Author: bugman
Date: Mon Mar 19 06:27:21 2007
New Revision: 3233
URL: http://svn.gna.org/viewcvs/relax?rev=3233&view=rev
Log:
Fixed the generic_fns.residue.delete() function and its associated unit tests.
An additional unit test for deletion using residue names has been added.
Modified:
1.3/generic_fns/residue.py
1.3/test_suite/unit_tests/generic_fns/test_residue.py
Modified: 1.3/generic_fns/residue.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/residue.py?rev=3233&r1=3232&r2=3233&view=diff
==============================================================================
--- 1.3/generic_fns/residue.py (original)
+++ 1.3/generic_fns/residue.py Mon Mar 19 06:27:21 2007
@@ -114,7 +114,7 @@
def delete(res_id=None):
"""Function for deleting residues from the current data pipe.
- @param res_id: The residue identifier string.
+ @param res_id: The molecule and residue identifier string.
@type res_id: str
"""
@@ -130,11 +130,25 @@
# Molecule loop.
for mol in molecule_loop(mol_token):
+ # List of indecies to delete.
+ indecies = []
+
# Loop over the residues of the molecule.
for i in xrange(len(mol.res)):
# Remove the residue is there is a match.
- if mol.res[i].num in residues:
- mol.res[i].pop()
+ if mol.res[i].num in residues or mol.res[i].name in residues:
+ indecies.append(i)
+
+ # Reverse the indecies.
+ indecies.reverse()
+
+ # Delete the residues.
+ for index in indecies:
+ mol.res.pop(index)
+
+ # Create an empty residue container if no residues remain.
+ if len(mol.res) == 0:
+ mol.res.add_item()
class Residue:
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=3233&r1=3232&r2=3233&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 Mon Mar 19 06:27:21
2007
@@ -27,7 +27,7 @@
from data import Data as relax_data_store
from data.pipe_container import PipeContainer
from generic_fns import residue
-from relax_errors import RelaxError, RelaxNoRunError, RelaxRunError
+from relax_errors import RelaxError, RelaxNoRunError, RelaxRunError,
RelaxSpinSelectDisallowError
@@ -143,29 +143,56 @@
self.assertRaises(RelaxError, residue.create, 1, 'Ala')
- def test_delete(self):
- """Test the deletion of a residue.
-
- The function used is generic_fns.residues.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')
+ def test_delete_name(self):
+ """Test residue deletion using residue name identifiers.
+
+ The function used is generic_fns.residues.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.residues.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 residue no longer exists (and defaults back to the
empty residue).
-
self.assertNotEqual(relax_data_store['orig'].mol[0].res[1].spin[0].num, 111)
- self.assert_(not
hasattr(relax_data_store['orig'].mol[0].res[1].spin[0], 'x'))
-
- # 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):
@@ -191,7 +218,7 @@
def test_delete_shift(self):
- """Test the deletion of multiple residue.
+ """Test the deletion of multiple residues.
The function used is generic_fns.residues.delete().
"""
@@ -207,18 +234,18 @@
# Delete the first and third residues.
residue.delete(res_id=':1,3')
- # Test that the residue no longer exists (and defaults back to the
empty residue).
+ # 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'))
- 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_fail(self):
- """Test the failure of the deletion of a non-existant residue.
-
- The function used is generic_fns.residues.delete().
- """
-
- # Delete a non-existant residue (2).
- self.assertRaises(RelaxError, residue.delete, res_id=':2')
+ """Test the failure of residue deletion when an atom id is supplied.
+
+ The function used is generic_fns.residues.delete().
+ """
+
+ # Supply an atom id.
+ self.assertRaises(RelaxSpinSelectDisallowError, residue.delete,
res_id='@2')
r3233 - in /1.3: generic_fns/residue.py test_suite/unit_tests/generic_fns/test_residue.py