Author: bugman
Date: Mon Apr 14 23:42:15 2008
New Revision: 5727
URL: http://svn.gna.org/viewcvs/relax?rev=5727&view=rev
Log:
Merged revisions 5711,5713-5725 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/spin_loop_bool
........
r5711 | bugman | 2008-04-14 21:20:26 +0200 (Mon, 14 Apr 2008) | 12 lines
Ok, lets try this again! Created a branch for some nasty breakages and
testing new ideas.
The command used was:
svn cp svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/spin_loop_bool
The spin_loop and its siblings cannot currently handle the branching tree
formed by the Selection
object (nested within Selection._union and Selection._intersect). For
example if there are two
molecules loaded into the data store, 'Ap4Aase' and 'RNA', the spin_loop
with the spin id string
'#Ap4Aase:Glu | #RNA@C8' loops over all spins of both molecules!!!
Therefore all the usages of the
Selection object need to be redesigned, and possibly the Selection object
itself.
........
r5713 | bugman | 2008-04-14 21:26:08 +0200 (Mon, 14 Apr 2008) | 3 lines
Modified the spin_loop to check the tuple of (mol, res, spin) against the
selection object.
........
r5714 | bugman | 2008-04-14 21:49:20 +0200 (Mon, 14 Apr 2008) | 5 lines
Redesigned the selection object method Selection.__contains__().
Now multiple MoleculeContainer, ResidueContainer, or SpinContainer
instances can be compared.
........
r5715 | bugman | 2008-04-14 21:54:34 +0200 (Mon, 14 Apr 2008) | 3 lines
Some fixes for the Selection.__contains__() method.
........
r5716 | bugman | 2008-04-14 21:59:10 +0200 (Mon, 14 Apr 2008) | 3 lines
Changed the spin_index_loop() function to use the same form as spin_loop().
........
r5717 | bugman | 2008-04-14 22:00:39 +0200 (Mon, 14 Apr 2008) | 3 lines
Updated the residue_loop() function.
........
r5718 | bugman | 2008-04-14 22:03:08 +0200 (Mon, 14 Apr 2008) | 3 lines
Updated all the other comparisons to the selection object.
........
r5719 | bugman | 2008-04-14 22:17:11 +0200 (Mon, 14 Apr 2008) | 3 lines
The Selection.__contains__() method now is complete and all the relevant
unit tests pass again.
........
r5720 | bugman | 2008-04-14 22:22:08 +0200 (Mon, 14 Apr 2008) | 3 lines
Small docstring updates.
........
Modified:
1.3/ (props changed)
1.3/generic_fns/selection.py
Propchange: 1.3/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Mon Apr 14 23:42:15 2008
@@ -1,1 +1,1 @@
-/branches/spin_loop_bool:1-5710
+/branches/spin_loop_bool:1-5726
Modified: 1.3/generic_fns/selection.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/selection.py?rev=5727&r1=5726&r2=5727&view=diff
==============================================================================
--- 1.3/generic_fns/selection.py (original)
+++ 1.3/generic_fns/selection.py Mon Apr 14 23:42:15 2008
@@ -61,15 +61,16 @@
class Selection(object):
"""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."""
+ 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"""
+ @param select_string: A mol-res-spin selection string.
+ @type select_string: string
+ """
self._union = None
self._intersect = None
@@ -106,10 +107,12 @@
def __contains__(self, obj):
"""Replacement function for determining if an object matches the
selection.
- @param obj: The data object.
- @type obj: MoleculeContainer, ResidueContainer, or
SpinContainer object.
+ @param obj: The data object. This can be a MoleculeContainer,
ResidueContainer, or
+ SpinContainer instance or a type of these instances.
If a tuple, only one
+ type of object can be in the tuple.
+ @type obj: instance or type of instances.
@return: The answer of whether the object matches the
selection.
- @rtype: Boolean
+ @rtype: bool
"""
# The selection object is a union.
@@ -120,29 +123,94 @@
elif self._intersect:
return (obj in self._intersect[0]) and (obj in
self._intersect[1])
- # The object is a molecule.
- elif isinstance(obj, MoleculeContainer):
+ # Initialise the molecule, residue, and spin objects.
+ mol = None
+ res = None
+ spin = None
+
+ # The object is not a tuple, so lets turn it into one.
+ if type(obj) != tuple:
+ obj = (obj,)
+
+ # Max 3 objects (cannot match, so False).
+ if len(obj) > 3:
+ return False
+
+ # Loop over the objects.
+ for i in range(len(obj)):
+ # The object is a molecule.
+ if isinstance(obj[i], MoleculeContainer):
+ # Error.
+ if mol != None:
+ raise RelaxError, "Comparing two molecular containers
simultaneously with the selection object is not supported."
+
+ # Unpack.
+ mol = obj[i]
+
+ # The object is a residue.
+ elif isinstance(obj[i], ResidueContainer):
+ # Error.
+ if res != None:
+ raise RelaxError, "Comparing two residue containers
simultaneously with the selection object is not supported."
+
+ # Unpack.
+ res = obj[i]
+
+ # The object is a spin.
+ elif isinstance(obj[i], SpinContainer):
+ # Error.
+ if spin != None:
+ raise RelaxError, "Comparing two spin containers
simultaneously with the selection object is not supported."
+
+ # Unpack.
+ spin = obj[i]
+
+ # Selection flags.
+ select_mol = False
+ select_res = False
+ select_spin = False
+
+ # Molecule container.
+ if mol:
+ # No molecules in selection object, therefore default to a match.
if not self.molecules:
- return True
- elif wildcard_match(obj.name, self.molecules):
- return True
-
- # The object is a residue.
- elif isinstance(obj, ResidueContainer):
+ select_mol = True
+
+ # A true match.
+ elif wildcard_match(mol.name, self.molecules):
+ select_mol = True
+ else:
+ # No molecule container sent in, therefore the molecule is
assumed to match.
+ select_mol = True
+
+ # Residue container.
+ if res:
+ # No residues in selection object, therefore default to a match.
if not self.residues:
- return True
- elif wildcard_match(obj.name, self.residues) or obj.num in
self.residues:
- return True
-
- # The object is a spin.
- elif isinstance(obj, SpinContainer):
+ select_res = True
+
+ # A true match.
+ elif wildcard_match(res.name, self.residues) or res.num in
self.residues:
+ select_res = True
+ else:
+ # No residue container sent in, therefore the residue is assumed
to match.
+ select_res = True
+
+ # Spin container.
+ if spin:
+ # No spins in selection object, therefore default to a match.
if not self.spins:
- return True
- elif wildcard_match(obj.name, self.spins) or obj.num in
self.spins:
- return True
-
- # No match.
- return False
+ select_spin = True
+
+ # A true match.
+ elif wildcard_match(spin.name, self.spins) or spin.num in
self.spins:
+ select_spin = True
+ else:
+ # No spin container sent in, therefore the spin is assumed to
match.
+ select_spin = True
+
+ # Return the selection status.
+ return select_mol and select_res and select_spin
def intersection(self, select_obj0, select_obj1):
@@ -597,14 +665,10 @@
# Loop over the molecules.
for mol in relax_data_store[pipe].mol:
- # Skip the molecule if there is no match to the selection.
- 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 res not in select_obj:
+ if (mol, res) not in select_obj:
continue
# Yield the residue data container.
@@ -687,14 +751,10 @@
res_num = 0
res_container = None
for mol in relax_data_store[pipe].mol:
- # Skip the molecule if there is no match to the selection.
- 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 res not in select_obj:
+ if (mol, res) not in select_obj:
continue
# Store the residue container.
@@ -737,20 +797,12 @@
spin_num = 0
spin_container = None
for mol in relax_data_store[pipe].mol:
- # Skip the molecule if there is no match to the selection.
- 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 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 spin not in select_obj:
+ if (mol, res, spin) not in select_obj:
continue
# Store the spin container.
@@ -1196,20 +1248,21 @@
# Loop over the molecules.
for mol_index in xrange(len(relax_data_store[pipe].mol)):
- # Skip the molecule if there is no match to the selection.
- if relax_data_store[pipe].mol[mol_index] not in select_obj:
- continue
+ # Alias the molecule container.
+ mol = relax_data_store[pipe].mol[mol_index]
# Loop over the residues.
for res_index in
xrange(len(relax_data_store[pipe].mol[mol_index].res)):
- # Skip the residue if there is no match to the selection.
- if relax_data_store[pipe].mol[mol_index].res[res_index] not in
select_obj:
- continue
+ # Alias the residue container.
+ res = relax_data_store[pipe].mol[mol_index].res[res_index]
# Loop over the spins.
for spin_index in
xrange(len(relax_data_store[pipe].mol[mol_index].res[res_index].spin)):
+ # Alias the spin container.
+ spin =
relax_data_store[pipe].mol[mol_index].res[res_index].spin[spin_index]
+
# Skip the spin if there is no match to the selection.
- if
relax_data_store[pipe].mol[mol_index].res[res_index].spin[spin_index] not in
select_obj:
+ if (mol, res, spin) not in select_obj:
continue
# Yield the spin system specific indecies.
@@ -1249,20 +1302,12 @@
# Loop over the molecules.
for mol in relax_data_store[pipe].mol:
- # Skip the molecule if there is no match to the selection.
- 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 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 spin not in select_obj:
+ if (mol, res, spin) not in select_obj:
continue
# Yield the spin system data container.
r5727 - in /1.3: ./ generic_fns/selection.py