Author: bugman
Date: Thu Oct 10 15:48:47 2013
New Revision: 21056
URL: http://svn.gna.org/viewcvs/relax?rev=21056&view=rev
Log:
Added support for the new 'dwH' dispersion parameter.
This is needed for the 'MQ NS CPMG 2-site' model support.
This follows the tutorial for adding relaxation dispersion models at:
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Adding_support_for_the_parameters.
Modified:
branches/relax_disp/specific_analyses/relax_disp/api.py
branches/relax_disp/specific_analyses/relax_disp/optimisation.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=21056&r1=21055&r2=21056&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/api.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/api.py Thu Oct 10
15:48:47 2013
@@ -90,6 +90,7 @@
self.PARAMS.add('phi_ex_C', scope='spin', default=5.0, desc='The
fast exchange factor between sites A and C (ppm^2)', set='params',
py_type=float, grace_string='\\xF\\B\\sex,C\\N (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\\B\\Q (ppm)', err=True, sim=True)
+ self.PARAMS.add('dwH', scope='spin', default=0.0, desc='The proton
chemical shift difference between states A and B (in ppm)', set='params',
py_type=float, grace_string='\\q\\xDw\\B\\sH\\N\\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('kB', scope='spin', default=10000.0,
desc='Approximate chemical exchange rate constant between sites A and B
(rad.s^-1)', set='params', py_type=float, grace_string='\\qk\\sB\\N\\Q
(rad.s\\S-1\\N)', err=True, sim=True)
self.PARAMS.add('kC', scope='spin', default=10000.0,
desc='Approximate chemical exchange rate constant between sites A and C
(rad.s^-1)', set='params', py_type=float, grace_string='\\qk\\sC\\N\\Q
(rad.s\\S-1\\N)', err=True, sim=True)
@@ -818,6 +819,7 @@
_table.add_row(["The pA.pB.dw**2 parameter of state C (ppm^2)",
"'phi_ex_C'", "5.0"])
_table.add_row(["The pA.dw**2 parameter (ppm^2)", "'padw2'", "1.0"])
_table.add_row(["Chemical shift difference between states A and B
(ppm)", "'dw'", "0.0"])
+ _table.add_row(["Proton chemical shift difference between states A and B
(ppm)", "'dwH'", "0.0"])
_table.add_row(["Exchange rate (rad/s)", "'kex'", "10000.0"])
_table.add_row(["Exchange rate between sites A and B (rad/s)", "'kB'",
"10000.0"])
_table.add_row(["Exchange rate between sites A and C (rad/s)", "'kC'",
"10000.0"])
@@ -1142,6 +1144,7 @@
_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(["Proton chemical shift difference between states A and B
(ppm)", "'dwH'"])
_table.add_row(["Exchange rate (rad/s)", "'kex'"])
_table.add_row(["Exchange rate from state A to state B (rad/s)",
"'k_AB'"])
_table.add_row(["Exchange rate from state B to state A (rad/s)",
"'k_BA'"])
Modified: branches/relax_disp/specific_analyses/relax_disp/optimisation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/optimisation.py?rev=21056&r1=21055&r2=21056&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/optimisation.py
(original)
+++ branches/relax_disp/specific_analyses/relax_disp/optimisation.py Thu Oct
10 15:48:47 2013
@@ -122,7 +122,7 @@
upper.append(10.0)
# Chemical shift difference between states A and B.
- elif spin.params[i] == 'dw':
+ elif spin.params[i] in ['dw', 'dwH']:
lower.append(0.0)
upper.append(10.0)
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=21056&r1=21055&r2=21056&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/parameters.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/parameters.py Thu Oct 10
15:48:47 2013
@@ -103,7 +103,7 @@
scaling_matrix[param_index, param_index] = 1
# Chemical shift difference between states A and B scaling.
- elif param_name == 'dw':
+ elif param_name in ['dw', 'dwH']:
scaling_matrix[param_index, param_index] = 1
# The population of state A.
@@ -533,7 +533,7 @@
j += 1
# Chemical exchange difference (dw >= 0).
- elif param_name == 'dw':
+ elif param_name in ['dw', 'dwH']:
A.append(zero_array * 0.0)
A[j][param_index] = 1.0
b.append(0.0)
@@ -657,7 +657,7 @@
# Yield the data.
yield 'r2b', param_index, spin_index, frq_index
- # Then the chemical shift difference parameters 'phi_ex',
'phi_ex_B', 'phi_ex_C', 'padw2' and 'dw' (one per spin).
+ # Then the chemical shift difference parameters 'phi_ex',
'phi_ex_B', 'phi_ex_C', 'padw2', 'dw' and 'dwH' (one per spin).
for spin_index in range(len(spins)):
# Yield the data.
if 'phi_ex' in spins[spin_index].params:
@@ -675,10 +675,13 @@
if 'dw' in spins[spin_index].params:
param_index += 1
yield 'dw', param_index, spin_index, None
+ if 'dwH' in spins[spin_index].params:
+ param_index += 1
+ yield 'dwH', param_index, spin_index, None
# All other parameters (one per spin cluster).
for param in spins[0].params:
- if not param in ['r2', 'r2a', 'r2b', 'phi_ex', 'phi_ex_B',
'phi_ex_C', 'padw2', 'dw']:
+ if not param in ['r2', 'r2a', 'r2b', 'phi_ex', 'phi_ex_B',
'phi_ex_C', 'padw2', 'dw', 'dwH']:
param_index += 1
yield param, param_index, None, None
@@ -774,7 +777,7 @@
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', 'phi_ex_B', 'phi_ex_C',
'padw2', 'dw']
+ spin_params = ['r2', 'r2a', 'r2b', 'phi_ex', 'phi_ex_B', 'phi_ex_C',
'padw2', 'dw', 'dwH']
num = 0
for spin in spins:
for i in range(len(spin.params)):
r21056 - in /branches/relax_disp/specific_analyses/relax_disp: api.py optimisation.py parameters.py