r20505 - /trunk/test_suite/system_tests/peak_lists.py -- August 02, 2013 - 13:53

Author: bugman
Date: Fri Aug  2 13:53:52 2013
New Revision: 20505

URL: http://svn.gna.org/viewcvs/relax?rev=20505&view=rev
Log:
Fix for handling reading spin of type heteronuc='NE1' and proton='HE1'.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for 
NMRPipe seriesTab format *.ser.

Troels E. Linnet provided this patch. Commit by: tlinset _aaattt_ 
gmail_dot_com

Signed-off-by: Edward d'Auvergne <edward _att_ nmr-relax _dott_ com>

Modified:
    trunk/test_suite/system_tests/peak_lists.py

Modified: trunk/test_suite/system_tests/peak_lists.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/peak_lists.py?rev=20505&r1=20504&r2=20505&view=diff
==============================================================================
--- trunk/test_suite/system_tests/peak_lists.py (original)
+++ trunk/test_suite/system_tests/peak_lists.py Fri Aug  2 13:53:52 2013
@@ -47,7 +47,7 @@
 
         # Missing module.
         if not dep_check.C_module_exp_fn and methodName in 
['test_bug_17276_peak_lists', 'test_bug_20873_peak_lists', 
'test_ccpn_analysis']:
-            # Store in the status object. 
+            # Store in the status object.
             status.skipped_tests.append([methodName, 'Relax curve-fitting C 
module', self._skip_type])
 
 
@@ -78,7 +78,7 @@
         self.interpreter.sequence.read(file='test.seq', dir=path, 
spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3, 
spin_num_col=4, spin_name_col=5, sep=None, spin_id=None)
 
         # Load the intensities.
-        self.interpreter.spectrum.read_intensities(file='test.seq', 
dir=path, spectrum_id=['2', '0'], heteronuc='N', proton='HN', 
int_method='height', int_col=[6, 7], spin_id_col=None, mol_name_col=1, 
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, 
spin_id=None, ncproc=None) 
+        self.interpreter.spectrum.read_intensities(file='test.seq', 
dir=path, spectrum_id=['2', '0'], heteronuc='N', proton='HN', 
int_method='height', int_col=[6, 7], spin_id_col=None, mol_name_col=1, 
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, 
spin_id=None, ncproc=None)
 
         # The peak intensities.
         data_2 = [337765.90000000002, 1697771.0, 867389.80000000005, 
2339480.0, 2574062.0, 1609356.0, 2179341.0, 1563795.0, 1535896.0, 3578841.0]
@@ -206,20 +206,23 @@
         """Test the reading of an NMRPipe seriesTab peak list."""
 
         # Create the sequence data, and name the spins.
-        self.interpreter.residue.create(res_num = 62, res_name=None, 
mol_name=None )
+        self.interpreter.residue.create(res_num = 62)
         self.interpreter.spin.name(name='NE1', spin_id=':62')
         self.interpreter.residue.create(res_num = 10)
         self.interpreter.spin.name(name='N', spin_id=':10')
         self.interpreter.residue.create(res_num = 6)
         self.interpreter.spin.name(name='N', spin_id=':6')
 
-        # Read the peak list.
-        self.interpreter.spectrum.read_intensities(file="seriesTab.ser", 
dir=status.install_path + 
sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', spectrum_id='test', 
int_method='height')
-
-        # Test the data.
-        
self.assertEqual(list(cdp.mol[0].res[0].spin[0].intensities['test']), 
+1.851056e+06)
-        
self.assertEqual(list(cdp.mol[0].res[1].spin[0].intensities['test']), 
+3.224387e+05)
-        
self.assertEqual(list(cdp.mol[0].res[2].spin[0].intensities['test']), 
+1.479366e+06)
+        # Read the peak list for W62NE1-W62HE1, with heteronuc=NE1 and 
proton=HE1.
+        self.interpreter.spectrum.read_intensities(file="seriesTab.ser", 
dir=status.install_path + 
sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', spectrum_id='test', 
heteronuc='NE1', proton='HE1', int_method='point sum')
+
+        # Read the peak list for heteronuc=N and proton=H.
+        self.interpreter.spectrum.read_intensities(file="seriesTab.ser", 
dir=status.install_path + 
sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', spectrum_id='test', 
int_method='point sum')
+
+        # Test the data.
+        self.assertEqual(cdp.mol[0].res[0].spin[0].intensities['test'], 
+1.851056e+06)
+        self.assertEqual(cdp.mol[0].res[1].spin[0].intensities['test'], 
+3.224387e+05)
+        self.assertEqual(cdp.mol[0].res[2].spin[0].intensities['test'], 
+1.479366e+06)
 
 
     def test_read_peak_list_sparky(self):