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a-r-j avatar a-r-j commented on July 3, 2024

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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a-r-j avatar a-r-j commented on July 3, 2024

Re docs, yes they're a little out of date at this point.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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l-Dr-MR-l avatar l-Dr-MR-l commented on July 3, 2024

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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a-r-j avatar a-r-j commented on July 3, 2024

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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l-Dr-MR-l avatar l-Dr-MR-l commented on July 3, 2024

Cheers that worked, it is now corrently following the deprotonate argument.

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