Hi Greg, I missed the @ bit for bonds: thanks for the tip: I will definitely use it. Still not matching donor and acceptors in the same ring is something I need to achieve. I'll work on Paul's suggestion and report back if I have any success in it.
Cheers, m 2016-09-29 17:03 GMT+02:00 Greg Landrum <[email protected]>: > Paul already mentioned an approach using the molecule's RingInfo > structure, which you could certainly use to see if the RDKit thinks the two > molecules are part of the same smallest ring. > I suspect that you might want something a bit more general (apologies that > I don't have a copy of that paper handy, so I can't read what the Roche > folks used). > > Fortunately, the more general case actually turns out to be easier. > I believe that what you want is to just determine whether or not the path > between the two atoms is composed solely of ring bonds. > You could express this in SMARTS as: > {DONOR}@*@*@{ACCEPTOR} > That's the three-bond separation case. > Where {DONOR} and {ACCEPTOR} are the SMARTS definitions you would like to > use for those atoms. The "@" in SMARTS means "Ring bond", so this pattern > corresponds to a donor separated by three ring bonds from an acceptor. > > This will, unfortunately, also match the case where the donor and acceptor > are adjacent to each other in a 5 membered ring. If it's important than you > not match that, you'll have to do a bit more work. > > Best, > -greg > > > > _____________________________ > From: Marco Stenta <[email protected]> > Sent: Thursday, September 29, 2016 4:13 PM > Subject: [Rdkit-discuss] Ring membership > To: <[email protected]> > > > > Dear Colleagues, > I am working on intramolecular hydrogen bonds, formed between > donor-acceptors separated by 2,3,4 atoms, as described in the Roche paper: > Kuhn, B.; Mohr, P.; Stahl, M. J. Med. Chem. 2010, 53, 2601. > > I will use SMARTS and RDKIT to identify and classify IMHB. > > I see from documentation how to identify atoms that are members of a ring, > how can I identify if two atoms are member of the same ring? > > > Example: > > Donor------X-----Y-------Acceptor > > NCC=O > > This will match > C1CC(NC1)C=O > > but I would lie to flag if two or more atoms belong to the same ring, as > this will impact the capability of IMHB to opne and close. > > > Do you have any suggestion? > > cheers, > Marco > > > > > >
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