Dear Navid,
“Zero conformations” mains that EmbedMolecule function return false. There is
no 3D. You use the default EmbedMolecule parameters.
You can try to change them to get 3D coordinates (increase maxAttempts for
example). I don’t see another way to get realistic “Angle” between atoms.
Dan already mentioned this in his reply, but I will reinforce: the RDKit
stores atom positions in conformers, so if a molecule has no conformers it
also has no atom positions. Without atom positions it doesn’t make sense to
calculate angles.
What exactly are you trying to do?
-greg
On Fri, 20
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