r26121 - /trunk/lib/structure/internal/object.py -- October 01, 2014 - 19:44

Author: bugman
Date: Wed Oct  1 19:44:39 2014
New Revision: 26121

URL: http://svn.gna.org/viewcvs/relax?rev=26121&view=rev
Log:
Bug fix for the CONECT records created by the structure.write_pdb user 
function.

The atom numbers inside the structural object were being used for the CONECT 
records rather than the
atom numbers used within the PDB file.

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=26121&r1=26120&r2=26121&view=diff
==============================================================================
--- trunk/lib/structure/internal/object.py      (original)
+++ trunk/lib/structure/internal/object.py      Wed Oct  1 19:44:39 2014
@@ -2937,11 +2937,7 @@
                         # Convert the atom indices to atom numbers.
                         for k in range(4):
                             if bonded[k] != '':
-                                if mol.atom_num[bonded[k]] != None:
-                                    bonded[k] = mol.atom_num[bonded[k]]
-                                else:
-                                    bonded[k] = bonded[k] + 1
-                                bonded_shifted[k] = bonded[k] + 
atom_counts[index]
+                                bonded_shifted[k] = bonded[k] + 1 + 
atom_counts[index]
 
                         # Write the CONECT record.
                         pdb_write.conect(file, 
serial=i+1+atom_counts[index], bonded1=bonded_shifted[0], 
bonded2=bonded_shifted[1], bonded3=bonded_shifted[2], 
bonded4=bonded_shifted[3])