On Wed, Oct 7, 2015 at 11:12 AM, Joos Kiener <joos.kie...@gmail.com> 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
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