Author: bugman
Date: Thu Apr 4 09:21:19 2013
New Revision: 19341
URL: http://svn.gna.org/viewcvs/relax?rev=19341&view=rev
Log:
Fixes for the dispersion specific analysis separating R2eff from R2.
There is one R2eff parameter per exponential curve, but only one R2 per
model. The code now better
handles this.
Modified:
branches/relax_disp/specific_analyses/relax_disp.py
Modified: branches/relax_disp/specific_analyses/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp.py?rev=19341&r1=19340&r2=19341&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp.py Thu Apr 4 09:21:19
2013
@@ -69,8 +69,9 @@
self.PARAMS.add('intensities', scope='spin', py_type=dict,
grace_string='\\qPeak intensities\\Q')
self.PARAMS.add('relax_times', scope='spin', py_type=dict,
grace_string='\\qRelaxation time period (s)\\Q')
self.PARAMS.add('cpmg_frqs', scope='spin', py_type=dict,
grace_string='\\qCPMG pulse train frequency (Hz)\\Q')
- self.PARAMS.add('r2', scope='spin', default=15.0, desc='The
effective transversal relaxation rate', set='params', py_type=dict,
grace_string='\\qR\\s2\\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=float, set='params', grace_string='\\qI\\s0\\Q',
err=True, sim=True)
+ 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=float,
grace_string='\\qR\\s2\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True)
self.PARAMS.add('rex', scope='spin', default=5.0, desc='The chemical
exchange contribution to R2', set='params', py_type=float,
grace_string='\\qR\\sex\\N\\Q (rad.s\\S-1\\N)', 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('r2a', scope='spin', default=15.0, desc='The
transversal relaxation rate for state A', set='params', py_type=float,
grace_string='\\qR\\s2,A\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True)
@@ -103,14 +104,14 @@
# Loop over the model parameters.
for i in range(len(spin.params)):
- # Transversal relaxation rate.
- if spin.params[i] == 'R2':
+ # Effective transversal relaxation rate.
+ if spin.params[i] == 'R2eff':
if sim_index != None:
- param_vector.append(spin.r2_sim[sim_index])
- elif spin.r2 == None:
+ param_vector.append(spin.r2eff_sim[sim_index])
+ elif spin.r2eff == None:
param_vector.append(0.0)
else:
- param_vector.append(spin.r2)
+ param_vector.append(spin.r2eff)
# Initial intensity.
elif spin.params[i] == 'I0':
@@ -124,6 +125,15 @@
# Then the spin block specific parameters, taking the values from
the first spin.
spin = spins[0]
for i in range(len(spin.params)):
+ # Transversal relaxation rate.
+ if spin.params[i] == 'R2':
+ if sim_index != None:
+ param_vector.append(spin.r2_sim[sim_index])
+ elif spin.r2 == None:
+ param_vector.append(0.0)
+ else:
+ param_vector.append(spin.r2)
+
# Chemical exchange contribution to 'R2'.
if spin.params[i] == 'Rex':
if sim_index != None:
@@ -198,7 +208,7 @@
# Alias the spin.
spin = spins[spin_index]
- # Transversal relaxation rate scaling.
+ # Effective transversal relaxation rate scaling.
scaling_matrix[param_index, param_index] = 1e-1
param_index += 1
@@ -209,8 +219,12 @@
# Then the spin block specific parameters.
spin = spins[0]
for i in range(len(spin.params)):
+ # Transversal relaxation rate scaling.
+ if spin.params[i] == 'R2':
+ scaling_matrix[param_index, param_index] = 1e-1
+
# Chemical exchange contribution to 'R2' scaling.
- if spin.params[i] == 'Rex':
+ elif spin.params[i] == 'Rex':
scaling_matrix[param_index, param_index] = 1e-1
# Exchange rate scaling.
@@ -525,8 +539,8 @@
# Loop over the parameters.
for i in range(len(spin.params)):
- # Relaxation rate (from 0 to 40 s^-1).
- if spin.params[i] == 'R2':
+ # R2eff relaxation rate (from 0 to 40 s^-1).
+ if spin.params[i] == 'R2eff':
min_options.append([inc[j], 0.0, 40.0])
# Intensity.
@@ -539,8 +553,12 @@
# Then the spin block specific parameters.
spin = spins[0]
for i in range(len(spin.params)):
+ # R2 relaxation rate (from 0 to 40 s^-1).
+ if spin.params[i] == 'R2':
+ min_options.append([inc[j], 0.0, 40.0])
+
# Chemical exchange contribution to 'R2'.
- if spin.params[i] == 'Rex':
+ elif spin.params[i] == 'Rex':
min_options.append([inc[j], 0.0, 20.0])
# Exchange rate.
@@ -653,8 +671,15 @@
# Then the spin block specific parameters.
spin = spins[0]
for k in range(len(spin.params)):
+ # The transversal relaxation rate >= 0.
+ if spin.params[k] == 'R2':
+ A.append(zero_array * 0.0)
+ A[j][i] = 1.0
+ b.append(0.0)
+ j += 1
+
# Relaxation rates and Rex.
- if search('^R', spin.params[k]):
+ elif search('^R', spin.params[k]):
# Rex, R2A >= 0.
A.append(zero_array * 0.0)
A[j][i] = 1.0
@@ -723,7 +748,7 @@
@rtype: int
"""
- # The number of spin specific parameters (R2 and I0 per spin), times
the total number of exponential curves.
+ # The number of spin specific parameters (R2eff and I0 per spin),
times the total number of exponential curves.
num = len(spins) * 2 * cdp.curve_count
# The block specific parameters.
@@ -783,17 +808,17 @@
# Fast-exchange regime.
if model == 'exp_fit':
print("Basic exponential curve-fitting.")
- params = ['R2', 'I0']
+ params = ['R2eff', 'I0']
# Fast-exchange regime.
elif model == 'fast 2-site':
print("2-site fast-exchange.")
- params = ['R2', 'I0', 'Rex', 'kex']
+ params = ['R2eff', 'I0', 'R2', 'Rex', 'kex']
# Slow-exchange regime.
elif model == 'slow 2-site':
print("2-site slow-exchange.")
- params = ['R2', 'I0', 'R2A', 'kA', 'dw']
+ params = ['R2eff', 'I0', 'R2', 'R2A', 'kA', 'dw']
# Invalid model.
else:
r19341 - /branches/relax_disp/specific_analyses/relax_disp.py