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
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--
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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