Author: bugman
Date: Sat Nov 16 17:12:38 2013
New Revision: 21462
URL: http://svn.gna.org/viewcvs/relax?rev=21462&view=rev
Log:
Created the 'MP05' model target function.
This is the Miloushev and Palmer 2005 R1rho analytic model for 2-site
off-resonance exchange.
This follows the tutorial for adding relaxation dispersion models at:
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_target_function
Modified:
branches/relax_disp/target_functions/relax_disp.py
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=21462&r1=21461&r2=21462&view=diff
==============================================================================
--- branches/relax_disp/target_functions/relax_disp.py (original)
+++ branches/relax_disp/target_functions/relax_disp.py Sat Nov 16 17:12:38
2013
@@ -36,6 +36,7 @@
from lib.dispersion.lm63_3site import r2eff_LM63_3site
from lib.dispersion.m61 import r1rho_M61
from lib.dispersion.m61b import r1rho_M61b
+from lib.dispersion.mp05 import r1rho_MP05
from lib.dispersion.mq_cr72 import r2eff_mq_cr72
from lib.dispersion.mmq_2site import r2eff_mmq_2site
from lib.dispersion.ns_cpmg_2site_3d import r2eff_ns_cpmg_2site_3D
@@ -47,7 +48,7 @@
from lib.dispersion.tsmfk01 import r2eff_TSMFK01
from lib.errors import RelaxError
from target_functions.chi2 import chi2
-from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG,
EXP_TYPE_MQ_CPMG, EXP_TYPE_MQ_R1RHO, EXP_TYPE_R1RHO, MODEL_CR72,
MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LIST_CPMG,
MODEL_LIST_CPMG_NUM, MODEL_LIST_FULL, MODEL_LIST_MQ_CPMG,
MODEL_LIST_MQ_R1RHO, MODEL_LIST_R1RHO, MODEL_LM63, MODEL_LM63_3SITE,
MODEL_M61, MODEL_M61B, MODEL_MMQ_2SITE, MODEL_MQ_CR72, MODEL_NOREX,
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_R2EFF, MODEL_TP02,
MODEL_TSMFK01
+from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG,
EXP_TYPE_MQ_CPMG, EXP_TYPE_MQ_R1RHO, EXP_TYPE_R1RHO, MODEL_CR72,
MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LIST_CPMG,
MODEL_LIST_CPMG_NUM, MODEL_LIST_FULL, MODEL_LIST_MQ_CPMG,
MODEL_LIST_MQ_R1RHO, MODEL_LIST_R1RHO, MODEL_LM63, MODEL_LM63_3SITE,
MODEL_M61, MODEL_M61B, MODEL_MMQ_2SITE, MODEL_MP05, MODEL_MQ_CR72,
MODEL_NOREX, 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_R2EFF, MODEL_TP02,
MODEL_TSMFK01
class Dispersion:
@@ -70,6 +71,7 @@
- '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.
- 'TP02': The Trott and Palmer (2002) 2-site exchange model for
R1rho-type experiments.
+ - 'MP05': The Miloushev and Palmer (2005) off-resonance 2-site
exchange model for R1rho-type experiments.
The following numerical models are currently supported:
@@ -126,7 +128,7 @@
raise RelaxError("No errors have been supplied to the target
function.")
if missing == None:
raise RelaxError("No missing data information has been supplied
to the target function.")
- if model in [MODEL_DPL94, MODEL_TP02]:
+ if model in [MODEL_DPL94, MODEL_TP02, MODEL_MP05]:
if chemical_shifts == None:
raise RelaxError("Chemical shifts must be supplied for the
'%s' R1rho off-resonance dispersion model." % model)
if r1 == None:
@@ -298,6 +300,8 @@
self.func = self.func_DPL94
if model == MODEL_TP02:
self.func = self.func_TP02
+ if model == MODEL_MP05:
+ self.func = self.func_MP05
if model == MODEL_NS_R1RHO_2SITE:
self.func = self.func_ns_r1rho_2site
if model == MODEL_MQ_CR72:
@@ -837,6 +841,56 @@
return chi2_sum
+ def func_MP05(self, params):
+ """Target function for the Miloushev and Palmer (2005) R1rho
off-resonance 2-site model.
+
+ @param params: The vector of parameter values.
+ @type params: numpy rank-1 float array
+ @return: The chi-squared value.
+ @rtype: float
+ """
+
+ # Scaling.
+ if self.scaling_flag:
+ params = dot(params, self.scaling_matrix)
+
+ # Unpack the parameter values.
+ R20 = params[:self.end_index[0]]
+ dw = params[self.end_index[0]:self.end_index[1]]
+ pA = params[self.end_index[1]]
+ kex = params[self.end_index[1]+1]
+
+ # Once off parameter conversions.
+ pB = 1.0 - pA
+
+ # Initialise.
+ chi2_sum = 0.0
+
+ # Loop over the spins.
+ for spin_index in range(self.num_spins):
+ # Loop over the spectrometer frequencies.
+ for frq_index in range(self.num_frq):
+ # The R20 index.
+ r20_index = frq_index + spin_index*self.num_frq
+
+ # Convert dw from ppm to rad/s.
+ dw_frq = dw[spin_index] * self.frqs[spin_index, frq_index]
+
+ # Back calculate the R1rho values.
+ r1rho_MP05(r1rho_prime=R20[r20_index],
omega=self.chemical_shifts[spin_index, frq_index],
offset=self.spin_lock_offsets[spin_index, frq_index], pA=pA, pB=pB,
dw=dw_frq, kex=kex, R1=self.r1[spin_index, frq_index],
spin_lock_fields=self.spin_lock_omega1[0][frq_index],
spin_lock_fields2=self.spin_lock_omega1_squared[0][frq_index],
back_calc=self.back_calc[spin_index][frq_index],
num_points=self.num_disp_points[0][frq_index])
+
+ # 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[0][frq_index]):
+ 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
+
+
def func_mmq_2site(self, params):
"""Target function for the combined SQ, ZQ, DQ and MQ CPMG numeric
solution.
r21462 - /branches/relax_disp/target_functions/relax_disp.py