Re: [Rdkit-discuss] Is it possible to create a reaction SMARTS with dative bonds?

2020-02-12 Thread Greg Landrum
On Wed, Feb 12, 2020 at 4:37 PM Grzegorz Skoraczyński < g.skoraczyn...@mimuw.edu.pl> wrote: > Hi Greg, > > Thanks for your reply. Could you explain more which pattern you use for > GetSubstructMatch? > Doh! Sorry I didn't include that: In [7]: pattern = Chem.MolFromSmarts('[O-]-[#1+]') How ca

Re: [Rdkit-discuss] Is it possible to create a reaction SMARTS with dative bonds?

2020-02-12 Thread Grzegorz Skoraczyński
Hi Greg, Thanks for your reply. Could you explain more which pattern you use for GetSubstructMatch? How can we guess which product' atoms are mapped to a reaction template? Best GS. śr., 12 lut 2020 o 15:50 Greg Landrum napisał(a): > Hi Grzegorz, > > Nice one! This is a bug in the way Reaction

Re: [Rdkit-discuss] Is it possible to create a reaction SMARTS with dative bonds?

2020-02-12 Thread Greg Landrum
Hi Grzegorz, Nice one! This is a bug in the way Reaction SMARTS (or Reaction SMILES for that matter) is parsed. At the moment there's not any way to directly work around the problem. You can add a single bond in the reaction and then manually convert that to a dative bond in the products. Somethin