Hi Greg, To be honest, I expected it to fail :)
I want to find structures with a defined topology, but allow for different bond types. My first idea was to use SMARTS with ~ bonds, and it works fine with GetSubstructMatch. I don't really need MCS, I just used it to check different patterns. But I expected that FindMCS will throw an exception, rather than produce SMARTS it cannot parse. Best, Marta 2016-07-05 11:32 GMT+02:00 Greg Landrum <[email protected]>: > Hi Maria, > > Output 11 is certainly wrong (the SMARTS generated is incorrect). > I suspect this is happening because the molecule "coa" (input 3 in your > notebook) is constructed from SMARTS and includes ~ bonds (which match any > bond type). I almost think that the MCS code should be generated to fail in > these cases. Do you really need to construct the input molecules from > SMARTS? > > Best, > -greg > > > On Tue, Jul 5, 2016 at 6:52 AM, Marta Stepniewska-Dziubinska > <[email protected]> wrote: >> >> Hi all, >> >> I got a very surprising error: RDKit generated a SMARTS string that it >> cannot parse. Here's my code: https://goo.gl/ETvjjT >> >> In order to explain the code: I create a structural pattern with SMARTS. >> It's a strange pattern, I admit, but I was able to find it in my >> molecule. I then try to use FindMCS for the pattern and the molecule, >> and I get some results, but the smartsString is incorrect. I see some >> inexplicable commas before several bonds, and when I remove them I get a >> valid SMARTS and a reasonable structure. >> >> I'm using RDKit 2016.03.1 and conda 4.0.4 on Ubuntu 14.04. >> >> Best, >> Marta >> >> >> ------------------------------------------------------------------------------ >> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >> present their vision of the future. This family event has something for >> everyone, including kids. Get more information and register today. >> http://sdm.link/attshape >> _______________________________________________ >> Rdkit-discuss mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > ------------------------------------------------------------------------------ Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San Francisco, CA to explore cutting-edge tech and listen to tech luminaries present their vision of the future. This family event has something for everyone, including kids. Get more information and register today. http://sdm.link/attshape _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
