Re: [Rdkit-discuss] rearomatize only benzene rigns after kekulize + clearAromaticFlags

2016-09-22 Thread Guillaume GODIN
+41 (0)79 536 1039 Firmenich SA RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8 De : Greg Landrum <greg.land...@gmail.com> Envoyé : jeudi 22 septembre 2016 10:22 À : Guillaume GODIN Cc : RDKit Discuss Objet : Re: [Rdkit-discuss] rearomatize only b

Re: [Rdkit-discuss] rearomatize only benzene rigns after kekulize + clearAromaticFlags

2016-09-22 Thread Greg Landrum
On Wed, Sep 21, 2016 at 4:31 PM, Guillaume GODIN < guillaume.go...@firmenich.com> wrote: > After testing the code, It works perfectly, thanks! > Well, there's at least that. ;-) > Unfortunatly, I discovered that it's still not compatible with the > aromaticity method used in the article i

Re: [Rdkit-discuss] rearomatize only benzene rigns after kekulize + clearAromaticFlags

2016-09-21 Thread Guillaume GODIN
Objet : Re: [Rdkit-discuss] rearomatize only benzene rigns after kekulize + clearAromaticFlags Guillaume, Here's how to read in a molecule and skip aromaticity perception: In [12]: m = Chem.MolFromSmiles('c1c1-c1cccnc1-c1cc[nH]c1',sanitize=False) In [13]: Chem.SanitizeMol(m,sanit

[Rdkit-discuss] rearomatize only benzene rigns after kekulize + clearAromaticFlags

2016-09-19 Thread Guillaume GODIN
Dear All, I would like to kekulize the molecule, but only conserve the aromaticity knowledge of C6 (benzene like) type rings So what to need to do after this command? Chem.rdmolops.Kekulize(mol, clearAromaticFlags=True) Should I need to store benzene like location before the Kekulize