How to obtain the embedding of molecular conformation

[Xinda]

Great Work!
Input：atom_type + xyz
How can we get the embedding of atom and xyz?

[Shengjie Luo]

The embedding of atom:

Transformer-M/Transformer-M/modules/transformer_m_layers.py

Line 25 in 45647e1

 class AtomFeature(nn.Module): 

The attention bias of 3D position:

Transformer-M/Transformer-M/modules/transformer_m_layers.py

Line 149 in 45647e1

 class Molecule3DBias(nn.Module):