r14794 - in /1.3/test_suite/system_tests/scripts/curve_fitting: ./ bug_18789_no_grace_errors.py -- October 05, 2011 - 18:49

Author: bugman
Date: Wed Oct  5 18:49:03 2011
New Revision: 14794

URL: http://svn.gna.org/viewcvs/relax?rev=14794&view=rev
Log:
Added the script for triggering bug #18789.

This script comes from the bug report submitted by Elio Cino <ecino att uwo 
dott ca> at
https://gna.org/bugs/?18789.



Added:
    1.3/test_suite/system_tests/scripts/curve_fitting/
    
1.3/test_suite/system_tests/scripts/curve_fitting/bug_18789_no_grace_errors.py

Added: 
1.3/test_suite/system_tests/scripts/curve_fitting/bug_18789_no_grace_errors.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/curve_fitting/bug_18789_no_grace_errors.py?rev=14794&view=auto
==============================================================================
--- 
1.3/test_suite/system_tests/scripts/curve_fitting/bug_18789_no_grace_errors.py
 (added)
+++ 
1.3/test_suite/system_tests/scripts/curve_fitting/bug_18789_no_grace_errors.py
 Wed Oct  5 18:49:03 2011
@@ -1,0 +1,107 @@
+###############################################################################
+#                                                                            
 #
+# Copyright (C) 2004-2008 Edward d'Auvergne                                  
 #
+#                                                                            
 #
+# This file is part of the program relax.                                    
 #
+#                                                                            
 #
+# relax 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 2 of the License, or          
 #
+# (at your option) any later version.                                        
 #
+#                                                                            
 #
+# relax 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 relax; if not, write to the Free Software                       
 #
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA  
 #
+#                                                                            
 #
+###############################################################################
+
+# Python module imports.
+from os import sep
+import sys
+
+# relax module imports.
+from data import Relax_data_store; ds = Relax_data_store()
+from status import Status; status = Status()
+
+
+# Script for relaxation curve fitting.
+######################################
+
+
+# Missing temp directory (allow this script to run outside of the system 
test framework).
+if not hasattr(ds, 'tmpdir'):
+    ds.tmpdir = 'temp_script'
+
+# Create the 'rx' data pipe.
+pipe.create('rx', 'relax_fit')
+
+# The path to the data files.
+data_path = status.install_path + 
sep+'test_suite'+sep+'shared_data'+sep+'curve_fitting'+sep+'bug_18789_no_grace_errors'
+
+# Quickly create the sequence.
+residue.create(13, 'ILE')
+residue.create(67, 'LEU')
+spin.name(name='N')
+
+# Spectrum names.
+names = [
+    '500',
+    '010',
+    '040',
+    '420',
+]
+
+# Relaxation times (in seconds).
+times = [
+    0.500,
+    0.010,
+    0.040,
+    0.420,
+]
+
+# Loop over the spectra.
+for i in xrange(len(names)):
+    # Load the peak intensities.
+    spectrum.read_intensities(file=names[i]+'.xpk', dir=data_path, 
spectrum_id=names[i], int_method='height')
+
+    # Set the relaxation times.
+    relax_fit.relax_time(time=times[i], spectrum_id=names[i])
+    
+
+spectrum.baseplane_rmsd(error=26500/1e6, spectrum_id='500', spin_id=None)
+spectrum.baseplane_rmsd(error=16700/1e6, spectrum_id='010', spin_id=None)   
+spectrum.baseplane_rmsd(error=18200/1e6, spectrum_id='040', spin_id=None)   
+spectrum.baseplane_rmsd(error=21100/1e6, spectrum_id='420', spin_id=None)   
+
+# Peak intensity error analysis.        
+spectrum.error_analysis()
+
+# Deselect unresolved spins.
+#deselect.read(file='unresolved')
+
+# Set the relaxation curve type.
+relax_fit.select_model('exp')
+
+# Grid search.
+grid_search(inc=3)
+
+# Minimise.
+minimise('simplex', scaling=False, constraints=False)
+
+# Monte Carlo simulations.
+monte_carlo.setup(number=5)
+monte_carlo.create_data()
+monte_carlo.initial_values()
+minimise('simplex', scaling=False, constraints=False)
+monte_carlo.error_analysis()
+
+# Save the relaxation rates.
+value.write(param='rx', file='rx.out', dir=ds.tmpdir, force=True)
+
+# Create Grace plots of the data.
+grace.write(y_data_type='rx', file='rx.agr', dir=ds.tmpdir, force=True)    # 
Relaxation rate.