r2669 - /1.3/generic_fns/sequence.py -- October 26, 2006 - 10:09

Author: bugman
Date: Thu Oct 26 10:09:12 2006
New Revision: 2669

URL: http://svn.gna.org/viewcvs/relax?rev=2669&view=rev
Log:
Fixed the nucleic acid residue names.

These names were being prefixed by 'R' by Scientific python, so residue 'G' 
would be labelled as
residue 'RG'!  This was causing the user function 'pdb.vectors()' to fail as 
the residue was
expected to be called 'G'.  The prefix 'R' is now stripped from the residue 
name.


Modified:
    1.3/generic_fns/sequence.py

Modified: 1.3/generic_fns/sequence.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/sequence.py?rev=2669&r1=2668&r2=2669&view=diff
==============================================================================
--- 1.3/generic_fns/sequence.py (original)
+++ 1.3/generic_fns/sequence.py Thu Oct 26 10:09:12 2006
@@ -145,8 +145,10 @@
         # Reassign the sequence of the first structure.
         if self.relax.data.pdb[run].structures[0].peptide_chains:
             res = 
self.relax.data.pdb[run].structures[0].peptide_chains[0].residues
+            molecule = 'protein'
         elif self.relax.data.pdb[run].structures[0].nucleotide_chains:
             res = 
self.relax.data.pdb[run].structures[0].nucleotide_chains[0].residues
+            molecule = 'nucleic acid'
         else:
             raise RelaxNoPdbChainError
 
@@ -158,9 +160,16 @@
             # Append a data container.
             self.relax.data.res[run].add_item()
 
-            # Insert the data.
+            # Residue number.
             self.relax.data.res[run][i].num = res[i].number
-            self.relax.data.res[run][i].name = res[i].name
+
+            # Residue name.
+            if molecule == 'nucleic acid':
+                self.relax.data.res[run][i].name = res[i].name[-1]
+            else:
+                self.relax.data.res[run][i].name = res[i].name
+
+            # Select the residue.
             self.relax.data.res[run][i].select = 1