Author: bugman
Date: Fri Jul 12 11:56:23 2013
New Revision: 20280
URL: http://svn.gna.org/viewcvs/relax?rev=20280&view=rev
Log:
Added support for the R2B parameter as required by the 'NS 2-site star' model.
This is the model of the numerical solution for the 2-site Bloch-McConnell
equations using complex
conjugate matrices.
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/api.py
branches/relax_disp/specific_analyses/relax_disp/parameters.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=20280&r1=20279&r2=20280&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/api.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/api.py Fri Jul 12
11:56:23 2013
@@ -89,7 +89,8 @@
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', set='params', py_type=float,
grace_string='\\qR\\s2,A\\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=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)
@@ -371,7 +372,7 @@
for spin in spins:
for i in range(len(spin.params)):
# R2 relaxation rates (from 1 to 40 s^-1).
- if spin.params[i] == 'r2':
+ if spin.params[i] in ['r2', 'r2a', 'r2b']:
lower.append(1.0)
upper.append(40.0)
@@ -388,11 +389,6 @@
# The cluster specific parameters (only use the values from
the first spin of the cluster).
spin = spins[0]
for i in range(len(spin.params)):
- # R2 relaxation rates (from 1 to 40 s^-1).
- if spin.params[i] == 'r2a':
- lower.append(1.0)
- upper.append(40.0)
-
# The population of state A.
elif spin.params[i] == 'pA':
if spin.model == MODEL_M61B:
@@ -1329,6 +1325,7 @@
_table.add_headings(["Data type", "Object name"])
_table.add_row(["Transversal relaxation rate (rad/s)", "'r2'"])
_table.add_row(["Transversal relaxation rate for state A (rad/s)",
"'r2a'"])
+ _table.add_row(["Transversal relaxation rate for state B (rad/s)",
"'r2b'"])
_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'"])
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=20280&r1=20279&r2=20280&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/parameters.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/parameters.py Fri Jul 12
11:56:23 2013
@@ -92,7 +92,7 @@
# Loop over the parameters of the cluster.
for param_name, param_index, spin_index, frq_index in
loop_parameters(spins=spins):
# Transversal relaxation rate scaling.
- if param_name == 'r2':
+ if param_name in ['r2', 'r2a', 'r2b']:
scaling_matrix[param_index, param_index] = 10
# The pA.pB.dw**2 and pA.dw**2 parameters.
@@ -102,10 +102,6 @@
# Chemical shift difference between states A and B scaling.
elif param_name == 'dw':
scaling_matrix[param_index, param_index] = 1
-
- # Transversal relaxation rate scaling.
- elif param_name == 'r2a':
- scaling_matrix[param_index, param_index] = 10
# The population of state A.
elif param_name == 'pA':
@@ -228,9 +224,9 @@
The different constraints used within different models are::
- R2 >= 0
- R2 <= -200
- R2A >= 0
+ 0 <= R2 <= 200
+ 0 <= R2A <= 200
+ 0 <= R2B <= 200
pB <= pA <= 1
pA >= 0.85 (the skewed condition, pA >> pB)
phi_ex >= 0
@@ -252,12 +248,18 @@
| | | | | |
| 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 | >= | -1 |
| | | | | |
| 1 0 0 | | pA | | 0.85 |
- | | . | | >= | |
+ | | | | | |
| 1 0 0 | | phi_ex | | 0 |
| | | | | |
| 1 0 0 | | padw2 | | 0 |
@@ -304,7 +306,7 @@
j += 1
# The transversal relaxation rates (0 <= r2 <= 200).
- elif param_name == 'r2':
+ elif param_name in ['r2', 'r2a', 'r2b']:
A.append(zero_array * 0.0)
A.append(zero_array * 0.0)
A[j][param_index] = 1.0
@@ -326,16 +328,6 @@
A[j][param_index] = 1.0
b.append(0.0)
j += 1
-
- # The transversal relaxation rates (0 <= r2 <= 200).
- elif param_name == 'r2a':
- A.append(zero_array * 0.0)
- A.append(zero_array * 0.0)
- A[j][param_index] = 1.0
- A[j+1][param_index] = -1.0
- b.append(0.0)
- b.append(-200.0 / scaling_matrix[param_index, param_index])
- j += 2
# The population of state A.
elif param_name == 'pA':
r20280 - in /branches/relax_disp/specific_analyses/relax_disp: api.py parameters.py