Comments (5)
diamondspark
commented on May 24, 2024
@a-r-j Any pointers to this?
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a-r-j
commented on May 24, 2024
Hi @diamondspark, apologies, will check this out by the end of the week. Looks like a bug to me. @kexinhuang12345 do you have bandwidth?
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kexinhuang12345
commented on May 24, 2024
Sure, I will take a look
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kexinhuang12345
commented on May 24, 2024
Hi, it seems like you are using pytorch geometric converter from networkx. Please use the graphein converter to get the PyG object:
from graphein.ml.conversion import GraphFormatConvertor
format_convertor = GraphFormatConvertor('nx', 'pyg',
verbose = 'gnn',
columns = None)
data = format_convertor(g)
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a-r-j
commented on May 24, 2024
Thanks, @kexinhuang12345 ! @diamondspark , can you kindly confirm if you're all good on this front so I can close the issue.
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Related Issues (20)
- PDB structure culstering HOT 4
- FoldCompDataset calls graphein.protein.tensor.Protein with incorrect __init__ arguments HOT 2
- Error during `Getting requirements to build wheel` HOT 3
- Running colab exmaple got an error ModuleNotFoundError: No module named 'torch_geometric' HOT 2
- `graphein.protein.edges.distance.add_distance_threshold` should allow computing distance by "any to any" atomistic even with "residue" granularity set
- can't read pdb ends with .pdb1.gz HOT 3
- [Docs] API Reference for `graphein.ml` is broken
- `ProteinGraphDataset` fails if a single graph construction fails.
- dssp version argument HOT 2
- add insertion code to node_id when insertoins are set to True HOT 2
- Sidechain torsion angle computation fails on examples containing Pyrolysin
- error in the tutorial HOT 1
- docker compose fails to build due to jupyter nbextension HOT 3
- keep_het parameter not working HOT 2
- deprotonate=False not working? HOT 5
- `pip install` fails on fresh `python==3.11` and `python==3.10` conda environment HOT 1
- Error occurred while Constructing edges when reading PDB file. HOT 7
- Error occurred while constructing edges from pdb files HOT 1
- TypeError: construct_graph() got an unexpected keyword argument 'pdb_path' HOT 2
- convert_nx_to_pyg doubles edge_index but not kind
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