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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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Passing CIF files directly into GearNet? #54

Closed gtamer2 closed 8 months ago

gtamer2 commented 8 months ago

Hi folks,

Is GearNet compatible with CIF files, or are there any sponsored solutions for converting CIF files into Gearnet-ready PDB files?

I have browsed through past issues and haven't seen CIF files mentioned previously. I know it is possible to convert CIF files to PDB files with a tool like BioPython, but this can be buggy.

Thanks in advance!

Oxer11 commented 8 months ago

Hi,

I've only used PDB files as the input and have little experience with the CIF format. So I may not know the solution to your problem. But there should be some tools to convert CIF to PDB files if you ask the Google. I think BioPython should be workable in this case.

gtamer2 commented 8 months ago

Okay good to know, thank you. If anything, sounds like adding native CIF support should come at the Torchdrug layer rather than at the model layer.