Author: semor
Date: Thu Jan 8 00:38:30 2009
New Revision: 8330
URL: http://svn.gna.org/viewcvs/relax?rev=8330&view=rev
Log:
Changed all instances of 'relax_times' to 'cpmg_frqs' and made other small
changes.
Modified:
branches/relax_disp/specific_fns/relax_disp.py
Modified: branches/relax_disp/specific_fns/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_fns/relax_disp.py?rev=8330&r1=8329&r2=8330&view=diff
==============================================================================
--- branches/relax_disp/specific_fns/relax_disp.py (original)
+++ branches/relax_disp/specific_fns/relax_disp.py Thu Jan 8 00:38:30 2009
@@ -123,7 +123,7 @@
# Intensity scaling.
elif search('^i', spin.params[i]):
# Find the position of the first time point.
- pos = cdp.relax_times.index(min(cdp.relax_times))
+ pos = cdp.cpmg_frqs.index(min(cdp.cpmg_frqs))
# Scaling.
scaling_matrix[i, i] = 1.0 / average(spin.intensities[pos])
@@ -156,7 +156,7 @@
scaling_matrix = self.assemble_scaling_matrix(spin=spin,
scaling=False)
# Initialise the relaxation fit functions.
- setup(num_params=len(spin.params), num_times=len(cdp.relax_times),
values=spin.intensities, sd=spin.intensity_err, relax_times=cdp.relax_times,
scaling_matrix=scaling_matrix)
+ setup(num_params=len(spin.params), num_times=len(cdp.cpmg_frqs),
values=spin.intensities, sd=spin.intensity_err, cpmg_frqs=cdp.cpmg_frqs,
scaling_matrix=scaling_matrix)
# Make a single function call. This will cause back calculation and
the data will be stored in the C module.
func(param_vector)
@@ -237,7 +237,7 @@
cdp = pipes.get_pipe()
# Loop over the spectral time points.
- for j in xrange(len(cdp.relax_times)):
+ for j in xrange(len(cdp.cpmg_frqs)):
# Back calculate the value.
value = self.back_calc(spin=spin, relax_time_index=j)
@@ -354,7 +354,7 @@
| Data type | Object name
| Value |
|___________________________________________________|_______________|__________|
| |
| |
- | Relaxation rate | 'R2'
| 8.0 |
+ | Transversal relaxation rate | 'R2'
| 8.0 |
| |
| |
| Chemical exchange contribution to 'R2' | 'Rex'
| 2.0 |
| |
| |
@@ -557,7 +557,7 @@
# Intensity
elif search('^I', spin.params[i]):
# Find the position of the first time point.
- pos = cdp.relax_times.index(min(cdp.relax_times))
+ pos = cdp.cpmg_frqs.index(min(cdp.cpmg_frqs))
# Scaling.
min_options.append([inc[j], 0.0,
average(spin.intensities[pos])])
@@ -761,7 +761,7 @@
else:
values = spin.sim_intensities[sim_index]
- setup(num_params=len(spin.params),
num_times=len(cdp.relax_times), values=values, sd=spin.intensity_err,
relax_times=cdp.relax_times, scaling_matrix=scaling_matrix)
+ setup(num_params=len(spin.params), num_times=len(cdp.cpmg_frqs),
values=values, sd=spin.intensity_err, cpmg_frqs=cdp.cpmg_frqs,
scaling_matrix=scaling_matrix)
# Setup the minimisation algorithm when constraints are present.
@@ -778,9 +778,9 @@
if match('[Ll][Mm]$', algor) or
match('[Ll]evenburg-[Mm]arquardt$', algor):
# Reconstruct the error data structure.
- lm_error = zeros(len(spin.relax_times), float64)
+ lm_error = zeros(len(spin.cpmg_frqs), float64)
index = 0
- for k in xrange(len(spin.relax_times)):
+ for k in xrange(len(spin.cpmg_frqs)):
lm_error[index:index+len(relax_error[k])] =
relax_error[k]
index = index + len(relax_error[k])
@@ -933,21 +933,25 @@
Relaxation curve fitting data type string matching patterns
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
__________________________________________________________________________________________
- | | |
|
- | Data type | Object name |
Patterns |
-
|___________________________________|______________________|_____________________________|
- | | |
|
- | Relaxation rate | 'rx' |
'^[Rr]x$' |
- | | |
|
- | Peak intensities (series) | 'intensities' |
'^[Ii]nt$' |
- | | |
|
- | Initial intensity | 'i0' |
'^[Ii]0$' |
- | | |
|
- | Intensity at infinity | 'iinf' |
'^[Ii]inf$' |
- | | |
|
- | Relaxation period times (series) | 'relax_times' |
'^[Rr]elax[ -_][Tt]imes$' |
-
|___________________________________|______________________|_____________________________|
+
_______________________________________________________________________________________________
+ | | |
|
+ | Data type | Object name |
Patterns |
+
|___________________________________________________|______________|__________________________|
+ | | |
|
+ | Transversal relaxation rate | 'R2' |
'^[Rr]2$' |
+ | | |
|
+ | Chemical exchange contribution to 'R2' | 'Rex' |
'^[Rr]ex$' |
+ | | |
|
+ | Exchange rate | 'kex' |
'^[Kk]ex$' |
+ | | |
|
+ | Relaxation rate for state A | 'R2A' |
'^[Rr]2A$' |
+ | | |
|
+ | Exchange rate from state A to state B | 'kA' |
'^[Kk]A$' |
+ | | |
|
+ | Chemical shift difference between states A and B | 'dw' |
'^[Dd]w$' |
+ | | |
|
+ | CPMG pulse train frequency (series) | 'cpmg_frqs' |
'^[Cc]pmg[ -_][Ff]rqs$' |
+
|___________________________________________________|______________|__________________________|
"""
@@ -967,9 +971,9 @@
if match('^[Ii]inf$', name):
return 'iinf'
- # Relaxation period times (series).
- if match('^[Rr]elax[ -_][Tt]imes$', name):
- return 'relax_times'
+ # CPMG pulse train frequency (series).
+ if match('^[Cc]pmg[ -_][Ff]rqs$', name):
+ return 'cpmg_frqs'
def return_grace_string(self, data_type):
@@ -995,8 +999,8 @@
grace_string = '\\qI\\sinf\\Q'
# Intensity at infinity.
- elif object_name == 'relax_times':
- grace_string = '\\qRelaxation time period (s)\\Q'
+ elif object_name == 'cpmg_frqs':
+ grace_string = '\\qCPMG pulse train frequency (Hz)\\Q'
# Return the Grace string.
return grace_string
r8330 - /branches/relax_disp/specific_fns/relax_disp.py