On 05/07/2013 17:54, Brett T. Hannigan wrote:
> I have a database of molecules in pdb files. I'd like to go through
> each molecule and see if it has certain substructures, and if they do
> identify which atoms are part of that substructure. So it's easy enough
> to read the pdb file in, convert
Hello,
You can "convert" from PDB to PDB using filter option (
http://openbabel.org/wiki/--filter_option)
obabel input.pdb -O output.pdb --filter "s='CN'"
If your database is really large, or you want to search multiple times,
then I'd suggest using FastSearch for performance reasons. For further
