Author: bugman
Date: Wed Dec 10 17:20:19 2014
New Revision: 27061
URL: http://svn.gna.org/viewcvs/relax?rev=27061&view=rev
Log:
Created the Structure.test_displacement_molecules system test.
This will be used to implement the new molecules argument for the
structure.displacement 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=27061&r1=27060&r2=27061&view=diff
==============================================================================
--- trunk/test_suite/system_tests/structure.py (original)
+++ trunk/test_suite/system_tests/structure.py Wed Dec 10 17:20:19 2014
@@ -3036,6 +3036,97 @@
self.assertAlmostEqual(cdp.structure.displacements._rotation_axis[models[i]][models[j]][k],
rot_axis[i][j][k])
+ def test_displacement_molecules(self):
+ """Test of the structure.displacement user function for different
molecules in one pipe.
+
+ This checks the molecules argument of the U{structure.displacement
user function<http://www.nmr-relax.com/manual/structure_displacement.html>}.
+ """
+
+ # Path of the structure file.
+ path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'structures'
+
+ # Load the file as two molecules.
+ self.interpreter.structure.read_pdb('Ap4Aase_res1-12.pdb', dir=path,
set_mol_name='1')
+ self.interpreter.structure.read_pdb('Ap4Aase_res1-12.pdb', dir=path,
set_mol_name='2')
+
+ # A rotation.
+ R = zeros((3, 3), float64)
+ euler_to_R_zyz(1.3, 0.4, 4.5, R)
+
+ # Rotate the second molecule.
+ self.interpreter.structure.rotate(R, atom_id='#2')
+
+ # Calculate the displacement.
+ self.interpreter.structure.displacement(molecules=['1', '2'])
+
+ # Shift a third structure back using the calculated displacement.
+ self.interpreter.structure.read_pdb('Ap4Aase_res1-12.pdb', dir=path,
set_mol_name='3')
+ self.interpreter.structure.rotate(R, atom_id='#3')
+
+ # The data to check.
+ molecules = ['1', '2']
+ trans_vect = [
+ [[0.0, 0.0, 0.0],
+ [ 2.270857972754659, -1.811667138656451,
1.878400649688508]],
+ [[ -2.270857972754659, 1.811667138656451,
-1.878400649688508],
+ [0.0, 0.0, 0.0]]
+ ]
+ dist = [
+ [0.0000000000000000, 3.4593818457148173],
+ [3.4593818457148173, 0.0000000000000000]
+ ]
+ rot_axis = [
+ [None,
+ [ 0.646165066909452, 0.018875759848125,
-0.762964227206007]],
+ [[ -0.646165066909452, -0.018875759848125,
0.762964227206007],
+ None]
+ ]
+ angle = [
+ [0.0000000000000000, 0.6247677290742989],
+ [0.6247677290742989, 0.0000000000000000]
+ ]
+
+ # Test the results.
+ self.assert_(hasattr(cdp.structure, 'displacements'))
+ for i in range(len(molecules)):
+ for j in range(len(molecules)):
+ # Check the translation.
+
self.assertAlmostEqual(cdp.structure.displacements._translation_distance[molecules[i]][molecules[j]],
dist[i][j])
+ for k in range(3):
+
self.assertAlmostEqual(cdp.structure.displacements._translation_vector[molecules[i]][molecules[j]][k],
trans_vect[i][j][k])
+
+ # Check the rotation.
+
self.assertAlmostEqual(cdp.structure.displacements._rotation_angle[molecules[i]][molecules[j]],
angle[i][j])
+ if rot_axis[i][j] != None:
+ for k in range(3):
+
self.assertAlmostEqual(cdp.structure.displacements._rotation_axis[molecules[i]][molecules[j]][k],
rot_axis[i][j][k])
+
+ # Save the results.
+ self.tmpfile = mktemp()
+ self.interpreter.state.save(self.tmpfile, dir=None, force=True)
+
+ # Reset relax.
+ self.interpreter.reset()
+
+ # Load the results.
+ self.interpreter.state.load(self.tmpfile)
+
+ # Test the re-loaded data.
+ self.assert_(hasattr(cdp.structure, 'displacements'))
+ for i in range(len(molecules)):
+ for j in range(len(molecules)):
+ # Check the translation.
+
self.assertAlmostEqual(cdp.structure.displacements._translation_distance[molecules[i]][molecules[j]],
dist[i][j])
+ for k in range(3):
+
self.assertAlmostEqual(cdp.structure.displacements._translation_vector[molecules[i]][molecules[j]][k],
trans_vect[i][j][k])
+
+ # Check the rotation.
+
self.assertAlmostEqual(cdp.structure.displacements._rotation_angle[molecules[i]][molecules[j]],
angle[i][j])
+ if rot_axis[i][j] != None:
+ for k in range(3):
+
self.assertAlmostEqual(cdp.structure.displacements._rotation_axis[molecules[i]][molecules[j]][k],
rot_axis[i][j][k])
+
+
def test_get_model(self):
"""Test the get_model() method of the internal structural object."""
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