Hi Jason,
I hope the following codes will help you a little.
from rdkit import Chem
from rdkit.Chem import Draw
from rdkit.Chem import AllChem
size = (120, 120)
m = Chem.MolFromSmiles('C#C')
m2=Chem.rdmolops.AddHs(m)
AllChem.EmbedMolecule(m2, AllChem.ETKDG())
Draw.MolToMPL(m2, size=size)
*** source code link (non specific to your question though)
https://github.com/rdkit/rdkit
Thanks. - malitha
On Fri, Dec 1, 2017 at 6:42 AM, Jason Biggs <jasondbi...@gmail.com> wrote:
>
> m = Chem.MolFromSmiles('C#C')
>
>
> renders fine
>
> [image: Inline image 1]
>
> but adding in the hydrogens, they don't snap to a linear arrangement
>
> m2=Chem.rdmolops.AddHs(m)
>
>
> [image: Inline image 3]
>
>
> This doesn't just affect acetylene, but any terminal alkyne, like
> 'c1ccc(CCC#C)cc1'.
>
> I can write a hack on my end to look for this special case, but where in
> the drawing code does it decide where to place hydrogens?
>
> Jason Biggs
>
>
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