Extract the structure embeddings

[Jerry888Chen]

Dear Team of GearNet,

Many many thanks for this wonderful package! I am new to programming (especially torchdrug and pytorch), so how to extract the structure representations confused me a lot after some explorations. If I want to embed my structure as an embedding using a GearNet model (for example, the GearNetIEConv model fold_mc_gearnet_edge_ieconv.pth), is there a convenient way to do that? Any instruction is appreciated and sorry for a naive question from a newbie.

Jerry

[Oxer11]

Hi, thanks for your interest in our work!

You can follow this tutorial, which describes how to use TorchDrug to construct data.Protein object and pass it into GearNet. Also, you can see this tutorial to learn about how to use pre-trained checkpoints.