Author: bugman
Date: Tue Jul 29 13:11:20 2014
New Revision: 24801
URL: http://svn.gna.org/viewcvs/relax?rev=24801&view=rev
Log:
Redesign and expansion of the nested model parameter copying in the frame
order auto-analysis.
The nested parameter protocol used to allow the analysis to complete in under
1,000,000 years was no
longer functional due to the switching to the axis alpha parameter to
decrease parameter number and
redundancy. The copying of the average domain position for the free rotor
models was also incorrect
as the dropping of the alpha Euler angle cause the translation parameters and
beta and gamma angles
to change drastically.
The new protocol has been split into four methods for the average domain
position, the pivot point,
the motional eigenframe and the parameters of ordering. These use the fact
that the free rotor and
torsionless models are the two extrema of the models where the torsion angle
is restricted. The
pivot copying is a new addition.
Modified:
branches/frame_order_cleanup/auto_analyses/frame_order.py
Modified: branches/frame_order_cleanup/auto_analyses/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/auto_analyses/frame_order.py?rev=24801&r1=24800&r2=24801&view=diff
==============================================================================
--- branches/frame_order_cleanup/auto_analyses/frame_order.py (original)
+++ branches/frame_order_cleanup/auto_analyses/frame_order.py Tue Jul 29
13:11:20 2014
@@ -20,7 +20,14 @@
###############################################################################
# Module docstring.
-"""The full frame order analysis."""
+"""The full frame order analysis.
+
+
+The nested model parameter copying protocol
+===========================================
+
+To allow the analysis to complete in under 1,000,000 years, the trick of
copying parameters from simpler nested models is used in this auto-analysis.
The protocol is split into four categories for the average domain position,
the pivot point, the motional eigenframe and the parameters of ordering.
These use the fact that the free rotor and torsionless models are the two
extrema of the models where the torsion angle is restricted, whereby
sigma_max is pi and 0 respectively.
+"""
# Python module imports.
@@ -35,7 +42,11 @@
from lib.geometry.coord_transform import spherical_to_cartesian
from prompt.interpreter import Interpreter
from lib.errors import RelaxError
+from lib.frame_order.conversions import convert_axis_alpha_to_spherical
from lib.io import open_write_file
+from lib.order import iso_cone_theta_to_S
+from pipe_control.structure.mass import pipe_centre_of_mass
+from specific_analyses.frame_order.data import generate_pivot
from specific_analyses.frame_order.variables import MODEL_FREE_ROTOR,
MODEL_ISO_CONE, MODEL_ISO_CONE_FREE_ROTOR, MODEL_ISO_CONE_TORSIONLESS,
MODEL_LIST_FREE_ROTORS, MODEL_LIST_NONREDUNDANT, MODEL_LIST_PSEUDO_ELLIPSE,
MODEL_PSEUDO_ELLIPSE, MODEL_PSEUDO_ELLIPSE_FREE_ROTOR,
MODEL_PSEUDO_ELLIPSE_TORSIONLESS, MODEL_RIGID, MODEL_ROTOR
from status import Status; status = Status()
@@ -250,64 +261,207 @@
return incs
- def nested_params(self, model):
- """Copy the parameters from the simpler nested models for faster
optimisation.
+ def nested_params_ave_dom_pos(self, model):
+ """Copy the average domain parameters from simpler nested models for
faster optimisation.
@param model: The frame order model.
@type model: str
"""
+ # Skip the following models to allow for full optimisation.
+ if model in [MODEL_RIGID, MODEL_FREE_ROTOR]:
+ # Printout.
+ print("No nesting of the average domain position parameters.")
+
+ # Exit.
+ return
+
# The average position from the rigid model.
- if model not in []:
+ if model not in MODEL_LIST_FREE_ROTORS:
+ # Printout.
+ print("Obtaining the average position from the rigid model.")
+
# Get the rigid data pipe.
- rigid_pipe = get_pipe(self.pipe_name_dict[MODEL_RIGID])
+ pipe = get_pipe(self.pipe_name_dict[MODEL_RIGID])
# Copy the average position parameters from the rigid model.
- if hasattr(rigid_pipe, 'ave_pos_x'):
- cdp.ave_pos_x = rigid_pipe.ave_pos_x
- if hasattr(rigid_pipe, 'ave_pos_y'):
- cdp.ave_pos_y = rigid_pipe.ave_pos_y
- if hasattr(rigid_pipe, 'ave_pos_z'):
- cdp.ave_pos_z = rigid_pipe.ave_pos_z
- if model not in MODEL_LIST_FREE_ROTORS:
- cdp.ave_pos_alpha = rigid_pipe.ave_pos_alpha
- cdp.ave_pos_beta = rigid_pipe.ave_pos_beta
- cdp.ave_pos_gamma = rigid_pipe.ave_pos_gamma
+ cdp.ave_pos_x = pipe.ave_pos_x
+ cdp.ave_pos_y = pipe.ave_pos_y
+ cdp.ave_pos_z = pipe.ave_pos_z
+ cdp.ave_pos_alpha = pipe.ave_pos_alpha
+ cdp.ave_pos_beta = pipe.ave_pos_beta
+ cdp.ave_pos_gamma = pipe.ave_pos_gamma
+
+ # The average position from the free rotor model.
+ else:
+ # Printout.
+ print("Obtaining the average position from the free rotor
model.")
+
+ # Get the free rotor data pipe.
+ pipe = get_pipe(self.pipe_name_dict[MODEL_FREE_ROTOR])
+
+ # Copy the average position parameters from the free rotor model.
+ cdp.ave_pos_x = pipe.ave_pos_x
+ cdp.ave_pos_y = pipe.ave_pos_y
+ cdp.ave_pos_z = pipe.ave_pos_z
+ cdp.ave_pos_beta = pipe.ave_pos_beta
+ cdp.ave_pos_gamma = pipe.ave_pos_gamma
+
+
+ def nested_params_eigenframe(self, model):
+ """Copy the eigenframe parameters from simpler nested models for
faster optimisation.
+
+ @param model: The frame order model.
+ @type model: str
+ """
+
+ # Skip the following models to allow for full optimisation.
+ if model in [MODEL_ROTOR, MODEL_PSEUDO_ELLIPSE]:
+ # Printout.
+ print("No nesting of the eigenframe parameters.")
+
+ # Exit.
+ return
# The cone axis from the rotor model.
- if model in [MODEL_ISO_CONE]:
+ if model in [MODEL_FREE_ROTOR, MODEL_ISO_CONE]:
+ # Printout.
+ print("Obtaining the cone axis from the rotor model.")
+
# Get the rotor data pipe.
- rotor_pipe = get_pipe(self.pipe_name_dict[MODEL_ROTOR])
+ pipe = get_pipe(self.pipe_name_dict[MODEL_ROTOR])
+
+ # The cone axis as the axis alpha angle.
+ if model == MODEL_FREE_ROTOR:
+ cdp.axis_alpha = pipe.axis_alpha
+
+ # The cone axis from the axis alpha angle to spherical angles.
+ if model == MODEL_ISO_CONE:
+ cdp.axis_theta, cdp_axis_phi =
convert_axis_alpha_to_spherical(alpha=pipe.axis_alpha,
pivot=generate_pivot(order=1, pipe_name=self.pipe_name_dict[MODEL_ROTOR]),
point=pipe_centre_of_mass(verbosity=0))
+
+ # The cone axis from the isotropic cone model.
+ elif model in [MODEL_ISO_CONE_FREE_ROTOR,
MODEL_ISO_CONE_TORSIONLESS]:
+ # Printout.
+ print("Obtaining the cone axis from the isotropic cone model.")
+
+ # Get the iso cone data pipe.
+ pipe = get_pipe(self.pipe_name_dict[MODEL_ISO_CONE])
+
+ # Copy the cone axis parameters.
+ cdp.axis_theta = pipe.axis_theta
+ cdp.axis_phi = pipe.axis_phi
+
+ # The full eigenframe from the pseudo-ellipse model.
+ elif model in [MODEL_PSEUDO_ELLIPSE_FREE_ROTOR,
MODEL_PSEUDO_ELLIPSE_TORSIONLESS, MODEL_DOUBLE_ROTOR]:
+ # Printout.
+ print("Obtaining the full eigenframe from the pseudo-ellipse
model.")
+
+ # Get the pseudo-ellipse data pipe.
+ pipe = get_pipe(self.pipe_name_dict[MODEL_PSEUDO_ELLIPSE])
+
+ # Copy the three Euler angles.
+ cdp.eigen_alpha = pipe.eigen_alpha
+ cdp.eigen_beta = pipe.eigen_beta
+ cdp.eigen_gamma = pipe.eigen_gamma
+
+
+ def nested_params_order(self, model):
+ """Copy the order parameters from simpler nested models for faster
optimisation.
+
+ @param model: The frame order model.
+ @type model: str
+ """
+
+ # Skip the following models to allow for full optimisation.
+ if model in [MODEL_ROTOR, MODEL_DOUBLE_ROTOR]:
+ # Printout.
+ print("No nesting of the order parameters.")
+
+ # Exit.
+ return
+
+ # The cone angle from the isotropic cone model.
+ if model in [MODEL_ISO_CONE_TORSIONLESS, MODEL_PSEUDO_ELLIPSE,
MODEL_ISO_CONE_FREE_ROTOR]:
+ # Get the iso cone data pipe.
+ pipe = get_pipe(self.pipe_name_dict[MODEL_ISO_CONE])
+
+ # Copy the cone angle directly.
+ if model == MODEL_ISO_CONE_TORSIONLESS:
+ print("Obtaining the cone angle from the isotropic cone
model.")
+ cdp.cone_theta = pipe.cone_theta
+
+ # Copy as the X cone angle.
+ elif model == MODEL_PSEUDO_ELLIPSE:
+ print("Obtaining the cone X angle from the isotropic cone
model.")
+ cdp.cone_theta_x = pipe.cone_theta
+
+ # Convert to the order parameter S.
+ elif model == MODEL_ISO_CONE_FREE_ROTOR:
+ print("Obtaining the cone order parameter from the isotropic
cone model.")
+ cdp.cone_s1 = iso_cone_theta_to_S(pipe.cone_theta)
+
+ # The X and Y cone angles from the pseudo-ellipse model.
+ elif model in [MODEL_PSEUDO_ELLIPSE_TORSIONLESS,
MODEL_PSEUDO_ELLIPSE_FREE_ROTOR]:
+ # Printout.
+ print("Obtaining the cone X and Y angles from the pseudo-ellipse
model.")
+
+ # Get the pseudo-ellipse data pipe.
+ pipe = get_pipe(self.pipe_name_dict[MODEL_PSEUDO_ELLIPSE])
# Copy the cone axis.
- cdp.axis_theta = rotor_pipe.axis_theta
- cdp.axis_phi = rotor_pipe.axis_phi
-
- # The cone axis from the free rotor model.
- if model in [MODEL_ISO_CONE_FREE_ROTOR]:
- # Get the rotor data pipe.
- free_rotor_pipe = get_pipe(self.pipe_name_dict[MODEL_FREE_ROTOR])
-
- # Copy the cone axis.
- cdp.axis_theta = free_rotor_pipe.axis_theta
- cdp.axis_phi = free_rotor_pipe.axis_phi
+ cdp.cone_theta_x = pipe.cone_theta_x
+ cdp.cone_theta_y = pipe.cone_theta_y
+
# The torsion from the rotor model.
if model in [MODEL_ISO_CONE, MODEL_PSEUDO_ELLIPSE]:
# Get the rotor data pipe.
- rotor_pipe = get_pipe(self.pipe_name_dict[MODEL_ROTOR])
+ pipe = get_pipe(self.pipe_name_dict[MODEL_ROTOR])
# Copy the cone axis.
- cdp.cone_sigma_max = rotor_pipe.cone_sigma_max
-
- # The cone angles from from the torsionless isotropic cone model.
- if model in MODEL_LIST_PSEUDO_ELLIPSE:
- # Get the rotor data pipe.
- pipe = get_pipe(self.pipe_name_dict[MODEL_ISO_CONE_TORSIONLESS])
-
- # Copy the cone axis.
- cdp.cone_theta_x = pipe.cone_theta
- cdp.cone_theta_y = pipe.cone_theta
+ cdp.cone_sigma_max = pipe.cone_sigma_max
+
+
+ def nested_params_pivot(self, model):
+ """Copy the pivot parameters from simpler nested models for faster
optimisation.
+
+ @param model: The frame order model.
+ @type model: str
+ """
+
+ # Skip the following models to allow for full optimisation.
+ if model in [MODEL_ROTOR]:
+ # Printout.
+ print("No nesting of the pivot parameters.")
+
+ # Exit.
+ return
+
+ # The pivot from the rotor model.
+ if model in [MODEL_ISO_CONE, MODEL_FREE_ROTOR]:
+ # Printout.
+ print("Obtaining the pivot point from the rotor model.")
+
+ # Get the iso cone data pipe.
+ pipe = get_pipe(self.pipe_name_dict[MODEL_ROTOR])
+
+ # Copy the pivot parameters.
+ cdp.pivot_x = pipe.pivot_x
+ cdp.pivot_y = pipe.pivot_y
+ cdp.pivot_z = pipe.pivot_z
+
+ # The pivot from the isotropic cone model.
+ else:
+ # Printout.
+ print("Obtaining the pivot point from the isotropic cone model.")
+
+ # Get the iso cone data pipe.
+ pipe = get_pipe(self.pipe_name_dict[MODEL_ISO_CONE])
+
+ # Copy the cone axis parameters.
+ cdp.pivot_x = pipe.pivot_x
+ cdp.pivot_y = pipe.pivot_y
+ cdp.pivot_z = pipe.pivot_z
def nested_models(self):
@@ -351,7 +505,11 @@
self.interpreter.frame_order.select_model(model=model)
# Copy nested parameters.
- self.nested_params(model)
+ subsection(file=sys.stdout, text="Parameter nesting.")
+ self.nested_params_ave_dom_pos(model)
+ self.nested_params_eigenframe(model)
+ self.nested_params_pivot(model)
+ self.nested_params_order(model)
# The optimisation settings.
self.interpreter.frame_order.num_int_pts(num=self.num_int_pts_grid)
r24801 - /branches/frame_order_cleanup/auto_analyses/frame_order.py