Author: bugman
Date: Fri Jul 12 12:31:02 2013
New Revision: 20283
URL: http://svn.gna.org/viewcvs/relax?rev=20283&view=rev
Log:
Better support for the R2A and R2B relaxation rate parameters in the
relaxation dispersion analysis.
This includes a number of fixes to allow these two parameters to be handled
correctly.
Modified:
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
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=20283&r1=20282&r2=20283&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/api.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/api.py Fri Jul 12
12:31:02 2013
@@ -82,6 +82,8 @@
self.PARAMS.add('r2eff', scope='spin', default=15.0, desc='The
effective transversal relaxation rate', set='params', py_type=dict,
grace_string='\\qR\\s2,eff\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True)
self.PARAMS.add('i0', scope='spin', default=10000.0, desc='The
initial intensity', py_type=dict, set='params', grace_string='\\qI\\s0\\Q',
err=True, sim=True)
self.PARAMS.add('r2', scope='spin', default=15.0, desc='The
transversal relaxation rate', set='params', py_type=list,
grace_string='\\qR\\s2\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True)
+ self.PARAMS.add('r2a', scope='spin', default=15.0, desc='The
transversal relaxation rate for state A in the absence of exchange',
set='params', py_type=list, grace_string='\\qR\\s2,A\\N\\Q (rad.s\\S-1\\N)',
err=True, sim=True)
+ self.PARAMS.add('r2b', scope='spin', default=15.0, desc='The
transversal relaxation rate for state B in the absence of exchange',
set='params', py_type=list, grace_string='\\qR\\s2,B\\N\\Q (rad.s\\S-1\\N)',
err=True, sim=True)
self.PARAMS.add('pA', scope='spin', default=0.5, desc='The
population for state A', set='params', py_type=float,
grace_string='\\qp\\sA\\N\\Q', err=True, sim=True)
self.PARAMS.add('pB', scope='spin', default=0.5, desc='The
population for state B', set='params', py_type=float,
grace_string='\\qp\\sB\\N\\Q', err=True, sim=True)
self.PARAMS.add('phi_ex', scope='spin', default=5.0, desc='The
phi_ex = pA.pB.dw**2 value (ppm^2)', set='params', py_type=float,
grace_string='\\xF\\B\\sex\\N = \\q p\\sA\\N.p\\sB\\N.\\xDw\\B\\S2\\N\\Q
(ppm\\S2\\N)', err=True, sim=True)
@@ -89,8 +91,6 @@
self.PARAMS.add('dw', scope='spin', default=0.0, desc='The chemical
shift difference between states A and B (in ppm)', set='params',
py_type=float, grace_string='\\q\\xDw\f{}\\Q (ppm)', err=True, sim=True)
self.PARAMS.add('kex', scope='spin', default=10000.0, desc='The
exchange rate', set='params', py_type=float, grace_string='\\qk\\sex\\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('r2a', scope='spin', default=15.0, desc='The
transversal relaxation rate for state A in the absence of exchange',
set='params', py_type=float, grace_string='\\qR\\s2,A\\N\\Q (rad.s\\S-1\\N)',
err=True, sim=True)
- self.PARAMS.add('r2b', scope='spin', default=15.0, desc='The
transversal relaxation rate for state B in the absence of exchange',
set='params', py_type=float, grace_string='\\qR\\s2,B\\N\\Q (rad.s\\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('params', scope='spin', desc='The model parameters',
py_type=list)
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=20283&r1=20282&r2=20283&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/parameters.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/parameters.py Fri Jul 12
12:31:02 2013
@@ -134,6 +134,7 @@
# Initialise parameters if needed.
for spin in spins:
+ # The R2 parameter.
if 'r2' in spin.params:
if sim_index != None:
spin.r2_sim[sim_index] = []
@@ -143,6 +144,28 @@
spin.r2 = []
for frq in loop_frq():
spin.r2.append(None)
+
+ # The R2A parameter.
+ if 'r2a' in spin.params:
+ if sim_index != None:
+ spin.r2a_sim[sim_index] = []
+ for frq in loop_frq():
+ spin.r2a_sim[sim_index].append(None)
+ else:
+ spin.r2a = []
+ for frq in loop_frq():
+ spin.r2a.append(None)
+
+ # The R2B parameter.
+ if 'r2b' in spin.params:
+ if sim_index != None:
+ spin.r2b_sim[sim_index] = []
+ for frq in loop_frq():
+ spin.r2b_sim[sim_index].append(None)
+ else:
+ spin.r2b = []
+ for frq in loop_frq():
+ spin.r2b.append(None)
# Loop over the parameters of the cluster, setting the values.
for param_name, param_index, spin_index, frq_index in
loop_parameters(spins=spins):
@@ -398,14 +421,38 @@
# Reset the frequency index.
frq_index = -1
- # Loop over the spectrometer frequencies.
- for frq in loop_frq():
- # First increment the indices.
- frq_index += 1
- param_index += 1
-
- # Yield the data.
- yield 'r2', param_index, spin_index, frq_index
+ # The R2 parameter.
+ if 'r2' in spins[0].params:
+ # Loop over the spectrometer frequencies.
+ for frq in loop_frq():
+ # First increment the indices.
+ frq_index += 1
+ param_index += 1
+
+ # Yield the data.
+ yield 'r2', param_index, spin_index, frq_index
+
+ # The R2A parameter.
+ if 'r2a' in spins[0].params:
+ # Loop over the spectrometer frequencies.
+ for frq in loop_frq():
+ # First increment the indices.
+ frq_index += 1
+ param_index += 1
+
+ # Yield the data.
+ yield 'r2a', param_index, spin_index, frq_index
+
+ # The R2B parameter.
+ if 'r2b' in spins[0].params:
+ # Loop over the spectrometer frequencies.
+ for frq in loop_frq():
+ # First increment the indices.
+ frq_index += 1
+ param_index += 1
+
+ # Yield the data.
+ yield 'r2b', param_index, spin_index, frq_index
# Then the chemical shift difference parameters 'phi_ex', 'padw2'
and 'dw' (one per spin).
for spin_index in range(len(spins)):
@@ -422,7 +469,7 @@
# All other parameters (one per spin cluster).
for param in spins[0].params:
- if not param in ['r2', 'phi_ex', 'padw2', 'dw']:
+ if not param in ['r2', 'r2a', 'r2b', 'phi_ex', 'padw2', 'dw']:
param_index += 1
yield param, param_index, None, None
@@ -508,7 +555,7 @@
raise RelaxError("The number of parameters for each spin in the
cluster are not the same.")
# Count the number of spin specific parameters for all spins.
- spin_params = ['r2', 'phi_ex', 'padw2', 'dw']
+ spin_params = ['r2', 'r2a', 'r2b', 'phi_ex', 'padw2', 'dw']
num = 0
for spin in spins:
for i in range(len(spin.params)):
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=20283&r1=20282&r2=20283&view=diff
==============================================================================
--- branches/relax_disp/target_functions/relax_disp.py (original)
+++ branches/relax_disp/target_functions/relax_disp.py Fri Jul 12 12:31:02
2013
@@ -118,11 +118,15 @@
# Create the structure for holding the back-calculated R2eff values
(matching the dimensions of the values structure).
self.back_calc = zeros((num_spins, num_frq, num_disp_points),
float64)
- # The post spin parameter indices.
+ # Initialise the post spin parameter indices.
self.end_index = []
+
+ # The spin and frequency dependent R2 parameters.
self.end_index.append(self.num_spins * self.num_frq)
if model == MODEL_NS_2SITE_STAR:
- self.end_index.append(self.num_spins * self.num_frq)
+ self.end_index.append(2 * self.num_spins * self.num_frq)
+
+ # The spin and dependent parameters (phi_ex, dw, padw2).
self.end_index.append(self.end_index[-1] + self.num_spins)
if model == MODEL_IT99:
self.end_index.append(self.end_index[-1] + self.num_spins)
r20283 - in /branches/relax_disp: specific_analyses/relax_disp/ target_functions/