Re: [Rdkit-discuss] sanitization removes Hs - is this expected?

[Michal K. <mic...@gm...>]

Hi Michal,
Hmm, wouldn't this do exactly what you wanted?
sdf_in=Chem.SDMolSupplier(in_file, removeHs=False)

Best wishes,
Michal

On 15 April 2015 at 16:40, Michał Nowotka <mm...@gm...> wrote:

> Hi,
>
> I have a question, directly related to this topic: I would like to
> achieve the following behavior from RDKit:
>
> 1. If input molfile has explicit hydrogens defined, then perform only
> partial sanitization and keep hydrogens.
> 2. Otherwise perform full sanitization as usual.
>
> Will that happen automatically or do I need to check if the molfile
> has explicit hydrogens? If the latter, how can I check this using
> RDKit without writing my own SDF parser?
>
> Michał Nowotka
>
> On Tue, Apr 7, 2015 at 11:50 AM, Greg Landrum <gre...@gm...>
> wrote:
> >
> > On Tue, Apr 7, 2015 at 12:13 PM, Michal Krompiec <
> mic...@gm...>
> > wrote:
> >>
> >> Thanks a lot!
> >
> >
> > Glad it works.
> >
> >>
> >> By the way, it would be useful to have this feature (MergeQueryHs) also
> in
> >> the substructure search KNIME node.
> >
> >
> > Indeed. :-)
> > We already have a version of the MolToRDKit node ready to allow this; it
> > just hasn't made it into the open-source version of the KNIME nodes yet
> (we
> > forgot to include this the last time we updated those nodes). It's coming
> > soon.
> >
> > -greg
> >
> >
> >
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