Author: bugman
Date: Fri Nov 16 20:08:22 2012
New Revision: 18004
URL: http://svn.gna.org/viewcvs/relax?rev=18004&view=rev
Log:
Added a script to perform a full frame order analysis on the synthetic CaM
test data.
Added:
branches/frame_order_testing/test_suite/shared_data/frame_order/cam/full_analysis.py
Added:
branches/frame_order_testing/test_suite/shared_data/frame_order/cam/full_analysis.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/shared_data/frame_order/cam/full_analysis.py?rev=18004&view=auto
==============================================================================
---
branches/frame_order_testing/test_suite/shared_data/frame_order/cam/full_analysis.py
(added)
+++
branches/frame_order_testing/test_suite/shared_data/frame_order/cam/full_analysis.py
Fri Nov 16 20:08:22 2012
@@ -1,0 +1,149 @@
+###############################################################################
+#
#
+# Copyright (C) 2004-2012 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 black-box Frame Order analysis.
+
+This script should be run from the directory where it is found with the
commands:
+
+$ ../../../../../relax full_analysis.py
+
+$ mpirun -n 3 ../../../../../relax --multi mpi4py full_analysis.py
+"""
+
+# Python module imports.
+from numpy import array
+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' integration points to use in the grid searches.
+NUM_INT_PTS_GRID = 50
+
+# The list of the number of Sobol' integration points to use iteratively in
the optimisations after the grid search (for the PCS data subset).
+NUM_INT_PTS_SUBSET = [100]
+
+# The list of the number of Sobol' integration points to use iteratively in
the optimisations after the grid search (for all PCS and RDC data).
+NUM_INT_PTS_FULL = [100, 1000]
+#NUM_INT_PTS_FULL = [100, 1000, 200000]
+
+# 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 = 3
+
+
+# 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('1J7O_1st_NH.pdb', dir='..', set_mol_name='N-dom')
+structure.read_pdb('1J7P_1st_NH_rot.pdb', dir='..', set_mol_name='C-dom')
+
+# Set up the 15N and 1H spins.
+structure.load_spins(spin_id='@N', ave_pos=False)
+structure.load_spins(spin_id='@H', ave_pos=False)
+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()
+
+# Loop over the alignments.
+ln = ['dy', 'tb', 'tm', 'er']
+for i in range(len(ln)):
+ # Load the RDCs.
+ rdc.read(align_id=ln[i], file='rdc_%s.txt'%ln[i], 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_%s_subset.txt'%ln[i], 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)
+ frq.set(id=ln[i], frq=900e6)
+
+# Load the N-domain tensors (the full tensors).
+script('../tensors.py')
+
+# Define the domains.
+domain(id='N', spin_id=":1-78")
+domain(id='C', spin_id=":80-148")
+
+# The tensor domains and reductions.
+full = ['Dy N-dom', 'Tb N-dom', 'Tm N-dom', 'Er N-dom']
+red = ['Dy C-dom', 'Tb C-dom', 'Tm C-dom', 'Er C-dom']
+ids = ['dy', 'tb', 'tm', 'er']
+for i in range(len(full)):
+ # Initialise the reduced tensor.
+ align_tensor.init(tensor=red[i], align_id=ids[i], params=(0, 0, 0, 0, 0))
+
+ # Set the domain info.
+ align_tensor.set_domain(tensor=full[i], domain='N')
+ align_tensor.set_domain(tensor=red[i], domain='C')
+
+ # Specify which tensor is reduced.
+ align_tensor.reduction(full_tensor=full[i], red_tensor=red[i])
+
+# Set the reference domain.
+frame_order.ref_domain('N')
+
+# Set the initial pivot point.
+pivot = array([ 37.254, 0.5, 16.7465])
+frame_order.pivot(pivot, fix=True)
+
+# Set the paramagnetic centre position.
+paramag.centre(pos=[35.934, 12.194, -4.206])
+
+# 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)
+
+# 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_%s.txt'%ln[i], mol_name_col=1,
res_num_col=2, spin_name_col=5, data_col=6, error_col=7)
+
+
+
+# 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, num_int_pts_full=NUM_INT_PTS_FULL,
mc_sim_num=MC_NUM)
r18004 - /branches/frame_order_testing/test_suite/shared_data/frame_order/cam/full_analysis.py