Author: bugman
Date: Tue Feb 4 16:03:48 2014
New Revision: 22119
URL: http://svn.gna.org/viewcvs/relax?rev=22119&view=rev
Log:
Merged revisions 22115 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r22115 | bugman | 2014-02-04 15:29:24 +0100 (Tue, 04 Feb 2014) | 9 lines
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:
branches/double_rotor/test_suite/shared_data/peak_lists/noe.140109.8.001.list
- copied unchanged from r22115,
trunk/test_suite/shared_data/peak_lists/noe.140109.8.001.list
branches/double_rotor/test_suite/shared_data/peak_lists/noe.140109.8.002.list
- copied unchanged from r22115,
trunk/test_suite/shared_data/peak_lists/noe.140109.8.002.list
Modified:
branches/double_rotor/ (props changed)
branches/double_rotor/test_suite/system_tests/noe.py
Propchange: branches/double_rotor/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Tue Feb 4 16:03:48 2014
@@ -1,1 +1,1 @@
-/trunk:1-22112
+/trunk:1-22112,22115
Modified: branches/double_rotor/test_suite/system_tests/noe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/double_rotor/test_suite/system_tests/noe.py?rev=22119&r1=22118&r2=22119&view=diff
==============================================================================
--- branches/double_rotor/test_suite/system_tests/noe.py (original)
+++ branches/double_rotor/test_suite/system_tests/noe.py Tue Feb 4 16:03:48
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.
r22119 - in /branches/double_rotor: ./ test_suite/shared_data/peak_lists/ test_suite/system_tests/