Re: [Rdkit-discuss] 2D coord for hydrogens

@lists.sourceforge.net Subject: Re: [Rdkit-discuss] 2D coord for hydrogens Hi Mark, further to Fio's reply, I think the confusion stems from the fact that when you call AddHs() after MolFromSmiles() no coordinates are actually generated; these are only generated on the fly for visualization

Re: [Rdkit-discuss] 2D coord for hydrogens

Hi Mark, further to Fio's reply, I think the confusion stems from the fact that when you call AddHs() after MolFromSmiles() no coordinates are actually generated; these are only generated on the fly for visualization, and hence are correct before and after AddHs(), as the layout is always

Re: [Rdkit-discuss] 2D coord for hydrogens

Hi Mark, it's best to add the hydrogens first and then set your coordinates: m=Chem.MolFromSmiles('Nc1nnc2n1CCS2') m2=rdmolops.AddHs(m, False, True); Chem.rdCoordGen.AddCoords(m2) Best, Fio On Thu, Aug 27, 2020 at 11:25 AM Mark Mackey wrote: > Hi all, > > > > I’m trying to generate a 2D

[Rdkit-discuss] 2D coord for hydrogens

Hi all, I'm trying to generate a 2D layout with sensible locations for hydrogens, and am struggling a bit. If I start from SMILES: m=Chem.MolFromSmiles('Nc1nnc2n1CCS2') m2=rdmolops.AddHs(m, False, True); Then m2 has perfectly sensible 2D cords for the hydrogens. If I use addCoords=False here