Re: [Rdkit-discuss] Check If Atom Is in Two Small Rings

Awesome! Thank you all so much!!! Here is my implementation of the function for reference: def passed_NA2SR(mol): #no atom shared by two small rings rings = mol.GetRingInfo().AtomRings() small_rings = [] for ring in rings: if len(ring) < 5:

Re: [Rdkit-discuss] Check If Atom Is in Two Small Rings

Peter, quite correct. To do that, you'll need to do operations on the rings themselves: >>> m = Chem.MolFromSmiles("C1CC12CCC2") >>> list(m.GetRingInfo().AtomRings()) [(0, 1, 2), (3, 4, 5, 2)] And set operations are probably your friend >>> m = Chem.MolFromSmiles("C1CCC12CCC2") >>>

Re: [Rdkit-discuss] Check If Atom Is in Two Small Rings

But Brian's solution won't help Jonathan find atoms that are in two three-membered or two four-membered rings, which I thought Jonathan also wanted, based on the wording of the original query. -P. On Tue, Apr 11, 2017 at 4:12 PM, Curt Fischer wrote: > Brian's solution

Re: [Rdkit-discuss] Check If Atom Is in Two Small Rings

Brian's solution is obviously better (shorter, uses less functions) than mine. (Although mine assumes that you want atoms that are part of _exactly_ two rings, not atoms that are part of _at least_ two rings as Brian's does. Probably Brian's solution is what you want but worth noting.) CF On

Re: [Rdkit-discuss] Check If Atom Is in Two Small Rings

You are so close! >>> from rdkit import Chem >>> m = Chem.MolFromSmiles("C1CC12CCC2") >>> for atom in m.GetAtoms(): ... if atom.IsInRingSize(3) and atom.IsInRingSize(4): print atom.GetIdx() ... 2 >>> Cheers, Brian On Tue, Apr 11, 2017 at 1:38 PM, Jonathan Saboury