Author: bugman
Date: Fri Dec 17 20:41:01 2010
New Revision: 11890
URL: http://svn.gna.org/viewcvs/relax?rev=11890&view=rev
Log:
Added test data and a script for testing the reading of CCPN Analysis 2.1
sparky peak lists.
This is data from bug #17341 (https://gna.org/bugs/?17341) submitted by
Madeleine Strickland <M dot
Strickland att bristol dot ac dott uk>.
Added:
1.3/test_suite/shared_data/peak_lists/ccpn_analysis/
1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0010.list
1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0020.list
1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0030.list
1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0050.list
1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0070.list
1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0100.list
1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0150.list
1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0200.list
1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0300.list
1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0400.list
1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0600.list
1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0800.list
1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_1000.list
1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_1200.list
1.3/test_suite/shared_data/peak_lists/ccpn_analysis/sequence.out
1.3/test_suite/system_tests/scripts/peak_lists/
1.3/test_suite/system_tests/scripts/peak_lists/ccpn_analysis.py
Added: 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0010.list
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0010.list?rev=11890&view=auto
==============================================================================
--- 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0010.list (added)
+++ 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0010.list Fri Dec
17 20:41:01 2010
@@ -1,0 +1,3 @@
+ Assignment w1 w2 Intensity
+ T1501N-T1501HN 104.038 6.715 1.41E+06 bx
+ V1504N-V1504HN 127.465 7.041 1.79E+06 bx
Added: 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0020.list
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0020.list?rev=11890&view=auto
==============================================================================
--- 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0020.list (added)
+++ 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0020.list Fri Dec
17 20:41:01 2010
@@ -1,0 +1,3 @@
+ Assignment w1 w2 Intensity
+ V1504N-V1504HN 127.465 7.041 1.76E+06 bx
+ T1501N-T1501HN 104.040 6.715 1.33E+06 bx
Added: 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0030.list
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0030.list?rev=11890&view=auto
==============================================================================
--- 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0030.list (added)
+++ 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0030.list Fri Dec
17 20:41:01 2010
@@ -1,0 +1,3 @@
+ Assignment w1 w2 Intensity
+ V1504N-V1504HN 127.465 7.041 1.71E+06 bx
+ T1501N-T1501HN 104.044 6.715 1.31E+06 bx
Added: 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0050.list
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0050.list?rev=11890&view=auto
==============================================================================
--- 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0050.list (added)
+++ 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0050.list Fri Dec
17 20:41:01 2010
@@ -1,0 +1,3 @@
+ Assignment w1 w2 Intensity
+ V1504N-V1504HN 127.465 7.041 1.70E+06 bx
+ T1501N-T1501HN 104.043 6.716 1.31E+06 bx
Added: 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0070.list
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0070.list?rev=11890&view=auto
==============================================================================
--- 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0070.list (added)
+++ 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0070.list Fri Dec
17 20:41:01 2010
@@ -1,0 +1,3 @@
+ Assignment w1 w2 Intensity
+ V1504N-V1504HN 127.465 7.041 1.66E+06 bx
+ T1501N-T1501HN 104.041 6.715 1.28E+06 bx
Added: 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0100.list
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0100.list?rev=11890&view=auto
==============================================================================
--- 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0100.list (added)
+++ 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0100.list Fri Dec
17 20:41:01 2010
@@ -1,0 +1,3 @@
+ Assignment w1 w2 Intensity
+ V1504N-V1504HN 127.465 7.041 1.56E+06 bx
+ T1501N-T1501HN 104.042 6.715 1.20E+06 bx
Added: 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0150.list
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0150.list?rev=11890&view=auto
==============================================================================
--- 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0150.list (added)
+++ 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0150.list Fri Dec
17 20:41:01 2010
@@ -1,0 +1,3 @@
+ Assignment w1 w2 Intensity
+ V1504N-V1504HN 127.465 7.041 1.51E+06 bx
+ T1501N-T1501HN 104.044 6.715 1.18E+06 bx
Added: 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0200.list
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0200.list?rev=11890&view=auto
==============================================================================
--- 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0200.list (added)
+++ 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0200.list Fri Dec
17 20:41:01 2010
@@ -1,0 +1,3 @@
+ Assignment w1 w2 Intensity
+ V1504N-V1504HN 127.465 7.041 1.41E+06 bx
+ T1501N-T1501HN 104.041 6.715 1.07E+06 bx
Added: 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0300.list
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0300.list?rev=11890&view=auto
==============================================================================
--- 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0300.list (added)
+++ 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0300.list Fri Dec
17 20:41:01 2010
@@ -1,0 +1,3 @@
+ Assignment w1 w2 Intensity
+ V1504N-V1504HN 127.465 7.041 1.24E+06 bx
+ T1501N-T1501HN 104.035 6.715 9.70E+05 bx
Added: 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0400.list
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0400.list?rev=11890&view=auto
==============================================================================
--- 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0400.list (added)
+++ 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0400.list Fri Dec
17 20:41:01 2010
@@ -1,0 +1,3 @@
+ Assignment w1 w2 Intensity
+ V1504N-V1504HN 127.465 7.041 1.11E+06 bx
+ T1501N-T1501HN 104.049 6.714 8.47E+05 bx
Added: 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0600.list
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0600.list?rev=11890&view=auto
==============================================================================
--- 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0600.list (added)
+++ 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0600.list Fri Dec
17 20:41:01 2010
@@ -1,0 +1,3 @@
+ Assignment w1 w2 Intensity
+ V1504N-V1504HN 127.465 7.041 8.43E+05 bx
+ T1501N-T1501HN 104.041 6.716 7.00E+05 bx
Added: 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0800.list
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0800.list?rev=11890&view=auto
==============================================================================
--- 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0800.list (added)
+++ 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_0800.list Fri Dec
17 20:41:01 2010
@@ -1,0 +1,4 @@
+ Assignment w1 w2 Intensity
+ V1504N-V1504HN 127.465 7.041 6.79E+05 bx
+ T1501N-T1501HN 104.044 6.716 5.25E+05 bx
+
Added: 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_1000.list
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_1000.list?rev=11890&view=auto
==============================================================================
--- 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_1000.list (added)
+++ 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_1000.list Fri Dec
17 20:41:01 2010
@@ -1,0 +1,3 @@
+ Assignment w1 w2 Intensity
+ V1504N-V1504HN 127.465 7.041 5.04E+05 bx
+ T1501N-T1501HN 104.016 6.715 4.23E+05 bx
Added: 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_1200.list
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_1200.list?rev=11890&view=auto
==============================================================================
--- 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_1200.list (added)
+++ 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/T1A_1200.list Fri Dec
17 20:41:01 2010
@@ -1,0 +1,3 @@
+ Assignment w1 w2 Intensity
+ V1504N-V1504HN 127.465 7.041 4.18E+05 bx
+ T1501N-T1501HN 104.045 6.716 3.10E+05 bx
Added: 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/sequence.out
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/peak_lists/ccpn_analysis/sequence.out?rev=11890&view=auto
==============================================================================
--- 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/sequence.out (added)
+++ 1.3/test_suite/shared_data/peak_lists/ccpn_analysis/sequence.out Fri Dec
17 20:41:01 2010
@@ -1,0 +1,4 @@
+1501 Thr N
+1502 Gly N
+1503 Tyr N
+1504 Val N
Added: 1.3/test_suite/system_tests/scripts/peak_lists/ccpn_analysis.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/peak_lists/ccpn_analysis.py?rev=11890&view=auto
==============================================================================
--- 1.3/test_suite/system_tests/scripts/peak_lists/ccpn_analysis.py (added)
+++ 1.3/test_suite/system_tests/scripts/peak_lists/ccpn_analysis.py Fri Dec
17 20:41:01 2010
@@ -1,0 +1,138 @@
+###############################################################################
+#
#
+# 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 0205-1307 USA
#
+#
#
+###############################################################################
+
+# Python module imports.
+import __main__
+from os import sep
+import sys
+
+
+# Script for relaxation curve fitting.
+######################################
+
+
+# The path to the data files.
+data_path = __main__.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'peak_lists'+sep+'ccpn_analysis'
+
+# Create the 'rx' data pipe.
+pipe.create('rx', 'relax_fit')
+
+# Load sequence and spins
+sequence.read('sequence.out', dir=data_path, res_num_col=1, res_name_col=2,
spin_name_col=3)
+
+# Spectrum names.
+names = [
+ 'T1A_0010',
+ 'T1A_0020',
+ 'T1A_0030',
+ 'T1A_0050',
+ 'T1A_0070',
+ 'T1A_0100',
+ 'T1A_0150',
+ 'T1A_0200',
+ 'T1A_0300',
+ 'T1A_0400',
+ 'T1A_0600',
+ 'T1A_0800',
+ 'T1A_1000',
+ 'T1A_1200'
+]
+
+# Relaxation times (in seconds).
+times = [
+ 0.01,
+ 0.02,
+ 0.03,
+ 0.05,
+ 0.07,
+ 0.1,
+ 0.15,
+ 0.2,
+ 0.3,
+ 0.4,
+ 0.6,
+ 0.8,
+ 1.0,
+ 1.2
+]
+
+# Loop over the spectra.
+for i in xrange(len(names)):
+ # Load the peak intensities.
+ spectrum.read_intensities(file=names[i]+'.list', 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])
+
+# Specify the duplicated spectra.
+spectrum.baseplane_rmsd(error=22980, spectrum_id='T1A_0010')
+spectrum.baseplane_rmsd(error=21982, spectrum_id='T1A_0020')
+spectrum.baseplane_rmsd(error=21916, spectrum_id='T1A_0030')
+spectrum.baseplane_rmsd(error=21780, spectrum_id='T1A_0050')
+spectrum.baseplane_rmsd(error=21015, spectrum_id='T1A_0070')
+spectrum.baseplane_rmsd(error=19957, spectrum_id='T1A_0100')
+spectrum.baseplane_rmsd(error=19064, spectrum_id='T1A_0150')
+spectrum.baseplane_rmsd(error=17618, spectrum_id='T1A_0200')
+spectrum.baseplane_rmsd(error=15592, spectrum_id='T1A_0300')
+spectrum.baseplane_rmsd(error=13681, spectrum_id='T1A_0400')
+spectrum.baseplane_rmsd(error=10938, spectrum_id='T1A_0600')
+spectrum.baseplane_rmsd(error=8898.4, spectrum_id='T1A_0800')
+spectrum.baseplane_rmsd(error=7541.9, spectrum_id='T1A_1000')
+spectrum.baseplane_rmsd(error=6772.1, spectrum_id='T1A_1200')
+
+
+# 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=11)
+
+# Minimise.
+minimise('simplex', scaling=False, constraints=False)
+
+# Monte Carlo simulations.
+monte_carlo.setup(number=500)
+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='devnull', force=True)
+
+# Save the results.
+results.write(file='devnull', force=True)
+
+# Create Grace plots of the data.
+grace.write(y_data_type='rx', file='devnull', force=True) # Relaxation
rate.
+
+# Display the Grace plots.
+grace.view(file='rx.agr')
+
+# Save the program state.
+state.save('devnull', force=True)
r11890 - in /1.3/test_suite: shared_data/peak_lists/ccpn_analysis/ system_tests/scripts/peak_lists/