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interactiongraphnet's Introduction

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interactiongraphnet's Issues

Need Your Kind Guidance

Hi @zjujdj ,
I am currently involved in the curation of the CAMP dataset. However, I have encountered some challenges along the way. I kindly request your guidance and assistance regarding these issues. Your expertise and support would be greatly appreciated.

Thank you for your attention and prompt response. I look forward to hearing from you soon.

运行出错

我想问一下,为什么运行完一个epoch之后会出现这样的错误?
epoch:0 train_rmse:7.3017 valid_rmse:6.7257 time:48.230 s
Traceback (most recent call last):
File "D:/DT/InteractionGraphNet-master/codes/ign_train.py", line 184, in
valid_true, valid_pred, _ = run_a_eval_epoch(DTIModel, valid_dataloader, device)
File "D:/DT/InteractionGraphNet-master/codes/ign_train.py", line 54, in run_a_eval_epoch
outputs = model(bg, bg3)
File "F:\anaconda1\envs\torchcpu\lib\site-packages\torch\nn\modules\module.py", line 541, in call
result = self.forward(*input, **kwargs)
File "D:\DT\InteractionGraphNet-master\codes\model.py", line 409, in forward
atom_feats = bg.ndata.pop('h')
File "F:\anaconda1\envs\torchcpu\lib_collections_abc.py", line 795, in pop
value = self[key]
File "F:\anaconda1\envs\torchcpu\lib\site-packages\dgl\view.py", line 60, in getitem
return self._graph.get_n_repr(self._nodes)[key]
KeyError: 'h'

about virtual screening model

Dear zjujdj,

Thanks for providing such an interesting script for the scoring,

Could you write a simple tutorial for how to train VS models, it looks like the methods in the example are not suitable for VS model training

Hope to receive your reply!

Process of PDBbind crystal pose

When I tried to reproduce the result of the paper, I met some problems.
The graph of PDBbind crystal structure is generated by extracting 10A pocket with chimera as docked pose or just using the pdbcode_pocket.pdb file provided by PDBbind.
Besides, RDKIT is failed to read some sdf ligand file, how to solve it?
Thank you a lot!

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