chain_selection returns KeyError: 'residue_name'

[johnnytam100]

Hi Arian, I'm sorry for the frequent opening of threads!

I want to do chain selection of PDB 2VVI, which has chains A, B, C and D.

g = construct_graph(config=config, pdb_code='2VVI', chain_selection="A")

However, it returns a KeyError: 'residue_name':

DEBUG:graphein.protein.graphs:Deprotonating protein. This removes H atoms from the pdb_df dataframe
DEBUG:graphein.protein.graphs:Detected 217 total nodes
INFO:graphein.protein.edges.distance:Found 411 hbond interactions.
INFO:graphein.protein.edges.distance:Found 42 hbond interactions.
---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
[<ipython-input-22-68026463de79>](https://localhost:8080/#) in <module>()
----> 1 g = construct_graph(config=config, pdb_code='2VVI', chain_selection="A")

3 frames
[/usr/local/lib/python3.7/dist-packages/graphein/protein/edges/distance.py](https://localhost:8080/#) in <listcomp>(.0)
    154     """
    155     # Check for existence of at least two Cysteine residues
--> 156     residues = [d["residue_name"] for _, d in G.nodes(data=True)]
    157     if residues.count("CYS") < 2:
    158         log.debug(

KeyError: 'residue_name'

Any idea how to resolve this error?
Thanks!

[a-r-j]

Hi @johnnytam100, no worries!

Could you please share the config? It looks like the trouble is occurring when you’re assigning the disulphide bonds. The key error says there is a node that doesn’t have a residue_name In the graph. Potentially, we’re not filtering out some unwanted HETATMS/Ligands properly which implies a potential bug. Are you including heteroatoms intentionally?

If you can share the config I can take a closer look this afternoon.

Also, could you please share the version of Graphein you’re using? pip list Should do the trick.

I just tried the following in a colab notebook and it seems to work as expected so I may be wrong about hetatms/ligands/waters causing the problem.

from graphein.protein.graphs import construct_graph
from graphein.protein.edges.distance import add_disulfide_interactions, add_hydrogen_bond_interactions
from graphein.protein.config import ProteinGraphConfig

config = ProteinGraphConfig(
    edge_construction_functions=[add_disulfide_interactions, add_hydrogen_bond_interactions],
     keep_hets=True,
     insertions=True,
     exclude_waters = False,
     )

g = construct_graph(pdb_code="2vvi", chain_selection="A", config=config)

DEBUG:graphein.protein.graphs:Deprotonating protein. This removes H atoms from the pdb_df dataframe
DEBUG:graphein.protein.graphs:Detected 217 total nodes
INFO:graphein.protein.edges.distance:Found 12 disulfide interactions.
INFO:graphein.protein.edges.distance:Found 411 hbond interactions.
INFO:graphein.protein.edges.distance:Found 42 hbond interactions.

[johnnytam100]

My graphein version is graphein 1.2.0

And I have tested your code, which worked! Then I found something strange, if you swap the positions of add_disulfide_interactions and add_hydrogen_bond_interactions, like this

from graphein.protein.graphs import construct_graph
from graphein.protein.edges.distance import add_disulfide_interactions, add_hydrogen_bond_interactions
from graphein.protein.config import ProteinGraphConfig

config = ProteinGraphConfig(
    edge_construction_functions=[add_hydrogen_bond_interactions, add_disulfide_interactions],
     keep_hets=True,
     insertions=True,
     exclude_waters = False,
     )

g = construct_graph(pdb_code="2vvi", chain_selection="A", config=config)

DEBUG:graphein.protein.graphs:Deprotonating protein. This removes H atoms from the pdb_df dataframe
DEBUG:graphein.protein.graphs:Detected 217 total nodes
INFO:graphein.protein.edges.distance:Found 411 hbond interactions.
INFO:graphein.protein.edges.distance:Found 42 hbond interactions.
---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
[<ipython-input-60-1e0f5c8e3c7b>](https://localhost:8080/#) in <module>()
     10      )
     11 
---> 12 g = construct_graph(pdb_code="2vvi", chain_selection="A", config=config)

3 frames
[/usr/local/lib/python3.7/dist-packages/graphein/protein/edges/distance.py](https://localhost:8080/#) in <listcomp>(.0)
    154     """
    155     # Check for existence of at least two Cysteine residues
--> 156     residues = [d["residue_name"] for _, d in G.nodes(data=True)]
    157     if residues.count("CYS") < 2:
    158         log.debug(

KeyError: 'residue_name'

My original config was

new_funcs = {"keep_hets": False,
             "edge_construction_functions": [add_peptide_bonds,
                                              add_hydrogen_bond_interactions,
                                              add_disulfide_interactions,
                                              add_ionic_interactions,
                                              add_aromatic_interactions,
                                              add_aromatic_sulphur_interactions,
                                              add_cation_pi_interactions],
            }

config = ProteinGraphConfig(**new_funcs)

# construct graph
g = construct_graph(config=config, pdb_code='2vvi', chain_selection="A")

Swapping only "add_hydrogen_bond_interactions" and "add_disulfide_interactions" didn't work.
Then I wonder what order of these arguments should work..

[a-r-j]

Huh, that is a bug. I’ll check it out

[a-r-j]

Ah, I see what’s going on. The hydrogen bonds are looking at the unfiltered dataframe and adding in new nodes from the other chains. These nodes don’t have any metadata attached because they weren’t added in the earlier steps where we add information to nodes and so we get the error.

This is definitely a bug and I’ll figure out a fix. What I would recommend you do for now is to not use the chain_selection=“A” Parameter but instead use chain_selection=“all”. You can then use graphein.protein.subgraphs.extract_subgraph_from_chains() to select the chains.

Tutorial notebook here

Good catch btw! Thanks for flagging this :)

[a-r-j]

Hey @johnnytam100 you should be able to proceed as normal now. v1.2.1 has fixes for this now and is on PyPI (pip install graphein==1.2.1). Would you mind giving it a try & letting me know if all's well so I can close the issues?

[johnnytam100]

Thank you @a-r-j ! It is fine now with pip install graphein==1.2.1! :)