Re: [Rdkit-discuss] Count carbon atoms

[Joos K. <joo...@gm...>]

Hi Greg,

thanks for your reply.

Can confirm it's way faster than other 2 options. For my use case it's fast
enough.

Best Regards,

Joos

2015-10-14 6:55 GMT+02:00 Greg Landrum <gre...@gm...>:

>
>
> On Wed, Oct 7, 2015 at 11:12 AM, Joos Kiener <joo...@gm...>
> wrote:
>
>> Hi all,
>>
>> is there an easy way I'm missing to get the number of C-Atoms in a
>> molecule?
>>
>> Currently I iterate all atoms and check if it's symbol is C. Doesn't seem
>> very efficient.
>>
>
> There's an, obviously under-documented, simple (and fast) way to do this:
>
> from rdkit.Chem import rdqueries
> q = rdqueries.AtomNumEqualsQueryAtom(6)
> len(mol.GetAtomsMatchingQuery(q))
>
> This is, based on the testing I just did, significantly faster than either
> the substructure-based or GetAtoms() based approaches. I'm not sure how
> generally useful it is, but this could be made even faster by adding a
> Mol.CountAtomsMatchingQuery() function to the C++ interface.
>
> You can find a bit of explanation, as well as a list of the types of
> QueryAtom functions available, by searching for QueryAtom here:
> https://github.com/rdkit/UGM_2014/blob/master/Notebooks/Whats_new.ipynb
>
> Best,
> -greg
>
>
>