Author: semor
Date: Wed Jan 7 21:53:01 2009
New Revision: 8322
URL: http://svn.gna.org/viewcvs/relax?rev=8322&view=rev
Log:
Added functions to select the experiment type and mathematical model used.
These functions allow the user to select the experiment type (cpmg or r1rho)
as well as the
mathematical model to fit the data (fast or slow).
These changes follow a discussion on relaxation dispersion, and mainly the
post at:
https://mail.gna.org/public/relax-devel/2009-01/msg00020.html
(Message-id: <7f080ed10901070529s397f7f23p914c820ced4d07f@xxxxxxxxxxxxxx>)
Modified:
branches/relax_disp/prompt/relax_disp.py
Modified: branches/relax_disp/prompt/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/prompt/relax_disp.py?rev=8322&r1=8321&r2=8322&view=diff
==============================================================================
--- branches/relax_disp/prompt/relax_disp.py (original)
+++ branches/relax_disp/prompt/relax_disp.py Wed Jan 7 21:53:01 2009
@@ -1,6 +1,7 @@
###############################################################################
#
#
# Copyright (C) 2004-2008 Edward d'Auvergne
#
+# Copyright (C) 2009 Sebastien Morin
#
#
#
# This file is part of the program relax.
#
#
#
@@ -21,7 +22,7 @@
###############################################################################
# Module docstring.
-"""Module containing the 'relax_fit' user function class."""
+"""Module containing the 'relax_disp' user function class."""
__docformat__ = 'plaintext'
# Python module imports.
@@ -30,14 +31,14 @@
# relax module imports.
import help
from relax_errors import RelaxNumError, RelaxStrError
-from specific_fns.setup import relax_fit_obj
+from specific_fns.setup import relax_disp_obj
-class Relax_fit:
+class Relax_disp:
def __init__(self, relax):
# Help.
self.__relax_help__ = \
- """Class for relaxation curve fitting."""
+ """Class for relaxation dispersion curve fitting."""
# Add the generic help string.
self.__relax_help__ = self.__relax_help__ + "\n" +
help.relax_class_help
@@ -46,70 +47,76 @@
self.__relax__ = relax
- def relax_time(self, time=0.0, spectrum_id=None):
- """Function for setting the relaxation time period associated with
each spectrum.
+ def exp_type(self, exp='cpmg'):
+ """Function for the selection of the relaxation dispersion
experiments to analyse.
Keyword Arguments
~~~~~~~~~~~~~~~~~
- time: The time, in seconds, of the relaxation period.
-
- spectrum_id: The spectrum identification string.
+ exp: The type of relaxation dispersion experiment performed.
- Description
- ~~~~~~~~~~~
+ The preet experiments
+ ~~~~~~~~~~~~~~~~~~~~~
- Peak intensities should be loaded before calling this user function
via the
- 'spectrum.read_intensities()' user function. The intensity values
will then be associated
- with a spectrum identifier. To associate each spectrum identifier
with a time point in the
- relaxation curve prior to optimisation, this user function should be
called.
+ The supported experiments will include CPMG ('cpmg') and R1rho
('r1rho').
+
+
+ Examples
+ ~~~~~~~~
+
+ To pick the experiment type 'cpmg' for all selected spins, type:
+
+ relax> relax_disp.exp_type('cpmg')
+ relax> relax_disp.exp_type(exp='cpmg')
"""
# Function intro text.
if self.__relax__.interpreter.intro:
- text = sys.ps3 + "relax_fit.relax_time("
- text = text + "time=" + `time`
- text = text + ", spectrum_id=" + `spectrum_id` + ")"
+ text = sys.ps3 + "relax_disp.exp_type("
+ text = text + "exp=" + `exp` + ")"
print text
- # The relaxation time.
- if type(time) != int and type(time) != float:
- raise RelaxNumError, ('relaxation time', time)
-
- # The spectrum identification string.
- if type(spectrum_id) != str:
- raise RelaxStrError, ('spectrum identification string',
spectrum_id)
+ # The exp argument.
+ if type(exp) != str:
+ raise RelaxStrError, ('exp', exp)
# Execute the functional code.
- relax_fit_obj.relax_time(time=time, spectrum_id=spectrum_id)
+ relax_disp_obj.exp_type(exp=exp)
- def select_model(self, model='exp'):
- """Function for the selection of the relaxation curve type.
+ def select_model(self, model='fast'):
+ """Function for the selection of the relaxation dispersion curve
type.
Keyword Arguments
~~~~~~~~~~~~~~~~~
- model: The type of relaxation curve to fit.
+ model: The type of relaxation dispersion curve to fit (relating to
the NMR time scale).
The preset models
~~~~~~~~~~~~~~~~~
- The supported relaxation experiments include the default two
parameter exponential fit,
- selected by setting the 'fit_type' argument to 'exp', and the three
parameter inversion
- recovery experiment in which the peak intensity limit is a non-zero
value, selected by
- setting the argument to 'inv'.
+ The supported equations will include the default fast-exchange limit
as well as the
+ slow-exchange limit.
The parameters of these two models are
- 'exp': [Rx, I0],
- 'inv': [Rx, I0, Iinf].
+ 'fast': [R2, Rex, kex],
+ 'slow': [R2A, kA, dw].
+
+
+ Examples
+ ~~~~~~~~
+
+ To pick the model 'fast' for all selected spins, type:
+
+ relax> relax_disp.select_model('fast')
+ relax> relax_disp.select_model(exp='fast')
"""
# Function intro text.
if self.__relax__.interpreter.intro:
- text = sys.ps3 + "relax_fit.select_model("
+ text = sys.ps3 + "relax_disp.select_model("
text = text + "model=" + `model` + ")"
print text
@@ -118,4 +125,4 @@
raise RelaxStrError, ('model', model)
# Execute the functional code.
- relax_fit_obj.select_model(model=model)
+ relax_disp_obj.select_model(model=model)
r8322 - /branches/relax_disp/prompt/relax_disp.py