Author: bugman
Date: Sat Nov 29 09:44:49 2014
New Revision: 26819
URL: http://svn.gna.org/viewcvs/relax?rev=26819&view=rev
Log:
Added a system test script for testing the saturation-recovery R1 experiment.
This was created by Andras Boeszoermenyi <Andras_Boeszoermenyi att hms dott
harvard dot edu>. The
file was taken from the saturation_recovery.tar.gaz file
(https://gna.org/task/download.php?file_id=22997) are attached to the task at
http://gna.org/task/?7415. The only difference with the original script is
that the grace.view user
function calls have been removed, as these cannot be used in a system test.
Added:
trunk/test_suite/system_tests/scripts/relax_fit_saturation_recovery.py
Added: trunk/test_suite/system_tests/scripts/relax_fit_saturation_recovery.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/relax_fit_saturation_recovery.py?rev=26819&view=auto
==============================================================================
--- trunk/test_suite/system_tests/scripts/relax_fit_saturation_recovery.py
(added)
+++ trunk/test_suite/system_tests/scripts/relax_fit_saturation_recovery.py
Sat Nov 29 09:44:49 2014
@@ -0,0 +1,132 @@
+###############################################################################
+#
#
+# Copyright (C) 2004-2014 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 relaxation curve fitting."""
+
+
+# Create the 'rx' data pipe.
+pipe.create('rx', 'relax_fit')
+
+# Load the backbone amide 15N spins from a PDB file.
+#structure.read_pdb('Ap4Aase_new_3.pdb')
+#structure.load_spins(spin_id='@N')
+
+# Load the sequence.
+sequence.read(file='wr10_43_relax.seq', res_name_col=1, res_num_col=2,
spin_num_col=3, spin_name_col=4)
+spin.name(name='H')
+spin.element(element='H')
+spin.isotope(isotope='1H', spin_id='@H')
+spin.name(name='HE1')
+spin.element(element='H')
+spin.isotope(isotope='1H', spin_id='@HE1')
+
+# Spectrum names.
+names = [
+ '0.070s',
+ '0.150s',
+ '0.250s',
+ '0.350s',
+ '0.500s',
+ '0.750s',
+ '1.000s',
+ '2.000s',
+ '3.000s',
+ '5.000s'
+]
+
+# Relaxation times (in seconds).
+times = [
+ 0.07,
+ 0.15,
+ 0.25,
+ 0.35,
+ 0.50,
+ 0.75,
+ 1.00,
+ 2.00,
+ 3.00,
+ 5.00
+]
+
+# Loop over the spectra.
+for i in range(len(names)):
+ # Load the peak intensities (first the backbone NH, then the tryptophan
indole NH).
+ spectrum.read_intensities(file=names[i]+'.list', spectrum_id=names[i],
int_method='height')
+
+ # Set the relaxation times.
+ relax_fit.relax_time(time=times[i], spectrum_id=names[i])
+
+# Specify the duplicated spectra.
+#spectrum.replicated(spectrum_ids=['T2_ncyc1_ave', 'T2_ncyc1b_ave'])
+#spectrum.replicated(spectrum_ids=['T2_ncyc4_ave', 'T2_ncyc4b_ave'])
+#spectrum.replicated(spectrum_ids=['T2_ncyc9_ave', 'T2_ncyc9b_ave'])
+#spectrum.replicated(spectrum_ids=['T2_ncyc11_ave', 'T2_ncyc11b_ave'])
+
+#maf# Spectrum baseplane noise for non-duplicated spectra
+spectrum.baseplane_rmsd(error=92440.562999, spectrum_id='0.070s',
spin_id=None)
+spectrum.baseplane_rmsd(error=91770.380636, spectrum_id='0.150s',
spin_id=None)
+spectrum.baseplane_rmsd(error=95226.122047, spectrum_id='0.250s',
spin_id=None)
+spectrum.baseplane_rmsd(error=94428.183988, spectrum_id='0.350s',
spin_id=None)
+spectrum.baseplane_rmsd(error=92478.391627, spectrum_id='0.500s',
spin_id=None)
+spectrum.baseplane_rmsd(error=92167.856579, spectrum_id='0.750s',
spin_id=None)
+spectrum.baseplane_rmsd(error=95071.442069, spectrum_id='1.000s',
spin_id=None)
+spectrum.baseplane_rmsd(error=92479.274501, spectrum_id='2.000s',
spin_id=None)
+spectrum.baseplane_rmsd(error=95735.516944, spectrum_id='3.000s',
spin_id=None)
+spectrum.baseplane_rmsd(error=106627.326030, spectrum_id='5.000s',
spin_id=None)
+
+
+# Peak intensity error analysis.
+spectrum.error_analysis()
+
+# Deselect unresolved spins.
+#deselect.read(file='unresolved', mol_name_col=1, res_num_col=2,
res_name_col=3, spin_num_col=4, spin_name_col=5)
+
+# Set the relaxation curve type.
+relax_fit.select_model('exp')
+
+# Grid search.
+minimise.grid_search(inc=11)
+
+# Minimise.
+minimise.execute('newton', constraints=False)
+
+# Monte Carlo simulations.
+monte_carlo.setup(number=5)
+monte_carlo.create_data()
+monte_carlo.initial_values()
+minimise.execute('newton', constraints=False)
+monte_carlo.error_analysis()
+
+# Save the relaxation rates.
+value.write(param='rx', file='rx.out', force=True)
+
+# Save the results.
+results.write(file='results', force=True)
+
+# Create Grace plots of the data.
+grace.write(y_data_type='chi2', file='chi2.agr', force=True) # Minimised
chi-squared value.
+grace.write(y_data_type='i0', file='i0.agr', force=True) # Initial peak
intensity.
+grace.write(y_data_type='rx', file='rx.agr', force=True) # Relaxation
rate.
+grace.write(x_data_type='relax_times', y_data_type='peak_intensity',
file='intensities.agr', force=True) # Average peak intensities.
+grace.write(x_data_type='relax_times', y_data_type='peak_intensity',
norm=True, file='intensities_norm.agr', force=True) # Average peak
intensities (normalised).
+
+# Save the program state.
+state.save('rx.save', force=True)
r26819 - /trunk/test_suite/system_tests/scripts/relax_fit_saturation_recovery.py