Author: bugman
Date: Fri Jul 19 15:41:05 2013
New Revision: 20415
URL: http://svn.gna.org/viewcvs/relax?rev=20415&view=rev
Log:
Added support for the 'LM63 3-site' parameters to the
specific_analyses.relax_disp.parameters module.
This is the Luz and Meiboom 1963 analytic model for three exchanging sites.
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/parameters.py
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=20415&r1=20414&r2=20415&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/parameters.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/parameters.py Fri Jul 19
15:41:05 2013
@@ -95,8 +95,8 @@
if param_name in ['r2', 'r2a', 'r2b']:
scaling_matrix[param_index, param_index] = 10
- # The pA.pB.dw**2 and pA.dw**2 parameters.
- elif param_name in ['phi_ex', 'padw2']:
+ # The pA.pB.dw**2, phi_ex_B, phi_ex_C and pA.dw**2 parameters.
+ elif param_name in ['phi_ex', 'phi_ex_B', 'phi_ex_C', 'padw2']:
scaling_matrix[param_index, param_index] = 1
# Chemical shift difference between states A and B scaling.
@@ -108,7 +108,7 @@
scaling_matrix[param_index, param_index] = 1
# Exchange rate scaling.
- elif param_name in ['kex', 'ka']:
+ elif param_name in ['kex', 'ka', 'kB', 'kC']:
scaling_matrix[param_index, param_index] = 10000
# Time of exchange scaling.
@@ -253,9 +253,13 @@
pB <= pA <= 1
pA >= 0.85 (the skewed condition, pA >> pB)
phi_ex >= 0
+ phi_ex_B >= 0
+ phi_ex_C >= 0
padw2 >= 0
dw >= 0
0 <= kex <= 2e6
+ 0 <= kB <= 2e6
+ 0 <= kC <= 2e6
tex >= 0
kA >= 0
@@ -265,37 +269,49 @@
In the notation A.x >= b, where A is a matrix of coefficients, x is an
array of parameter values, and b is a vector of scalars, these inequality
constraints are::
- | 1 0 0 | | R2 | | 0 |
- | | | | | |
- |-1 0 0 | | R2 | | -200 |
- | | | | | |
- | 1 0 0 | | R2A | | 0 |
- | | | | | |
- |-1 0 0 | | R2A | | -200 |
- | | | | | |
- | 1 0 0 | | R2B | | 0 |
- | | | | | |
- |-1 0 0 | | R2B | | -200 |
- | | | | | |
- | 1 0 0 | | pA | | 0.5 |
- | | | | | |
- |-1 0 0 | . | pA | >= | -1 |
- | | | | | |
- | 1 0 0 | | pA | | 0.85 |
- | | | | | |
- | 1 0 0 | | phi_ex | | 0 |
- | | | | | |
- | 1 0 0 | | padw2 | | 0 |
- | | | | | |
- | 1 0 0 | | dw | | 0 |
- | | | | | |
- | 1 0 0 | | kex | | 0 |
- | | | | | |
- |-1 0 0 | | kex | | -2e6 |
- | | | | | |
- | 1 0 0 | | tex | | 0 |
- | | | | | |
- | 1 0 0 | | kA | | 0 |
+ | 1 0 0 | | R2 | | 0 |
+ | | | | | |
+ |-1 0 0 | | R2 | | -200 |
+ | | | | | |
+ | 1 0 0 | | R2A | | 0 |
+ | | | | | |
+ |-1 0 0 | | R2A | | -200 |
+ | | | | | |
+ | 1 0 0 | | R2B | | 0 |
+ | | | | | |
+ |-1 0 0 | | R2B | | -200 |
+ | | | | | |
+ | 1 0 0 | | pA | | 0.5 |
+ | | | | | |
+ |-1 0 0 | | pA | | -1 |
+ | | | | | |
+ | 1 0 0 | | pA | | 0.85 |
+ | | | | | |
+ | 1 0 0 | | phi_ex | | 0 |
+ | | | | | |
+ | 1 0 0 | . | phi_ex_B | >= | 0 |
+ | | | | | |
+ | 1 0 0 | | phi_ex_C | | 0 |
+ | | | | | |
+ | 1 0 0 | | padw2 | | 0 |
+ | | | | | |
+ | 1 0 0 | | dw | | 0 |
+ | | | | | |
+ | 1 0 0 | | kex | | 0 |
+ | | | | | |
+ |-1 0 0 | | kex | | -2e6 |
+ | | | | | |
+ | 1 0 0 | | kB | | 0 |
+ | | | | | |
+ |-1 0 0 | | kB | | -2e6 |
+ | | | | | |
+ | 1 0 0 | | kC | | 0 |
+ | | | | | |
+ |-1 0 0 | | kC | | -2e6 |
+ | | | | | |
+ | 1 0 0 | | tex | | 0 |
+ | | | | | |
+ | 1 0 0 | | kA | | 0 |
@keyword spins: The list of spin data containers for the
block.
@@ -340,8 +356,8 @@
b.append(-200.0 / scaling_matrix[param_index, param_index])
j += 2
- # The pA.pB.dw**2 and pA.dw**2 parameters (phi_ex >= 0 and padw2 >=
0).
- elif param_name in ['phi_ex', 'padw2']:
+ # The pA.pB.dw**2, phi_ex_B, phi_ex_C and pA.dw**2 parameters
(phi_ex* >= 0 and padw2 >= 0).
+ elif param_name in ['phi_ex', 'phi_ex_B', 'phi_ex_C', 'padw2']:
A.append(zero_array * 0.0)
A[j][param_index] = 1.0
b.append(0.0)
@@ -377,7 +393,7 @@
j += 1
# Exchange rates and times (0 <= k <= 2e6).
- elif param_name in ['kex', 'ka']:
+ elif param_name in ['kex', 'ka', 'kB', 'kC']:
A.append(zero_array * 0.0)
A.append(zero_array * 0.0)
A[j][param_index] = 1.0
@@ -472,12 +488,18 @@
# 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).
+ # Then the chemical shift difference parameters 'phi_ex',
'phi_ex_B', 'phi_ex_C', '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 'phi_ex_B' in spins[spin_index].params:
+ param_index += 1
+ yield 'phi_ex_B', param_index, spin_index, None
+ if 'phi_ex_C' in spins[spin_index].params:
+ param_index += 1
+ yield 'phi_ex_C', param_index, spin_index, None
if 'padw2' in spins[spin_index].params:
param_index += 1
yield 'padw2', param_index, spin_index, None
@@ -487,7 +509,7 @@
# All other parameters (one per spin cluster).
for param in spins[0].params:
- if not param in ['r2', 'r2a', 'r2b', 'phi_ex', 'padw2', 'dw']:
+ if not param in ['r2', 'r2a', 'r2b', 'phi_ex', 'phi_ex_B',
'phi_ex_C', 'padw2', 'dw']:
param_index += 1
yield param, param_index, None, None
@@ -573,7 +595,7 @@
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', 'r2a', 'r2b', 'phi_ex', 'padw2', 'dw']
+ spin_params = ['r2', 'r2a', 'r2b', 'phi_ex', 'phi_ex_B', 'phi_ex_C',
'padw2', 'dw']
num = 0
for spin in spins:
for i in range(len(spin.params)):
r20415 - /branches/relax_disp/specific_analyses/relax_disp/parameters.py