Author: bugman
Date: Mon Mar 4 15:54:46 2013
New Revision: 18616
URL: http://svn.gna.org/viewcvs/relax?rev=18616&view=rev
Log:
Added a script to test the displacement found in the rigid frame order model.
Added:
branches/frame_order_testing/test_suite/shared_data/frame_order/displacements/rigid_test.py
Added:
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=18616&view=auto
==============================================================================
---
branches/frame_order_testing/test_suite/shared_data/frame_order/displacements/rigid_test.py
(added)
+++
branches/frame_order_testing/test_suite/shared_data/frame_order/displacements/rigid_test.py
Mon Mar 4 15:54:46 2013
@@ -1,0 +1,202 @@
+###############################################################################
+#
#
+# Copyright (C) 2004-2013 Edward d'Auvergne
#
+#
#
+# This file is part of the program relax (http://www.nmr-relax.com).
#
+#
#
+# This program is free software: you can redistribute it and/or modify
#
+# it under the terms of the GNU General Public License as published by
#
+# the Free Software Foundation, either version 3 of the License, or
#
+# (at your option) any later version.
#
+#
#
+# This program is distributed in the hope that it will be useful,
#
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
+# GNU General Public License for more details.
#
+#
#
+# You should have received a copy of the GNU General Public License
#
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
+#
#
+###############################################################################
+
+"""Script for testing translation and rotation in the frame order analyses.
+
+This script should be run from the directory where it is found with the
commands:
+
+$ ../../../../relax full_analysis.py
+"""
+
+# 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)
+
+# Read the structures.
+structure.read_pdb('displaced.pdb', set_mol_name='fancy_mol')
+
+# Set up the 15N and 1H spins.
+structure.load_spins()
+spin.isotope(isotope='15N', spin_id='@N')
+spin.isotope(isotope='1H', spin_id='@H')
+
+# Define the magnetic dipole-dipole relaxation interaction.
+dipole_pair.define(spin_id1='@N', spin_id2='@H', direct_bond=True)
+dipole_pair.set_dist(spin_id1='@N', spin_id2='@H', ave_dist=1.041 * 1e-10)
+dipole_pair.unit_vectors()
+
+# The lanthanides and data files.
+ln = ['dy', 'tb', 'tm', 'er', 'yb', 'ho']
+pcs_files = [
+ 'pcs_dy.txt',
+ 'pcs_tb.txt',
+ 'pcs_tm.txt',
+ 'pcs_er.txt',
+ 'pcs_yb.txt',
+ 'pcs_ho.txt'
+]
+pcs_files_subset = pcs_files
+rdc_files = [
+ 'rdc_dy.txt',
+ 'rdc_tb.txt',
+ 'rdc_tm.txt',
+ 'rdc_er.txt',
+ 'rdc_yb.txt',
+ 'rdc_ho.txt'
+]
+
+# Loop over the alignments.
+for i in range(len(ln)):
+ # Load the RDCs.
+ 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)
+
+ # The temperature and field strength.
+ temperature(id=ln[i], temp=303.0)
+ frq.set(id=ln[i], frq=800.0, units="MHz")
+
+# Load the tensors (the full tensors).
+align_tensor.init(tensor='Dy fixed', align_id='dy',
params=(-0.000283041921495, 0.00017331020651, 0.000348144461756,
0.00109678563394, -0.000261126459214), param_types=2)
+align_tensor.init(tensor='Dy fixed', align_id='dy',
params=(1.32405973595e-05, 1.69451339335e-05, 1.11420056339e-05,
1.2902359091e-05, 1.06231229491e-05), param_types=2, errors=True)
+align_tensor.init(tensor='Tb fixed', align_id='tb',
params=(0.000167738428636, -0.000311103377008, 0.000231043994111,
0.000927908442481, -0.00042448381621), param_types=2)
+align_tensor.init(tensor='Tb fixed', align_id='tb',
params=(9.23106516114e-06, 1.23864406564e-05, 9.25138110416e-06,
1.0025121852e-05, 8.6027985631e-06), param_types=2, errors=True)
+align_tensor.init(tensor='Tm fixed', align_id='tm',
params=(-0.000214531334757, 0.000250016686133, -0.000318452894707,
-0.000566585709341, 0.000458689017372), param_types=2)
+align_tensor.init(tensor='Tm fixed', align_id='tm',
params=(8.18656207912e-06, 1.09649975373e-05, 8.43998269558e-06,
8.63599444168e-06, 7.95937745247e-06), param_types=2, errors=True)
+align_tensor.init(tensor='Er fixed', align_id='er',
params=(-9.34632913359e-05, 7.71986454118e-05, -0.000234020357448,
-0.000363596427557, 0.000177874820425), param_types=2)
+align_tensor.init(tensor='Er fixed', align_id='er',
params=(6.32851257036e-06, 9.3721066722e-06, 7.36682050165e-06,
7.52806731357e-06, 9.79003188793e-06), param_types=2, errors=True)
+align_tensor.init(tensor='Yb fixed', align_id='yb',
params=(2.20524016343e-05, -6.04903356962e-05, -0.000114723702615,
-0.000214855846027, 0.000143730520814), param_types=2)
+align_tensor.init(tensor='Yb fixed', align_id='yb',
params=(4.2812326053e-06, 5.43186247053e-06, 4.83605375312e-06,
5.10468453851e-06, 4.31847329676e-06), param_types=2, errors=True)
+align_tensor.init(tensor='Ho fixed', align_id='ho',
params=(-6.99147985047e-05, -8.00899711508e-06, 0.000102219102441,
0.000424559081645, -0.000255281322523), param_types=2)
+align_tensor.init(tensor='Ho fixed', align_id='ho',
params=(7.74711876341e-06, 9.55677606858e-06, 9.13852550558e-06,
7.82230105216e-06, 7.33515152376e-06), param_types=2, errors=True)
+
+# Define the domains.
+domain(id='moving', spin_id=":0-100")
+domain(id='fixed', spin_id=":101-200")
+
+# The tensor domains and reductions.
+full = ['Dy fixed', 'Tb fixed', 'Tm fixed', 'Er fixed', 'Yb fixed', 'Ho
fixed']
+red = ['Dy moving', 'Tb moving', 'Tm moving', 'Er moving', 'Yb moving', 'Ho
moving']
+for i in range(len(full)):
+ # Initialise the reduced tensors (fitted during optimisation).
+ align_tensor.init(tensor=red[i], align_id=ln[i], params=(0, 0, 0, 0, 0))
+
+ # Set the domain info.
+ align_tensor.set_domain(tensor=full[i], domain='fixed')
+ align_tensor.set_domain(tensor=red[i], domain='moving')
+
+ # Specify which tensor is reduced.
+ align_tensor.reduction(full_tensor=full[i], red_tensor=red[i])
+
+# Set the reference domain.
+frame_order.ref_domain('fixed')
+
+# Link the domains to the PDB files.
+frame_order.domain_to_pdb(domain='fixed', pdb='displaced.pdb')
+
+# 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)
+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)
+
+# Set the real parameter values.
+cdp.ave_pos_x = -1
+cdp.ave_pos_y = -2
+cdp.ave_pos_z = -3
+cdp.ave_pos_alpha = 0.14159265359
+cdp.ave_pos_beta = 2.0
+cdp.ave_pos_gamma = 2.14159265359
+
+
+# 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)
r18616 - /branches/frame_order_testing/test_suite/shared_data/frame_order/displacements/rigid_test.py