Author: bugman
Date: Wed Nov 2 17:21:15 2011
New Revision: 14959
URL: http://svn.gna.org/viewcvs/relax?rev=14959&view=rev
Log:
Monte Carlo simulations are now implemented for the frame order analysis.
Modified:
1.3/specific_fns/frame_order.py
Modified: 1.3/specific_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/frame_order.py?rev=14959&r1=14958&r2=14959&view=diff
==============================================================================
--- 1.3/specific_fns/frame_order.py (original)
+++ 1.3/specific_fns/frame_order.py Wed Nov 2 17:21:15 2011
@@ -57,6 +57,7 @@
"""Initialise the class by placing API_common methods into the
API."""
# Place methods into the API.
+ self.eliminate = self._eliminate_false
self.overfit_deselect = self._overfit_deselect_dummy
self.return_conversion_factor = self._return_no_conversion_factor
self.return_data_name = self._return_data_name
@@ -78,44 +79,82 @@
return lower, upper
- def _assemble_param_vector(self):
+ def _assemble_param_vector(self, sim_index=None):
"""Assemble and return the parameter vector.
- @return: The parameter vector.
- @rtype: numpy rank-1 array
- """
-
- # Initialise the parameter array using the tensor rotation Euler
angles (average domain position).
- if cdp.model in ['free rotor', 'iso cone, torsionless', 'iso cone,
free rotor']:
- param_vect = [cdp.ave_pos_beta, cdp.ave_pos_gamma]
+ @return: The parameter vector.
+ @rtype: numpy rank-1 array
+ @keyword sim_index: The Monte Carlo simulation index.
+ @type sim_index: int
+ """
+
+ # Normal values.
+ if sim_index == None:
+ # Initialise the parameter array using the tensor rotation Euler
angles (average domain position).
+ if cdp.model in ['free rotor', 'iso cone, torsionless', 'iso
cone, free rotor']:
+ param_vect = [cdp.ave_pos_beta, cdp.ave_pos_gamma]
+ else:
+ param_vect = [cdp.ave_pos_alpha, cdp.ave_pos_beta,
cdp.ave_pos_gamma]
+
+ # Frame order eigenframe - the full frame.
+ if cdp.model in ['iso cone', 'pseudo-ellipse', 'pseudo-ellipse,
torsionless', 'pseudo-ellipse, free rotor']:
+ param_vect.append(cdp.eigen_alpha)
+ param_vect.append(cdp.eigen_beta)
+ param_vect.append(cdp.eigen_gamma)
+
+ # Frame order eigenframe - the isotropic cone axis.
+ elif cdp.model in ['free rotor', 'iso cone, torsionless', 'iso
cone, free rotor', 'rotor']:
+ param_vect.append(cdp.axis_theta)
+ param_vect.append(cdp.axis_phi)
+
+ # Cone parameters - pseudo-elliptic cone parameters.
+ if cdp.model in ['pseudo-ellipse', 'pseudo-ellipse,
torsionless', 'pseudo-ellipse, free rotor']:
+ param_vect.append(cdp.cone_theta_x)
+ param_vect.append(cdp.cone_theta_y)
+
+ # Cone parameters - single isotropic angle or order parameter.
+ elif cdp.model in ['iso cone', 'iso cone, torsionless']:
+ param_vect.append(cdp.cone_theta)
+ elif cdp.model in ['iso cone, free rotor']:
+ param_vect.append(cdp.cone_s1)
+
+ # Cone parameters - torsion angle.
+ if cdp.model in ['rotor', 'line', 'iso cone', 'pseudo-ellipse']:
+ param_vect.append(cdp.cone_sigma_max)
+
+ # Simulation values.
else:
- param_vect = [cdp.ave_pos_alpha, cdp.ave_pos_beta,
cdp.ave_pos_gamma]
-
- # Frame order eigenframe - the full frame.
- if cdp.model in ['iso cone', 'pseudo-ellipse', 'pseudo-ellipse,
torsionless', 'pseudo-ellipse, free rotor']:
- param_vect.append(cdp.eigen_alpha)
- param_vect.append(cdp.eigen_beta)
- param_vect.append(cdp.eigen_gamma)
-
- # Frame order eigenframe - the isotropic cone axis.
- elif cdp.model in ['free rotor', 'iso cone, torsionless', 'iso cone,
free rotor', 'rotor']:
- param_vect.append(cdp.axis_theta)
- param_vect.append(cdp.axis_phi)
-
- # Cone parameters - pseudo-elliptic cone parameters.
- if cdp.model in ['pseudo-ellipse', 'pseudo-ellipse, torsionless',
'pseudo-ellipse, free rotor']:
- param_vect.append(cdp.cone_theta_x)
- param_vect.append(cdp.cone_theta_y)
-
- # Cone parameters - single isotropic angle or order parameter.
- elif cdp.model in ['iso cone', 'iso cone, torsionless']:
- param_vect.append(cdp.cone_theta)
- elif cdp.model in ['iso cone, free rotor']:
- param_vect.append(cdp.cone_s1)
-
- # Cone parameters - torsion angle.
- if cdp.model in ['rotor', 'line', 'iso cone', 'pseudo-ellipse']:
- param_vect.append(cdp.cone_sigma_max)
+ # Initialise the parameter array using the tensor rotation Euler
angles (average domain position).
+ if cdp.model in ['free rotor', 'iso cone, torsionless', 'iso
cone, free rotor']:
+ param_vect = [cdp.ave_pos_beta_sim[sim_index],
cdp.ave_pos_gamma_sim[sim_index]]
+ else:
+ param_vect = [cdp.ave_pos_alpha_sim[sim_index],
cdp.ave_pos_beta_sim[sim_index], cdp.ave_pos_gamma_sim[sim_index]]
+
+ # Frame order eigenframe - the full frame.
+ if cdp.model in ['iso cone', 'pseudo-ellipse', 'pseudo-ellipse,
torsionless', 'pseudo-ellipse, free rotor']:
+ param_vect.append(cdp.eigen_alpha_sim[sim_index])
+ param_vect.append(cdp.eigen_beta_sim[sim_index])
+ param_vect.append(cdp.eigen_gamma_sim[sim_index])
+
+ # Frame order eigenframe - the isotropic cone axis.
+ elif cdp.model in ['free rotor', 'iso cone, torsionless', 'iso
cone, free rotor', 'rotor']:
+ param_vect.append(cdp.axis_theta_sim[sim_index])
+ param_vect.append(cdp.axis_phi_sim[sim_index])
+
+ # Cone parameters - pseudo-elliptic cone parameters.
+ if cdp.model in ['pseudo-ellipse', 'pseudo-ellipse,
torsionless', 'pseudo-ellipse, free rotor']:
+ param_vect.append(cdp.cone_theta_x_sim[sim_index])
+ param_vect.append(cdp.cone_theta_y_sim[sim_index])
+
+ # Cone parameters - single isotropic angle or order parameter.
+ elif cdp.model in ['iso cone', 'iso cone, torsionless']:
+ param_vect.append(cdp.cone_theta_sim[sim_index])
+ elif cdp.model in ['iso cone, free rotor']:
+ param_vect.append(cdp.cone_s1_sim[sim_index])
+
+ # Cone parameters - torsion angle.
+ if cdp.model in ['rotor', 'line', 'iso cone', 'pseudo-ellipse']:
+ param_vect.append(cdp.cone_sigma_max_sim[sim_index])
# Return as a numpy array.
return array(param_vect, float64)
@@ -221,6 +260,7 @@
# Rotations and inversions.
axis_pos = axis
axis_neg = dot(inv_mat, axis)
+ print inv_mat
# Simulation central axis.
axis_sim_pos = None
@@ -234,8 +274,9 @@
spherical_to_cartesian([1.0, getattr(cdp,
theta_name+'_sim')[i], getattr(cdp, phi_name+'_sim')[i]], axis_sim[i])
# Inversion.
- axis_sim_pos = axis_sim_pos
- axis_sim_neg = dot(inv_mat, axis_sim_pos)
+ axis_sim_pos = axis_sim
+ print axis_sim_pos
+ axis_sim_neg = transpose(dot(inv_mat, transpose(axis_sim_pos)))
# Generate the axis vectors.
print("\nGenerating the axis vectors.")
@@ -715,11 +756,11 @@
# Eigenframe parameters.
if eigen_alpha != None:
- cdp.eigen_alpha[sim_index] = wrap_angles(eigen_alpha, 0.0,
2.0*pi)
+ cdp.eigen_alpha_sim[sim_index] = wrap_angles(eigen_alpha,
0.0, 2.0*pi)
if eigen_beta != None:
- cdp.eigen_beta[sim_index] = wrap_angles(eigen_beta, 0.0,
2.0*pi)
+ cdp.eigen_beta_sim[sim_index] = wrap_angles(eigen_beta,
0.0, 2.0*pi)
if eigen_gamma != None:
- cdp.eigen_gamma[sim_index] = wrap_angles(eigen_gamma, 0.0,
2.0*pi)
+ cdp.eigen_gamma_sim[sim_index] = wrap_angles(eigen_gamma,
0.0, 2.0*pi)
if axis_theta != None:
cdp.axis_theta_sim[sim_index] = axis_theta
if axis_phi != None:
@@ -730,13 +771,13 @@
cdp.cone_theta_sim[sim_index] = cone_theta
if cone_s1 != None:
cdp.cone_s1_sim[sim_index] = cone_s1
- cdp.cone_theta[sim_index] =
order_parameters.iso_cone_S_to_theta(cone_s1)
+ cdp.cone_theta_sim[sim_index] =
order_parameters.iso_cone_S_to_theta(cone_s1)
if cone_theta_x != None:
- cdp.cone_theta_x[sim_index] = cone_theta_x
+ cdp.cone_theta_x_sim[sim_index] = cone_theta_x
if cone_theta_y != None:
- cdp.cone_theta_y[sim_index] = cone_theta_y
+ cdp.cone_theta_y_sim[sim_index] = cone_theta_y
if cone_sigma_max != None:
- cdp.cone_sigma_max[sim_index] = abs(cone_sigma_max)
+ cdp.cone_sigma_max_sim[sim_index] = abs(cone_sigma_max)
# Optimisation stats.
cdp.chi2_sim[sim_index] = func
@@ -945,6 +986,35 @@
# Return the names.
return names
+
+
+ def get_param_names(self, model_info=None):
+ """Return a vector of parameter names.
+
+ @keyword model_info: The model index from model_info().
+ @type model_info: int
+ @return: The vector of parameter names.
+ @rtype: list of str
+ """
+
+ # Return the parameter object names.
+ param_names = self.data_names(set='params')
+ return param_names
+
+
+ def get_param_values(self, model_info=None, sim_index=None):
+ """Return a vector of parameter values.
+
+ @keyword model_info: The model index from model_info(). This is
zero for the global models or equal to the global spin index (which covers
the molecule, residue, and spin indices).
+ @type model_info: int
+ @keyword sim_index: The Monte Carlo simulation index.
+ @type sim_index: int
+ @return: The vector of parameter values.
+ @rtype: list of str
+ """
+
+ # Assemble the values and return it.
+ return self._assemble_param_vector(sim_index=sim_index)
def grid_search(self, lower=None, upper=None, inc=None,
constraints=False, verbosity=0, sim_index=None):
r14959 - /1.3/specific_fns/frame_order.py