r8505 - /branches/multi_structure/generic_fns/structure/scientific.py -- January 19, 2009 - 11:11

Author: bugman
Date: Mon Jan 19 11:11:16 2009
New Revision: 8505

URL: http://svn.gna.org/viewcvs/relax?rev=8505&view=rev
Log:
Modified the bond_vectors() method for the new structural object design.


Modified:
    branches/multi_structure/generic_fns/structure/scientific.py

Modified: branches/multi_structure/generic_fns/structure/scientific.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/multi_structure/generic_fns/structure/scientific.py?rev=8505&r1=8504&r2=8505&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/scientific.py (original)
+++ branches/multi_structure/generic_fns/structure/scientific.py Mon Jan 19 
11:11:16 2009
@@ -387,7 +387,7 @@
         return pos
 
 
-    def bond_vectors(self, atom_id=None, attached_atom=None, 
struct_index=None, return_name=False, return_warnings=False):
+    def bond_vectors(self, atom_id=None, attached_atom=None, model_num=None, 
return_name=False, return_warnings=False):
         """Find the bond vectors between the atoms of 'attached_atom' and 
'atom_id'.
 
         @keyword atom_id:           The molecule, residue, and atom 
identifier string.  This must
@@ -395,10 +395,10 @@
         @type atom_id:              str
         @keyword attached_atom:     The name of the bonded atom.
         @type attached_atom:        str
-        @keyword struct_index:      The index of the structure to return the 
vectors from.  If not
-                                    supplied and multiple structures/models 
exist, then vectors from
-                                    all structures will be returned.
-        @type struct_index:         None or int
+        @keyword model_num:         The model of which to return the vectors 
from.  If not supplied
+                                    and multiple models exist, then vectors 
from all models will be
+                                    returned.
+        @type model_num:            None or int
         @keyword return_name:       A flag which if True will cause the name 
of the attached atom to
                                     be returned together with the bond 
vectors.
         @type return_name:          bool
@@ -416,17 +416,17 @@
         attached_name = None
         warnings = None
 
-        # Loop over the structures.
-        for i in xrange(len(self.structural_data)):
-            # Single structure.
-            if struct_index and struct_index != i:
+        # Loop over the models.
+        for model in self.structural_data:
+            # Single model.
+            if model_num and model_num != model.num:
                 continue
 
             # Init.
             atom_found = False
 
             # Loop over each individual molecule.
-            for mol, mol_name, mol_type in 
self.__molecule_loop(self.structural_data[i], sel_obj):
+            for mol, mol_name, mol_type in self.__molecule_loop(model, 
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_name, mol_type, sel_obj):
                     # Loop over the atoms of the residue.