Author: bugman
Date: Tue Feb 4 15:29:24 2014
New Revision: 22115
URL: http://svn.gna.org/viewcvs/relax?rev=22115&view=rev
Log:
Created the Noe.test_bug_21591_noe_calculation_fail system test.
This is to catch bug #21591 (https://gna.org/bugs/?21591) submitted by Martin
Ballaschk
(https://gna.org/users/mab). This is the complete failure of the NOE
analysis.
The peak lists attached to the bug report have been included in the test
suite to create the system
test.
Added:
trunk/test_suite/shared_data/peak_lists/noe.140109.8.001.list
trunk/test_suite/shared_data/peak_lists/noe.140109.8.002.list
Modified:
trunk/test_suite/system_tests/noe.py
Added: trunk/test_suite/shared_data/peak_lists/noe.140109.8.001.list
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/peak_lists/noe.140109.8.001.list?rev=22115&view=auto
==============================================================================
--- trunk/test_suite/shared_data/peak_lists/noe.140109.8.001.list (added)
+++ trunk/test_suite/shared_data/peak_lists/noe.140109.8.001.list Tue Feb 4
15:29:24 2014
@@ -1,0 +1,3 @@
+ Assignment w1 w2 Data Height
+
+ G120N-HN 101.980 9.089 7471594
Added: trunk/test_suite/shared_data/peak_lists/noe.140109.8.002.list
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/peak_lists/noe.140109.8.002.list?rev=22115&view=auto
==============================================================================
--- trunk/test_suite/shared_data/peak_lists/noe.140109.8.002.list (added)
+++ trunk/test_suite/shared_data/peak_lists/noe.140109.8.002.list Tue Feb 4
15:29:24 2014
@@ -1,0 +1,3 @@
+ Assignment w1 w2 Data Height
+
+ G120N-HN 101.980 9.089 3888023
Modified: trunk/test_suite/system_tests/noe.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/noe.py?rev=22115&r1=22114&r2=22115&view=diff
==============================================================================
--- trunk/test_suite/system_tests/noe.py (original)
+++ trunk/test_suite/system_tests/noe.py Tue Feb 4 15:29:24 2014
@@ -62,6 +62,61 @@
"2AT7_fmf_mol1 12 PHE 150 N
0.803029108487728 0.0199040298831904 \n",
"2AT7_fmf_mol1 13 ASN 170 N
0.829415981681132 0.0339996453012768 \n",
"2AT7_fmf_mol1 14 LYS 184 N
0.755789564728523 0.0250941717735858 \n"
+ ]
+
+ # Printout of the real and generated data.
+ print("\n\nThe real data:")
+ for i in range(len(lines)):
+ print(repr(data[i]))
+ print("\nThe generated data:")
+ for i in range(len(lines)):
+ print(repr(lines[i]))
+ print("\n")
+
+ # Check each line.
+ for i in range(len(lines)):
+ self.assertEqual(data[i], lines[i])
+
+
+ def test_bug_21591_noe_calculation_fail(self):
+ """Catch U{bug #21591<https://gna.org/bugs/?21591>}, the failure of
the NOE analysis."""
+
+ # Generate the sequence.
+ self.interpreter.spin.create(mol_name='XYZ_mol1', res_num=120,
res_name='GLY', spin_num=1865, spin_name='N')
+
+ # Load the reference spectrum and saturated spectrum peak
intensities.
+ path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'peak_lists'
+
self.interpreter.spectrum.read_intensities(file='noe.140109.8.001.list',
dir=path, spectrum_id='ref_ave')
+
self.interpreter.spectrum.read_intensities(file='noe.140109.8.002.list',
dir=path, spectrum_id='sat_ave')
+
+ # Set the spectrum types.
+ self.interpreter.noe.spectrum_type('ref', 'ref_ave')
+ self.interpreter.noe.spectrum_type('sat', 'sat_ave')
+
+ # Set the errors.
+ self.interpreter.spectrum.baseplane_rmsd(error=1.3e06,
spectrum_id='ref_ave')
+ self.interpreter.spectrum.baseplane_rmsd(error=1.4e06,
spectrum_id='sat_ave')
+
+ # Peak intensity error analysis.
+ self.interpreter.spectrum.error_analysis()
+
+ # Calculate the NOEs.
+ self.interpreter.calc()
+
+ # Save the NOEs.
+ self.interpreter.value.write(param='noe', file=ds.tmpfile)
+
+ # Open the NOE output file.
+ file = open(ds.tmpfile)
+ lines = file.readlines()
+ file.close()
+
+ # How the file should look like.
+ data = [
+ "# Parameter description: The NOE.\n",
+ "#\n",
+ "# mol_name res_num res_name spin_num spin_name
value error \n",
+ "XYZ_mol1 120 GLY 1865 N
0.5203739657160172 0.20810473864150658 \n",
]
# Printout of the real and generated data.
r22115 - in /trunk/test_suite: shared_data/peak_lists/ system_tests/