Author: bugman
Date: Wed Apr 3 11:50:44 2013
New Revision: 19315
URL: http://svn.gna.org/viewcvs/relax?rev=19315&view=rev
Log:
The specific_analyses.relax_disp module now uses the parameter list object to
define parameters.
This allows the now unused methods data_names(), default_value(),
return_data_name(), and
return_grace_string() to be deleted and their contents copied into the
parameter definitions in the
class __init__() method.
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=19315&r1=19314&r2=19315&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp.py Wed Apr 3 11:50:44
2013
@@ -44,6 +44,29 @@
class Relax_disp(API_base, API_common):
"""Class containing functions for relaxation dispersion curve fitting."""
+ def __init__(self):
+ """Initialise the class by placing API_common methods into the
API."""
+
+ # Execute the base class __init__ method.
+ super(Relax_disp, self).__init__()
+
+ # Set up the spin parameters.
+ self.PARAMS.add('intensities', scope='spin', py_type=dict,
grace_string='\\qPeak intensities\\Q')
+ self.PARAMS.add('relax_times', scope='spin', py_type=dict,
grace_string='\\qRelaxation time period (s)\\Q')
+ self.PARAMS.add('cpmg_frqs', scope='spin', py_type=dict,
grace_string='\\qCPMG pulse train frequency (Hz)\\Q')
+ self.PARAMS.add('r2', scope='spin', default=15.0, desc='The
effective transversal relaxation rate', set='params', py_type=dict,
grace_string='\\qR\\s2\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True)
+ self.PARAMS.add('i0', scope='spin', default=10000.0, desc='The
initial intensity', py_type=float, set='params', grace_string='\\qI\\s0\\Q',
err=True, sim=True)
+ self.PARAMS.add('rex', scope='spin', default=5.0, desc='The chemical
exchange contribution to R2', set='params', py_type=float,
grace_string='\\qR\\sex\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True)
+ self.PARAMS.add('kex', scope='spin', default=10000.0, desc='The
exchange rate', set='params', py_type=float, grace_string='\\qk\\sex\\N\\Q
(rad.s\\S-1\\N)', err=True, sim=True)
+ self.PARAMS.add('r2a', scope='spin', default=15.0, desc='The
transversal relaxation rate for state A', set='params', py_type=float,
grace_string='\\qR\\s2,A\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True)
+ self.PARAMS.add('ka', scope='spin', default=10000.0, desc='The
exchange rate from state A to state B', set='params', py_type=float,
grace_string='\\qk\\sA\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True)
+ self.PARAMS.add('dw', scope='spin', default=1000.0, desc='The
chemical shift difference between states A and B', set='params',
py_type=float, grace_string='\\q\\xDw\\f{}\\Q (Hz)', err=True, sim=True)
+ self.PARAMS.add('params', scope='spin', desc='The model parameters',
py_type=list)
+
+ # Add the minimisation data.
+ self.PARAMS.add_min_data(min_stats_global=False, min_stats_spin=True)
+
+
def assemble_param_vector(self, spin=None, sim_index=None):
"""Assemble the dispersion relaxation dispersion curve fitting
parameter vector (as a numpy array).
@@ -402,141 +425,6 @@
# If the name is not in 'spin', add it.
if not hasattr(spin, name):
setattr(spin, name, init_data)
-
-
- def data_names(self, set='all', error_names=False, sim_names=False):
- """Function for returning a list of names of data structures.
-
- Description
- ===========
-
- The names are as follows:
-
- - 'params', an array of the parameter names associated with the
model.
- - 'r2', the transversal relaxation rate.
- - 'rex', the chemical exchange contribution to 'R2'.
- - 'kex', the exchange rate.
- - 'r2a', the transversal relaxation rate for state A.
- - 'ka', the exchange rate from state A to state B.
- - 'dw', the chemical shift difference between states A and B.
- - 'chi2', chi-squared value.
- - 'iter', iterations.
- - 'f_count', function count.
- - 'g_count', gradient count.
- - 'h_count', hessian count.
- - 'warning', minimisation warning.
-
-
- @keyword set: The set of object names to return. This can
be set to 'all' for all
- names, to 'generic' for generic object
names, 'params' for parameter
- names,or to 'min' for minimisation specific
object names.
- @type set: str
- @keyword error_names: A flag which if True will add the error
object names as well.
- @type error_names: bool
- @keyword sim_names: A flag which if True will add the Monte
Carlo simulation object
- names as well.
- @type sim_names: bool
- @return: The list of object names.
- @rtype: list of str
- """
-
- # Initialise.
- names = []
-
- # Generic.
- if set == 'all' or set == 'generic':
- names.append('params')
-
- # Parameters.
- if set == 'all' or set == 'params':
- names.append('r2')
- names.append('rex')
- names.append('kex')
- names.append('r2a')
- names.append('ka')
- names.append('dw')
-
- # Minimisation statistics.
- if set == 'all' or set == 'min':
- names.append('chi2')
- names.append('iter')
- names.append('f_count')
- names.append('g_count')
- names.append('h_count')
- names.append('warning')
-
- # Parameter errors.
- if error_names and (set == 'all' or set == 'params'):
- names.append('r2_err')
- names.append('rex_err')
- names.append('kex_err')
- names.append('r2a_err')
- names.append('ka_err')
- names.append('dw_err')
-
- # Parameter simulation values.
- if sim_names and (set == 'all' or set == 'params'):
- names.append('r2_sim')
- names.append('rex_sim')
- names.append('kex_sim')
- names.append('r2a_sim')
- names.append('ka_sim')
- names.append('dw_sim')
-
- # Return the names.
- return names
-
-
- def default_value(self, param):
- """
- Relaxation dispersion curve fitting default values
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- These values are arbitrary and will depend on the system studied.
-
________________________________________________________________________________
- | |
| |
- | Data type | Object name
| Value |
-
|___________________________________________________|_______________|__________|
- | |
| |
- | Transversal relaxation rate | 'R2'
| 15.0 |
- | |
| |
- | Chemical exchange contribution to 'R2' | 'Rex'
| 5.0 |
- | |
| |
- | Exchange rate | 'kex'
| 10000.0 |
- | |
| |
- | Transversal relaxation rate for state A | 'R2A'
| 15.0 |
- | |
| |
- | Exchange rate from state A to state B | 'kA'
| 10000.0 |
- | |
| |
- | Chemical shift difference between states A and B | 'dw'
| 1000.0 |
- | |
| |
-
|___________________________________________________|_______________|__________|
-
- """
-
- # Transversal relaxation rate.
- if param == 'R2':
- return 15.0
-
- # Chemical exchange contribution to 'R2'.
- if param == 'Rex':
- return 5.0
-
- # Exchange rate.
- if param == 'kex':
- return 10000.0
-
- # Transversal relaxation rate for state A.
- if param == 'R2A' :
- return 15.0
-
- # Exchange rate from state A to state B.
- if param == 'kA' :
- return 10000
-
- # Chemical shift difference between states A and B.
- if param == 'dw' :
- return 1000.0
def disassemble_param_vector(self, param_vector=None, spin=None,
sim_index=None):
@@ -1092,47 +980,6 @@
_table.add_row(["CPMG pulse train frequency (series)", "'cpmg_frqs'"])
return_data_name_doc.add_table(_table.label)
- def return_data_name(self, name):
- """Return a unique identifying string for the relaxation dispersion
curve-fitting parameter.
-
- @param name: The relaxation dispersion curve-fitting parameter.
- @type name: str
- @return: The unique parameter identifying string.
- @rtype: str
- """
-
- # Transversal relaxation rate.
- if match('^[Rr]2$', name):
- return 'r2'
-
- # Chemical exchange contribution to 'R2'.
- if match('^[Rr]ex$', name):
- return 'rex'
-
- # Exchange rate.
- if match('^[Kk]ex$', name):
- return 'kex'
-
- # Transversal relaxation rate for state A.
- if match('^[Rr]2A$', name):
- return 'r2a'
-
- # Exchange rate from state A to state B.
- if match('^[Kk]A$', name):
- return 'ka'
-
- # Chemical shift difference between states A and B.
- if match ('^[Dd]w$', name):
- return 'dw'
-
- # Peak intensities (series)
- if match('^[Ii]nt$', name):
- return 'intensities'
-
- # CPMG pulse train frequency (series).
- if match('^[Cc]pmg[ -_][Ff]rqs$', name):
- return 'cpmg_frqs'
-
def return_error(self, spin_id):
"""Return the standard deviation data structure.
@@ -1151,48 +998,6 @@
return spin.intensity_err
- def return_grace_string(self, data_type):
- """Function for returning the Grace string representing the data
type for axis labelling."""
-
- # Get the object name.
- object_name = self.return_data_name(data_type)
-
- # Peak intensities.
- if object_name == 'intensities':
- grace_string = '\\qPeak intensities\\Q'
-
- # Transversal relaxation rate.
- elif object_name == 'r2':
- grace_string = '\\qR\\s2\\N (s\\S-1\\N)\\Q'
-
- # Chemical exchange contribution to 'R2'.
- elif object_name == 'rex':
- grace_string = '\\qR\\sex\\N (s\\S-1\\N)\\Q'
-
- # Exchange rate.
- elif object_name == 'kex':
- grace_string = '\\qk\\sex\\N (s\\S-1\\N)\\Q'
-
- # Transversal relaxation rate for state A.
- elif object_name == 'r2a':
- grace_string = '\\qR\\s2,A\\N (s\\S-1\\N)\\Q'
-
- # Exchange rate from state A to state B.
- elif object_name == 'ka':
- grace_string = '\\qk\\sA\\N (s\\S-1\\N)\\Q'
-
- # Chemical shift difference between states A and B.
- elif object_name == 'dw':
- grace_string = '\\q\\xDw\\f{} (Hz)\\Q'
-
- # CPMG pulse train frequency
- elif object_name == 'cpmg_frqs':
- grace_string = '\\qCPMG pulse train frequency (Hz)\\Q'
-
- # Return the Grace string.
- return grace_string
-
-
def return_units(self, stat_type):
"""Dummy function which returns None as the stats have no units."""
r19315 - /branches/relax_disp/specific_analyses/relax_disp.py