Author: bugman
Date: Tue Sep 3 17:07:38 2013
New Revision: 20773
URL: http://svn.gna.org/viewcvs/relax?rev=20773&view=rev
Log:
Moved the ordering of the model TSMF. Ordering conventions mentioned in this
post: http://article.gmane.org/gmane.science.nmr.relax.devel/4500
Progress sr #3071: https://gna.org/support/index.php?3071 - Implementation of
Tollinger/Kay dispersion model (2001)
Following the guide at:
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax
Troels E. Linnet provided this patch. Commit by: tlinnet _aaattt_
gmail_dot_com
Signed-off-by: Edward d'Auvergne <edward@xxxxxxxxxxxxx>
Modified:
branches/relax_disp/lib/dispersion/__init__.py
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/lib/dispersion/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/dispersion/__init__.py?rev=20773&r1=20772&r2=20773&view=diff
==============================================================================
--- branches/relax_disp/lib/dispersion/__init__.py (original)
+++ branches/relax_disp/lib/dispersion/__init__.py Tue Sep 3 17:07:38 2013
@@ -27,7 +27,6 @@
'dpl94',
'it99',
'lm63',
- 'tsmfk01',
'lm63_3site',
'm61',
'm61b',
@@ -37,5 +36,6 @@
'ns_r1rho_2site',
'ns_matrices',
'tp02',
+ 'tsmfk01',
'two_point'
]
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=20773&r1=20772&r2=20773&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/api.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/api.py Tue Sep 3
17:07:38 2013
@@ -659,6 +659,48 @@
for frq in loop_frq():
params.append('r2')
+ # LM63 model.
+ elif model == MODEL_LM63:
+ print("The Luz and Meiboom (1963) 2-site fast exchange model.")
+ params = []
+ for frq in loop_frq():
+ params.append('r2')
+ params += ['phi_ex', 'kex']
+
+ # LM63 3-site model.
+ elif model == MODEL_LM63_3SITE:
+ print("The Luz and Meiboom (1963) 3-site fast exchange model.")
+ params = []
+ for frq in loop_frq():
+ params.append('r2')
+ params += ['phi_ex_B', 'phi_ex_C', 'kB', 'kC']
+
+ # Full CR72 model.
+ elif model == MODEL_CR72_FULL:
+ print("The full Carver and Richards (1972) 2-site model for all
time scales.")
+ params = []
+ for frq in loop_frq():
+ params.append('r2a')
+ for frq in loop_frq():
+ params.append('r2b')
+ params += ['pA', 'dw', 'kex']
+
+ # Reduced CR72 model.
+ elif model == MODEL_CR72:
+ print("The reduced Carver and Richards (1972) 2-site model for
all time scales, whereby the simplification R20A = R20B is assumed.")
+ params = []
+ for frq in loop_frq():
+ params.append('r2')
+ params += ['pA', 'dw', 'kex']
+
+ # IT99 model.
+ elif model == MODEL_IT99:
+ print("The Ishima and Torchia (1999) CPMG 2-site model for all
time scales with pA >> pB.")
+ params = []
+ for frq in loop_frq():
+ params.append('r2')
+ params += ['phi_ex', 'padw2', 'tex']
+
# TSMFK01 model.
elif model == MODEL_TSMFK01:
print("The Tollinger, Kay et al. (2001) 2-site very-slow
exchange model, range of microsecond to second time scale.")
@@ -666,48 +708,6 @@
for frq in loop_frq():
params.append('r2a')
params += ['dw', 'kA']
-
- # LM63 model.
- elif model == MODEL_LM63:
- print("The Luz and Meiboom (1963) 2-site fast exchange model.")
- params = []
- for frq in loop_frq():
- params.append('r2')
- params += ['phi_ex', 'kex']
-
- # LM63 3-site model.
- elif model == MODEL_LM63_3SITE:
- print("The Luz and Meiboom (1963) 3-site fast exchange model.")
- params = []
- for frq in loop_frq():
- params.append('r2')
- params += ['phi_ex_B', 'phi_ex_C', 'kB', 'kC']
-
- # Full CR72 model.
- elif model == MODEL_CR72_FULL:
- print("The full Carver and Richards (1972) 2-site model for all
time scales.")
- params = []
- for frq in loop_frq():
- params.append('r2a')
- for frq in loop_frq():
- params.append('r2b')
- params += ['pA', 'dw', 'kex']
-
- # Reduced CR72 model.
- elif model == MODEL_CR72:
- print("The reduced Carver and Richards (1972) 2-site model for
all time scales, whereby the simplification R20A = R20B is assumed.")
- params = []
- for frq in loop_frq():
- params.append('r2')
- params += ['pA', 'dw', 'kex']
-
- # IT99 model.
- elif model == MODEL_IT99:
- print("The Ishima and Torchia (1999) CPMG 2-site model for all
time scales with pA >> pB.")
- params = []
- for frq in loop_frq():
- params.append('r2')
- params += ['phi_ex', 'padw2', 'tex']
# Full NS CPMG 2-site 3D model.
elif model == MODEL_NS_CPMG_2SITE_3D_FULL:
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=20773&r1=20772&r2=20773&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/variables.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/variables.py Tue Sep 3
17:07:38 2013
@@ -47,9 +47,6 @@
MODEL_LM63 = 'LM63'
"""The CPMG 2-site fast exchange model of Luz and Meiboom (1963)."""
-MODEL_TSMFK01 = 'TSMFK01'
-"""The CPMG 2-site very-slow exchange model, range of microsecond to second
time scale, of M. Tollinger, N.R. Skrynnikov, F.A.A. Mulder, J.D.F. Kay and
L.E. Kay (2001)."""
-
MODEL_LM63_3SITE = 'LM63 3-site'
"""The CPMG 3-site fast exchange model of Luz and Meiboom (1963)."""
@@ -61,6 +58,9 @@
MODEL_IT99 = 'IT99'
"""The CPMG 2-site model for all time scales with pA >> pB of Ishima and
Torchia (1999)."""
+
+MODEL_TSMFK01 = 'TSMFK01'
+"""The CPMG 2-site very-slow exchange model, range of microsecond to second
time scale, of M. Tollinger, N.R. Skrynnikov, F.A.A. Mulder, J.D.F. Kay and
L.E. Kay (2001)."""
MODEL_M61 = 'M61'
"""The R1rho 2-site fast exchange model of Meiboom (1961)."""
@@ -96,16 +96,16 @@
# 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_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]
+MODEL_LIST_DISP = [MODEL_NOREX, MODEL_LM63, MODEL_LM63_3SITE, MODEL_CR72,
MODEL_CR72_FULL, MODEL_IT99, MODEL_TSMFK01, 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_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]
+MODEL_LIST_FULL = [MODEL_R2EFF, MODEL_NOREX, MODEL_LM63, MODEL_LM63_3SITE,
MODEL_CR72, MODEL_CR72_FULL, MODEL_IT99, MODEL_TSMFK01, 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]
+MODEL_LIST_CPMG = [MODEL_NOREX, MODEL_LM63, MODEL_LM63_3SITE, MODEL_CR72,
MODEL_CR72_FULL, MODEL_IT99, MODEL_TSMFK01, 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 all dispersion models specifically for CPMG-type experiments
(excluding the R2eff model)."""
-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]
+MODEL_LIST_CPMG_FULL = [MODEL_R2EFF, MODEL_NOREX, MODEL_LM63,
MODEL_LM63_3SITE, MODEL_CR72, MODEL_CR72_FULL, MODEL_IT99, MODEL_TSMFK01,
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_M61B, MODEL_DPL94,
MODEL_TP02, MODEL_NS_R1RHO_2SITE]
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=20773&r1=20772&r2=20773&view=diff
==============================================================================
--- branches/relax_disp/target_functions/relax_disp.py (original)
+++ branches/relax_disp/target_functions/relax_disp.py Tue Sep 3 17:07:38
2013
@@ -57,11 +57,11 @@
- 'No Rex': The model for no chemical exchange relaxation.
- 'LM63': The Luz and Meiboom (1963) 2-site fast exchange model.
- - 'TSMFK01': The Tollinger, Kay et al. (2001) 2-site very-slow
exchange model, range of microsecond to second time scale.
- 'LM63 3-site': The Luz and Meiboom (1963) 3-site fast
exchange model.
- 'CR72': The reduced Carver and Richards (1972) 2-site model
for all time scales with R20A = R20B.
- 'CR72 full': The full Carver and Richards (1972) 2-site model
for all time scales.
- 'IT99': The Ishima and Torchia (1999) 2-site model for all
time scales with skewed populations (pA >> pB).
+ - 'TSMFK01': The Tollinger, Kay et al. (2001) 2-site very-slow
exchange model, range of microsecond to second time scale.
- 'M61': The Meiboom (1961) 2-site fast exchange model for
R1rho-type experiments.
- 'DPL94': The Davis, Perlman and London (1994) 2-site fast
exchange model for R1rho-type experiments.
- 'M61 skew': The Meiboom (1961) on-resonance 2-site model with
skewed populations (pA >> pB) for R1rho-type experiments.
@@ -211,8 +211,6 @@
self.func = self.func_NOREX
if model == MODEL_LM63:
self.func = self.func_LM63
- if model == MODEL_TSMFK01:
- self.func = self.func_TSMFK01
if model == MODEL_LM63_3SITE:
self.func = self.func_LM63_3site
if model == MODEL_CR72_FULL:
@@ -221,6 +219,8 @@
self.func = self.func_CR72
if model == MODEL_IT99:
self.func = self.func_IT99
+ if model == MODEL_TSMFK01:
+ self.func = self.func_TSMFK01
if model == MODEL_NS_CPMG_2SITE_3D_FULL:
self.func = self.func_ns_cpmg_2site_3D_full
if model == MODEL_NS_CPMG_2SITE_3D:
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=20773&r1=20772&r2=20773&view=diff
==============================================================================
--- branches/relax_disp/user_functions/relax_disp.py (original)
+++ branches/relax_disp/user_functions/relax_disp.py Tue Sep 3 17:07:38 2013
@@ -40,7 +40,7 @@
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 MODEL_CR72,
MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LM63, MODEL_TSMFK01,
MODEL_LM63_3SITE, MODEL_M61, MODEL_M61B, MODEL_NOREX, MODEL_R2EFF,
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_R1RHO_2SITE, MODEL_TP02
+from specific_analyses.relax_disp.variables import MODEL_CR72,
MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LM63, MODEL_LM63_3SITE,
MODEL_M61, MODEL_M61B, MODEL_NOREX, MODEL_R2EFF, 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_R1RHO_2SITE, MODEL_TP02, MODEL_TSMFK01
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
@@ -477,11 +477,11 @@
u"%s: {R\u2082eff/R\u2081\u1D68, I\u2080}" % MODEL_R2EFF,
u"%s: {R\u2082, ...}" % MODEL_NOREX,
u"%s: {R\u2082, ..., \u03D5\u2091\u2093, k\u2091\u2093}" %
MODEL_LM63,
- u"%s: {R\u2082A, ..., d\u03C9, kA}" % MODEL_TSMFK01,
u"%s: {R\u2082, ..., \u03D5\u2091\u2093B, kB, \u03D5\u2091\u2093C,
kC}" % MODEL_LM63_3SITE,
u"%s: {R\u2082, ..., pA, d\u03C9, k\u2091\u2093}" % MODEL_CR72,
u"%s: {R\u2082A, R\u2082B, ..., pA, d\u03C9, k\u2091\u2093}" %
MODEL_CR72_FULL,
u"%s: {R\u2082, ..., \u03D5\u2091\u2093, pA.d\u03C9\u00B2,
k\u2091\u2093}" % MODEL_IT99,
+ u"%s: {R\u2082A, ..., d\u03C9, kA}" % MODEL_TSMFK01,
u"%s: {R\u2082, ..., pA, d\u03C9, k\u2091\u2093}" %
MODEL_NS_CPMG_2SITE_3D,
u"%s: {R\u2082A, R\u2082B, ..., pA, d\u03C9, k\u2091\u2093}" %
MODEL_NS_CPMG_2SITE_3D_FULL,
u"%s: {R\u2082, ..., pA, d\u03C9, k\u2091\u2093}" %
MODEL_NS_CPMG_2SITE_STAR,
@@ -497,11 +497,11 @@
MODEL_R2EFF,
MODEL_NOREX,
MODEL_LM63,
- MODEL_TSMFK01,
MODEL_LM63_3SITE,
MODEL_CR72,
MODEL_CR72_FULL,
MODEL_IT99,
+ MODEL_TSMFK01,
MODEL_NS_CPMG_2SITE_3D,
MODEL_NS_CPMG_2SITE_3D_FULL,
MODEL_NS_CPMG_2SITE_STAR,
@@ -524,11 +524,11 @@
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_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_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| << kA,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, kA}.")
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_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| << kA,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, kA}.")
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,")
r20773 - in /branches/relax_disp: lib/dispersion/ specific_analyses/relax_disp/ target_functions/ user_functions/