Author: bugman
Date: Thu Jul 31 18:25:05 2014
New Revision: 24896
URL: http://svn.gna.org/viewcvs/relax?rev=24896&view=rev
Log:
Created the Bruker.test_bug_22411_T1_read_fail system test.
This is to catch bug #22411 (https://gna.org/bugs/?22411) as reported by
Olena Dobrovolska.
Added:
trunk/test_suite/shared_data/bruker_files/bug_22411_T1.txt (with props)
trunk/test_suite/shared_data/bruker_files/bug_22411_T1_sequence
Modified:
trunk/test_suite/system_tests/bruker.py
Added: trunk/test_suite/shared_data/bruker_files/bug_22411_T1.txt
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/bruker_files/bug_22411_T1.txt?rev=24896&view=auto
==============================================================================
--- trunk/test_suite/shared_data/bruker_files/bug_22411_T1.txt (added)
+++ trunk/test_suite/shared_data/bruker_files/bug_22411_T1.txt Thu Jul 31
18:25:05 2014
@@ -0,0 +1,89 @@
+$##1.0
+
+Project: Dynamic method/T1
+Date: Tuesday, May 27, 2014 2:17:20 PM
+User: olena
+Computer: STR340AG093177
+generated by: Dynamics Center 2.1.5
+
+
+SECTION: sample information
+sample name: UreE
+Description/Title: standard demo sample
+Origin: in-house
+Date of preparation: 06 / 2012
+Solvent: 90% H2O + 10% D2O
+pH: 7.5
+Sample tube: normal
+Tube diameter (mm): 5
+Concentration (mM): 1.00
+Temperature (K): 298.0
+Weight (Daltons): 17500
+Correlation time (ns): 17.00
+Labelling: 15N
+AminoAcid storage: FASTA file
+AminoAcid file: C:\Users\olena\Desktop\Anna\BpUreE_AM_relax_from
Stefano\BpUreE_AM_relax\NOE\BpUreE_aa.fa
+
+ 140 H Q H
+ 220 L
+PDB file: C:\Users\olena\Desktop\Anna\BpUreE_AM_relax_from
Stefano\BpUreE_AM_relax\NOE\hadded_2.pdb
+
+
+SECTION: relevant parameters
+Proton frequency[MHz]: 500.125
+X nucleus frequency[MHz]: 50.677
+
+
+SECTION: integrals
+Mixing time [s]: 0.01000000 0.05000000
0.10000000 0.20000000 0.40000000
0.60000000 0.80000000 1.00000000
1.50000000 2.50000000
+Peak name I0 I1
I2 I3 I4 I5
I6 I7 I8
I9
+
+
+ H145 13756498.00000000 15514689.00000000
15055511.00000000 13609771.00000000 10062429.00000000
7974869.00000000 6169520.00000000 4629481.00000000
2547361.00000000 898870.00000000
+ Q146 8733461.00000000 10080191.00000000
9981142.00000000 8620576.00000000 6590677.00000000
4630599.00000000 3602645.00000000 2718771.00000000
1506067.00000000 436106.00000000
+ H147 224716698.00000000 253388645.00000000
248053592.00000000 216045891.00000000 161293601.00000000
119337670.00000000 88886202.00000000 67943841.00000000
37367369.00000000 11560388.00000000
+ L222 15759159.00000000 18560944.00000000
18865908.00000000 17809151.00000000 15700416.00000000
13595993.00000000 11816930.00000000 10332890.00000000
7792819.00000000 4579760.00000000
+
+SECTION: integral errors
+Mixing time [s]: 0.01000000 0.05000000
0.10000000 0.20000000 0.40000000
0.60000000 0.80000000 1.00000000
1.50000000 2.50000000
+Peak name I0 I1
I2 I3 I4 I5
I6 I7 I8
I9
+
+ H145 93740.22047434 86246.24327553
86512.35134207 98214.16028465 83166.68544343
102285.80593267 86477.22470018 86533.28148070
90750.07835281 85573.61522123
+ Q146 93740.22047434 86246.24327553
86512.35134207 98214.16028465 83166.68544343
102285.80593267 86477.22470018 86533.28148070
90750.07835281 85573.61522123
+ H147 93740.22047434 86246.24327553
86512.35134207 98214.16028465 83166.68544343
102285.80593267 86477.22470018 86533.28148070
90750.07835281 85573.61522123
+ L222 93740.22047434 86246.24327553
86512.35134207 98214.16028465 83166.68544343
102285.80593267 86477.22470018 86533.28148070
90750.07835281 85573.61522123
+
+
+
+SECTION: integrals back calculated from fit
+Mixing time [s]: 0.01000000 0.05000000
0.10000000 0.20000000 0.40000000
0.60000000 0.80000000 1.00000000
1.50000000 2.50000000
+Peak name I0 I1
I2 I3 I4 I5
I6 I7 I8
I9
+
+ H145 15738604.20090525 15026510.70680394
14181529.06515528 12631440.70947580 10021034.21322855
7950092.86845353 6307131.10764571 5003702.90853851
2805050.33175678 881533.74821077
+ Q146 10254719.90269907 9754883.24076119
9164207.55688108 8087989.88264072 6299875.46308338
4907082.15839184 3822211.31993968 2977186.62592412
1594169.41220471 457079.02996617
+ H147 258326604.85790733 245549161.68237550
230462413.29953182 203012792.17669052 157532441.01064360
122240917.45496067 94855648.80709809 73605420.32851373
39041481.78350179 10983968.61860609
+ L222 18614264.92121686 18204408.56909731
17704755.28321164 16746214.00305464 14982009.01175903
13403662.10460977 11991593.22848775 10728285.07875159
8122016.13957740 4655120.56867706
+
+
+SECTION: details
+Fitted function: f(t) = Io * exp (-t/T)
+Random error estimation of data: RMS per spectrum (or trace/plane)
+Systematic error estimation of data: average variance calculation
+Fit parameter Error estimation method: from fit using calculated y
uncertainties
+Confidence level: 95%
+Used peaks: peaks from
C:\Users\olena\Desktop\Anna\SpUreE_SC_dyn_500\SpUreE_SC_dyn_500\SpUreE_500.xml
+Used integrals: peak intensities
+Used Mixing time: all values (including replicates) used
+
+
+SECTION: results
+Peak name F1 [ppm] F2 [ppm] T1 [s] error
errorScale R1 [rad/s] R1 sd [rad/s]
+
+H145 118.656 8.099 0.863921 0.0174326
2.3060041 1.157513 0.0101287
+Q146 121.783 8.277 0.800479 0.0247820
2.3060041 1.249252 0.0167716
+H147 125.284 7.972 0.788527 0.0009692
2.3060041 1.268188 0.0006760
+L222 122.595 8.283 1.796588 0.0340993
2.3060041 0.556611 0.0045813
+
+
+
+
Propchange: trunk/test_suite/shared_data/bruker_files/bug_22411_T1.txt
------------------------------------------------------------------------------
svn:eol-style = native
Added: trunk/test_suite/shared_data/bruker_files/bug_22411_T1_sequence
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/bruker_files/bug_22411_T1_sequence?rev=24896&view=auto
==============================================================================
--- trunk/test_suite/shared_data/bruker_files/bug_22411_T1_sequence
(added)
+++ trunk/test_suite/shared_data/bruker_files/bug_22411_T1_sequence Thu
Jul 31 18:25:05 2014
@@ -0,0 +1,4 @@
+H 145
+Q 146
+H 147
+L 222
Modified: trunk/test_suite/system_tests/bruker.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/bruker.py?rev=24896&r1=24895&r2=24896&view=diff
==============================================================================
--- trunk/test_suite/system_tests/bruker.py (original)
+++ trunk/test_suite/system_tests/bruker.py Thu Jul 31 18:25:05 2014
@@ -1,4 +1,4 @@
-###############################################################################
+##############################################################################
#
#
# Copyright (C) 2011-2013 Edward d'Auvergne
#
#
#
@@ -37,6 +37,18 @@
# Create a data pipe.
self.interpreter.pipe.create('mf', 'mf')
+
+
+ def test_bug_22411_T1_read_fail(self):
+ """Test catching U{bug #22411<https://gna.org/bugs/?22411>}, the
failure in reading a Bruker DC T1 file as submitted by Olena Dobrovolska."""
+
+ # The data path.
+ path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'bruker_files'
+
+ # Create a data pipe, read the sequence, and read the Bruker DC file
to trigger the bug.
+ self.interpreter.pipe.create('bug_22411', 'mf')
+ self.interpreter.sequence.read(file='bug_22411_T1_sequence',
dir=path, res_num_col=2, res_name_col=1)
+ self.interpreter.bruker.read(ri_id='T1', file='bug_22411_T1.txt',
dir=path)
def test_bruker_read_noe(self):
r24896 - in /trunk/test_suite: shared_data/bruker_files/ system_tests/