deprotonate=False not working?

[l-Dr-MR-l]

Hi, I'm probably not understanding something correctly but I'm setting deprotonate to False and still get deprotonation happening:

        self.graphein_config = ProteinGraphConfig(granularity='atom',
                                                  deprotonate=False,
                                                  edge_construction_functions= [
                                                                                add_peptide_bonds,
                                                                                add_atomic_edges,
                                                                                #add_hydrogen_bond_interactions,
                                                                                #add_hydrophobic_interactions,
                                                                                add_bond_order,
                                                                                #partial(add_distance_threshold, long_interaction_threshold=5, threshold=10.)
                                                                                #partial(add_k_nn_edges, k=3, long_interaction_threshold=0)
                                                                                ],
                                                  node_metadata_functions= [amino_acid_one_hot, expasy_protein_scale])
        print(self.graphein_config.dict())

and run using:
graph_list.append(construct_graph(config=self.graphein_config, path=file_path))

output:

2024-03-13 13:12:00,703 - INFO - Initialising data loader.
{'granularity': 'atom', 'keep_hets': [], 'insertions': True, 'alt_locs': 'max_occupancy', 'pdb_dir': None, 'verbose': False, 'exclude_waters': True, 'deprotonate': False, 'protein_df_processing_functions': None, 'edge_construction_functions': [<function add_peptide_bonds at 0x7f4ace2c7ec0>, <function add_atomic_edges at 0x7f4ace2d1120>, <function add_bond_order at 0x7f4ace2d1260>], 'node_metadata_functions': [<function amino_acid_one_hot at 0x7f4ace2d2f20>, <function expasy_protein_scale at 0x7f4ace2d2b60>], 'edge_metadata_functions': None, 'graph_metadata_functions': None, 'get_contacts_config': None, 'dssp_config': None}
2024-03-13 13:12:00,703 - INFO - Building graphs with batch_size 5
                    DEBUG    Deprotonating protein. This removes H atoms from the       graphs.py:188
                             pdb_df dataframe

if I'm reading this correctly it is applied out of this graphs.py, where I see deprotonate's default value is true so I'm not assigning it properly somehow?

def process_dataframe(
    protein_df: pd.DataFrame,
    atom_df_processing_funcs: Optional[List[Callable]] = None,
    hetatom_df_processing_funcs: Optional[List[Callable]] = None,
    granularity: str = "centroids",
    chain_selection: str = "all",
    insertions: bool = False,
    alt_locs: bool = False,
    deprotonate: bool = True,

I've also tried simply copying and running the code in https://graphein.ai/notebooks/atom_graph_tutorial.html to see if deprotonation=False works there.
But I get a TypeError: construct_graph() got an unexpected keyword argument 'pdb_code'
Is the documentation site out of date?

[a-r-j]

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

[a-r-j]

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.

[l-Dr-MR-l]

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

[a-r-j]

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

[l-Dr-MR-l]

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