Author: bugman
Date: Tue Nov 20 13:25:41 2007
New Revision: 3653
URL: http://svn.gna.org/viewcvs/relax?rev=3653&view=rev
Log:
Updated the generic_fns.test_residue unit test module to use the newly
created base class.
Modified:
1.3/test_suite/unit_tests/generic_fns/test_residue.py
Modified: 1.3/test_suite/unit_tests/generic_fns/test_residue.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/unit_tests/generic_fns/test_residue.py?rev=3653&r1=3652&r2=3653&view=diff
==============================================================================
--- 1.3/test_suite/unit_tests/generic_fns/test_residue.py (original)
+++ 1.3/test_suite/unit_tests/generic_fns/test_residue.py Tue Nov 20 13:25:41
2007
@@ -25,489 +25,13 @@
# relax module imports.
from data import Data as relax_data_store
-from data.pipe_container import PipeContainer
from generic_fns import residue
from relax_errors import RelaxError, RelaxNoPipeError,
RelaxSpinSelectDisallowError
+from test_suite.unit_tests.residue_testing_base import Residue_base_class
-class Test_residue(TestCase):
+class Test_residue(Residue_base_class, TestCase):
"""Unit tests for the functions of the 'generic_fns.residue' module."""
- def setUp(self):
- """Set up for all the residue unit tests."""
-
- # Reset the relax data storage object.
- relax_data_store.__reset__()
-
- # Add a data pipe to the data store.
- relax_data_store.add(pipe_name='orig', pipe_type='mf')
-
- # Add a second data pipe for copying tests.
- relax_data_store.add(pipe_name='test', pipe_type='mf')
-
- # Set the current data pipe to 'orig'.
- relax_data_store.current_pipe = 'orig'
-
-
- def tearDown(self):
- """Reset the relax data storage object."""
-
- relax_data_store.__reset__()
-
-
- def setup_data(self):
- """Function for setting up some data for the unit tests."""
-
- # Create the first residue and add some data to its spin container.
- residue.create(1, 'Ala')
- relax_data_store['orig'].mol[0].res[0].spin[0].num = 111
- relax_data_store['orig'].mol[0].res[0].spin[0].x = 1
- relax_data_store['orig'].mol[0].name = 'Old mol'
-
- # Create a second molecule.
- relax_data_store['orig'].mol.add_item('New mol')
-
- # Copy the residue to the new molecule.
- residue.copy(res_from=':1', res_to='#New mol')
- residue.copy(res_from='#Old mol:1', res_to='#New mol:5')
-
- # Change the first residue's data.
- relax_data_store['orig'].mol[0].res[0].spin[0].num = 222
- relax_data_store['orig'].mol[0].res[0].spin[0].x = 2
-
-
- def test_copy_between_molecules(self):
- """Test the copying of the residue data between different molecules.
-
- The function used is generic_fns.residue.copy().
- """
-
- # Set up some data.
- self.setup_data()
-
- # Test the original residue.
- self.assertEqual(relax_data_store['orig'].mol[0].res[0].num, 1)
- self.assertEqual(relax_data_store['orig'].mol[0].res[0].name, 'Ala')
- self.assertEqual(relax_data_store['orig'].mol[0].res[0].spin[0].num,
222)
- self.assertEqual(relax_data_store['orig'].mol[0].res[0].spin[0].x, 2)
-
- # Test the new residue 1.
- self.assertEqual(relax_data_store['orig'].mol[1].name, 'New mol')
- self.assertEqual(relax_data_store['orig'].mol[1].res[0].num, 1)
- self.assertEqual(relax_data_store['orig'].mol[1].res[0].name, 'Ala')
- self.assertEqual(relax_data_store['orig'].mol[1].res[0].spin[0].num,
111)
- self.assertEqual(relax_data_store['orig'].mol[1].res[0].spin[0].x, 1)
-
- # Test the new residue 5.
- self.assertEqual(relax_data_store['orig'].mol[1].res[1].num, 5)
- self.assertEqual(relax_data_store['orig'].mol[1].res[1].name, 'Ala')
- self.assertEqual(relax_data_store['orig'].mol[1].res[1].spin[0].num,
111)
- self.assertEqual(relax_data_store['orig'].mol[1].res[1].spin[0].x, 1)
-
-
-
- def test_copy_between_pipes(self):
- """Test the copying of the residue data between different data pipes.
-
- The function used is generic_fns.residue.copy().
- """
-
- # Create the first residue and add some data to its spin container.
- residue.create(1, 'Ala')
- relax_data_store['orig'].mol[0].res[0].spin[0].num = 111
- relax_data_store['orig'].mol[0].res[0].spin[0].x = 1
-
- # Copy the residue to the second data pipe.
- residue.copy(res_from=':1', pipe_to='test')
- residue.copy(pipe_from='orig', res_from=':1', pipe_to='test',
res_to=':5')
-
- # Change the first residue's data.
- relax_data_store['orig'].mol[0].res[0].spin[0].num = 222
- relax_data_store['orig'].mol[0].res[0].spin[0].x = 2
-
- # Test the original residue.
- self.assertEqual(relax_data_store['orig'].mol[0].res[0].num, 1)
- self.assertEqual(relax_data_store['orig'].mol[0].res[0].name, 'Ala')
- self.assertEqual(relax_data_store['orig'].mol[0].res[0].spin[0].num,
222)
- self.assertEqual(relax_data_store['orig'].mol[0].res[0].spin[0].x, 2)
-
- # Test the new residue 1.
- self.assertEqual(relax_data_store['test'].mol[0].res[0].num, 1)
- self.assertEqual(relax_data_store['test'].mol[0].res[0].name, 'Ala')
- self.assertEqual(relax_data_store['test'].mol[0].res[0].spin[0].num,
111)
- self.assertEqual(relax_data_store['test'].mol[0].res[0].spin[0].x, 1)
-
- # Test the new residue 5.
- self.assertEqual(relax_data_store['test'].mol[0].res[1].num, 5)
- self.assertEqual(relax_data_store['test'].mol[0].res[1].name, 'Ala')
- self.assertEqual(relax_data_store['test'].mol[0].res[1].spin[0].num,
111)
- self.assertEqual(relax_data_store['test'].mol[0].res[1].spin[0].x, 1)
-
-
- def test_copy_between_pipes_fail_no_pipe(self):
- """Test the copying of the residue data between different data pipes.
-
- The function used is generic_fns.residue.copy().
- """
-
- # Create the first residue and add some data to its spin container.
- residue.create(1, 'Ala')
- relax_data_store['orig'].mol[0].res[0].spin[0].num = 111
- relax_data_store['orig'].mol[0].res[0].spin[0].x = 1
-
- # Copy the residue to the second data pipe.
- self.assertRaises(RelaxNoPipeError, residue.copy, res_from=':1',
pipe_to='test2')
-
-
- def test_copy_within_molecule(self):
- """Test the copying of the residue data within a single molecule.
-
- The function used is generic_fns.residue.copy().
- """
-
- # Create the first residue and add some data to its spin container.
- residue.create(1, 'Ala')
- relax_data_store['orig'].mol[0].res[0].spin[0].num = 111
- relax_data_store['orig'].mol[0].res[0].spin[0].x = 1
-
- # Copy the residue a few times.
- residue.copy(res_from=':1', res_to=':2')
- residue.copy(res_from=':1', pipe_to='orig', res_to=':3')
-
- # Change the first residue's data.
- relax_data_store['orig'].mol[0].res[0].spin[0].num = 222
- relax_data_store['orig'].mol[0].res[0].spin[0].x = 2
-
- # Copy the residue once more.
- residue.copy(res_from=':1', res_to=':4,Met')
-
- # Test the original residue.
- self.assertEqual(relax_data_store['orig'].mol[0].res[0].num, 1)
- self.assertEqual(relax_data_store['orig'].mol[0].res[0].name, 'Ala')
- self.assertEqual(relax_data_store['orig'].mol[0].res[0].spin[0].num,
222)
- self.assertEqual(relax_data_store['orig'].mol[0].res[0].spin[0].x, 2)
-
- # Test the new residue 2.
- self.assertEqual(relax_data_store['orig'].mol[0].res[1].num, 2)
- self.assertEqual(relax_data_store['orig'].mol[0].res[1].name, 'Ala')
- self.assertEqual(relax_data_store['orig'].mol[0].res[1].spin[0].num,
111)
- self.assertEqual(relax_data_store['orig'].mol[0].res[1].spin[0].x, 1)
-
- # Test the new residue 3.
- self.assertEqual(relax_data_store['orig'].mol[0].res[2].num, 3)
- self.assertEqual(relax_data_store['orig'].mol[0].res[2].name, 'Ala')
- self.assertEqual(relax_data_store['orig'].mol[0].res[2].spin[0].num,
111)
- self.assertEqual(relax_data_store['orig'].mol[0].res[2].spin[0].x, 1)
-
- # Test the new residue 4.
- self.assertEqual(relax_data_store['orig'].mol[0].res[3].num, 4)
- self.assertEqual(relax_data_store['orig'].mol[0].res[3].name, 'Met')
- self.assertEqual(relax_data_store['orig'].mol[0].res[3].spin[0].num,
222)
- self.assertEqual(relax_data_store['orig'].mol[0].res[3].spin[0].x, 2)
-
-
- def test_copy_within_molecule_fail1(self):
- """The failure of copying residue data within a molecule of a
non-existent residue.
-
- The function used is generic_fns.residue.copy().
- """
-
- # Create a few residues.
- residue.create(1, 'Ala')
- residue.create(-1, 'His')
-
- # Copy a non-existent residue (1 Met).
- self.assertRaises(RelaxError, residue.copy, res_from=':Met',
res_to=':2,Gly')
-
-
- def test_copy_within_molecule_fail2(self):
- """The failure of copying residue data within a molecule to a
residue which already exists.
-
- The function used is generic_fns.residue.copy().
- """
-
- # Create a few residues.
- residue.create(1, 'Ala')
- residue.create(-1, 'His')
-
- # Copy a residue to a number which already exists.
- self.assertRaises(RelaxError, residue.copy, res_from=':1',
res_to=':-1,Gly')
-
-
- def test_creation(self):
- """Test the creation of a residue.
-
- The function used is generic_fns.residue.create().
- """
-
- # Create a few new residues.
- residue.create(1, 'Ala')
- residue.create(2, 'Leu')
- residue.create(-3, 'Ser')
-
- # Test that the residue numbers are correct.
- self.assertEqual(relax_data_store['orig'].mol[0].res[0].num, 1)
- self.assertEqual(relax_data_store['orig'].mol[0].res[1].num, 2)
- self.assertEqual(relax_data_store['orig'].mol[0].res[2].num, -3)
-
- # Test that the residue names are correct.
- self.assertEqual(relax_data_store['orig'].mol[0].res[0].name, 'Ala')
- self.assertEqual(relax_data_store['orig'].mol[0].res[1].name, 'Leu')
- self.assertEqual(relax_data_store['orig'].mol[0].res[2].name, 'Ser')
-
-
- def test_creation_fail(self):
- """Test the failure of residue creation (by supplying two residues
with the same number).
-
- The function used is generic_fns.residue.create().
- """
-
- # Create the first residue.
- residue.create(1, 'Ala')
-
- # Assert that a RelaxError occurs when the next added residue has
the same sequence number as the first.
- self.assertRaises(RelaxError, residue.create, 1, 'Ala')
-
-
- def test_delete_name(self):
- """Test residue deletion using residue name identifiers.
-
- The function used is generic_fns.residue.delete().
- """
-
- # Create some residues and add some data to the spin containers.
- residue.create(1, 'Ala')
- residue.create(2, 'Ala')
- residue.create(3, 'Ala')
- residue.create(4, 'Gly')
- relax_data_store['orig'].mol[0].res[3].spin[0].num = 111
- relax_data_store['orig'].mol[0].res[3].spin[0].x = 1
-
- # Delete the first residue.
- residue.delete(res_id=':Ala')
-
- # Test that the first residue is 4 Gly.
- self.assertEqual(relax_data_store['orig'].mol[0].res[0].num, 4)
- self.assertEqual(relax_data_store['orig'].mol[0].res[0].name, 'Gly')
- self.assertEqual(relax_data_store['orig'].mol[0].res[0].spin[0].num,
111)
- self.assert_(hasattr(relax_data_store['orig'].mol[0].res[0].spin[0],
'x'))
-
-
- def test_delete_num(self):
- """Test residue deletion using residue number identifiers.
-
- The function used is generic_fns.residue.delete().
- """
-
- # Create some residues and add some data to the spin containers.
- residue.create(1, 'Ala')
- residue.create(2, 'Ala')
- residue.create(3, 'Ala')
- residue.create(4, 'Gly')
- relax_data_store['orig'].mol[0].res[3].spin[0].num = 111
- relax_data_store['orig'].mol[0].res[3].spin[0].x = 1
-
- # Delete the first residue.
- residue.delete(res_id=':1')
-
- # Test that the sequence.
- self.assertEqual(relax_data_store['orig'].mol[0].res[0].num, 2)
- self.assertEqual(relax_data_store['orig'].mol[0].res[0].name, 'Ala')
- self.assertEqual(relax_data_store['orig'].mol[0].res[1].num, 3)
- self.assertEqual(relax_data_store['orig'].mol[0].res[1].name, 'Ala')
- self.assertEqual(relax_data_store['orig'].mol[0].res[2].num, 4)
- self.assertEqual(relax_data_store['orig'].mol[0].res[2].name, 'Gly')
- self.assertEqual(relax_data_store['orig'].mol[0].res[2].spin[0].num,
111)
- self.assert_(hasattr(relax_data_store['orig'].mol[0].res[2].spin[0],
'x'))
-
-
- def test_delete_all(self):
- """Test the deletion of all residues.
-
- The function used is generic_fns.residue.delete().
- """
-
- # Create some residues and add some data to the spin containers.
- residue.create(1, 'Ala')
- residue.create(2, 'Ala')
- residue.create(3, 'Ala')
- residue.create(4, 'Ala')
- relax_data_store['orig'].mol[0].res[3].spin[0].num = 111
- relax_data_store['orig'].mol[0].res[3].spin[0].x = 1
-
- # Delete all residues.
- residue.delete(res_id=':1-4')
-
- # Test that the first residue defaults back to the empty residue.
- self.assertEqual(relax_data_store['orig'].mol[0].res[0].num, None)
- self.assertEqual(relax_data_store['orig'].mol[0].res[0].name, None)
-
-
- def test_delete_shift(self):
- """Test the deletion of multiple residues.
-
- The function used is generic_fns.residue.delete().
- """
-
- # Create some residues and add some data to the spin containers.
- residue.create(1, 'Ala')
- residue.create(2, 'Ala')
- residue.create(3, 'Ala')
- residue.create(4, 'Ala')
- relax_data_store['orig'].mol[0].res[3].spin[0].num = 111
- relax_data_store['orig'].mol[0].res[3].spin[0].x = 1
-
- # Delete the first and third residues.
- residue.delete(res_id=':1,3')
-
- # Test that the remaining residues.
- self.assertEqual(relax_data_store['orig'].mol[0].res[0].num, 2)
- self.assertEqual(relax_data_store['orig'].mol[0].res[1].num, 4)
- self.assertEqual(relax_data_store['orig'].mol[0].res[1].spin[0].num,
111)
- self.assert_(hasattr(relax_data_store['orig'].mol[0].res[1].spin[0],
'x'))
-
-
- def test_delete_fail(self):
- """Test the failure of residue deletion when an atom id is supplied.
-
- The function used is generic_fns.residue.delete().
- """
-
- # Supply an atom id.
- self.assertRaises(RelaxSpinSelectDisallowError, residue.delete,
res_id='@2')
-
-
- def test_display(self):
- """Test the display of residue information.
-
- The function used is generic_fns.residue.display().
- """
-
- # Set up some data.
- self.setup_data()
-
- # The following should all work without error.
- residue.display()
- residue.display(':1')
- residue.display('#New mol:5')
- residue.display('#Old mol:1')
-
-
- def test_display_fail(self):
- """Test the failure of the display of residue information.
-
- The function used is generic_fns.residue.display().
- """
-
- # Set up some data.
- self.setup_data()
-
- # The following should fail.
- self.assertRaises(RelaxSpinSelectDisallowError, residue.display,
'@N')
-
-
- def test_rename(self):
- """Test the renaming of a residue.
-
- The function tested is generic_fns.residue.rename().
- """
-
- # Create the first residue and add some data to its spin container.
- residue.create(-10, 'His')
-
- # Rename the residue.
- residue.rename(res_id=':-10', new_name='K')
-
- # Test that the residue has been renamed.
- self.assertEqual(relax_data_store['orig'].mol[0].res[0].name, 'K')
-
-
- def test_rename_many(self):
- """Test the renaming of multiple residues.
-
- The function used is generic_fns.residue.rename().
- """
-
- # Create the first residue and add some data to its spin container.
- residue.create(1, 'Ala')
- relax_data_store['orig'].mol[0].res[0].spin[0].num = 111
-
- # Copy the residue a few times.
- residue.copy(res_from=':1', res_to=':2')
- residue.copy(res_from=':1', res_to=':3')
-
- # Change the first residue's data.
- relax_data_store['orig'].mol[0].res[0].name = 'His'
-
- # Copy the residue once more.
- residue.copy(res_from=':1', res_to=':4,Met')
-
- # Rename all alanines.
- residue.rename(res_id=':Ala', new_name='Gln')
-
- # Test the renaming of alanines.
- self.assertEqual(relax_data_store['orig'].mol[0].res[1].name, 'Gln')
- self.assertEqual(relax_data_store['orig'].mol[0].res[2].name, 'Gln')
-
- # Test that the other residues have not changed.
- self.assertEqual(relax_data_store['orig'].mol[0].res[0].name, 'His')
- self.assertEqual(relax_data_store['orig'].mol[0].res[3].name, 'Met')
-
-
- def test_rename_no_spin(self):
- """Test the failure of renaming a residue when a spin id is given.
-
- The function tested is generic_fns.residue.rename().
- """
-
- # Try renaming using a atom id.
- self.assertRaises(RelaxSpinSelectDisallowError, residue.rename,
res_id='@111', new_name='K')
-
-
- def test_renumber(self):
- """Test the renumbering of a residue.
-
- The function tested is generic_fns.residue.renumber().
- """
-
- # Create the first residue and add some data to its spin container.
- residue.create(-10, 'His')
-
- # Rename the residue.
- residue.renumber(res_id=':-10', new_number=10)
-
- # Test that the residue has been renumbered.
- self.assertEqual(relax_data_store['orig'].mol[0].res[0].num, 10)
-
-
- def test_renumber_many_fail(self):
- """Test the renaming of multiple residues.
-
- The function used is generic_fns.residue.renumber().
- """
-
- # Create the first residue and add some data to its spin container.
- residue.create(1, 'Ala')
-
- # Copy the residue a few times.
- residue.copy(res_from=':1', res_to=':2')
- residue.copy(res_from=':1', res_to=':3')
-
- # Change the first residue's data.
- relax_data_store['orig'].mol[0].res[0].spin[0].name = 'His'
-
- # Copy the residue once more.
- residue.copy(res_from=':1', res_to=':4,Met')
-
- # Try renumbering all alanines.
- self.assertRaises(RelaxError, residue.renumber, res_id=':Ala',
new_number=10)
-
-
- def test_renumber_no_spin(self):
- """Test the failure of renaming a residue when a spin id is given.
-
- The function tested is generic_fns.residue.renumber().
- """
-
- # Try renaming using a atom id.
- self.assertRaises(RelaxSpinSelectDisallowError, residue.renumber,
res_id='@111', new_number=10)
+ # Place the generic_fns.residue module into the class namespace.
+ residue_fns = residue
r3653 - /1.3/test_suite/unit_tests/generic_fns/test_residue.py