Re: [Rdkit-discuss] Cleaning SD files

[Paul E. <pau...@bi...>]

On 17/09/10 07:57, markus kossner wrote:
>
> some time ago I implemented a filter function during a pdb mining 
> campaign. The Idea was to exclude compounds to far away from drug like 
> chemical matter.
>

As a matter of interest, how did you convert from a pdb file that might 
contain a ligand to an RDKit mol?  Look for residues with HETATMs? In 
making the RDKit mol, how did you know the bonds and the bond orders 
(look them up in the Chemical Component Library, perhaps)? (non-trivial 
AFAICS).

Paul.