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

[Maciek W. <ma...@wo...>]

I correct myself, all residue types are available
from Chem.SplitMolByPDBResidues().

----
Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
ma...@wo...

2016-03-22 9:50 GMT+01:00 Maciek Wójcikowski <ma...@wo...>:

> Hi Greg,
> 2016-03-22 6:28 GMT+01:00 Greg Landrum <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.
>
> Ok, you're right I've just noticed your comment, while the example was
> still using atom indices (although they worked for the sample mol -
> fortunatelly aligned with atom indices).
>
> >
> >
> >>
> >> 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?
> >
> >
>
> Not really. I want to get each amino acid separately, so I'd have to do
> SplitMolByPDBChainId() -> SplitMolByPDBResidues() -> break the peptide
> bonds (to eliminate series of aa) -> split disconnected molecules. And that
> only outputs valid PDB amino acids. Accessing non-standard ones, like HOH,
> LIG, UNL, although present in PDB would be also desired. In other words the
> unique key should be "monomer index + chain id" instead of only three
> letter name as in SplitMolByPDBResidues().
>
> Maciek
>
> >
> > -greg
> >
>