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

[Michał N. <mm...@gm...>]

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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