Author: bugman
Date: Mon Mar 19 05:47:57 2007
New Revision: 3217
URL: http://svn.gna.org/viewcvs/relax?rev=3217&view=rev
Log:
Implemented the generic_fns.residue.delete() function (although it doesn't
work yet).
This function has been coded to use the UCSF selection syntax as described in
Gary Thompson's post
located at https://mail.gna.org/public/relax-devel/2007-01/msg00014.html
(Message-id:
<f001463a0701071417w6bd7927cp8fdd052e698575ec@xxxxxxxxxxxxxx>).
The function makes use of three new selection functions - tokenise,
parse_token, and molecule_loop.
The first two are described at
https://mail.gna.org/public/relax-devel/2007-01/msg00036.html
(Message-ID: <1168883717.7569.511.camel@mrspell>). The last function is
similar to the spin_loop
function described in the same post. All three are yet to be implemented
(although stubs have been
created for the functions).
The RelaxError 'RelaxSpinSelectDisallowError' has been created to prevent
spins from being selected
by the user function.
The unit tests for generic_fns.residue.delete() have been updated and two
more added:
test_delete_all() and test_delete_shift().
Modified:
1.3/generic_fns/residue.py
1.3/generic_fns/selection.py
1.3/relax_errors.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=3217&r1=3216&r2=3217&view=diff
==============================================================================
--- 1.3/generic_fns/residue.py (original)
+++ 1.3/generic_fns/residue.py Mon Mar 19 05:47:57 2007
@@ -22,10 +22,8 @@
# relax module imports.
from data import Data as relax_data_store
-from relax_errors import RelaxError, RelaxFileEmptyError,
RelaxNoPdbChainError, RelaxNoRunError, RelaxNoSequenceError,
RelaxSequenceError
-
-
-# The relax data storage object.
+from relax_errors import RelaxError, RelaxFileEmptyError,
RelaxNoPdbChainError, RelaxNoRunError, RelaxNoSequenceError,
RelaxSequenceError, RelaxSpinSelectDisallowError
+from selection import molecule_loop, parse_token, tokenise
@@ -113,6 +111,32 @@
cdp.mol[0].res.add_item(res_num=res_num, res_name=res_name)
+def delete(res_id=None):
+ """Function for deleting residues from the current data pipe.
+
+ @param res_id: The residue identifier string.
+ @type res_id: str
+ """
+
+ # Split up the selection string.
+ mol_token, res_token, spin_token = tokenise(res_id)
+
+ # Disallow spin selections.
+ if spin_token != None:
+ raise RelaxSpinSelectDisallowError
+
+ # Parse the tokens.
+ residues = parse_token(res_token)
+
+ # Molecule loop.
+ for mol in molecule_loop(mol_token):
+ # 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()
+
+
class Residue:
def __init__(self, relax):
"""Class containing functions specific to amino-acid sequence."""
@@ -124,24 +148,6 @@
"""Function for returning a list of names of data structures
associated with the sequence."""
return [ 'res' ]
-
-
- def delete(self, run=None):
- """Function for deleting the sequence."""
-
- # Test if the run exists.
- if not run in relax_data_store.run_names:
- raise RelaxNoRunError, run
-
- # Test if the sequence data is loaded.
- if not relax_data_store.res.has_key(run):
- raise RelaxNoSequenceError, run
-
- # Delete the data.
- del(relax_data_store.res[run])
-
- # Clean up the runs.
- self.relax.generic.runs.eliminate_unused_runs()
def display(self, run=None):
Modified: 1.3/generic_fns/selection.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/selection.py?rev=3217&r1=3216&r2=3217&view=diff
==============================================================================
--- 1.3/generic_fns/selection.py (original)
+++ 1.3/generic_fns/selection.py Mon Mar 19 05:47:57 2007
@@ -32,6 +32,15 @@
# The relax data storage object.
+def tokenise(selection):
+ return None, None, None
+
+def molecule_loop(selection):
+ for mol in relax_data_store[relax_data_store.current_pipe].mol:
+ yield mol
+
+def parse_token(token):
+ return []
class Selection:
def __init__(self, relax):
Modified: 1.3/relax_errors.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/relax_errors.py?rev=3217&r1=3216&r2=3217&view=diff
==============================================================================
--- 1.3/relax_errors.py (original)
+++ 1.3/relax_errors.py Mon Mar 19 05:47:57 2007
@@ -532,6 +532,17 @@
self.save_state()
+# Selection errors.
+###################
+
+# Disallow spin selection.
+class RelaxSpinSelectDisallowError(BaseError):
+ def __init__(self):
+ self.text = "The selection of spin systems is not allowed."
+ if Debug:
+ self.save_state()
+
+
# Setup errors.
###############
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=3217&r1=3216&r2=3217&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 05:47:57
2007
@@ -149,19 +149,69 @@
The function used is generic_fns.residues.delete().
"""
- # 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
-
- # Delete the residue.
- residue.delete(res_num=1, res_name='Ala')
+ # 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 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')
+
+
+ def test_delete_all(self):
+ """Test the deletion of all residues.
+
+ 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')
+ 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=':1-4')
+
+ # 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)
-
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'))
+
+
+ def test_delete_shift(self):
+ """Test the deletion of multiple 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')
+ 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 residue no longer exists (and defaults back to the
empty residue).
+ 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):
@@ -170,5 +220,5 @@
The function used is generic_fns.residues.delete().
"""
- # Delete a non-existant residue (1 Met).
- self.assertRaises(RelaxError, residue.delete, 1, 'Met')
+ # Delete a non-existant residue (2).
+ self.assertRaises(RelaxError, residue.delete, res_id=':2')
r3217 - in /1.3: ./ generic_fns/ test_suite/unit_tests/generic_fns/