Author: bugman
Date: Wed Mar 27 14:09:39 2013
New Revision: 19195
URL: http://svn.gna.org/viewcvs/relax?rev=19195&view=rev
Log:
Ported r8354 from the old relax_disp branch into the new branch.
The command used was:
svn merge -r8353:8354
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/relax_disp/specific_fns/@r18123
specific_analyses
.....
r8354 | semor | 2009-01-09 23:13:27 +0100 (Fri, 09 Jan 2009) | 7 lines
Changed paths:
M /branches/relax_disp/specific_fns/relax_disp.py
Corrected a few formatting issues and still added parameters for the slow-
and fast-exchange regime.
Formatting issues corrected were spotted by Ed in a post at:
https://mail.gna.org/public/relax-devel/2009-01/msg00045.html
(Message-id: <7f080ed10901091243k76e08449ld2d1a4d273b97f71@xxxxxxxxxxxxxx>)
.....
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=19195&r1=19194&r2=19195&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp.py Wed Mar 27 14:09:39
2013
@@ -62,7 +62,7 @@
# Loop over the model parameters.
for i in xrange(len(spin.params)):
# Transversal relaxation rate.
- if spin.params[i] == 'r2':
+ if spin.params[i] == 'R2':
if sim_index != None:
param_vector.append(spin.r2_sim[sim_index])
elif spin.r2 == None:
@@ -71,7 +71,7 @@
param_vector.append(spin.r2)
# Chemical exchange contribution to 'R2'.
- elif spin.params[i] == 'rex':
+ elif spin.params[i] == 'Rex':
if sim_index != None:
param_vector.append(spin.rex_sim[sim_index])
elif spin.rex == None:
@@ -89,7 +89,7 @@
param_vector.append(spin.kex)
# Relaxation rate for state A.
- if spin.params[i] == 'r2a':
+ if spin.params[i] == 'R2A':
if sim_index != None:
param_vector.append(spin.r2a_sim[sim_index])
elif spin.r2a == None:
@@ -98,7 +98,7 @@
param_vector.append(spin.r2a)
# Exchange rate from state A to state B.
- if spin.params[i] == 'ka':
+ if spin.params[i] == 'kA':
if sim_index != None:
param_vector.append(spin.ka_sim[sim_index])
elif spin.ka == None:
@@ -334,11 +334,11 @@
The names are as follows:
- 'params', an array of the parameter names associated with the
model.
- - 'r2', the transversal relaxation rate.
- - 'rex', the chemical exchange contribution to 'R2'.
+ - 'R2', the transversal relaxation rate.
+ - 'Rex', the chemical exchange contribution to 'R2'.
- 'kex', the exchange rate.
- - 'r2a', the transversal relaxation rate for state A.
- - 'ka', the exchange rate from state A to state B.
+ - 'R2A', the transversal relaxation rate for state A.
+ - 'kA', the exchange rate from state A to state B.
- 'dw', the chemical shift difference between states A and B.
- 'chi2', chi-squared value.
- 'iter', iterations.
@@ -370,11 +370,11 @@
# Parameters.
if set == 'all' or set == 'params':
- names.append('r2')
- names.append('rex')
+ names.append('R2')
+ names.append('Rex')
names.append('kex')
- names.append('r2a')
- names.append('ka')
+ names.append('R2A')
+ names.append('kA')
names.append('dw')
# Minimisation statistics.
@@ -419,15 +419,15 @@
| Data type | Object name
| Value |
|___________________________________________________|_______________|__________|
| |
| |
- | Transversal relaxation rate | 'r2'
| 8.0 |
+ | Transversal relaxation rate | 'R2'
| 8.0 |
| |
| |
- | Chemical exchange contribution to 'R2' | 'rex'
| 2.0 |
+ | Chemical exchange contribution to 'R2' | 'Rex'
| 2.0 |
| |
| |
| Exchange rate | 'kex'
| 10000.0 |
| |
| |
- | Transversal relaxation rate for state A | 'r2a'
| 8.0 |
+ | Transversal relaxation rate for state A | 'R2A'
| 8.0 |
| |
| |
- | Exchange rate from state A to state B | 'ka'
| 10000.0 |
+ | Exchange rate from state A to state B | 'kA'
| 10000.0 |
| |
| |
| Chemical shift difference between states A and B | 'dw'
| 100 |
| |
| |
@@ -436,23 +436,23 @@
"""
# Transversal relaxation rate.
- if param == 'r2':
+ if param == 'R2':
return 8.0
# Chemical exchange contribution to 'R2'.
- if param == 'rex':
+ if param == 'Rex':
return 2.0
# Exchange rate.
- if param == 'kes':
+ if param == 'kex':
return 10000.0
# Transversal relaxation rate for state A.
- if param == 'r2a' :
+ if param == 'R2A' :
return 8.0
# Exchange rate from state A to state B.
- if param == 'ka' :
+ if param == 'kA' :
return 10000
# Chemical shift difference between states A and B.
@@ -476,27 +476,43 @@
# Monte Carlo simulations.
if sim_index != None:
- # The relaxation rate.
- spin.rx_sim[sim_index] = param_vector[0]
-
- # Initial intensity.
- spin.i0_sim[sim_index] = param_vector[1]
-
- # Intensity at infinity.
- if cdp.curve_type == 'inv':
- spin.iinf_sim[sim_index] = param_vector[2]
+ # Transversal relaxation rate.
+ spin.r2_sim[sim_index] = param_vector[0]
+
+ # Chemical exchange contribution to 'R2'.
+ spin.rex_sim[sim_index] = param_vector[1]
+
+ # Exchange rate.
+ spin.kex_sim[sim_index] = param_vector[2]
+
+ # Relaxation rate for state A.
+ spin.r2a_sim[sim_index] = param_vector[3]
+
+ # Exchange rate from state A to state B.
+ spin.ka_sim[sim_index] = param_vector[4]
+
+ # Chemical shift difference between states A and B.
+ spin.dw_sim[sim_index] = param_vector[5]
# Parameter values.
else:
- # The relaxation rate.
- spin.rx = param_vector[0]
-
- # Initial intensity.
- spin.i0 = param_vector[1]
-
- # Intensity at infinity.
- if cdp.curve_type == 'inv':
- spin.iinf = param_vector[2]
+ # Transversal relaxation rate.
+ spin.r2 = param_vector[0]
+
+ # Chemical exchange contribution to 'R2'.
+ spin.rex = param_vector[1]
+
+ # Exchange rate.
+ spin.kex = param_vector[2]
+
+ # Relaxation rate for state A.
+ spin.r2a = param_vector[3]
+
+ # Exchange rate from state A to state B.
+ spin.ka = param_vector[4]
+
+ # Chemical shift difference between states A and B.
+ spin.dw = param_vector[5]
def exp_type(self, exp='cpmg'):
@@ -1015,15 +1031,15 @@
| Data type | Object name |
Patterns |
|___________________________________________________|______________|__________________________|
| | |
|
- | Transversal relaxation rate | 'r2' |
'^[Rr]2$' |
+ | Transversal relaxation rate | 'R2' |
'^[Rr]2$' |
| | |
|
- | Chemical exchange contribution to 'R2' | 'rex' |
'^[Rr]ex$' |
+ | Chemical exchange contribution to 'R2' | 'Rex' |
'^[Rr]ex$' |
| | |
|
| Exchange rate | 'kex' |
'^[Kk]ex$' |
| | |
|
- | Transversal relaxation rate for state A | 'r2a' |
'^[Rr]2A$' |
+ | Transversal relaxation rate for state A | 'R2A' |
'^[Rr]2A$' |
| | |
|
- | Exchange rate from state A to state B | 'ka' |
'^[Kk]A$' |
+ | Exchange rate from state A to state B | 'kA' |
'^[Kk]A$' |
| | |
|
| Chemical shift difference between states A and B | 'dw' |
'^[Dd]w$' |
| | |
|
@@ -1115,12 +1131,12 @@
# Fast-exchange regime.
if model == 'fast':
print "Two parameter exponential fit."
- params = ['r2', 'rex', 'kex']
+ params = ['R2', 'Rex', 'kex']
# Slow-exchange regime.
elif model == 'slow':
print "Three parameter inversion recovery fit."
- params = ['r2a', 'ka', 'dw']
+ params = ['R2A', 'kA', 'dw']
# Invalid model.
else:
r19195 - /branches/relax_disp/specific_analyses/relax_disp.py