r5890 - /1.3/generic_fns/structure/scientific.py -- April 21, 2008 - 00:29

Author: bugman
Date: Mon Apr 21 00:21:33 2008
New Revision: 5890

URL: http://svn.gna.org/viewcvs/relax?rev=5890&view=rev
Log:
A number of fixes for the Scientific_data.attached_atom() method.


Modified:
    1.3/generic_fns/structure/scientific.py

Modified: 1.3/generic_fns/structure/scientific.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/scientific.py?rev=5890&r1=5889&r2=5890&view=diff
==============================================================================
--- 1.3/generic_fns/structure/scientific.py (original)
+++ 1.3/generic_fns/structure/scientific.py Mon Apr 21 00:21:33 2008
@@ -244,13 +244,8 @@
                                 name (str), and atomic position (array of 
len 3, or list of arrays)
         """
 
-        # Split up the selection string.
-        mol_token, res_token, atom_token = tokenise(atom_id)
-
-        # Parse the tokens.
-        molecules = parse_token(mol_token)
-        residues = parse_token(res_token)
-        atoms = parse_token(atom_token)
+        # Generate the selection object.
+        sel_obj = Selection(atom_id)
 
         # Init.
         atom_found = False
@@ -262,13 +257,13 @@
                 continue
 
             # Loop over each individual molecule.
-            for mol, mol_name, mol_type in self.__molecule_loop(struct, 
molecules):
+            for mol, mol_name, mol_type in self.__molecule_loop(struct, 
sel_obj):
                 # Loop over the residues of the protein in the PDB file.
-                for res, res_num, res_name in self.__residue_loop(mol, 
mol_type, residues):
+                for res, res_num, res_name in self.__residue_loop(mol, 
mol_type, sel_obj):
                     # Loop over the atoms of the residue.
                     for atom in res:
                         # Skip non-matching atoms.
-                        if atom_token and not (wildcard_match(atom.name, 
atoms) or atom.properties['serial_number'] in atoms):
+                        if sel_obj and not 
sel_obj.contains_spin(atom.properties['serial_number'], atom.name, res_num, 
res_name, mol_name):
                             continue
 
                         # More than one matching atom!