Author: macraild
Date: Fri Mar 30 18:41:01 2007
New Revision: 3258
URL: http://svn.gna.org/viewcvs/relax?rev=3258&view=rev
Log:
Further mol-res-spin selection improvements. Work still needed on
boolean logic.
Modified:
1.3/generic_fns/selection.py
1.3/test_suite/unit_tests/generic_fns/test_selection.py
Modified: 1.3/generic_fns/selection.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/selection.py?rev=3258&r1=3257&r2=3258&view=diff
==============================================================================
--- 1.3/generic_fns/selection.py (original)
+++ 1.3/generic_fns/selection.py Fri Mar 30 18:41:01 2007
@@ -58,9 +58,17 @@
class Selection(object):
- """An object containing mol-res-spin selections"""
+ """An object containing mol-res-spin selections.
+
+ A Selection object represents either a set of selected
+ molecules, residues and spins, or the union or intersection
+ of two other Selection objects."""
def __init__(self, select_string):
+ """Initialise a Selection object.
+
+ @type select_string: string
+ @param select_string: a mol-res-spin selection string"""
self._union = None
self._intersect = None
@@ -91,29 +99,49 @@
self.spins = parse_token(spin_token)
def __contains__(self, obj):
-
if self._union:
return (obj in self._union[0]) or (obj in self._union[1])
elif self._intersect:
return (obj in self._intersect[0]) and (obj in
self._intersect[1])
- elif isinstance(obj, MoleculeContainer) and obj.name in
self.molecules:
- return True
- elif isinstance(obj, ResidueContainer) and obj.name in self.residues:
- return True
- elif isinstance(obj, SpinContainer) and obj.name in self.spins:
- return True
- else:
- return False
+ elif isinstance(obj, MoleculeContainer):
+ if not self.molecules:
+ return True
+ elif obj.name in self.molecules:
+ return True
+ elif isinstance(obj, ResidueContainer):
+ if not self.residues:
+ return True
+ elif obj.name in self.residues or obj.num in self.residues:
+ return True
+ elif isinstance(obj, SpinContainer):
+ if not self.spins:
+ return True
+ elif obj.name in self.spins or obj.num in self.spins:
+ return True
+
+ return False
def intersection(self, select_obj0, select_obj1):
+ """Make a Selection object the intersection of two Selection objects
- if self._union or self._intersect:
+ @type select_obj0: Instance of class Selection
+ @param select_obj0: First Selection object in intersection
+ @type select_obj1: Instance of class Selection
+ @param select_obj1: First Selection object in intersection"""
+
+ if self._union or self._intersect or self.molecules or self.residues
or self.spins:
raise RelaxError, "Cannot define multiple Boolean relationships
between Selection objects"
self._intersect = (select_obj0, select_obj1)
def union(self, select_obj0, select_obj1):
-
- if self._union or self._intersect:
+ """Make a Selection object the union of two Selection objects
+
+ @type select_obj0: Instance of class Selection
+ @param select_obj0: First Selection object in union
+ @type select_obj1: Instance of class Selection
+ @param select_obj1: First Selection object in union"""
+
+ if self._union or self._intersect or self.molecules or self.residues
or self.spins:
raise RelaxError, "Cannot define multiple Boolean relationships
between Selection objects"
self._union = (select_obj0, select_obj1)
@@ -278,18 +306,18 @@
"""
# Parse the selection string.
- selectObj = Selection(selection)
+ select_obj = Selection(selection)
# Disallowed selections.
- if selectObj.residues:
+ if select_obj.residues:
raise RelaxResSelectDisallowError
- if selectObj.spins:
+ if select_obj.spins:
raise RelaxSpinSelectDisallowError
# Loop over the molecules.
for mol in relax_data_store[relax_data_store.current_pipe].mol:
# Skip the molecule if there is no match to the selection.
- if selectObj.molecules and mol.name not in selectObj:
+ if mol not in select_obj:
continue
# Yield the molecule data container.
@@ -379,23 +407,25 @@
"""
# Parse the selection string.
- selectObj = Selection(selection)
+ select_obj = Selection(selection)
# Disallowed selections.
- if selectObj.spins:
+ if select_obj.spins:
raise RelaxSpinSelectDisallowError
# Loop over the molecules.
for mol in relax_data_store[relax_data_store.current_pipe].mol:
# Skip the molecule if there is no match to the selection.
- if selectObj.molecules and mol.name not in selectObj:
+ if mol not in select_obj:
continue
+ print mol
# Loop over the residues.
for res in mol.res:
# Skip the residue if there is no match to the selection.
- if selectObj.residues and res.name not in selectObj:
+ if res not in select_obj:
continue
+ print res
# Yield the residue data container.
yield res
@@ -630,24 +660,24 @@
"""
# Parse the selection string.
- selectObj = Selection(selection)
+ select_obj = Selection(selection)
# Loop over the molecules.
for mol in relax_data_store[relax_data_store.current_pipe].mol:
# Skip the molecule if there is no match to the selection.
- if selectObj.molecules and mol.name not in selectObj:
+ if mol not in select_obj:
continue
# Loop over the residues.
for res in mol.res:
# Skip the residue if there is no match to the selection.
- if selectObj.residues and res.name not in selectObj:
+ if res not in select_obj:
continue
# Loop over the spins.
for spin in res.spin:
# Skip the spin if there is no match to the selection.
- if selectObj.spins and spin.name not in selectObj:
+ if spin not in select_obj:
continue
# Yield the spin system data container.
Modified: 1.3/test_suite/unit_tests/generic_fns/test_selection.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/unit_tests/generic_fns/test_selection.py?rev=3258&r1=3257&r2=3258&view=diff
==============================================================================
--- 1.3/test_suite/unit_tests/generic_fns/test_selection.py (original)
+++ 1.3/test_suite/unit_tests/generic_fns/test_selection.py Fri Mar 30
18:41:01 2007
@@ -85,6 +85,9 @@
# Test the molecule name.
self.assertEqual(mol.name, 'RNA')
+ # Test loop length.
+ self.assertEqual(len(list(selection.molecule_loop('#RNA'))), 1)
+
def test_molecule_loop_no_selection(self):
"""Test the proper operation of the molecule loop when no selection
is present.
@@ -103,6 +106,10 @@
# Increment i.
i = i + 1
+
+ # Test loop length.
+ self.assertEqual(len(list(selection.molecule_loop())), 2)
+
def test_parse_token_single_element_num(self):
@@ -268,7 +275,10 @@
for res in selection.residue_loop('#Ap4Aase:Glu'):
# Test the selection.
self.assertEqual(res.num, 2)
-
+
+ # Test loop length.
+ self.assertEqual(len(list(selection.residue_loop('#Ap4Aase:Glu'))),
1)
+
def test_residue_loop_no_selection(self):
"""Test the proper operation of the residue loop when no selection
is present.
@@ -292,7 +302,9 @@
# Increment i.
i = i + 1
-
+ # Test loop length.
+ self.assertEqual(i, 5)
+
def test_reverse(self):
"""Test spin system selection reversal.
@@ -335,6 +347,10 @@
# Increment i.
i = i + 1
+
+ # Test loop length.
+ self.assertEqual(i, 2)
+
def test_spin_loop_no_selection(self):
@@ -358,12 +374,10 @@
# Increment i.
i = i + 1
-
- def test_boolean_selection1(self):
- """Test boolean mol-res-spin selections."""
-
- # The selection object:
- sel = selection.Selection("#Ap4Aase | #RNA@N5")
+
+ # Test loop length.
+ self.assertEqual(i, 7)
+
def test_tokenise1(self):
"""Test the generic_fns.selection.tokenise() function on the string
'@1'."""
@@ -662,26 +676,41 @@
def test_boolean_or_selection(self):
"""Test boolean or in mol-res-spin selections."""
- self.assert_(list(selection.spin_loop("#Ap4Aase | #RNA@N5")) ==
list(selection.spin_loop())
+ self.assert_(list(selection.spin_loop("#Ap4Aase | #RNA@N5")) ==
list(selection.spin_loop()))
def test_boolean_and_selection(self):
"""Test boolean and in mol-res-spin selections."""
# The selection loop:
- sel = selection.residue_loop("#Ap4Aase:4 & :Pro")
+ sel = list(selection.residue_loop("#Ap4Aase:4 & :Pro"))
# Test:
+ self.assertEqual(len(sel), 1)
for res in sel:
self.assert_(res.name == "Pro" and res.num == 4)
def test_boolean_complex_selection(self):
"""Test complex boolean mol-res-spin selections."""
- a syntax error
- # The selection loops:
- sel = selection.residue_loop("#Ap4Aase:4 & :Pro | #RNA@N5")
+
+ # The selection loop:
+ sel = list(selection.residue_loop("#Ap4Aase:4 & :Pro | #RNA"))
# Test:
+ self.assertEqual(len(sel), 3)
for res in sel:
self.assert_(res.num in [-5,-4,4])
+
+
+ def test_boolean_parenthesis_selection(self):
+ """Test complex boolean mol-res-spin selections with parenthesis."""
+
+ # The selection loop:
+ sel = list(selection.residue_loop("(#Ap4Aase & :Pro) | (#RNA &
:-4)"))
+
+ # Test:
+ self.assertEqual(len(sel), 2)
+ for res in sel:
+ self.assert_(res.num in [-4,4])
+
r3258 - in /1.3: generic_fns/selection.py test_suite/unit_tests/generic_fns/test_selection.py