Author: bugman
Date: Tue Sep 1 10:15:08 2009
New Revision: 9418
URL: http://svn.gna.org/viewcvs/relax?rev=9418&view=rev
Log:
Rearrangement of the handling of frame order models.
The tensor rotation Euler angles are now model independent, the 'rigid' model
is better supported,
and a clear isolation of the isotropic cone model has been made.
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=9418&r1=9417&r2=9418&view=diff
==============================================================================
--- 1.3/specific_fns/frame_order.py (original)
+++ 1.3/specific_fns/frame_order.py Tue Sep 1 10:15:08 2009
@@ -161,41 +161,29 @@
if not hasattr(cdp, 'params'):
cdp.params = []
- # The rigid model.
- if cdp.model == 'rigid':
- # Set up the parameter arrays.
- if not len(cdp.params):
- cdp.params.append('alpha')
- cdp.params.append('beta')
- cdp.params.append('gamma')
-
- # Initialise the tensor rotation angles.
- if not hasattr(cdp, 'alpha'):
- cdp.alpha = 0.0
- if not hasattr(cdp, 'beta'):
- cdp.beta = 0.0
- if not hasattr(cdp, 'gamma'):
- cdp.gamma = 0.0
-
+ # Set up the tensor rotation parameter arrays.
+ if not len(cdp.params):
+ cdp.params.append('alpha')
+ cdp.params.append('beta')
+ cdp.params.append('gamma')
+
+ # Initialise the tensor rotation angles.
+ if not hasattr(cdp, 'alpha'):
+ cdp.alpha = 0.0
+ if not hasattr(cdp, 'beta'):
+ cdp.beta = 0.0
+ if not hasattr(cdp, 'gamma'):
+ cdp.gamma = 0.0
# Isotropic cone model.
if cdp.model == 'iso cone':
# Set up the parameter arrays.
if not len(cdp.params):
- cdp.params.append('alpha')
- cdp.params.append('beta')
- cdp.params.append('gamma')
cdp.params.append('theta_axis')
cdp.params.append('phi_axis')
cdp.params.append('theta_cone')
# Initialise the cone axis angles and cone angle values.
- if not hasattr(cdp, 'alpha'):
- cdp.alpha = 0.0
- if not hasattr(cdp, 'beta'):
- cdp.beta = 0.0
- if not hasattr(cdp, 'gamma'):
- cdp.gamma = 0.0
if not hasattr(cdp, 'theta_axis'):
cdp.theta_axis = 0.0
if not hasattr(cdp, 'phi_axis'):
@@ -233,27 +221,8 @@
# Disassemble the parameter vector.
alpha, beta, gamma = param_vector
- # Wrap the Euler angles.
- alpha = wrap_angles(alpha, 0.0, 2.0*pi)
- beta = wrap_angles(beta, 0.0, 2.0*pi)
- gamma = wrap_angles(gamma, 0.0, 2.0*pi)
-
- # Monte Carlo simulation data structures.
- if sim_index != None:
- # Model parameters.
- cdp.alpha_sim[sim_index] = alpha
- cdp.beta_sim[sim_index] = beta
- cdp.gamma_sim[sim_index] = gamma
-
- # Normal data structures.
- else:
- # Model parameters.
- cdp.alpha = alpha
- cdp.beta = beta
- cdp.gamma = gamma
-
# Isotropic cone model.
- if cdp.model == 'iso cone':
+ elif cdp.model == 'iso cone':
# Disassemble the parameter vector.
alpha, beta, gamma, theta_axis, phi_axis, theta_cone =
param_vector
@@ -263,17 +232,9 @@
if theta_cone > pi:
theta_cone = 2.0*pi - theta_cone
- # Wrap the Euler angles.
- alpha = wrap_angles(alpha, 0.0, 2.0*pi)
- beta = wrap_angles(beta, 0.0, 2.0*pi)
- gamma = wrap_angles(gamma, 0.0, 2.0*pi)
-
# Monte Carlo simulation data structures.
if sim_index != None:
# Model parameters.
- cdp.alpha_sim[sim_index] = alpha
- cdp.beta_sim[sim_index] = beta
- cdp.gamma_sim[sim_index] = gamma
cdp.theta_axis_sim[sim_index] = theta_axis
cdp.phi_axis_sim[sim_index] = phi_axis
cdp.theta_cone_sim[sim_index] = theta_cone
@@ -281,15 +242,23 @@
# Normal data structures.
else:
# Model parameters.
- cdp.alpha = alpha
- cdp.beta = beta
- cdp.gamma = gamma
cdp.theta_axis = theta_axis
cdp.phi_axis = phi_axis
cdp.theta_cone = theta_cone
- # Monte Carlo simulation optimisation data structures.
+ # Wrap the Euler angles.
+ alpha = wrap_angles(alpha, 0.0, 2.0*pi)
+ beta = wrap_angles(beta, 0.0, 2.0*pi)
+ gamma = wrap_angles(gamma, 0.0, 2.0*pi)
+
+ # Monte Carlo simulation data structures.
if sim_index != None:
+ # Tensor rotation.
+ cdp.alpha_sim[sim_index] = alpha
+ cdp.beta_sim[sim_index] = beta
+ cdp.gamma_sim[sim_index] = gamma
+
+ # Optimisation stats.
cdp.chi2_sim[sim_index] = func
cdp.iter_sim[sim_index] = iter_count
cdp.f_count_sim[sim_index] = f_count
@@ -299,6 +268,12 @@
# Normal optimisation data structures.
else:
+ # Tensor rotation.
+ cdp.alpha = alpha
+ cdp.beta = beta
+ cdp.gamma = gamma
+
+ # Optimisation stats.
cdp.chi2 = func
cdp.iter = iter_count
cdp.f_count = f_count
@@ -318,19 +293,22 @@
# Alias the current data pipe.
cdp = pipes.get_pipe()
- # Isotropic cone model.
- if cdp.model == 'iso cone':
- # The initial parameter vector (the cone axis angles and the
cone angle).
+ # The rigid model initial parameter vector (the cone axis angles and
the cone angle).
+ if cdp.model == 'rigid':
+ param_vector = array([cdp.alpha, cdp.beta, cdp.gamma], float64)
+
+ # The isotropic cone model initial parameter vector (the cone axis
angles and the cone angle).
+ elif cdp.model == 'iso cone':
param_vector = array([cdp.alpha, cdp.beta, cdp.gamma,
cdp.theta_axis, cdp.phi_axis, cdp.theta_cone], float64)
- # Get the data structures for optimisation using the tensors as
base data sets.
- full_tensors, red_tensors, red_tensor_err, full_in_ref_frame =
self.__minimise_setup_tensors()
-
- # Set up the optimisation function.
- target = frame_order_models.Frame_order(model=cdp.model,
full_tensors=full_tensors, red_tensors=red_tensors,
red_errors=red_tensor_err, full_in_ref_frame=full_in_ref_frame)
-
- # Make a single function call. This will cause back calculation
and the data will be stored in the class instance.
- target.func(param_vector)
+ # Get the data structures for optimisation using the tensors as base
data sets.
+ full_tensors, red_tensors, red_tensor_err, full_in_ref_frame =
self.__minimise_setup_tensors()
+
+ # Set up the optimisation function.
+ target = frame_order_models.Frame_order(model=cdp.model,
full_tensors=full_tensors, red_tensors=red_tensors,
red_errors=red_tensor_err, full_in_ref_frame=full_in_ref_frame)
+
+ # Make a single function call. This will cause back calculation and
the data will be stored in the class instance.
+ target.func(param_vector)
# Return the reduced tensors.
return target.red_tensors_bc
@@ -354,19 +332,22 @@
# Alias the current data pipe.
cdp = pipes.get_pipe()
- # Isotropic cone model.
- if cdp.model == 'iso cone':
- # The initial parameter vector (the cone axis angles and the
cone angle).
+ # The rigid model initial parameter vector (the cone axis angles and
the cone angle).
+ if cdp.model == 'rigid':
+ param_vector = array([cdp.alpha, cdp.beta, cdp.gamma], float64)
+
+ # The isotropic cone model initial parameter vector (the cone axis
angles and the cone angle).
+ elif cdp.model == 'iso cone':
param_vector = array([cdp.alpha, cdp.beta, cdp.gamma,
cdp.theta_axis, cdp.phi_axis, cdp.theta_cone], float64)
- # Get the data structures for optimisation using the tensors as
base data sets.
- full_tensors, red_tensors, red_tensor_err, full_in_ref_frame =
self.__minimise_setup_tensors()
-
- # Set up the optimisation function.
- target = frame_order_models.Frame_order(model=cdp.model,
full_tensors=full_tensors, red_tensors=red_tensors,
red_errors=red_tensor_err, full_in_ref_frame=full_in_ref_frame)
-
- # Make a single function call. This will cause back calculation
and the data will be stored in the class instance.
- chi2 = target.func(param_vector)
+ # Get the data structures for optimisation using the tensors as base
data sets.
+ full_tensors, red_tensors, red_tensor_err, full_in_ref_frame =
self.__minimise_setup_tensors()
+
+ # Set up the optimisation function.
+ target = frame_order_models.Frame_order(model=cdp.model,
full_tensors=full_tensors, red_tensors=red_tensors,
red_errors=red_tensor_err, full_in_ref_frame=full_in_ref_frame)
+
+ # Make a single function call. This will cause back calculation and
the data will be stored in the class instance.
+ chi2 = target.func(param_vector)
# Set the chi2.
cdp.chi2 = chi2
@@ -394,6 +375,10 @@
# Alias the current data pipe.
cdp = pipes.get_pipe()
+ # Test the model.
+ if not cdp.model in ['iso cone']:
+ raise RelaxError("A cone PDB representation of the '%s' model
cannot be made." % cdp.model)
+
# Test for the data structures.
if not hasattr(cdp, 'theta_cone'):
raise RelaxError("The cone angle theta_cone does not exist.")
@@ -497,15 +482,18 @@
The names are as follows:
- 'params', an array of the parameter names associated with the
model.
- - 'theta_axis', the cone axis polar angle (for the isotropic
cone model).
- - 'phi_axis', the cone axis azimuthal angle (for the isotropic
cone model).
- - 'theta_cone', the isotropic cone angle.
- 'chi2', chi-squared value.
- 'iter', iterations.
- 'f_count', function count.
- 'g_count', gradient count.
- 'h_count', hessian count.
- 'warning', minimisation warning.
+
+ The isotropic cone specific model parameters are:
+
+ - 'theta_axis', the cone axis polar angle (for the isotropic
cone model).
+ - 'phi_axis', the cone axis azimuthal angle (for the isotropic
cone model).
+ - 'theta_cone', the isotropic cone angle.
@keyword set: The set of object names to return. This can
be set to 'all' for all
@@ -534,9 +522,12 @@
names.append('alpha')
names.append('beta')
names.append('gamma')
- names.append('theta_axis')
- names.append('phi_axis')
- names.append('theta_cone')
+
+ # The isotropic cone model.
+ if cdp.model == 'iso cone':
+ names.append('theta_axis')
+ names.append('phi_axis')
+ names.append('theta_cone')
# Minimisation statistics.
if set == 'all' or set == 'min':
@@ -552,18 +543,24 @@
names.append('alpha_err')
names.append('beta_err')
names.append('gamma_err')
- names.append('theta_axis_err')
- names.append('phi_axis_err')
- names.append('theta_cone_err')
+
+ # The isotropic cone model.
+ if cdp.model == 'iso cone':
+ names.append('theta_axis_err')
+ names.append('phi_axis_err')
+ names.append('theta_cone_err')
# Parameter simulation values.
if sim_names and (set == 'all' or set == 'params'):
names.append('alpha_sim')
names.append('beta_sim')
names.append('gamma_sim')
- names.append('theta_axis_sim')
- names.append('phi_axis_sim')
- names.append('theta_cone_sim')
+
+ # The isotropic cone model.
+ if cdp.model == 'iso cone':
+ names.append('theta_axis_sim')
+ names.append('phi_axis_sim')
+ names.append('theta_cone_sim')
# Return the names.
return names
@@ -620,15 +617,17 @@
if cdp.params[i] == 'gamma':
grid_ops.append([inc[i], 0.0, 2*pi])
- # Cone axis angles and cone angle.
- if cdp.params[i] == 'theta_axis':
- grid_ops.append([inc[i], 0.0, pi])
- if cdp.params[i] == 'phi_axis':
- grid_ops.append([inc[i], 0.0, 2*pi])
-
- # The cone angle.
- if cdp.params[i] == 'theta_cone':
- grid_ops.append([inc[i], 0.0, pi])
+ # The isotropic cone model.
+ if cdp.model == 'iso cone':
+ # Cone axis angles and cone angle.
+ if cdp.params[i] == 'theta_axis':
+ grid_ops.append([inc[i], 0.0, pi])
+ if cdp.params[i] == 'phi_axis':
+ grid_ops.append([inc[i], 0.0, 2*pi])
+
+ # The cone angle.
+ if cdp.params[i] == 'theta_cone':
+ grid_ops.append([inc[i], 0.0, pi])
# Lower bound (if supplied).
if lower:
@@ -686,14 +685,12 @@
# Throw a warning.
warn(RelaxWarning("Constraints are as of yet not implemented -
turning this option off."))
- # The rigid model.
+ # The rigid model initial parameter vector (the cone axis angles and
the cone angle).
if cdp.model == 'rigid':
- # The initial parameter vector (tensor rotation Euler angles).
param_vector = array([cdp.alpha, cdp.beta, cdp.gamma], float64)
- # Isotropic cone model.
- if cdp.model == 'iso cone':
- # The initial parameter vector (tensor rotation Euler angles,
the cone axis angles and the cone angle).
+ # The isotropic cone model initial parameter vector (the cone axis
angles and the cone angle).
+ elif cdp.model == 'iso cone':
param_vector = array([cdp.alpha, cdp.beta, cdp.gamma,
cdp.theta_axis, cdp.phi_axis, cdp.theta_cone], float64)
# Get the data structures for optimisation using the tensors as base
data sets.
r9418 - /1.3/specific_fns/frame_order.py