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 <m...@cresset-group.com> wrote:
> 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 then the hydrogens are all at the origin, which is
> more-or-less expected.
>
>
>
> If, however, I generate new 2D coords for the heavy atoms with CoordGen:
>
>
>
> m=Chem.MolFromSmiles('Nc1nnc2n1CCS2')
>
> Chem.rdCoordGen.AddCoords(m)
>
> m2=rdmolops.AddHs(m, False, True);
>
>
>
> then the 2D coords for the hydrogens are poor on the 5-membered ring, and
> the two hydrogens on the NH2 are superimposed.
>
>
>
> (In practise I’m starting from a 3D SDF and trying to generate 2D coords
> for it, hence the need for CoordGen).
>
>
>
> What am I doing wrong?
>
>
>
> Regards,
>
> Mark
>
>
>
> *-- *
>
> *Mark Mackey*
>
> *Chief Scientific Officer*
>
> *Cresset*
>
> New Cambridge House, Bassingbourn Road, Litlington, Cambridgeshire, SG8
> 0SS, UK
>
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>
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>
>
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