How to get 3D coordinates?

Hi, I'm a beginner of Molecular field and cheminformatics.
So I have a difficulty in using this github code.

I try to get a atom's 3D coordinates of molecules, when inferencing using this model.
I already read issue #100 , but I couldn't understand how to utilize this part, single_dock_with_gradient.

Would you explain more details of changing 3D embedding vector to 3D coordinates method?

I'd really appreciate for it if anyone advise me this problem.
Thank you.