Re: [Rdkit-discuss] Submol: bond vs atom indicies

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

Hi Maciek,


On Mon, Mar 21, 2016 at 8:33 PM, Maciek Wójcikowski <ma...@wo...>
wrote:

>
> I came across one problem with RDKit today, namely Chem.PathToSubmol()
> function. Does the "path" mean atom or bond indices? On this very list I
> fount the examples showing usage with atom idx [
> https://www.mail-archive.com/rdk...@li.../msg03966.html],
> while the example on "Getting started in python" is feeding
> Chem.FindAtomEnvironmentOfRadiusN() which gives a list of bond indices. The
> documentation could be more explicit here... After my brief analysis of the
> code I found out that the bonds should be used (correct me if I'm wrong).
>

The function is still not documented, but it's definitely bonds. I think
the thread you reference from the mailing list says the same thing.


> So here comes the question: is there an equivalent function or a clever
> way to do Chem.PathToSubmol() on atom indices? Currently I do: 1) get the
> atom path; 2) get bonds between every atom in path (their indices); 3) get
> submol with Chem.PathToSubmol()
>

I don't think so.


> PS.
> I use it to get each proteins residue (amino acid) in separate mol. It
> would be much easier if we could use "Molecule -> Residues ->  Atoms"
> instead of "Molecule -> Atoms -> (grouping of monomers) -> Residues".
>
>
SplitMolByPDBResidues() doesn't do what you want?

-greg