Author: bugman
Date: Wed Mar 27 13:02:20 2013
New Revision: 19179
URL: http://svn.gna.org/viewcvs/relax?rev=19179&view=rev
Log:
Ported r8328 from the old relax_disp branch into the new branch.
The command used was:
svn merge -r8327:8328
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/relax_disp/specific_fns/@r18123
specific_analyses
.....
r8328 | semor | 2009-01-08 00:16:20 +0100 (Thu, 08 Jan 2009) | 5 lines
Changed paths:
M /branches/relax_disp/specific_fns/relax_disp.py
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_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=19179&r1=19178&r2=19179&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp.py Wed Mar 27 13:02:20
2013
@@ -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.
r19179 - /branches/relax_disp/specific_analyses/relax_disp.py