Author: bugman
Date: Wed Dec 10 13:58:30 2014
New Revision: 27052
URL: http://svn.gna.org/viewcvs/relax?rev=27052&view=rev
Log:
Created the Structure.test_align_molecules system test.
This will be used to extend the functionality of the structure.align user
function to be able to
align different molecules in the same data pipe, rather than requiring either
models or identically
named structures in different data pipes.
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=27052&r1=27051&r2=27052&view=diff
==============================================================================
--- trunk/test_suite/system_tests/structure.py (original)
+++ trunk/test_suite/system_tests/structure.py Wed Dec 10 13:58:30 2014
@@ -170,6 +170,111 @@
self.assertEqual(len(data),
len(cdp.structure.structural_data[1].mol[0].atom_name))
i = 0
for res_num, res_name, atom_name, pos in
cdp.structure.atom_loop(selection=selection, model_num=2, res_num_flag=True,
res_name_flag=True, atom_name_flag=True, pos_flag=True):
+ self.assertEqual(atom_name, data[i][0])
+ self.assertEqual(res_name, data[i][1])
+ self.assertEqual(res_num, data[i][2])
+ self.assertAlmostEqual(pos[0][0], data[i][3])
+ self.assertAlmostEqual(pos[0][1], data[i][4])
+ self.assertAlmostEqual(pos[0][2], data[i][5])
+ i += 1
+
+
+ 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."""
+
+ # Path of the PDB file.
+ path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'diffusion_tensor'+sep+'spheroid'
+
+ # Load the reference structure.
+ self.interpreter.structure.read_pdb('uniform.pdb', dir=path,
set_mol_name='ref')
+
+ # Delete a residue and atom.
+ self.interpreter.structure.delete("#ref:8")
+ self.interpreter.structure.delete("#ref:2@N")
+
+ # Output PDB to stdout to help in debugging.
+ self.interpreter.structure.write_pdb(file=sys.stdout)
+
+ # Load the PDB twice as different models.
+ self.interpreter.structure.read_pdb('uniform.pdb', dir=path,
set_mol_name='1')
+ self.interpreter.structure.read_pdb('uniform.pdb', dir=path,
set_mol_name='2')
+
+ # Delete a residue and atom from these two structures.
+ self.interpreter.structure.delete("#1,2:12")
+ self.interpreter.structure.delete("#1,2:20@H")
+
+ # Translate and rotate the models.
+ R = zeros((3, 3), float64)
+ axis_angle_to_R(array([1, 0, 0], float64), 1.0, R)
+ self.interpreter.structure.rotate(R=R, model=1, atom_id='#1')
+ axis_angle_to_R(array([0, 0, 1], float64), 2.0, R)
+ self.interpreter.structure.rotate(R=R, model=2, atom_id='#2')
+ self.interpreter.structure.translate(T=[1., 1., 1.], model=1,
atom_id='#1')
+ 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')
+
+ # Output PDB to stdout to help in debugging.
+ self.interpreter.structure.write_pdb(file=sys.stdout)
+
+ # The atomic data.
+ data = [
+ ["N", "NH", 1, 0.000, 0.000, 0.000],
+ ["H", "NH", 1, 0.000, 0.000, -1.020],
+ ["N", "NH", 2, 0.000, 0.000, 0.000],
+ ["H", "NH", 2, 0.883, 0.000, -0.510],
+ ["N", "NH", 3, 0.000, 0.000, 0.000],
+ ["H", "NH", 3, 0.883, 0.000, 0.510],
+ ["N", "NH", 4, 0.000, 0.000, 0.000],
+ ["H", "NH", 4, 0.000, 0.000, 1.020],
+ ["N", "NH", 5, 0.000, 0.000, 0.000],
+ ["H", "NH", 5, 0.000, 0.000, -1.020],
+ ["N", "NH", 6, 0.000, 0.000, 0.000],
+ ["H", "NH", 6, 0.273, 0.840, -0.510],
+ ["N", "NH", 7, 0.000, 0.000, 0.000],
+ ["H", "NH", 7, 0.273, 0.840, 0.510],
+ ["N", "NH", 8, 0.000, 0.000, 0.000],
+ ["H", "NH", 8, 0.000, 0.000, 1.020],
+ ["N", "NH", 9, 0.000, 0.000, 0.000],
+ ["H", "NH", 9, -0.000, 0.000, -1.020],
+ ["N", "NH", 10, 0.000, 0.000, 0.000],
+ ["H", "NH", 10, -0.715, 0.519, -0.510],
+ ["N", "NH", 11, 0.000, 0.000, 0.000],
+ ["H", "NH", 11, -0.715, 0.519, 0.510],
+ #["N", "NH", 12, 0.000, 0.000, 0.000],
+ #["H", "NH", 12, -0.000, 0.000, 1.020],
+ ["N", "NH", 13, 0.000, 0.000, 0.000],
+ ["H", "NH", 13, -0.000, -0.000, -1.020],
+ ["N", "NH", 14, 0.000, 0.000, 0.000],
+ ["H", "NH", 14, -0.715, -0.519, -0.510],
+ ["N", "NH", 15, 0.000, 0.000, 0.000],
+ ["H", "NH", 15, -0.715, -0.519, 0.510],
+ ["N", "NH", 16, 0.000, 0.000, 0.000],
+ ["H", "NH", 16, -0.000, -0.000, 1.020],
+ ["N", "NH", 17, 0.000, 0.000, 0.000],
+ ["H", "NH", 17, 0.000, -0.000, -1.020],
+ ["N", "NH", 18, 0.000, 0.000, 0.000],
+ ["H", "NH", 18, 0.273, -0.840, -0.510],
+ ["N", "NH", 19, 0.000, 0.000, 0.000],
+ ["H", "NH", 19, 0.273, -0.840, 0.510],
+ ["N", "NH", 20, 0.000, 0.000, 0.000],
+ #["H", "NH", 20, 0.000, -0.000, 1.020]
+ ]
+
+ # The selection object.
+ selection = cdp.structure.selection()
+
+ # 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
self.assertEqual(atom_name, data[i][0])
self.assertEqual(res_name, data[i][1])
self.assertEqual(res_num, data[i][2])
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