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Code for our Nature Scientific Reports paper "A universal framework for accurate and efficient geometric deep learning of molecular systems"

Home Page: https://www.nature.com/articles/s41598-023-46382-8

Python 100.00%
computational-biology computational-chemistry docking geometric-deep-learning graph-neural-networks machine-learning protein-ligand-interactions rna-structure-prediction

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physics-aware-multiplex-gnn's Issues

Encountered an in-place operation error when using the PAMNet model

I have encountered an error while using the PAMNet model for RNA structure prediction. Specifically, the error occurred when executing the following line of code:

torch.arange(1, self.freq.numel() + 1, out=self.freq).mul_(PI)

The program threw the following error:
RuntimeError: a leaf Variable that requires grad is being used in an in-place operation.

I have consulted the relevant documentation but still cannot resolve this issue. Could you please advise on how to modify the code to avoid this error?

Not able to replicate the environment

I have been trying to replicate the environment, I create a new conda env and pip install -r requirements.txt but I'm constantly getting the error "torch_scatter-2.0.4+cu101-cp37-cp37m-linux_x86_64.whl is not a supported wheel on this platform." I have tried on three different linux machines I'm getting same error. Please let me know what can be done.

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