Author: bugman
Date: Wed Dec 3 14:12:31 2008
New Revision: 8099
URL: http://svn.gna.org/viewcvs/relax?rev=8099&view=rev
Log:
Added all the files necessary to reproduce bug #12670
(https://gna.org/bugs/index.php?12670).
This bug was reported by Michael Funk (mifu att nmr dot mpibpc dot mpg dot
de).
The script needs to be modified to point to the correct locations and needs
to be activated as a
system test.
Added:
1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-02.listb
1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-04.listb
1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-06.listb
1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-08.listb
1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-10.listb
1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-12.listb
1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-14.listb
1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-16.listb
1.3/test_suite/shared_data/sequence/1UBQ.seq
1.3/test_suite/system_tests/scripts/1UBQ_relax_fit.py
Added: 1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-02.listb
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-02.listb?rev=8099&view=auto
==============================================================================
--- 1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-02.listb (added)
+++ 1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-02.listb Wed Dec 3
14:12:31 2008
@@ -1,0 +1,3 @@
+ Assignment w1 w2 Data Height S/N Spectrum
+
+ Q2N-H 122.592 9.103 487178 28
Added: 1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-04.listb
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-04.listb?rev=8099&view=auto
==============================================================================
--- 1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-04.listb (added)
+++ 1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-04.listb Wed Dec 3
14:12:31 2008
@@ -1,0 +1,3 @@
+ Assignment w1 w2 Data Height S/N Spectrum
+
+ Q2N-H 122.581 9.100 394412 23
Added: 1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-06.listb
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-06.listb?rev=8099&view=auto
==============================================================================
--- 1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-06.listb (added)
+++ 1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-06.listb Wed Dec 3
14:12:31 2008
@@ -1,0 +1,3 @@
+ Assignment w1 w2 Data Height S/N Spectrum
+
+ Q2N-H 122.583 9.101 298711 41
Added: 1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-08.listb
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-08.listb?rev=8099&view=auto
==============================================================================
--- 1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-08.listb (added)
+++ 1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-08.listb Wed Dec 3
14:12:31 2008
@@ -1,0 +1,3 @@
+ Assignment w1 w2 Data Height S/N
+
+ Q2N-H 122.611 9.101 295565 25
Added: 1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-10.listb
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-10.listb?rev=8099&view=auto
==============================================================================
--- 1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-10.listb (added)
+++ 1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-10.listb Wed Dec 3
14:12:31 2008
@@ -1,0 +1,3 @@
+ Assignment w1 w2 Data Height S/N
+
+ Q2N-H 122.591 9.101 198763 13
Added: 1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-12.listb
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-12.listb?rev=8099&view=auto
==============================================================================
--- 1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-12.listb (added)
+++ 1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-12.listb Wed Dec 3
14:12:31 2008
@@ -1,0 +1,3 @@
+ Assignment w1 w2 Data Height S/N
+
+ Q2N-H 122.601 9.103 182650 13
Added: 1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-14.listb
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-14.listb?rev=8099&view=auto
==============================================================================
--- 1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-14.listb (added)
+++ 1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-14.listb Wed Dec 3
14:12:31 2008
@@ -1,0 +1,3 @@
+ Assignment w1 w2 Data Height S/N
+
+ Q2N-H 122.595 9.107 132678 8
Added: 1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-16.listb
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-16.listb?rev=8099&view=auto
==============================================================================
--- 1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-16.listb (added)
+++ 1.3/test_suite/shared_data/peak_lists/700mhz-263k-1m-16.listb Wed Dec 3
14:12:31 2008
@@ -1,0 +1,3 @@
+ Assignment w1 w2 Data Height S/N
+
+ Q2N-H 122.552 9.100 102729 8
Added: 1.3/test_suite/shared_data/sequence/1UBQ.seq
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/sequence/1UBQ.seq?rev=8099&view=auto
==============================================================================
--- 1.3/test_suite/shared_data/sequence/1UBQ.seq (added)
+++ 1.3/test_suite/shared_data/sequence/1UBQ.seq Wed Dec 3 14:12:31 2008
@@ -1,0 +1,77 @@
+Mol_name Res_num Res_name Spin_num Spin_name
+A 1 MET 1 N
+A 2 GLN 9 N
+A 3 ILE 18 N
+A 4 PHE 26 N
+A 5 VAL 37 N
+A 6 LYS 44 N
+A 7 THR 53 N
+A 8 LEU 60 N
+A 9 THR 68 N
+A 10 GLY 75 N
+A 11 LYS 79 N
+A 12 THR 88 N
+A 13 ILE 95 N
+A 14 THR 103 N
+A 15 LEU 110 N
+A 16 GLU 118 N
+A 17 VAL 127 N
+A 18 GLU 134 N
+A 19 PRO 143 N
+A 20 SER 150 N
+A 21 ASP 156 N
+A 22 THR 164 N
+A 23 ILE 171 N
+A 24 GLU 179 N
+A 25 ASN 188 N
+A 26 VAL 196 N
+A 27 LYS 203 N
+A 28 ALA 212 N
+A 29 LYS 217 N
+A 30 ILE 226 N
+A 31 GLN 234 N
+A 32 ASP 243 N
+A 33 LYS 251 N
+A 34 GLU 260 N
+A 35 GLY 269 N
+A 36 ILE 273 N
+A 37 PRO 281 N
+A 38 PRO 288 N
+A 39 ASP 295 N
+A 40 GLN 303 N
+A 41 GLN 312 N
+A 42 ARG 321 N
+A 43 LEU 332 N
+A 44 ILE 340 N
+A 45 PHE 348 N
+A 46 ALA 359 N
+A 47 GLY 364 N
+A 48 LYS 368 N
+A 49 GLN 377 N
+A 50 LEU 386 N
+A 51 GLU 394 N
+A 52 ASP 403 N
+A 53 GLY 411 N
+A 54 ARG 415 N
+A 55 THR 426 N
+A 56 LEU 433 N
+A 57 SER 441 N
+A 58 ASP 447 N
+A 59 TYR 455 N
+A 60 ASN 467 N
+A 61 ILE 475 N
+A 62 GLN 483 N
+A 63 LYS 492 N
+A 64 GLU 501 N
+A 65 SER 510 N
+A 66 THR 516 N
+A 67 LEU 523 N
+A 68 HIS 531 N
+A 69 LEU 541 N
+A 70 VAL 549 N
+A 71 LEU 556 N
+A 72 ARG 564 N
+A 73 LEU 575 N
+A 74 ARG 583 N
+A 75 GLY 594 N
+A 76 GLY 598 N
Added: 1.3/test_suite/system_tests/scripts/1UBQ_relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/1UBQ_relax_fit.py?rev=8099&view=auto
==============================================================================
--- 1.3/test_suite/system_tests/scripts/1UBQ_relax_fit.py (added)
+++ 1.3/test_suite/system_tests/scripts/1UBQ_relax_fit.py Wed Dec 3 14:12:31
2008
@@ -1,0 +1,89 @@
+# Script for catching bug #12670 (https://gna.org/bugs/index.php?12670) as
submitted by Michael Funk (mifu att nmr dot mpibpc dot mpg dot de).
+
+# Create the 'rx' data pipe.
+pipe.create('rx', 'relax_fit')
+
+# Load the sequence.
+sequence.read('1UBQ.seq', mol_name_col=0, res_num_col=1, res_name_col=2,
spin_num_col=3, spin_name_col=4)
+
+# Spectrum names.
+names = [
+ '700mhz-263k-1m-02',
+ '700mhz-263k-1m-04',
+ '700mhz-263k-1m-06',
+ '700mhz-263k-1m-08',
+ '700mhz-263k-1m-10',
+ '700mhz-263k-1m-12',
+ '700mhz-263k-1m-14',
+ '700mhz-263k-1m-16'
+ ]
+
+# Relaxation times (in seconds).
+times = [
+ 0.004,
+ 0.008,
+ 0.012,
+ 0.016,
+ 0.020,
+ 0.024,
+ 0.028,
+ 0.032
+]
+
+#maf# Definte data path
+data_path = '.'
+
+# Loop over the spectra.
+for i in xrange(len(names)):
+ # Load the peak intensities.
+ spectrum.read_intensities(file=names[i]+'.listb', dir=data_path,
spectrum_id=names[i], int_method='height', proton='H')
+
+ # Set the relaxation times.
+ relax_fit.relax_time(time=times[i], spectrum_id=names[i])
+
+# Specify the duplicated spectra.
+
+#maf# Spectrum baseplane noise for non-duplicated spectra
+spectrum.baseplane_rmsd(error=20570, spectrum_id='700mhz-263k-1m-02',
spin_id=None)
+spectrum.baseplane_rmsd(error=20570, spectrum_id='700mhz-263k-1m-04',
spin_id=None)
+spectrum.baseplane_rmsd(error=18125, spectrum_id='700mhz-263k-1m-06',
spin_id=None)
+spectrum.baseplane_rmsd(error=15560, spectrum_id='700mhz-263k-1m-08',
spin_id=None)
+spectrum.baseplane_rmsd(error=15652, spectrum_id='700mhz-263k-1m-10',
spin_id=None)
+spectrum.baseplane_rmsd(error=16500, spectrum_id='700mhz-263k-1m-12',
spin_id=None)
+spectrum.baseplane_rmsd(error=16000, spectrum_id='700mhz-263k-1m-14',
spin_id=None)
+spectrum.baseplane_rmsd(error=16700, spectrum_id='700mhz-263k-1m-16',
spin_id=None)
+
+# Peak intensity error analysis.
+spectrum.error_analysis()
+
+# 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=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='devnull', force=True)
+
+# Save the results.
+results.write(file='devnull', force=True)
+
+# Create Grace plots of the data.
+grace.write(y_data_type='chi2', file='devnull', force=True) # Minimised
chi-squared value.
+grace.write(y_data_type='i0', file='devnull', force=True) # Initial peak
intensity.
+grace.write(y_data_type='rx', file='devnull', force=True) # Relaxation
rate.
+grace.write(x_data_type='relax_times', y_data_type='int', file='devnull',
force=True) # Average peak intensities.
+grace.write(x_data_type='relax_times', y_data_type='int', norm=True,
file='devnull', force=True) # Average peak intensities (normalised).
+
+# Save the program state.
+state.save('devnull', force=True)
r8099 - in /1.3/test_suite: shared_data/peak_lists/ shared_data/sequence/ system_tests/scripts/