r5451 - /1.3/test_suite/system_tests/sequence.py -- April 08, 2008 - 17:56

Author: bugman
Date: Tue Apr  8 17:56:35 2008
New Revision: 5451

URL: http://svn.gna.org/viewcvs/relax?rev=5451&view=rev
Log:
Created the test_load_protein_gly_N_Ca_spins_from_pdb() system test.

This tests the loading of glycine backbone amide N and Ca spins from a loaded 
protein PDB file.


Modified:
    1.3/test_suite/system_tests/sequence.py

Modified: 1.3/test_suite/system_tests/sequence.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/sequence.py?rev=5451&r1=5450&r2=5451&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/sequence.py (original)
+++ 1.3/test_suite/system_tests/sequence.py Tue Apr  8 17:56:35 2008
@@ -42,6 +42,54 @@
         """Reset the relax data storage object."""
 
         relax_data_store.__reset__()
+
+
+    def test_load_protein_gly_N_Ca_spins_from_pdb(self):
+        """Load the glycine backbone amide N and Ca spins from a loaded 
protein PDB file."""
+
+        # Read the PDB file.
+        self.relax.interpreter._Structure.read_pdb(file='test.pdb', 
dir=sys.path[-1] + '/test_suite/system_tests/data', model=1)
+
+        # Generate the sequence of nitrogen spins (1 molecule, all GLY 
residues, and only N spins).
+        self.relax.interpreter._Structure.load_spins(spin_id=':GLY@N')
+
+        # Append to the sequence the alpha carbon spins (1 molecule, all GLY 
residues, and only Ca spins).
+        self.relax.interpreter._Structure.load_spins(spin_id=':GLY@CA')
+
+        # Alias the current data pipe.
+        cdp = relax_data_store[relax_data_store.current_pipe]
+
+        # Test some of the sequence.
+        self.assertEqual(len(cdp.mol), 1)
+        self.assertEqual(cdp.mol[0].name, None)
+        self.assertEqual(len(cdp.mol[0].res), 3)
+
+        # 1st residue.
+        self.assertEqual(cdp.mol[0].res[0].num, 1)
+        self.assertEqual(cdp.mol[0].res[0].name, 'GLY')
+        self.assertEqual(len(cdp.mol[0].res[0].spin), 2)
+        self.assertEqual(cdp.mol[0].res[0].spin[0].num, 1)
+        self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'N')
+        self.assertEqual(cdp.mol[0].res[0].spin[1].num, 2)
+        self.assertEqual(cdp.mol[0].res[0].spin[1].name, 'CA')
+
+        # 2nd residue.
+        self.assertEqual(cdp.mol[0].res[1].num, 4)
+        self.assertEqual(cdp.mol[0].res[1].name, 'GLY')
+        self.assertEqual(len(cdp.mol[0].res[1].spin), 2)
+        self.assertEqual(cdp.mol[0].res[1].spin[0].num, 51)
+        self.assertEqual(cdp.mol[0].res[1].spin[0].name, 'N')
+        self.assertEqual(cdp.mol[0].res[1].spin[1].num, 53)
+        self.assertEqual(cdp.mol[0].res[1].spin[1].name, 'CA')
+
+        # 3rd residue.
+        self.assertEqual(cdp.mol[0].res[2].num, 12)
+        self.assertEqual(cdp.mol[0].res[2].name, 'GLY')
+        self.assertEqual(len(cdp.mol[0].res[2].spin), 2)
+        self.assertEqual(cdp.mol[0].res[2].spin[0].num, 167)
+        self.assertEqual(cdp.mol[0].res[2].spin[0].name, 'N')
+        self.assertEqual(cdp.mol[0].res[2].spin[1].num, 169)
+        self.assertEqual(cdp.mol[0].res[2].spin[1].name, 'CA')
 
 
     def test_load_protein_gly_N_spins_from_pdb(self):