Author: bugman
Date: Thu Apr 10 19:52:05 2014
New Revision: 22701
URL: http://svn.gna.org/viewcvs/relax?rev=22701&view=rev
Log:
Converted all of the N-state model parameters to use the parameter list
object.
The default_value(), return_data_name() and return_grace_string() API methods
have also been deleted
as these have been superseded by the parameter list object.
Modified:
trunk/specific_analyses/n_state_model/api.py
trunk/specific_analyses/n_state_model/parameter_object.py
Modified: trunk/specific_analyses/n_state_model/api.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/n_state_model/api.py?rev=22701&r1=22700&r2=22701&view=diff
==============================================================================
--- trunk/specific_analyses/n_state_model/api.py (original)
+++ trunk/specific_analyses/n_state_model/api.py Thu Apr 10 19:52:05
2014
@@ -62,7 +62,6 @@
# Place methods into the API.
self.model_loop = self._model_loop_single_global
self.overfit_deselect = self._overfit_deselect_dummy
- self.return_conversion_factor = self._return_no_conversion_factor
self.set_selected_sim = self._set_selected_sim_global
self.sim_return_selected = self._sim_return_selected_global
@@ -255,31 +254,6 @@
# Return the data.
return mc_data
-
-
- def default_value(self, param):
- """The default N-state model parameter values.
-
- @param param: The N-state model parameter.
- @type param: str
- @return: The default value.
- @rtype: float
- """
-
- # Split the parameter into its base name and index.
- name = self.return_data_name(param)
- index = param_model_index(param)
-
- # The number of states as a float.
- N = float(cdp.N)
-
- # Probability.
- if name == 'probs':
- return 1.0 / N
-
- # Euler angles.
- elif name == 'alpha' or name == 'beta' or name == 'gamma':
- return (float(index)+1) * pi / (N+1.0)
def grid_search(self, lower=None, upper=None, inc=None,
constraints=False, verbosity=0, sim_index=None):
@@ -671,48 +645,6 @@
return data
- def return_data_name(self, param):
- """Return a unique identifying string for the N-state model
parameter.
-
- @param param: The N-state model parameter.
- @type param: str
- @return: The unique parameter identifying string.
- @rtype: str
- """
-
- # Probability.
- if search('^p[0-9]*$', param):
- return 'probs'
-
- # Alpha Euler angle.
- if search('^alpha', param):
- return 'alpha'
-
- # Beta Euler angle.
- if search('^beta', param):
- return 'beta'
-
- # Gamma Euler angle.
- if search('^gamma', param):
- return 'gamma'
-
- # Bond length.
- if search('^r$', param) or search('[Bb]ond[ -_][Ll]ength', param):
- return 'r'
-
- # Heteronucleus type.
- if param == 'heteronuc_type':
- return 'heteronuc_type'
-
- # Proton type.
- if param == 'proton_type':
- return 'proton_type'
-
- # Paramagnetic centre.
- if search('^paramag_[xyz]$', param):
- return param
-
-
def return_error(self, data_id=None):
"""Create and return the spin specific Monte Carlo Ri error
structure.
@@ -773,34 +705,6 @@
# Return the errors.
return mc_errors
-
-
- def return_grace_string(self, param):
- """Return the Grace string representation of the parameter.
-
- This is used for axis labelling.
-
- @param param: The specific analysis parameter.
- @type param: str
- @return: The Grace string representation of the parameter.
- @rtype: str
- """
-
- # The measured PCS.
- if param == 'pcs':
- return "Measured PCS"
-
- # The back-calculated PCS.
- if param == 'pcs_bc':
- return "Back-calculated PCS"
-
- # The measured RDC.
- if param == 'rdc':
- return "Measured RDC"
-
- # The back-calculated RDC.
- if param == 'rdc_bc':
- return "Back-calculated RDC"
def set_error(self, model_info, index, error):
@@ -831,13 +735,15 @@
return getattr(tensor, names[param_index]+'_err')
- def set_param_values(self, param=None, value=None, spin_id=None,
error=False, force=True):
+ def set_param_values(self, param=None, value=None, index=None,
spin_id=None, error=False, force=True):
"""Set the N-state model parameter values.
@keyword param: The parameter name list.
@type param: list of str
@keyword value: The parameter value list.
@type value: list
+ @keyword index: The index for parameters which are of the
list-type (probs, alpha, beta, and gamma). This is ignored for all other
types.
+ @type index: None or int
@keyword spin_id: The spin identification string (unused).
@type spin_id: None
@keyword error: A flag which if True will allow the parameter
errors to be set instead of the values.
@@ -854,6 +760,8 @@
for i in range(len(param)):
# Get the object's name.
obj_name = self.return_data_name(param[i])
+ print param
+ print obj_name
# Is the parameter is valid?
if not obj_name:
@@ -865,29 +773,8 @@
# Set the indexed parameter.
if obj_name in ['probs', 'alpha', 'beta', 'gamma']:
- # The index.
- index = param_model_index(param[i])
-
- # Set.
obj = getattr(cdp, obj_name)
obj[index] = value[i]
-
- # The paramagnetic centre.
- if search('^paramag_[xyz]$', obj_name):
- # Init.
- if not hasattr(cdp, 'paramagnetic_centre'):
- cdp.paramagnetic_centre = zeros(3, float64)
-
- # Set the coordinate.
- if obj_name == 'paramag_x':
- index = 0
- elif obj_name == 'paramag_y':
- index = 1
- else:
- index = 2
-
- # Set the value in Angstrom.
- cdp.paramagnetic_centre[index] = value[i]
# Set the spin parameters.
else:
Modified: trunk/specific_analyses/n_state_model/parameter_object.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/n_state_model/parameter_object.py?rev=22701&r1=22700&r2=22701&view=diff
==============================================================================
--- trunk/specific_analyses/n_state_model/parameter_object.py (original)
+++ trunk/specific_analyses/n_state_model/parameter_object.py Thu Apr 10
19:52:05 2014
@@ -42,5 +42,12 @@
self.add_align_data()
self.add_csa()
+ # Add up the model parameters.
+ self.add('probs', scope='global', default=0.0, desc='The
probabilities of each state', py_type=list, set='params', err=True, sim=True)
+ self.add('alpha', scope='global', units='rad', default=0.0,
desc='The alpha Euler angles (for the rotation of each state)', py_type=list,
set='params', err=True, sim=True)
+ self.add('beta', scope='global', units='rad', default=0.0, desc='The
beta Euler angles (for the rotation of each state)', py_type=list,
set='params', err=True, sim=True)
+ self.add('gamma', scope='global', units='rad', default=0.0,
desc='The gamma Euler angles (for the rotation of each state)', py_type=list,
set='params', err=True, sim=True)
+ self.add('paramagnetic_centre', scope='global', units='Angstrom',
desc='The paramagnetic centre', py_type=float, set='params', err=True,
sim=True)
+
# Add the minimisation data.
self.add_min_data(min_stats_global=False, min_stats_spin=True)
r22701 - in /trunk/specific_analyses/n_state_model: api.py parameter_object.py