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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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Edge_list set to [0,0,0] #40

Closed andrew7shen closed 1 year ago

andrew7shen commented 1 year ago

Hi, thanks for your work!

In the Fold3D dataset class, why is the edge_list field set to an empty edge list of [[0,0,0]] when the input hdf5 files are loaded (on line 85 in dataset.py)? I'm trying to load in my own protein graphs into the GearNetIEConv model to get an output embedding, and if I don't set edge_list=[[0,0,0]], I run into an IndexOutOfBounds error later on when the protein graph is getting passed through the "message" function of the GeometricRelationalGraphConv layer.

Oxer11 commented 1 year ago

Hi, we need to set a placeholder for edge_list when loading the protein and the real edges are constructed during the model forward process.

andrew7shen commented 1 year ago

Makes sense, thanks!