Thank you, Sereina.
I understand importance of addition of hydrogens to get a reasonable 3D
coordinates. But the situation may be not that simple.
1. Addition of hydrogen is only required for custom coordinates supplied
from an external file. If coordinates of a template is generated with
rdk
Makes sense :)
> On Jul 7, 2020, at 12:35 PM, Sereina Riniker
> wrote:
>
> Dear Pavel and Sunhwan,
>
> Please note that hydrogens should always be added for the embedding algorithm
> to work properly (i.e. it’s not a walk around but what should be done).
> See also Section “Working with 3D M
Dear Pavel and Sunhwan,
Please note that hydrogens should always be added for the embedding algorithm
to work properly (i.e. it’s not a walk around but what should be done).
See also Section “Working with 3D Molecules” in
https://www.rdkit.org/docs/GettingStartedInPython.html
Best regards,
Sere
The reason constraint embed didn’t work is the molecule simply can’t be
embedded using the rdkit’s algorithm.
> In [25]: mol_child = Chem.MolFromSmiles('C[C@@H]1CC[C@H](O)CC1=O')
>
>
> In [26]: AllChem.EmbedMolecule(mol_child)
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