Author: bugman
Date: Mon Jun 10 15:39:03 2013
New Revision: 20012
URL: http://svn.gna.org/viewcvs/relax?rev=20012&view=rev
Log:
Added the support for the pA.dw^2 parameter 'padw2' to the dispersion
specific analysis.
This is needed for the Ishima and Torchia 1999 2-site model for all
timescales with pA >> pB.
This commit follows step 5 of the relaxation dispersion model addition
tutorial
(http://thread.gmane.org/gmane.science.nmr.relax.devel/3907).
Modified:
branches/relax_disp/specific_analyses/relax_disp/__init__.py
branches/relax_disp/specific_analyses/relax_disp/parameters.py
Modified: branches/relax_disp/specific_analyses/relax_disp/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/__init__.py?rev=20012&r1=20011&r2=20012&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/__init__.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/__init__.py Mon Jun 10
15:39:03 2013
@@ -97,6 +97,7 @@
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)
+ self.PARAMS.add('padw2', scope='spin', default=1.0, desc='The
pA.dw**2 value (ppm^2)', set='params', py_type=float,
grace_string='\\qp\\sA\\N.\\xDw\\B\\S2\\N\\Q (ppm\\S2\\N)', err=True,
sim=True)
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('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)
@@ -385,8 +386,8 @@
lower.append(1.0)
upper.append(40.0)
- # The pA.pB.dw**2 parameter.
- elif spin.params[i] == 'phi_ex':
+ # The pA.pB.dw**2 and pA.dw**2 parameters.
+ elif spin.params[i] in ['phi_ex', 'padw2']:
lower.append(0.0)
upper.append(10.0)
@@ -1571,6 +1572,7 @@
_table.add_row(["Population of state A", "'pA'"])
_table.add_row(["Population of state B", "'pB'"])
_table.add_row(["The pA.pB.dw**2 parameter (ppm^2)", "'phi_ex'"])
+ _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'"])
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=20012&r1=20011&r2=20012&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/parameters.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/parameters.py Mon Jun 10
15:39:03 2013
@@ -136,8 +136,8 @@
if param_name == 'r2':
scaling_matrix[param_index, param_index] = 10
- # The pA.pB.dw**2 parameter.
- elif param_name == 'phi_ex':
+ # The pA.pB.dw**2 and pA.dw**2 parameters.
+ elif param_name in ['phi_ex', 'padw2']:
scaling_matrix[param_index, param_index] = 1
# Chemical shift difference between states A and B scaling.
@@ -254,6 +254,7 @@
pB <= pA <= 1
pA >= 0.85 (the skewed condition, pA >> pB)
phi_ex >= 0
+ padw2 >= 0
dw >= 0
kex >= 0
kA >= 0
@@ -277,6 +278,8 @@
| 1 0 0 | | pA | | 0.85 |
| | | | | |
| 1 0 0 | | phi_ex | | 0 |
+ | | | | | |
+ | 1 0 0 | | padw2 | | 0 |
| | | | | |
| 1 0 0 | | dw | | 0 |
| | | | | |
@@ -327,8 +330,8 @@
b.append(-200.0 / scaling_matrix[param_index, param_index])
j += 2
- # The pA.pB.dw**2 parameter (phi_ex >= 0).
- elif param_name == 'phi_ex':
+ # The pA.pB.dw**2 and pA.dw**2 parameters (phi_ex >= 0 and padw2 >=
0).
+ elif param_name in ['phi_ex', 'padw2']:
A.append(zero_array * 0.0)
A[j][param_index] = 1.0
b.append(0.0)
@@ -429,19 +432,22 @@
# Yield the data.
yield 'r2', param_index, spin_index, frq_index
- # Then the chemical shift difference parameters 'phi_ex' and 'dw'
(one per spin).
+ # Then the chemical shift difference parameters 'phi_ex', 'padw2'
and 'dw' (one per spin).
for spin_index in range(len(spins)):
# Yield the data.
if 'phi_ex' in spins[spin_index].params:
param_index += 1
yield 'phi_ex', param_index, spin_index, None
+ if 'padw2' in spins[spin_index].params:
+ param_index += 1
+ yield 'padw2', param_index, spin_index, None
if 'dw' in spins[spin_index].params:
param_index += 1
yield 'dw', param_index, spin_index, None
# All other parameters (one per spin cluster).
for param in spins[0].params:
- if not param in ['r2', 'phi_ex', 'dw']:
+ if not param in ['r2', 'phi_ex', 'padw2', 'dw']:
param_index += 1
yield param, param_index, None, None
@@ -490,7 +496,7 @@
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', 'dw']
+ spin_params = ['r2', 'phi_ex', 'padw2', 'dw']
num = 0
for spin in spins:
for i in range(len(spin.params)):
r20012 - in /branches/relax_disp/specific_analyses/relax_disp: __init__.py parameters.py