Author: macraild
Date: Thu Mar 29 18:46:15 2007
New Revision: 3245
URL: http://svn.gna.org/viewcvs/relax?rev=3245&view=rev
Log:
A proposal for a modified mol-res-spin selection mechanism.
This simple modification, based on a selection object, permits
the use of booleans in selection strings, eg:
':leu@xxxxxxx | :val@CG1,CG2'
selects leucine and valine methyls.
Also, modification of Selection.__contains__() will allow for
wildcards, regex, etc as desired.
Modified:
1.3/generic_fns/selection.py
Modified: 1.3/generic_fns/selection.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/selection.py?rev=3245&r1=3244&r2=3245&view=diff
==============================================================================
--- 1.3/generic_fns/selection.py (original)
+++ 1.3/generic_fns/selection.py Thu Mar 29 18:46:15 2007
@@ -28,6 +28,7 @@
# relax module imports.
from data import Data as relax_data_store
+from data.mol_res_spin import MoleculeContainer, ResidueContainer,
SpinContainer
from relax_errors import RelaxError, RelaxNoRunError, RelaxNoSequenceError,
RelaxRegExpError, RelaxResSelectDisallowError, RelaxSpinSelectDisallowError
@@ -55,6 +56,67 @@
id_string_doc = string
+
+class Selection(object):
+ """An object containing mol-res-spin selections"""
+
+ def __init__(self, selectString):
+
+ self._union = None
+ self._intersect = None
+
+ self.molecules = None
+ self.residues = None
+ self.spins = None
+
+ if not selectString:
+ return
+
+ if '&' in selectString:
+ and_split = selectString.split('&')
+ part0 = Selection(and_split[0])
+ part1 = Selection(and_split[1])
+ return part0.intersection(part1)
+
+ elif '|' in selectString:
+ and_split = selectString.split('|')
+ part0 = Selection(and_split[0])
+ part1 = Selection(and_split[1])
+ return part0.union(part1)
+
+ else:
+ mol_token, res_token, spin_token = tokenise(selectString)
+ self.molecules = parse_token(mol_token)
+ self.residues = parse_token(res_token)
+ self.spins = parse_token(spin_token)
+
+ def __contains__(self, obj):
+
+ in_self = False
+ if isinstance(obj, MoleculeContainer) and obj.name in self.molecules:
+ in_self = True
+ elif isinstance(obj, ResidueContainer) and obj.name in self.residues:
+ in_self = True
+ elif isinstance(obj, SpinContainer) and obj.name in self.spins:
+ in_self = True
+ if self._union:
+ return in_self or (obj in self._union)
+ if self._intersect:
+ return in_self and (obj in self._union)
+ else:
+ return in_self
+
+ def intersection(self, selectObj):
+
+ if self._union or self._intersect:
+ raise RelaxError, "Cannot define multiple Boolean relationships
between Selection objects"
+ self._intersect = selectObj
+
+ def union(self, selectObj):
+
+ if self._union or self._intersect:
+ raise RelaxError, "Cannot define multiple Boolean relationships
between Selection objects"
+ self._union = selectObj
def desel_all(self, run=None):
@@ -216,22 +278,19 @@
@rtype: instance of the MoleculeContainer class.
"""
- # Split up the selection string.
- mol_token, res_token, spin_token = tokenise(selection)
+ # Parse the selection string.
+ selectObj = Selection(selection)
# Disallowed selections.
- if res_token:
+ if selectObj.residues:
raise RelaxResSelectDisallowError
- if spin_token:
+ if selectObj.spins:
raise RelaxSpinSelectDisallowError
-
- # Parse the token.
- molecules = parse_token(mol_token)
# 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 mol_token and mol.name not in molecules:
+ if selectObj.molecules and mol.name not in selectObj:
continue
# Yield the molecule data container.
@@ -320,27 +379,23 @@
@rtype: instance of the MoleculeContainer class.
"""
- # Split up the selection string.
- mol_token, res_token, spin_token = tokenise(selection)
-
+ # Parse the selection string.
+ selectObj = Selection(selection)
+
# Disallowed selections.
- if spin_token:
+ if selectObj.spins:
raise RelaxSpinSelectDisallowError
-
- # Parse the tokens.
- molecules = parse_token(mol_token)
- residues = parse_token(res_token)
# 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 mol_token and mol.name not in molecules:
+ if selectObj.molecules and mol.name not in selectObj:
continue
# Loop over the residues.
for res in mol.res:
# Skip the residue if there is no match to the selection.
- if res_token and res.name not in residues:
+ if selectObj.residues and res.name not in selectObj:
continue
# Yield the residue data container.
@@ -575,30 +630,25 @@
@rtype: instance of the SpinContainer class.
"""
- # Split up the selection string.
- mol_token, res_token, spin_token = tokenise(selection)
-
- # Parse the tokens.
- molecules = parse_token(mol_token)
- residues = parse_token(res_token)
- spins = parse_token(spin_token)
+ # Parse the selection string.
+ selectObj = 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 mol_token and mol.name not in molecules:
+ if selectObj.molecules and mol.name not in selectObj:
continue
# Loop over the residues.
for res in mol.res:
# Skip the residue if there is no match to the selection.
- if res_token and res.name not in residues:
+ if selectObj.residues and res.name not in selectObj:
continue
# Loop over the spins.
for spin in res.spin:
# Skip the spin if there is no match to the selection.
- if spin_token and spin.name not in spins:
+ if selectObj.spins and spin.name not in selectObj:
continue
# Yield the spin system data container.
@@ -697,3 +747,4 @@
# Return the three tokens.
return mol_token, res_token, spin_token
+
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Re: r3245 - /1.3/generic_fns/selection.py