r23340 - /trunk/lib/structure/internal/object.py -- May 22, 2014 - 17:21

Author: bugman
Date: Thu May 22 17:21:05 2014
New Revision: 23340

URL: http://svn.gna.org/viewcvs/relax?rev=23340&view=rev
Log:
Important bug fix for the structure.delete user function when multiple models 
are present.

This is to fix bug #22070 (https://gna.org/bugs/index.php?22070), the failure 
of the
structure.superimpose user function after deleting atoms with 
structure.delete.

The problem is that structure.delete was removing the atoms from the first 
model but none of the
others.  This is because it was using the structural object atom_loop() 
method to find the atoms to
be deleted, but this method operates on the first model.  So when the second 
model is reached, the
atoms are already gone.


Modified:
    trunk/lib/structure/internal/object.py

Modified: trunk/lib/structure/internal/object.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/internal/object.py?rev=23340&r1=23339&r2=23340&view=diff
==============================================================================
--- trunk/lib/structure/internal/object.py      (original)
+++ trunk/lib/structure/internal/object.py      Thu May 22 17:21:05 2014
@@ -1532,6 +1532,12 @@
             if atom_id:
                 sel_obj = Selection(atom_id)
 
+            # Loop over the atoms and find the indices of the atoms to 
delete.
+            indices = []
+            for i in self.atom_loop(atom_id=atom_id, index_flag=True):
+                indices.append(i)
+            indices.reverse()
+
             # Loop over the models.
             del_res_nums = []
             for model in self.model_loop():
@@ -1543,16 +1549,10 @@
                     if sel_obj and not sel_obj.contains_mol(mol.mol_name):
                         continue
 
-                    # Loop over the atoms.
-                    indices = []
-                    for i in self.atom_loop(atom_id=atom_id, 
model_num=model.num, index_flag=True):
-                        indices.append(i)
-
                     # Generate a residue data dictionary for the metadata 
trimming (prior to atom deletion).
                     res_data = self._residue_data(res_nums=mol.res_num, 
res_names=mol.res_name)
 
                     # Loop over the reverse indices and pop out the data.
-                    indices.reverse()
                     for i in indices:
                         mol.atom_num.pop(i)
                         mol.atom_name.pop(i)