Author: bugman
Date: Fri Nov 23 16:00:59 2012
New Revision: 18023
URL: http://svn.gna.org/viewcvs/relax?rev=18023&view=rev
Log:
The models used in the frame order auto-analysis can now be specified in the
user script.
Modified:
branches/frame_order_testing/auto_analyses/frame_order.py
Modified: branches/frame_order_testing/auto_analyses/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/auto_analyses/frame_order.py?rev=18023&r1=18022&r2=18023&view=diff
==============================================================================
--- branches/frame_order_testing/auto_analyses/frame_order.py (original)
+++ branches/frame_order_testing/auto_analyses/frame_order.py Fri Nov 23
16:00:59 2012
@@ -45,7 +45,7 @@
class Frame_order_analysis:
"""The frame order auto-analysis protocol."""
- def __init__(self, data_pipe_full=None, data_pipe_subset=None,
pipe_bundle=None, results_dir=None, grid_inc=11, grid_inc_rigid=21,
min_algor='simplex', num_int_pts_grid=50, num_int_pts_subset=[20, 100],
func_tol_subset=[1e-2, 1e-2], num_int_pts_full=[100, 1000, 200000],
func_tol_full=[1e-2, 1e-3, 1e-4], mc_sim_num=500, mc_int_pts=1000,
mc_func_tol=1e-3):
+ def __init__(self, data_pipe_full=None, data_pipe_subset=None,
pipe_bundle=None, results_dir=None, grid_inc=11, grid_inc_rigid=21,
min_algor='simplex', num_int_pts_grid=50, num_int_pts_subset=[20, 100],
func_tol_subset=[1e-2, 1e-2], num_int_pts_full=[100, 1000, 200000],
func_tol_full=[1e-2, 1e-3, 1e-4], mc_sim_num=500, mc_int_pts=1000,
mc_func_tol=1e-3, models=['rigid', 'free rotor', 'rotor', 'iso cone,
torsionless', 'iso cone, free rotor', 'iso cone', 'pseudo-ellipse,
torsionless', 'pseudo-ellipse']):
"""Perform the full frame order analysis.
@param data_pipe_full: The name of the data pipe containing
all of the RDC and PCS data.
@@ -78,6 +78,8 @@
@type mc_int_num: int
@keyword mc_func_tol: The minimisation function tolerance
cutoff to terminate optimisation during Monte Carlo simulations.
@type mc_func_tol: float
+ @keyword models: The frame order models to use in the
analysis. The 'rigid' model must be included as this is essential for the
analysis.
+ @type models: list of str
"""
# Execution lock.
@@ -98,10 +100,11 @@
self.mc_sim_num = mc_sim_num
self.mc_int_pts = mc_int_pts
self.mc_func_tol = mc_func_tol
-
- # A dictionary of the data pipe names.
- self.models = {}
- self.pipes = []
+ self.models = models
+
+ # A dictionary and list of the data pipe names.
+ self.pipe_name_dict = {}
+ self.pipe_name_list = []
# Project directory (i.e. directory containing the model-free model
results and the newly generated files)
if results_dir:
@@ -125,7 +128,7 @@
# The final results does not already exist.
if not self.read_results(model='final', pipe_name='final'):
# Model selection.
- self.interpreter.model_selection(method='AIC',
modsel_pipe='final', pipes=self.pipes)
+ self.interpreter.model_selection(method='AIC',
modsel_pipe='final', pipes=self.pipe_name_list)
# The number of integration points.
self.interpreter.frame_order.num_int_pts(num=self.mc_int_pts)
@@ -245,7 +248,7 @@
# The average position from the rigid model.
if model not in []:
# Get the rigid data pipe.
- rigid_pipe = get_pipe(self.models['rigid'])
+ rigid_pipe = get_pipe(self.pipe_name_dict['rigid'])
# Copy the average position parameters from the rigid model.
if model not in ['free rotor', 'iso cone, free rotor']:
@@ -256,7 +259,7 @@
# The cone axis from the rotor model.
if model in ['iso cone']:
# Get the rotor data pipe.
- rotor_pipe = get_pipe(self.models['rotor'])
+ rotor_pipe = get_pipe(self.pipe_name_dict['rotor'])
# Copy the cone axis.
cdp.axis_theta = rotor_pipe.axis_theta
@@ -265,7 +268,7 @@
# The cone axis from the free rotor model.
if model in ['iso cone, free rotor']:
# Get the rotor data pipe.
- free_rotor_pipe = get_pipe(self.models['free rotor'])
+ free_rotor_pipe = get_pipe(self.pipe_name_dict['free rotor'])
# Copy the cone axis.
cdp.axis_theta = free_rotor_pipe.axis_theta
@@ -274,7 +277,7 @@
# The torsion from the rotor model.
if model in ['iso cone', 'pseudo-ellipse']:
# Get the rotor data pipe.
- rotor_pipe = get_pipe(self.models['rotor'])
+ rotor_pipe = get_pipe(self.pipe_name_dict['rotor'])
# Copy the cone axis.
cdp.cone_sigma_max = rotor_pipe.cone_sigma_max
@@ -282,7 +285,7 @@
# The cone angles from from the torsionless isotropic cone model.
if model in ['pseudo-ellipse, torsionless', 'pseudo-ellipse, free
rotor', 'pseudo-ellipse']:
# Get the rotor data pipe.
- pipe = get_pipe(self.models['iso cone, torsionless'])
+ pipe = get_pipe(self.pipe_name_dict['iso cone, torsionless'])
# Copy the cone axis.
cdp.cone_theta_x = pipe.cone_theta
@@ -296,8 +299,11 @@
self.optimise_rigid()
# Iteratively optimise the frame order models.
- models = ['rotor', 'free rotor', 'iso cone, torsionless', 'iso cone,
free rotor', 'iso cone', 'pseudo-ellipse, torsionless', 'pseudo-ellipse, free
rotor', 'pseudo-ellipse']
- for model in models:
+ for model in self.models:
+ # Skip the already optimised rigid model.
+ if model == 'rigid':
+ continue
+
# The model title.
title = model[0].upper() + model[1:]
@@ -305,11 +311,11 @@
self.print_title(title)
# The data pipe name.
- self.models[model] = '%s - %s' % (title, self.pipe_bundle)
- self.pipes.append(self.models[model])
+ self.pipe_name_dict[model] = '%s - %s' % (title,
self.pipe_bundle)
+ self.pipe_name_list.append(self.pipe_name_dict[model])
# The results file already exists, so read its contents instead.
- if self.read_results(model=model, pipe_name=self.models[model]):
+ if self.read_results(model=model,
pipe_name=self.pipe_name_dict[model]):
# Re-perform model elimination just in case.
self.interpreter.eliminate()
@@ -317,8 +323,8 @@
continue
# Create the data pipe using the full data set, and switch to it.
- self.interpreter.pipe.copy(self.data_pipe_subset,
self.models[model], bundle_to=self.pipe_bundle)
- self.interpreter.pipe.switch(self.models[model])
+ self.interpreter.pipe.copy(self.data_pipe_subset,
self.pipe_name_dict[model], bundle_to=self.pipe_bundle)
+ self.interpreter.pipe.switch(self.pipe_name_dict[model])
# Select the Frame Order model.
self.interpreter.frame_order.select_model(model=model)
@@ -340,7 +346,7 @@
self.interpreter.minimise(self.min_algor,
func_tol=self.func_tol_subset[i], constraints=False)
# Copy the PCS data.
- self.interpreter.pcs.copy(pipe_from=self.data_pipe_full,
pipe_to=self.models[model])
+ self.interpreter.pcs.copy(pipe_from=self.data_pipe_full,
pipe_to=self.pipe_name_dict[model])
# Minimise (for the full data set).
for i in range(len(self.num_int_pts_full)):
@@ -371,16 +377,16 @@
self.print_title(title)
# The data pipe name.
- self.models[model] = '%s - %s' % (title, self.pipe_bundle)
- self.pipes.append(self.models[model])
+ self.pipe_name_dict[model] = '%s - %s' % (title, self.pipe_bundle)
+ self.pipe_name_list.append(self.pipe_name_dict[model])
# The results file already exists, so read its contents instead.
- if self.read_results(model=model, pipe_name=self.models[model]):
+ if self.read_results(model=model,
pipe_name=self.pipe_name_dict[model]):
return
# Create the data pipe using the full data set, and switch to it.
- self.interpreter.pipe.copy(self.data_pipe_full, self.models[model],
bundle_to=self.pipe_bundle)
- self.interpreter.pipe.switch(self.models[model])
+ self.interpreter.pipe.copy(self.data_pipe_full,
self.pipe_name_dict[model], bundle_to=self.pipe_bundle)
+ self.interpreter.pipe.switch(self.pipe_name_dict[model])
# Select the Frame Order model.
self.interpreter.frame_order.select_model(model=model)
@@ -514,7 +520,7 @@
"""
# Loop over all models.
- for pipe_name in self.models.values() + ['final']:
+ for pipe_name in self.pipe_name_list + ['final']:
# Switch to the data pipe.
self.interpreter.pipe.switch(pipe_name)
r18023 - /branches/frame_order_testing/auto_analyses/frame_order.py