Comments (5)
Hi @l-Dr-MR-l thanks for finding this. It appears the argument was not wired up. I've made a PR; would you be able to test it out & see if it resolves your issue? #375
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Re docs, yes they're a little out of date at this point. I've been meaning to get around to updating them. Is the error with pdb_code
or pdb_path
? pdb_path
was renamed to just path
but pdb_code
shouldn't have been touched for some time.
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Hi @l-Dr-MR-l thanks for finding this. It appears the argument was not wired up. I've made a PR; would you be able to test it out & see if it resolves your issue? #375
Hi @a-r-j , I've run
pip install --update pip
pip install --update graphein[all]
and then ran my code again, unfortunately it seems to still deprotonate despite being set to False.
Did I need to update it in a different way?
self.graphein_config = ProteinGraphConfig(granularity='atom',
deprotonate=False,
edge_construction_functions= [
add_peptide_bonds,
add_atomic_edges, # Covalent bonds
add_ring_status, # Needs other edges to add to. Adds ring structures.
add_bond_order, # Needs other edges to add to. Adds single/double bond.
add_disulfide_interactions,
],
node_metadata_functions= [amino_acid_one_hot,
expasy_protein_scale,
hydrogen_bond_acceptor,
hydrogen_bond_donor
])
graph_list.append(construct_graph(config=self.graphein_config, path=file_path))
terminal output:
DEBUG Deprotonating protein. This removes H atoms from the graphs.py:188
pdb_df dataframe
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Hi, yes. I've not pushed a new version to PyPI yet (will be doing so today) as there were a few other PRs I was hoping to squeeze in. You can try the change if you pip install from the github repository though pip install git+https://github.com/a-r-j/graphein
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Cheers that worked, it is now corrently following the deprotonate argument.
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Related Issues (20)
- 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
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- 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
- `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
- Can not find a function ProteinGraph function anymore HOT 3
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