Author: bugman
Date: Fri Sep 6 16:12:15 2013
New Revision: 20905
URL: http://svn.gna.org/viewcvs/relax?rev=20905&view=rev
Log:
Converted references of ka and kA to k_AB.
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/tsmfk01.py
branches/relax_disp/specific_analyses/relax_disp/api.py
branches/relax_disp/specific_analyses/relax_disp/parameters.py
branches/relax_disp/target_functions/relax_disp.py
branches/relax_disp/test_suite/system_tests/relax_disp.py
branches/relax_disp/user_functions/relax_disp.py
Modified: branches/relax_disp/lib/dispersion/tsmfk01.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/dispersion/tsmfk01.py?rev=20905&r1=20904&r2=20905&view=diff
==============================================================================
--- branches/relax_disp/lib/dispersion/tsmfk01.py (original)
+++ branches/relax_disp/lib/dispersion/tsmfk01.py Fri Sep 6 16:12:15 2013
@@ -23,7 +23,7 @@
# Module docstring.
"""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-R2bj| << kA,kB <<
1/tau_CP. R20A is the transverse relaxation rate of site A in the absence of
exchange.
+Applicable in the limit of slow exchange, when |R2A-R2B| << 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.
This module is for the function, gradient and Hessian of the TSMFK01 model.
The model is named after the reference:
@@ -32,22 +32,22 @@
The equation used is::
- sin(delta_omega * tau_CP)
- R2Aeff = R20A + kA - kA * ------------------------- ,
- delta_omega * tau_CP
+ sin(delta_omega * tau_CP)
+ R2Aeff = R20A + k_AB - k_AB * ------------------------- ,
+ delta_omega * tau_CP
where::
tau_CP = 1.0/(4*nu_cpmg) ,
-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, kA is the forward
chemical exchange rate constant, delta_omega is the chemical shift difference
between the two states.
+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, k_AB is the
forward chemical exchange rate constant, delta_omega is the chemical shift
difference between the two states.
"""
# Python module imports.
from math import sin
-def r2eff_TSMFK01(r20a=None, dw=None, kA=None, cpmg_frqs=None,
back_calc=None, num_points=None):
+def r2eff_TSMFK01(r20a=None, dw=None, k_AB=None, cpmg_frqs=None,
back_calc=None, num_points=None):
"""Calculate the R2eff values for the TSMFK01 model.
See the module docstring for details.
@@ -57,8 +57,8 @@
@type r20a: float
@keyword dw: The chemical exchange difference between states
A and B in rad/s.
@type dw: float
- @keyword kA: The kA parameter value (the forward exchange
rate in rad/s).
- @type kA: float
+ @keyword k_AB: The k_AB parameter value (the forward exchange
rate in rad/s).
+ @type k_AB: float
@keyword cpmg_frqs: The CPMG nu1 frequencies.
@type cpmg_frqs: numpy rank-1 float array
@keyword back_calc: The array for holding the back calculated R2eff
values. Each element corresponds to one of the CPMG nu1 frequencies.
@@ -82,7 +82,7 @@
# Catch zeros (to avoid pointless mathematical operations).
if numer == 0.0:
- back_calc[i] = r20a + kA
+ back_calc[i] = r20a + k_AB
continue
# Denominator.
@@ -95,4 +95,4 @@
# The full formula.
else:
- back_calc[i] = r20a + kA - kA * numer / denom
+ back_calc[i] = r20a + k_AB - k_AB * numer / denom
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=20905&r1=20904&r2=20905&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/api.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/api.py Fri Sep 6
16:12:15 2013
@@ -96,7 +96,7 @@
self.PARAMS.add('kB', scope='spin', default=10000.0,
desc='Approximate chemical exchange rate constant between sites A and B
(rad.s^-1)', set='params', py_type=float, grace_string='\\qk\\sB\\N\\Q
(rad.s\\S-1\\N)', err=True, sim=True)
self.PARAMS.add('kC', scope='spin', default=10000.0,
desc='Approximate chemical exchange rate constant between sites A and C
(rad.s^-1)', set='params', py_type=float, grace_string='\\qk\\sC\\N\\Q
(rad.s\\S-1\\N)', err=True, sim=True)
self.PARAMS.add('tex', scope='spin', default=1.0/20000.0, desc='The
time of exchange (tex = 1/(2kex))', set='params', py_type=float,
grace_string='\\q\\xt\\B\\sex\\N\\Q (s.rad\\S-1\\N)', err=True, sim=True)
- self.PARAMS.add('kA', scope='spin', default=10000.0, desc='The
exchange rate from state A to state B', set='params', py_type=float,
grace_string='\\qk\\sA\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True)
+ self.PARAMS.add('k_AB', scope='spin', default=10000.0, desc='The
exchange rate from state A to state B', set='params', py_type=float,
grace_string='\\qk\\sA\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True)
self.PARAMS.add('params', scope='spin', desc='The model parameters',
py_type=list)
# Add the minimisation data.
@@ -382,7 +382,7 @@
upper.append(1.0)
# Exchange rates.
- elif spin.params[i] in ['kex', 'kA', 'kB', 'kC']:
+ elif spin.params[i] in ['kex', 'k_AB', 'kB', 'kC']:
lower.append(1.0)
upper.append(100000.0)
@@ -675,7 +675,7 @@
params = []
for frq in loop_frq():
params.append('r2a')
- params += ['dw', 'kA']
+ params += ['dw', 'k_AB']
# Full NS CPMG 2-site 3D model.
elif model == MODEL_NS_CPMG_2SITE_3D_FULL:
@@ -1382,7 +1382,7 @@
_table.add_row(["The pA.dw**2 parameter (ppm^2)", "'padw2'"])
_table.add_row(["Chemical shift difference between states A and B
(ppm)", "'dw'"])
_table.add_row(["Exchange rate (rad/s)", "'kex'"])
- _table.add_row(["Exchange rate from state A to state B (rad/s)", "'kA'"])
+ _table.add_row(["Exchange rate from state A to state B (rad/s)",
"'k_AB'"])
_table.add_row(["Time of exchange (s/rad)", "'tex'"])
_table.add_row(["Peak intensities (series)", "'intensities'"])
_table.add_row(["CPMG pulse train frequency (series, Hz)",
"'cpmg_frqs'"])
@@ -1421,7 +1421,7 @@
set_doc = Desc_container("Relaxation dispersion curve fitting set
details")
- set_doc.add_paragraph("Only three parameters can be set for either the
slow- or the fast-exchange regime. For the slow-exchange regime, these
parameters include the transversal relaxation rate for state A (R2A), the
exchange rate from state A to state (kA) and the chemical shift difference
between states A and B (dw). For the fast-exchange regime, these include the
transversal relaxation rate (R2), the chemical exchange contribution to R2
(Rex) and the exchange rate (kex). Setting parameters for a non selected
model has no effect.")
+ set_doc.add_paragraph("Only three parameters can be set for either the
slow- or the fast-exchange regime. For the slow-exchange regime, these
parameters include the transversal relaxation rate for state A (R2A), the
exchange rate from state A to state (k_AB) and the chemical shift difference
between states A and B (dw). For the fast-exchange regime, these include the
transversal relaxation rate (R2), the chemical exchange contribution to R2
(Rex) and the exchange rate (kex). Setting parameters for a non selected
model has no effect.")
def set_error(self, model_info, index, error):
Modified: branches/relax_disp/specific_analyses/relax_disp/parameters.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/parameters.py?rev=20905&r1=20904&r2=20905&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/parameters.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/parameters.py Fri Sep 6
16:12:15 2013
@@ -113,7 +113,7 @@
scaling_matrix[param_index, param_index] = 1
# Exchange rate scaling.
- elif param_name in ['kex', 'ka', 'kB', 'kC']:
+ elif param_name in ['kex', 'k_AB', 'kB', 'kC']:
scaling_matrix[param_index, param_index] = 10000
# Time of exchange scaling.
@@ -423,7 +423,7 @@
0 <= kB <= 2e6
0 <= kC <= 2e6
tex >= 0
- kA >= 0
+ k_AB >= 0
Matrix notation
@@ -473,7 +473,7 @@
| | | | | |
| 1 0 0 | | tex | | 0 |
| | | | | |
- | 1 0 0 | | kA | | 0 |
+ | 1 0 0 | | k_AB | | 0 |
@keyword spins: The list of spin data containers for the
block.
@@ -555,7 +555,7 @@
j += 1
# Exchange rates and times (0 <= k <= 2e6).
- elif param_name in ['kex', 'ka', 'kB', 'kC']:
+ elif param_name in ['kex', 'k_AB', 'kB', 'kC']:
A.append(zero_array * 0.0)
A.append(zero_array * 0.0)
A[j][param_index] = 1.0
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=20905&r1=20904&r2=20905&view=diff
==============================================================================
--- branches/relax_disp/target_functions/relax_disp.py (original)
+++ branches/relax_disp/target_functions/relax_disp.py Fri Sep 6 16:12:15
2013
@@ -1084,7 +1084,7 @@
# Unpack the parameter values.
R20A = params[:self.end_index[0]]
dw = params[self.end_index[0]:self.end_index[1]]
- kA = params[self.end_index[1]]
+ k_AB = params[self.end_index[1]]
# Initialise.
chi2_sum = 0.0
@@ -1100,15 +1100,15 @@
dw_frq = dw[spin_index] * self.frqs[spin_index, frq_index]
# Back calculate the R2eff values.
- r2eff_TSMFK01(r20a=R20A[r20a_index], dw=dw_frq, kA=kA,
cpmg_frqs=self.cpmg_frqs, back_calc=self.back_calc[spin_index, frq_index],
num_points=self.num_disp_points)
-
- # For all missing data points, set the back-calculated value
to the measured values so that it has no effect on the chi-squared value.
- for point_index in range(self.num_disp_points):
- if self.missing[spin_index, frq_index, point_index]:
- self.back_calc[spin_index, frq_index, point_index] =
self.values[spin_index, frq_index, point_index]
-
- # Calculate and return the chi-squared value.
- chi2_sum += chi2(self.values[spin_index, frq_index],
self.back_calc[spin_index, frq_index], self.errors[spin_index, frq_index])
-
- # Return the total chi-squared value.
- return chi2_sum
+ r2eff_TSMFK01(r20a=R20A[r20a_index], dw=dw_frq, k_AB=k_AB,
cpmg_frqs=self.cpmg_frqs, back_calc=self.back_calc[spin_index, frq_index],
num_points=self.num_disp_points)
+
+ # For all missing data points, set the back-calculated value
to the measured values so that it has no effect on the chi-squared value.
+ for point_index in range(self.num_disp_points):
+ if self.missing[spin_index, frq_index, point_index]:
+ self.back_calc[spin_index, frq_index, point_index] =
self.values[spin_index, frq_index, point_index]
+
+ # Calculate and return the chi-squared value.
+ chi2_sum += chi2(self.values[spin_index, frq_index],
self.back_calc[spin_index, frq_index], self.errors[spin_index, frq_index])
+
+ # Return the total chi-squared value.
+ return chi2_sum
Modified: branches/relax_disp/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/relax_disp.py?rev=20905&r1=20904&r2=20905&view=diff
==============================================================================
--- branches/relax_disp/test_suite/system_tests/relax_disp.py (original)
+++ branches/relax_disp/test_suite/system_tests/relax_disp.py Fri Sep 6
16:12:15 2013
@@ -250,7 +250,7 @@
]
# List of parameters which do not belong to the model.
- blacklist = ['cpmg_frqs', 'r2', 'rex', 'kex', 'r2a', 'ka', 'dw']
+ blacklist = ['cpmg_frqs', 'r2', 'rex', 'kex', 'r2a', 'k_AB', 'dw']
# Checks for each residue.
for i in range(len(res_data)):
@@ -1066,11 +1066,11 @@
{Representative 15N CPMG relaxation dispersion curve measured on the
cross peaks from residue L61 in folded ACBP at pH 5.3, 1 M GuHCl, and 40C.}
1. The dotted line represents a residue-specific fit of all
parameters in Eq. 1.
- - ka = 11.3 +/- 0.7 s^{-1}
+ - k_AB = 11.3 +/- 0.7 s^{-1}
- dw = (2.45 +/- 0.09) * 10^3 s^{-1}
- R2 = 8.0 +/- 0.5 s^{-1}.
- 2. The solid line represents a global fit of ka to all protein
residues and a residue-specific fit of dw and R2.}
- -.ka = 10.55 +/- 0.08 s^{-1}
+ 2. The solid line represents a global fit of k_AB to all protein
residues and a residue-specific fit of dw and R2.}
+ -.k_AB = 10.55 +/- 0.08 s^{-1}
- dw = (2.44 +/- 0.08) * 10^3 s^{-1}
- R2 = 8.4 +/- 0.3 s^{-1}.
@@ -1089,7 +1089,7 @@
# Set the initial parameter values.
res61L.r2a = [8]
res61L.dw = 6.5
- res61L.kA = 11.0
+ res61L.k_AB = 11.0
# Low precision optimisation.
self.interpreter.minimise(min_algor='simplex', line_search=None,
hessian_mod=None, hessian_type=None, func_tol=1e-05, grad_tol=None,
max_iter=1000, constraints=True, scaling=True, verbosity=1)
@@ -1099,14 +1099,14 @@
print("%-20s %-20s" % ("Parameter", "Value (:61)"))
print("%-20s %20.15g" % ("R2A (600 MHz)", res61L.r2a[0]))
print("%-20s %20.15g" % ("dw", res61L.dw))
- print("%-20s %20.15g" % ("kA", res61L.kA))
+ print("%-20s %20.15g" % ("k_AB", res61L.k_AB))
print("%-20s %20.15g\n" % ("chi2", res61L.chi2))
# Checks for residue :61. Reference values from paper
self.assertAlmostEqual(res61L.r2a[0], 8.4, -1)
self.assertAlmostEqual(res61L.dw, 6.41, 2)
- self.assertAlmostEqual(res61L.kA, 10.55, 0)
+ self.assertAlmostEqual(res61L.k_AB, 10.55, 0)
self.assertAlmostEqual(res61L.chi2, 60.0, 5)
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=20905&r1=20904&r2=20905&view=diff
==============================================================================
--- branches/relax_disp/user_functions/relax_disp.py (original)
+++ branches/relax_disp/user_functions/relax_disp.py Fri Sep 6 16:12:15 2013
@@ -469,7 +469,7 @@
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\u2082A, ..., d\u03C9, k_AB}") % 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,
@@ -516,7 +516,7 @@
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_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,")
r20905 - in /branches/relax_disp: lib/dispersion/ specific_analyses/relax_disp/ target_functions/ test_suite/system_tests/ u...