Can not find a function ProteinGraph function anymore

[velocirraptor23]

I was trying to reproduce the notebooks to train the PSCDB data set but I can not find this function:
from graphein.construct_graphs import ProteinGraph

Any way you can help me with this?

BW,

Cesar

[a-r-j]

Could you point me to the line in question? I suspect it should be ProteinGraphConfig.

[velocirraptor23]

Thanks a lot for your response. seems there is a change in the code from the newer versions. And your suggestion worked. Now I am facing another issue:
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AttributeError Traceback (most recent call last)
Cell In[7], line 12
5 pg = ProteinGraphConfig(granularity='CA', insertions=False, keep_hets=[],
6 node_featuriser='meiler', get_contacts_path='/Users/arianjamasb/github/getcontacts',
7 pdb_dir='../../examples/pdbs/',
8 contacts_dir='../../examples/contacts/',
9 exclude_waters=True, covalent_bonds=False, include_ss=True)
11 # Build Graphs
---> 12 train_graphs = [pg.dgl_graph_from_pdb_code(pdb_code=x_train['Free PDB'].iloc[i],
13 chain_selection=list(x_train['Free Chains'].iloc[i])) for i in tqdm(range(len(x_train)))]
15 test_graphs = [pg.dgl_graph_from_pdb_code(pdb_code=x_test['Free PDB'].iloc[i],
16 chain_selection=list(x_test['Free Chains'].iloc[i])) for i in tqdm(range(len(x_test)))]

Cell In[7], line 12, in (.0)
5 pg = ProteinGraphConfig(granularity='CA', insertions=False, keep_hets=[],
6 node_featuriser='meiler', get_contacts_path='/Users/arianjamasb/github/getcontacts',
7 pdb_dir='../../examples/pdbs/',
8 contacts_dir='../../examples/contacts/',
9 exclude_waters=True, covalent_bonds=False, include_ss=True)
11 # Build Graphs
---> 12 train_graphs = [pg.dgl_graph_from_pdb_code(pdb_code=x_train['Free PDB'].iloc[i],
13 chain_selection=list(x_train['Free Chains'].iloc[i])) for i in tqdm(range(len(x_train)))]
15 test_graphs = [pg.dgl_graph_from_pdb_code(pdb_code=x_test['Free PDB'].iloc[i],
16 chain_selection=list(x_test['Free Chains'].iloc[i])) for i in tqdm(range(len(x_test)))]

AttributeError: 'ProteinGraphConfig' object has no attribute 'dgl_graph_from_pdb_code'

This function is not found anymore. dgl_graph_from_pdb_code.

Just wonderign if this outdated as well.

BW,

Cesar

[a-r-j]

Yes, I think it is.

I think the method you want is this one:

graphein/graphein/ml/conversion.py

Line 190 in 27463a5

def convert_nx_to_dgl(self, G: nx.Graph) -> dgl.DGLGraph:

[velocirraptor23]

Perfect. I am going to try this.

BW,

Cesar