Author: bugman
Date: Wed Dec 10 14:05:33 2014
New Revision: 27053
URL: http://svn.gna.org/viewcvs/relax?rev=27053&view=rev
Log:
Modified the Structure.test_align_molecules system test.
This now simultaneously checks both the pipes and molecules arguments to the
structure.align user
function.
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=27053&r1=27052&r2=27053&view=diff
==============================================================================
--- trunk/test_suite/system_tests/structure.py (original)
+++ trunk/test_suite/system_tests/structure.py Wed Dec 10 14:05:33 2014
@@ -182,10 +182,14 @@
def test_align_molecules(self):
"""Test the U{structure.align user
function<http://www.nmr-relax.com/manual/structure_align.html>} for aligning
different molecules in one pipe."""
+ # Reset relax.
+ self.interpreter.reset()
+
# Path of the PDB file.
path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'diffusion_tensor'+sep+'spheroid'
- # Load the reference structure.
+ # Create a data pipe for the reference structure, then load it.
+ self.interpreter.pipe.create('ref', 'N-state')
self.interpreter.structure.read_pdb('uniform.pdb', dir=path,
set_mol_name='ref')
# Delete a residue and atom.
@@ -194,6 +198,9 @@
# Output PDB to stdout to help in debugging.
self.interpreter.structure.write_pdb(file=sys.stdout)
+
+ # Create a second data pipe for the structures to align and
superimpose.
+ self.interpreter.pipe.create('align', 'N-state')
# Load the PDB twice as different models.
self.interpreter.structure.read_pdb('uniform.pdb', dir=path,
set_mol_name='1')
@@ -213,7 +220,7 @@
self.interpreter.structure.translate(T=[0., 0., 1.], model=2,
atom_id='#2')
# The alignment.
- self.interpreter.structure.align(molecules=['ref', '1', '2'],
method='fit to first', atom_id='@N,H')
+ self.interpreter.structure.align(pipes=['ref', 'align'],
molecules=['ref', '1', '2'], method='fit to first', atom_id='@N,H')
# Output PDB to stdout to help in debugging.
self.interpreter.structure.write_pdb(file=sys.stdout)
@@ -268,10 +275,8 @@
# Check the molecules.
self.assertEqual(len(data),
len(cdp.structure.structural_data[0].mol[0].atom_name))
self.assertEqual(len(data),
len(cdp.structure.structural_data[0].mol[1].atom_name))
- self.assertEqual(len(data),
len(cdp.structure.structural_data[0].mol[2].atom_name))
current_mol = ''
for mol_name, res_num, res_name, atom_name, pos in
cdp.structure.atom_loop(selection=selection, model_num=1, mol_name_flag=True,
res_num_flag=True, res_name_flag=True, atom_name_flag=True, pos_flag=True):
- print mol_name, res_num, res_name, atom_name, pos
if mol_name != current_mol:
current_mol = mol_name
i = 0
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