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a-r-j / graphein

Protein Graph Library
https://graphein.ai/
MIT License
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Error in tdc_developability.ipynb notebook #400

Open velocirraptor23 opened 3 months ago

velocirraptor23 commented 3 months ago

I was trying to follow this notebook but in the part for training (Creating Datasets) I got this error:

File /cluster/ddu/cmmartinez001/graphein/notebooks/../graphein/ml/conversion.py:274, in GraphFormatConvertor.convert_nx_to_pyg(self, G) 264 """ 265 Converts NetworkX graph to pytorch_geometric.data.Data object. Requires PyTorch Geometric (https://pytorch-geometric.readthedocs.io/en/latest/) to be installed. 266 (...) 270 :rtype: pytorch_geometric.data.Data 271 """ 273 # Initialise dict used to construct Data object & Assign node ids as a feature --> 274 data = {"node_id": list(G.nodes())} 275 G = nx.convert_node_labels_to_integers(G) 277 # Construct Edge Index

AttributeError: 'NoneType' object has no attribute 'nodes'

I think I instaled everything but I am not sure why i got this.

BW,

Cesar

a-r-j commented 2 weeks ago

Could you narrow down which PDB id is failing? I suspect this is related to #409 through deprecation of a PDB accession.