Hi Maciek,
On Mon, Mar 21, 2016 at 8:33 PM, Maciek Wójcikowski <[email protected]>
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/[email protected]/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
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