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DeepGraphLearning / GearNet

GearNet and Geometric Pretraining Methods for Protein Structure Representation Learning, ICLR'2023 (https://arxiv.org/abs/2203.06125)
MIT License
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Extract the structure embeddings #58

Open Jerry888Chen opened 6 months ago

Jerry888Chen commented 6 months ago

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_edgeieconv.pth), is there a convenient way to do that? Any instruction is appreciated and sorry for a naive question from a newbie.

Jerry

Oxer11 commented 6 months ago

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.