Author: bugman
Date: Mon Mar 4 16:01:12 2013
New Revision: 18617
URL: http://svn.gna.org/viewcvs/relax?rev=18617&view=rev
Log:
Simplified the rigid frame order model displacement testing script.
Modified:
branches/frame_order_testing/test_suite/shared_data/frame_order/displacements/rigid_test.py
Modified:
branches/frame_order_testing/test_suite/shared_data/frame_order/displacements/rigid_test.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/shared_data/frame_order/displacements/rigid_test.py?rev=18617&r1=18616&r2=18617&view=diff
==============================================================================
---
branches/frame_order_testing/test_suite/shared_data/frame_order/displacements/rigid_test.py
(original)
+++
branches/frame_order_testing/test_suite/shared_data/frame_order/displacements/rigid_test.py
Mon Mar 4 16:01:12 2013
@@ -28,61 +28,10 @@
# Python module imports.
from numpy import array, float64
-from time import asctime, localtime
-
-# relax module imports.
-from auto_analyses.frame_order import Frame_order_analysis
-# Analysis variables.
-#####################
-
-# The grid search size (the number of increments per dimension).
-GRID_INC = 11
-
-# The more precise grid search size for the initial rigid model (the number
of increments per dimension).
-GRID_INC_RIGID = 31
-
-# The number of Sobol' points for the PCS numerical integration in the grid
searches.
-NUM_INT_PTS_GRID = 50
-
-# The list of the number of Sobol' points for the PCS numerical integration
to use iteratively in the optimisations after the grid search (for the PCS
data subset).
-NUM_INT_PTS_SUBSET = [100]
-
-# The minimisation function tolerance cutoff to terminate optimisation (for
the PCS data subset, see the minimise user function).
-FUNC_TOL_SUBSET = [1e-2]
-
-# The list of the number of Sobol' points for the PCS numerical integration
to use iteratively in the optimisations after the grid search (for all PCS
and RDC data).
-NUM_INT_PTS_FULL = [100, 1000, 10000]
-
-# The minimisation function tolerance cutoff to terminate optimisation (for
all PCS and RDC data, see the minimise user function).
-FUNC_TOL_FULL = [1e-2, 1e-3, 1e-4]
-
-# The optimisation technique.
-MIN_ALGOR = 'simplex'
-
-# The number of Monte Carlo simulations to be used for error analysis at the
end of the protocol.
-MC_NUM = 100
-
-# The number of Sobol' points for the PCS numerical integration during Monte
Carlo simulations.
-MC_INT_PTS = 100
-
-# The minimisation function tolerance cutoff to terminate optimisation
during Monte Carlo simulations.
-MC_FUNC_TOL = 1e-2
-
-# The frame order models to use.
-MODELS = ['rigid']
-
-
-# Set up the base data pipes.
-#############################
-
-# The data pipe bundle to group all data pipes.
-PIPE_BUNDLE = "Frame Order (%s)" % asctime(localtime())
-
-# Create the base data pipe containing only a subset of the PCS data.
-SUBSET = "Data subset - " + PIPE_BUNDLE
-pipe.create(pipe_name=SUBSET, pipe_type='frame order', bundle=PIPE_BUNDLE)
+# Create the data pipe.
+pipe.create(pipe_name='rigid test', pipe_type='frame order')
# Read the structures.
structure.read_pdb('displaced.pdb', set_mol_name='fancy_mol')
@@ -107,7 +56,6 @@
'pcs_yb.txt',
'pcs_ho.txt'
]
-pcs_files_subset = pcs_files
rdc_files = [
'rdc_dy.txt',
'rdc_tb.txt',
@@ -123,7 +71,7 @@
rdc.read(align_id=ln[i], file=rdc_files[i], dir='.', spin_id1_col=1,
spin_id2_col=2, data_col=3, error_col=4)
# The PCS (only a subset of ~5 spins for fast initial optimisations).
- pcs.read(align_id=ln[i], file=pcs_files_subset[i], dir='.',
mol_name_col=1, res_num_col=2, spin_name_col=5, data_col=6, error_col=7)
+ pcs.read(align_id=ln[i], file=pcs_files[i], dir='.', mol_name_col=1,
res_num_col=2, spin_name_col=5, data_col=6, error_col=7)
# The temperature and field strength.
temperature(id=ln[i], temp=303.0)
@@ -170,21 +118,15 @@
# Allow the average domain to be translated during optimisation.
frame_order.ave_pos_translate()
-# Set the initial pivot point.
-pivot = array([ 0, 0, 0], float64)
+# Set the initial pivot point (should make no difference for the rigid
model).
+pivot = array([0, 0, 0], float64)
frame_order.pivot(pivot, fix=True)
# Set the paramagnetic centre position.
paramag.centre(pos=[-5, -7, -9])
-# Duplicate the PCS data subset data pipe to create a data pipe containing
all the PCS data.
-DATA = "Data - " + PIPE_BUNDLE
-pipe.copy(pipe_from=SUBSET, pipe_to=DATA, bundle_to=PIPE_BUNDLE)
-pipe.switch(DATA)
-
-# Load the complete PCS data into the already filled data pipe.
-for i in range(len(ln)):
- pcs.read(align_id=ln[i], file=pcs_files[i], mol_name_col=1,
res_num_col=2, spin_name_col=5, data_col=6, error_col=7)
+# Select the Frame Order model.
+frame_order.select_model(model='rigid')
# Set the real parameter values.
cdp.ave_pos_x = -1
@@ -194,9 +136,8 @@
cdp.ave_pos_beta = 2.0
cdp.ave_pos_gamma = 2.14159265359
+# Calculate the chi2 value.
+calc()
-# Execution.
-############
-
-# Do not change!
-Frame_order_analysis(data_pipe_full=DATA, data_pipe_subset=SUBSET,
pipe_bundle=PIPE_BUNDLE, grid_inc=GRID_INC, grid_inc_rigid=GRID_INC_RIGID,
min_algor=MIN_ALGOR, num_int_pts_grid=NUM_INT_PTS_GRID,
num_int_pts_subset=NUM_INT_PTS_SUBSET, func_tol_subset=FUNC_TOL_SUBSET,
num_int_pts_full=NUM_INT_PTS_FULL, func_tol_full=FUNC_TOL_FULL,
mc_sim_num=MC_NUM, mc_int_pts=MC_INT_PTS, mc_func_tol=MC_FUNC_TOL,
models=MODELS)
+# Attempt to mimimise.
+minimise('simplex', constraints=False)
r18617 - /branches/frame_order_testing/test_suite/shared_data/frame_order/displacements/rigid_test.py