Author: bugman
Date: Thu Jan 15 18:41:28 2009
New Revision: 8486
URL: http://svn.gna.org/viewcvs/relax?rev=8486&view=rev
Log:
Added an amino acid translation table for determining elements from PDB atom
names.
Modified:
branches/multi_structure/generic_fns/structure/internal.py
Modified: branches/multi_structure/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_structure/generic_fns/structure/internal.py?rev=8486&r1=8485&r2=8486&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/internal.py (original)
+++ branches/multi_structure/generic_fns/structure/internal.py Thu Jan 15
18:41:28 2009
@@ -1333,8 +1333,22 @@
# Strip away atom numbering, from the front and end.
element = strip(atom_name, digits)
+ # Amino acid atom translation table (note, numbers have been stripped
already!).
+ table = {'C': ['CA', 'CB', 'CG', 'CD', 'CE', 'CZ'],
+ 'N': ['NE', 'NH'],
+ 'H': ['HA', 'HB', 'HG', 'HD', 'HE', 'HT'],
+ 'O': ['OG', 'OD', 'OE'],
+ 'S': ['SD']
+ }
+
+ # Translate amino acids.
+ for key in table.keys():
+ if element in table[key]:
+ element = key
+ break
+
# Allowed element list.
- elements = ['H', 'C', 'N', 'O', 'F', 'P']
+ elements = ['H', 'C', 'N', 'O', 'F', 'P', 'S']
# Return the element, if in the list.
if element in elements:
_______________________________________________
relax (http://nmr-relax.com)
This is the relax-commits mailing list
[email protected]
To unsubscribe from this list, get a password
reminder, or change your subscription options,
visit the list information page at
https://mail.gna.org/listinfo/relax-commits
