Dear Jose Manuel,
On Tue, Jan 5, 2016 at 8:58 AM, Jose Manuel Gally < [email protected]> wrote: > Hi, > > currently when I generate conformations with RDKit and want to use them > for docking experiments, I have to first rewrite them using the > MolConverter node in Knime. > I need to do this because some docking software read the information > about charges in the atom block rather than in the molecule properties. > > Is there a way to specify to SDWriter to write according to the > "standard" V2000 format? (1) > To be a bit picky: the RDKit's current behavior is perfectly correct and follows the v2000 standard in this regard. The CTAB document you reference, which is from 2005, says this about the atom charge lines: Wider range of values in M CHG and M RAD lines below. Retained for compatibility with older Ctabs, M CHG and M RAD lines take precedence The problem you are encountering is that the docking software you are using doesn't follow the (>10 year old) standard. Having said that, it's probably possible to modify the RDKit's behavior to populate the CHG field in the atom blocks. I'll look into it. -greg
------------------------------------------------------------------------------
_______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
