Re: [Rdkit-discuss] canonical atom indexing

[Greg L. <gre...@gm...>]

On Thu, Mar 10, 2016 at 2:04 PM, Brian Kelley <fus...@gm...> wrote:

> Yes, I actually exposed that function to Python  in Rdkit :)
>
> Be aware that the canonical rank and the output order aren't the same
> thing.  The rank is what is used during graph traversal, when making the
> smiles string, to choose what atom to go to next.  The output order is what
> atoms where output first, second, third in the output smiles string.  They
> are not necessarily the same.
>
> Both should, however, be unique for the input graph, but in either case
> explicit hydrogens should be added.
>

Exactly. If you just want a canonical ordering of the atoms, there is no
reason to generate the SMILES. You can just use Chem.CanonicalRankAtoms().

The "_smilesAtomOutputOrder" property used to be the only way to get a
canonical ordering. It is still useful if you care about the order of atoms
in the output SMILES, but is quite inefficient if all you want is a
canonical ordering.

-greg