r27100 - /trunk/test_suite/system_tests/structure.py -- December 11, 2014 - 19:10

Author: bugman
Date: Thu Dec 11 19:10:37 2014
New Revision: 27100

URL: http://svn.gna.org/viewcvs/relax?rev=27100&view=rev
Log:
Modified some system tests of the structure.align and structure.superimpose 
user functions.

The displace_id argument has been introduced for both of these user functions 
for finer control over
which atoms are translated and rotated by the algorithm.  This allows, for 
example, to align
structures based on a set of backbone heavy atoms while the protons and side 
chains are displaced by
default.  Or if a domain is aligned, then just that domain can be displaced.


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=27100&r1=27099&r2=27100&view=diff
==============================================================================
--- trunk/test_suite/system_tests/structure.py  (original)
+++ trunk/test_suite/system_tests/structure.py  Thu Dec 11 19:10:37 2014
@@ -105,7 +105,7 @@
         self.interpreter.structure.add_atom(mol_name='uniform_mol1', 
atom_name='Ti', res_name='TST', res_num=1, pos=[[1.0, 2.0, 3.0], [1.0, 2.0, 
3.0]], element='Ti', pdb_record='HETATM')
 
         # The alignment.
-        self.interpreter.structure.align(pipes=['ref', 'align'], method='fit 
to first', atom_id='@N,H')
+        self.interpreter.structure.align(pipes=['ref', 'align'], method='fit 
to first', atom_id='@N,H', displace_id='@N,H')
 
         # Output PDB to stdout to help in debugging.
         self.interpreter.structure.write_pdb(file=sys.stdout)
@@ -4335,7 +4335,7 @@
         self.interpreter.structure.add_atom(mol_name='uniform_mol1', 
atom_name='Ti', res_name='TST', res_num=1, pos=[[1.0, 2.0, 3.0], [2.0, 3.0, 
4.0]], element='Ti', pdb_record='HETATM')
 
         # Superimpose the backbone heavy atoms.
-        self.interpreter.structure.superimpose(method='fit to mean', 
atom_id='@N,C,CA,O')
+        self.interpreter.structure.superimpose(method='fit to mean', 
atom_id='@N,C,CA,O', displace_id=':82-114')
 
         # Check that the two structures now have the same atomic coordinates.
         model1 = cdp.structure.structural_data[0].mol[0]
@@ -4346,9 +4346,9 @@
             self.assertAlmostEqual(model1.z[i], model2.z[i], 2)
 
         # The last atom must be different.
-        self.assertNotAlmostEqual(model1.x[-1], model2.x[-1], 2)
-        self.assertNotAlmostEqual(model1.y[-1], model2.y[-1], 2)
-        self.assertNotAlmostEqual(model1.z[-1], model2.z[-1], 2)
+        self.assertAlmostEqual(model1.x[-1] - model2.x[-1], -1.0, 2)
+        self.assertAlmostEqual(model1.y[-1] - model2.y[-1], -1.0, 2)
+        self.assertAlmostEqual(model1.z[-1] - model2.z[-1], -1.0, 2)
 
 
     def test_superimpose_fit_to_mean2(self):