Hi Markus, I do not use RDKit for handling protein structures (I do not think this is supported); instead, I use Bio.PDB to parse PDB files. This is one of the best PDB parsers (in my opinion), and better then the open babel or OEChem implementations. Unfortunately, there is no software I am aware of which can handle small molecules as well as protein structures reliably, i.e. keep track of disordered atoms, insertions code, ligand identifiers, atom names, alternative atom locations etc.
There is an implementation of the KDTree algorithm in Bio.PDB, which I use to get all contacts between ligand and amino acid atoms. I am working on a paper at the moment which describes the methods I used to get the SIFts from protein-ligand complexes. I intend to make my protein-ligand interaction database including the API publicly available (as database dumps) maybe that will be helpful. Bio.PDB uses the Biopython license which is extremely liberal; maybe there is way to use it as the foundation for a PDBMolSupplier and a RDBioMol class...okay I am dreaming a bit here! ;) Adrian On Fri, May 23, 2008 at 9:49 AM, markus <[email protected]> wrote: > Hi there, > > some questions about File input: > 1. I want to read in large multiconformer sdf file. > This could be done by checking the canonical isomeric smiles. > However I wonder if that could be (or already is) implemented in some > Supplier > as I suspect my Python Code to be slow. > 2. How about Proteins / binding Pockets? As RDKit explicitly is designed > for > small Mols, I wonder if anyone has already loaded a Protein? > I found a post by Adrian Schreyer (*[Rdkit-discuss] Atom-level SMARTS > matching*) > mentioning SIFTs, This implies the perception of Pocket-residues. > Was that done / Can that be done by the RDKit? > > Cheers Markus > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Rdkit-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
