MODEL_TP02:
self.func = self.func_TP02
if model == MODEL_NS_R1RHO_2SITE:
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=20769&r1=20768&r2=20769&view=diff
==============================================================================
--- branches/relax_disp/user_functions/relax_disp.py (original)
+++ branches/relax_disp/user_functions/relax_disp.py Tue Sep 3 13:47:19 2013
@@ -488,8 +488,8 @@
u"%s: {R\u2082A, R\u2082B, ..., pA, d\u03C9, k\u2091\u2093}" %
MODEL_NS_CPMG_2SITE_STAR_FULL,
u"%s: {R\u2082, ..., pA, d\u03C9, k\u2091\u2093}" %
MODEL_NS_CPMG_2SITE_EXPANDED,
u"%s: {R\u2081\u1D68', ..., \u03D5\u2091\u2093, k\u2091\u2093}" %
MODEL_M61,
+ u"%s: {R\u2081\u1D68', ..., pA, d\u03C9, k\u2091\u2093}" %
MODEL_M61B,
u"%s: {R\u2081\u1D68', ..., \u03D5\u2091\u2093, k\u2091\u2093}" %
MODEL_DPL94,
- u"%s: {R\u2081\u1D68', ..., pA, d\u03C9, k\u2091\u2093}" %
MODEL_M61B,
u"%s: {R\u2081\u1D68', ..., pA, d\u03C9, k\u2091\u2093}" %
MODEL_TP02,
u"%s: {R\u2082, ..., pA, d\u03C9, k\u2091\u2093}" %
MODEL_NS_R1RHO_2SITE
],
@@ -508,8 +508,8 @@
MODEL_NS_CPMG_2SITE_STAR_FULL,
MODEL_NS_CPMG_2SITE_EXPANDED,
MODEL_M61,
+ MODEL_M61B,
MODEL_DPL94,
- MODEL_M61B,
MODEL_TP02,
MODEL_NS_R1RHO_2SITE
],
@@ -533,8 +533,8 @@
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_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_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_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.
r20769 - in /branches/relax_disp: specific_analyses/relax_disp/ target_functions/ user_functions/