Re: [Rdkit-discuss] Count carbon atoms

[John M <joh...@gm...>]

On 8 October 2015 at 00:21, Andrew Dalke <da...@da...> wrote:

> I fed it some ChEBI structures and found the molecular formula was about
> 2x faster than the SMARTS match, and almost 10x faster than iterating over
> the atoms.
>

This seems odd... surely you can't go faster that iterating over the atoms
and counting element 6? To get the molecular formula or match a SMARTS you
must at a minimum iterate over all atoms so by definition they must be
slower.

Does RDKit precompute formulas in sanitise for example hence the times
aren't really reflective? Perhaps the python iter is indeed slower than a
SMARTS match but that can't be true?

Regards,
John W May
joh...@gm...