Re: [Rdkit-discuss] ReactionFromSmarts and RunReactants

Now I think I know and I very much look forward to a more detailed documentation. many thanks, -Monica At 2016-04-22 17:48:39, "Greg Landrum" wrote: There isn't great documentation for this, but the way the current code works is reasonably simple. If your

Re: [Rdkit-discuss] ReactionFromSmarts and RunReactants

There isn't great documentation for this, but the way the current code works is reasonably simple. If your reaction has two products (i.e. two molecules separated by a dot), you will get two products (i.e. two separate molecules) when you call RunReactants(); that's what you asked for. Here's a

Re: [Rdkit-discuss] ReactionFromSmarts and RunReactants

Hi Grégori, Maybe I don't have a clear understanding of this function, I know the dot represent disconncction of two fragments ,and I suppose changes just occurs in mapped molecular fragment, the remaining part of reactant is invariable, in other words, if mapped molecular fragment breaks

Re: [Rdkit-discuss] ReactionFromSmarts and RunReactants

Hi Monica, As Greg stated, why do you expect your product not to be fragmented? I suggest you to have a careful look at the SMARTS definition (for instance from Daylight: http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html) In SMARTS patterns, the dot indicates disconnected fragments.

[Rdkit-discuss] ReactionFromSmarts and RunReactants

Greg, After changing the pattern into "[C:1][C:2](=[O:3])[N+0:4][C:5]=[C:6][C:7]([O-:8])=[O:9].[OH2:10].[OH2:11]>>[C:1][C:2]([O-:10])=[O:3].[O:8]=[C:7]=[O:9].[N+:4].[C:6][C:5]=[O:11] , I get the same result .A ring structure just like you said is broken into pieces.

Re: [Rdkit-discuss] ReactionFromSmarts and RunReactants

Monica, Why do you think you should get a single chain from the ring structure? If you look at the atom mapping in your input reaction: [C:1][C:2](=[O:3])[N+0:4][C:5]=[C:6][C:7]([O-:8])=[O:9].[OH2:10].[OH2:11]>>[C:1][C:2]([O-:10])=[O:3].[O:7]=[C:8]=[O:9].[N+:4].[C:6][C:5]=[O:11] You've told it