Author: bugman
Date: Fri Apr 5 17:25:48 2013
New Revision: 19387
URL: http://svn.gna.org/viewcvs/relax?rev=19387&view=rev
Log:
Converted all relaxation dispersion parameters to lowercase.
This is so the variable names match the parameter names identically, avoiding
problems with some of
the shared methods of the specific analysis API.
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=19387&r1=19386&r2=19387&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp.py Fri Apr 5 17:25:48
2013
@@ -102,7 +102,7 @@
# Loop over the model parameters.
for i in range(len(spin.params)):
# Effective transversal relaxation rate.
- if spin.params[i] == 'R2eff':
+ if spin.params[i] == 'r2eff':
if sim_index != None:
param_vector.append(spin.r2eff_sim[key][sim_index])
elif spin.r2eff == None or key not in spin.r2eff:
@@ -111,7 +111,7 @@
param_vector.append(spin.r2eff[key])
# Initial intensity.
- elif spin.params[i] == 'I0':
+ elif spin.params[i] == 'i0':
if sim_index != None:
param_vector.append(spin.i0_sim[key][sim_index])
elif spin.i0 == None or key not in spin.i0:
@@ -123,7 +123,7 @@
spin = spins[0]
for i in range(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:
@@ -132,7 +132,7 @@
param_vector.append(spin.r2)
# Chemical exchange contribution to 'R2'.
- if spin.params[i] == 'Rex':
+ if spin.params[i] == 'rex':
if sim_index != None:
param_vector.append(spin.rex_sim[sim_index])
elif spin.rex == None:
@@ -150,7 +150,7 @@
param_vector.append(spin.kex)
# Transversal 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:
@@ -159,7 +159,7 @@
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:
@@ -219,11 +219,11 @@
spin = spins[0]
for i in range(len(spin.params)):
# Transversal relaxation rate scaling.
- if spin.params[i] == 'R2':
+ if spin.params[i] == 'r2':
scaling_matrix[param_index, param_index] = 10
# Chemical exchange contribution to 'R2' scaling.
- elif spin.params[i] == 'Rex':
+ elif spin.params[i] == 'rex':
scaling_matrix[param_index, param_index] = 10
# Exchange rate scaling.
@@ -231,11 +231,11 @@
scaling_matrix[param_index, param_index] = 10000
# Transversal relaxation rate for state A scaling
- elif spin.params[i] == 'R2A':
+ elif spin.params[i] == 'r2a':
scaling_matrix[param_index, param_index] = 10
# Exchange rate from state A to state B scaling.
- elif spin.params[i] == 'kA':
+ elif spin.params[i] == 'ka':
scaling_matrix[param_index, param_index] = 10000
# Chemical shift difference between states A and B scaling.
@@ -415,14 +415,14 @@
# Loop over the model parameters.
for i in range(len(spin.params)):
# Effective transversal relaxation rate.
- if spin.params[i] == 'R2eff':
+ if spin.params[i] == 'r2eff':
if sim_index != None:
spin.r2eff_sim[sim_index][key] =
param_vector[index]
else:
spin.r2eff[key] = param_vector[index]
# Initial intensity.
- elif spin.params[i] == 'I0':
+ elif spin.params[i] == 'i0':
if sim_index != None:
spin.i0_sim[sim_index][key] =
param_vector[index+1]
else:
@@ -432,14 +432,14 @@
spin = spins[0]
for i in range(len(spin.params)):
# Transversal relaxation rate.
- if spin.params[i] == 'R2':
+ if spin.params[i] == 'r2':
if sim_index != None:
spin.r2_sim[sim_index] = param_vector[param_index]
else:
spin.r2 = param_vector[param_index]
# Chemical exchange contribution to 'R2'.
- if spin.params[i] == 'Rex':
+ if spin.params[i] == 'rex':
if sim_index != None:
spin.rex_sim[sim_index] = param_vector[param_index]
else:
@@ -453,14 +453,14 @@
spin.kex = param_vector[param_index]
# Transversal relaxation rate for state A.
- if spin.params[i] == 'R2A':
+ if spin.params[i] == 'r2a':
if sim_index != None:
spin.r2a_sim[sim_index] = param_vector[param_index]
else:
spin.r2a = param_vector[param_index]
# Exchange rate from state A to state B.
- if spin.params[i] == 'kA':
+ if spin.params[i] == 'ka':
if sim_index != None:
spin.ka_sim[sim_index] = param_vector[param_index]
else:
@@ -622,12 +622,12 @@
# Loop over the parameters.
for i in range(len(spin.params)):
# R2eff relaxation rate (from 0 to 40 s^-1).
- if spin.params[i] == 'R2eff':
+ if spin.params[i] == 'r2eff':
lower.append(0.0)
upper.append(40.0)
# Intensity.
- elif spin.params[i] == 'I0':
+ elif spin.params[i] == 'i0':
lower.append(0.0)
upper.append(max(spin.intensities.values()))
@@ -635,12 +635,12 @@
spin = spins[0]
for i in range(len(spin.params)):
# R2 relaxation rate (from 0 to 40 s^-1).
- if spin.params[i] == 'R2':
+ if spin.params[i] == 'r2':
lower.append(0.0)
upper.append(40.0)
# Chemical exchange contribution to 'R2'.
- elif spin.params[i] == 'Rex':
+ elif spin.params[i] == 'rex':
lower.append(0.0)
upper.append(20.0)
@@ -650,12 +650,12 @@
upper.append(100000.0)
# Transversal relaxation rate for state A.
- elif spin.params[i] == 'R2A':
+ elif spin.params[i] == 'r2a':
lower.append(0.0)
upper.append(20.0)
# Exchange rate from state A to state B.
- elif spin.params[i] == 'kA':
+ elif spin.params[i] == 'ka':
lower.append(0.0)
upper.append(100000.0)
@@ -814,7 +814,7 @@
# Loop over the parameters.
for k in range(len(spin.params)):
# The transversal relaxation rate >= 0.
- if spin.params[k] == 'R2':
+ if spin.params[k] == 'r2':
A.append(zero_array * 0.0)
A[j][i] = 1.0
b.append(0.0)
@@ -824,14 +824,14 @@
spin = spins[0]
for k in range(len(spin.params)):
# The transversal relaxation rate >= 0.
- if spin.params[k] == 'R2':
+ if spin.params[k] == 'r2':
A.append(zero_array * 0.0)
A[j][i] = 1.0
b.append(0.0)
j += 1
# Relaxation rates and Rex.
- elif search('^R', spin.params[k]):
+ elif search('^r', spin.params[k]):
# Rex, R2A >= 0.
A.append(zero_array * 0.0)
A[j][i] = 1.0
@@ -1015,17 +1015,17 @@
# Fast-exchange regime.
if model == 'exp_fit':
print("Basic exponential curve-fitting.")
- params = ['R2eff', 'I0']
+ params = ['r2eff', 'i0']
# Fast-exchange regime.
elif model == 'fast 2-site':
print("2-site fast-exchange.")
- params = ['R2eff', 'I0', 'R2', 'Rex', 'kex']
+ params = ['r2eff', 'i0', 'r2', 'rex', 'kex']
# Slow-exchange regime.
elif model == 'slow 2-site':
print("2-site slow-exchange.")
- params = ['R2eff', 'I0', 'R2', 'R2A', 'kA', 'dw']
+ params = ['r2eff', 'i0', 'r2', 'r2a', 'ka', 'dw']
# Invalid model.
else:
r19387 - /branches/relax_disp/specific_analyses/relax_disp.py