Just wondering - why do you want to do this? Most algorithms just need a
ring check like OBAtom::IsInRing().
Regards,
- Noel
On Sun, 16 Sep 2018 at 22:46, <tayeb...@gmail.com> wrote:
> Thank you, Dr. Forli. It worked!
>
> -Tayeb
>
> -----Original Message-----
> From: Stefano Forli <fo...@scripps.edu>
> Sent: Thursday, September 13, 2018 10:09 PM
> To: tayeb...@gmail.com; openbabel-disc...@lists.sf.net
> Cc: Cesar Plascencia <plasc...@chemistry.msu.edu>
> Subject: Re: [Open Babel] Ring Perception Using Pybel
>
> I don't know how to do that with PyBel only, but you can access OB from it
> and get roughly the same results with something like this:
>
> import pybel
> ob=pybel.ob
>
> pmol=pybel.readfile('sdf', 'filename.sdf').next() mol=pmol.OBMol
> ring_list=list(mol.GetSSSR())
> size=len(ring_list)
> print "size", size
> for ring in ring_list:
> members=tuple(ring._path)
> print "members", members
>
>
>
> On 09/13/2018 06:01 PM, tayeb...@gmail.com wrote:
> > Hi,
> >
> > Does anybody know how I can use pybel to find rings (sssr) in compounds
> and output the indices of the atoms in those rings?
> >
> > I have already figured out how to do it using rdkit, but I am interested
> in accomplishing the same thing with pybel:
> >
> > >>> *m = Chem.MolFromMolFile('temp.mol')*
> >
> > >>> *ssr = Chem.GetSymmSSSR(m)*
> >
> > # and then I can print the indices of the atoms in the rings:
> >
> > >>> *list(ssr[0])*# print for the first ring for example
> >
> > [6, 5 , 2, 1, 3, 0]
> >
> > >>> *len(ssr)*# or print the number of rings
> >
> > 3
> >
> >
> >
> >
> >
> > _______________________________________________
> > OpenBabel-discuss mailing list
> > OpenBabel-discuss@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
> >
>
> --
>
> Stefano Forli, PhD
>
> Assistant Professor
> Dept. of Integrative Structural
> and Computational Biology, MB-112A
> The Scripps Research Institute
> 10550 North Torrey Pines Road
> La Jolla, CA 92037-1000, USA.
>
> tel: +1 (858)784-2055
> fax: +1 (858)784-2860
> email: fo...@scripps.edu
> http://www.scripps.edu/faculty/forli/
>
>
>
>
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