r27340 - /trunk/test_suite/system_tests/structure.py -- January 28, 2015 - 13:07

Author: bugman
Date: Wed Jan 28 13:07:29 2015
New Revision: 27340

URL: http://svn.gna.org/viewcvs/relax?rev=27340&view=rev
Log:
Created the Structure.test_align_molecules_end_truncation system test.

This is to demonstrate a failure of the common residue detection algorithm 
using multiple pairwise
alignments in the backend of the structure.align and other multiple structure 
based user functions.


Modified:
    trunk/test_suite/system_tests/structure.py

Modified: trunk/test_suite/system_tests/structure.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/structure.py?rev=27340&r1=27339&r2=27340&view=diff
==============================================================================
--- trunk/test_suite/system_tests/structure.py  (original)
+++ trunk/test_suite/system_tests/structure.py  Wed Jan 28 13:07:29 2015
@@ -354,6 +354,42 @@
         # Add an atom that should not be superimposed.
         self.interpreter.structure.add_atom(mol_name='CaM A', 
atom_name='Ti', res_name='TST', res_num=1, pos=[1.0, 2.0, 3.0], element='Ti', 
pdb_record='HETATM')
         self.interpreter.structure.add_atom(mol_name='CaM B', 
atom_name='Ti', res_name='TST', res_num=1, pos=[2.0, 3.0, 4.0], element='Ti', 
pdb_record='HETATM')
+
+        # Superimpose the backbone heavy atoms.
+        self.interpreter.structure.align(method='fit to mean', 
atom_id='@N,C,CA,O', displace_id=':82-5000')
+
+        # Check that the two structures now have the same atomic coordinates.
+        mol1 = cdp.structure.structural_data[0].mol[0]
+        mol2 = cdp.structure.structural_data[0].mol[1]
+        for i in range(len(mol1.atom_name)):
+            if mol1.res_num[i] == 1:
+                continue
+            self.assertAlmostEqual(mol1.x[i], mol2.x[i], 2)
+            self.assertAlmostEqual(mol1.y[i], mol2.y[i], 2)
+            self.assertAlmostEqual(mol1.z[i], mol2.z[i], 2)
+
+        # The last atom must be different - it is not displaced.
+        self.assertAlmostEqual(mol1.x[-1] - mol2.x[-1], -1.0, 2)
+        self.assertAlmostEqual(mol1.y[-1] - mol2.y[-1], -1.0, 2)
+        self.assertAlmostEqual(mol1.z[-1] - mol2.z[-1], -1.0, 2)
+
+
+    def test_align_molecules_end_truncation(self):
+        """Test of the structure.align user function, fitting to the mean 
structure."""
+
+        # Path of the structure file.
+        path = status.install_path + 
sep+'test_suite'+sep+'shared_data'+sep+'structures'
+
+        # Load the two rotated structures.
+        self.interpreter.structure.read_pdb('1J7O.pdb', dir=path, 
read_model=1, set_model_num=1, set_mol_name='CaM A')
+        self.interpreter.structure.read_pdb('1J7O.pdb', dir=path, 
read_model=1, set_model_num=1, set_mol_name='CaM B')
+        self.interpreter.structure.read_pdb('1J7O.pdb', dir=path, 
read_model=1, set_model_num=1, set_mol_name='CaM C')
+
+        # Delete some end residues.
+        self.interpreter.structure.delete(atom_id="#CaM A:1-4")
+        self.interpreter.structure.delete(atom_id="#CaM A:60-100")
+        self.interpreter.structure.delete(atom_id="#CaM C:1-3")
+        self.interpreter.structure.delete(atom_id="#CaM C:75-100")
 
         # Superimpose the backbone heavy atoms.
         self.interpreter.structure.align(method='fit to mean', 
atom_id='@N,C,CA,O', displace_id=':82-5000')