Seb,
I might send a seperate message explaining the hidden, unitless radian
unit. All the relaxation dispersion equations and their parameters
are in radial units, and therefore care has to be taken when setting
or using the input and output values. I.e. rotational correlation
times are in s/rad, kex is in rad/s, R2 is in rad/s, etc. This is why
using published NMR data from the literature would be very useful for
the system test - relax in the end should match the published values.
This test, or maybe a few tests, will be very useful for determining
if relax is returning rubbish or good results. If relax can't be made
to match certain published results, it may even uncover incorrect
published data ;)
Regards,
Edward
On Thu, Jan 8, 2009 at 12:16 AM, <sebastien.morin.1@xxxxxxxxx> wrote:
Author: semor
Date: Thu Jan 8 00:16:20 2009
New Revision: 8328
URL: http://svn.gna.org/viewcvs/relax?rev=8328&view=rev
Log:
Moved the relax_time() function to cpmg_frq() and made other small changes.
Still much (!) work is needed for this code to be complete.
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=8328&r1=8327&r2=8328&view=diff
==============================================================================
--- branches/relax_disp/specific_fns/relax_disp.py (original)
+++ branches/relax_disp/specific_fns/relax_disp.py Thu Jan 8 00:16:20 2009
@@ -168,6 +168,43 @@
return results[relax_time_index]
+ def cpmg_frq(self, frq=0, spectrum_id=None):
+ """Set the CPMG frequency associated with a given spectrum.
+
+ @keyword frq: The frequency, in Hz, of the CPMG train.
+ @type frq: int
+ @keyword spectrum_id: The spectrum identification string.
+ @type spectrum_id: str
+ """
+
+ # Alias the current data pipe.
+ cdp = pipes.get_pipe()
+
+ # Test if the spectrum id exists.
+ if spectrum_id not in cdp.spectrum_ids:
+ raise RelaxError, "The peak heights corresponding to spectrum
id '%s' have not been loaded." % spectrum_id
+
+ # Store the CPMG frequency in the class instance.
+ self.__cpmg_frq = int(frq)
+
+ # The index.
+ index = cdp.spectrum_ids.index(spectrum_id)
+
+ # Initialise the global CPMG frequency data structure if needed.
+ if not hasattr(cdp, 'frq'):
+ cdp.frq = [None] * len(cdp.spectrum_ids)
+
+ # Index not present in the global CPMG frequency data structure.
+ while 1:
+ if index > len(cdp.frq) - 1:
+ cdp.frq.append(None)
+ else:
+ break
+
+ # Add the frequency at the correct position.
+ cdp.frq[index] = frq
+
+
def create_mc_data(self, spin_id):
"""Create the Monte Carlo peak intensity data.
@@ -311,20 +348,25 @@
Relaxation curve fitting default values
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- These values are completely arbitrary as peak heights (or volumes)
are extremely variable
- and the Rx value is a compensation for both the R1 and R2 values.
- ___________________________________________________________________
- | | | |
- | Data type | Object name | Value |
- |________________________|_______________|________________________|
- | | | |
- | Relaxation rate | 'rx' | 8.0 |
- | | | |
- | Initial intensity | 'i0' | 10000.0 |
- | | | |
- | Intensity at infinity | 'iinf' | 0.0 |
- | | | |
- |________________________|_______________|________________________|
+ These values are arbitrary and will depend on the system studied.
+
________________________________________________________________________________
+ | |
| |
+ | Data type | Object name
| Value |
+
|___________________________________________________|_______________|__________|
+ | |
| |
+ | Relaxation rate | 'R2'
| 8.0 |
+ | |
| |
+ | Chemical exchange contribution to 'R2' | 'Rex'
| 2.0 |
+ | |
| |
+ | Exchange rate | 'kex'
| 10000.0 |
+ | |
| |
+ | Relaxation rate for state A | 'R2A'
| 0.0 |
+ | |
| |
+ | Exchange rate from state A to state B | 'kA'
| 10000.0 |
+ | |
| |
+ | Chemical shift difference between states A and B | 'dw'
| 100 |
+ | |
| |
+
|___________________________________________________|_______________|__________|
"""
@@ -854,43 +896,6 @@
continue
- def relax_time(self, time=0.0, spectrum_id=None):
- """Set the relaxation time period associated with a given spectrum.
-
- @keyword time: The time, in seconds, of the relaxation
period.
- @type time: float
- @keyword spectrum_id: The spectrum identification string.
- @type spectrum_id: str
- """
-
- # Alias the current data pipe.
- cdp = pipes.get_pipe()
-
- # Test if the spectrum id exists.
- if spectrum_id not in cdp.spectrum_ids:
- raise RelaxError, "The peak heights corresponding to spectrum
id '%s' have not been loaded." % spectrum_id
-
- # Store the relaxation time in the class instance.
- self.__relax_time = float(time)
-
- # The index.
- index = cdp.spectrum_ids.index(spectrum_id)
-
- # Initialise the global relaxation time data structure if needed.
- if not hasattr(cdp, 'relax_times'):
- cdp.relax_times = [None] * len(cdp.spectrum_ids)
-
- # Index not present in the global relaxation time data structure.
- while 1:
- if index > len(cdp.relax_times) - 1:
- cdp.relax_times.append(None)
- else:
- break
-
- # Add the time at the correct position.
- cdp.relax_times[index] = time
-
-
def return_data(self, spin):
"""Function for returning the peak intensity data structure.
_______________________________________________
relax (http://nmr-relax.com)
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Re: r8328 - /branches/relax_disp/specific_fns/relax_disp.py