Re: [Rdkit-discuss] explicit H atoms

Hello Mark, I thought you could depict it like the attached, since only the narrow end of a wedged bond counts. Sure, it is confusing, but it is doable. Except that in section ST-0.5 of the IUPAC guidelines pointed out by Greg https://www.degruyter.com/document/doi/10.1351/pac200678101897/html it

Re: [Rdkit-discuss] two molecules in mol object

Have you looked at GetMolFrags? if you define >m=MolFromSmiles('CCC.CC') then >rdmolops.GetMolFrags(m,asMols=True) returns two molecules, keeping any coordinates or non-computed properties in the process. Jason Biggs On Wed, Mar 10, 2021 at 9:42 AM Shani Zev wrote: > Hi all, > I have

[Rdkit-discuss] two molecules in mol object

Hi all, I have mol object that contains two molecules, I want to delete one of the molecules but without going through smiles (if I will go through smiles it could be easy but I need to do it directly for the mol object.) There is a way to get to each molecule while they are in the same mol

Re: [Rdkit-discuss] explicit H atoms

Dear Mark, Many thanks for this nice example ! Best, Jean-Marc Le 10/03/2021 à 09:52, Mark Mackey a écrit : I believe it's not possible to represent the chirality of the attached molecule's ring fusion carbons without using an explicit H. Regards, Mark -- Mark Mackey Chief Scientific

Re: [Rdkit-discuss] explicit H atoms

I believe it's not possible to represent the chirality of the attached molecule's ring fusion carbons without using an explicit H. Regards, Mark -- Mark Mackey Chief Scientific Officer Cresset New Cambridge House, Bassingbourn Road, Litlington, Cambridgeshire, SG8 0SS, UK tel: +44 (0)1223

Re: [Rdkit-discuss] explicit H atoms

Dear Greg, Jason, and Maciek, many thanks for your feedback. The reading of the IUPAC guidelines will certainly bring useful information. Best, Jean-Marc Le 10/03/2021 à 09:28, Greg Landrum a écrit : On Wed, Mar 10, 2021 at 9:05 AM Jean-Marc Nuzillard mailto:jm.nuzill...@univ-reims.fr>>

Re: [Rdkit-discuss] explicit H atoms

On Wed, Mar 10, 2021 at 9:05 AM Jean-Marc Nuzillard < jm.nuzill...@univ-reims.fr> wrote: > > Your answer about tetragonal carbons goes in the same direction as my > initial feeling did, > but my feeling was only a feeling, just like yours. > I was wondering whether someone had some more formal

Re: [Rdkit-discuss] explicit H atoms

Dear Ling, Your answer about tetragonal carbons goes in the same direction as my initial feeling did, but my feeling was only a feeling, just like yours. I was wondering whether someone had some more formal view about this question. Many thanks! Jean-Marc Le 09/03/2021 à 20:42, Ling Chan