Re: [Rdkit-discuss] Incorrect SMARTS from FindMCS

Thanks Greg! BondCompare.CompareAny is exactly what I needed Best, Marta 2016-07-06 7:47 GMT+02:00 Greg Landrum : > Marta, > > On Tue, Jul 5, 2016 at 11:14 AM, Marta Stępniewska-Dziubińska > wrote: >> >> >> To be honest, I expected it to fail :) > > >

Re: [Rdkit-discuss] Incorrect SMARTS from FindMCS

On Tue, Jul 5, 2016 at 1:38 PM, Peter S. Shenkin wrote: > But we have learned that RDKit can do the imparsable > > Oh... Peter... you should be ashamed. :-) -- Attend Shape: An AT Tech Expo July

Re: [Rdkit-discuss] Incorrect SMARTS from FindMCS

But we have learned that RDKit can do the imparsable -P. On Tue, Jul 5, 2016 at 6:14 AM, Marta Stępniewska-Dziubińska < mart...@ibb.waw.pl> wrote: > Hi Greg, > > To be honest, I expected it to fail :) > > I want to find structures with a defined topology, but allow for > different bond

Re: [Rdkit-discuss] Incorrect SMARTS from FindMCS

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

Re: [Rdkit-discuss] Incorrect SMARTS from FindMCS

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

[Rdkit-discuss] Incorrect SMARTS from FindMCS

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