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 it to SMILES representation, > and then do a SMARTS query to look for my substructures. However, if > the SMARTS query reports that the substructure is present in the > molecule, I'm not sure how to identify the atoms in the pdb file which make > up the match. > Any ideas?
I would suggest that you can browser the ligand-expo service provided by PDB and download the smiles or 3D structures of small molecules http://ligand-expo.rcsb.org/ld-download.html Lirong Wang, PhD School of Pharmacy University of Pittsburgh ------------------------------------------------------------------------------ This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
