Error occurred while Constructing edges when reading PDB file.

[1412140736]

The error message is as follows:
Constructing edges... ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 0% -:--:--
Traceback (most recent call last):
File "/media/aita130/anaconda_space/envs/ZeroBind/lib/python3.9/site-packages/pandas/core/indexes/base.py", line 3803, in get_loc
return self._engine.get_loc(casted_key)
File "pandas/_libs/index.pyx", line 138, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/index.pyx", line 165, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/hashtable_class_helper.pxi", line 2263, in pandas._libs.hashtable.Int64HashTable.get_item
File "pandas/_libs/hashtable_class_helper.pxi", line 2273, in pandas._libs.hashtable.Int64HashTable.get_item
KeyError: 230

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/home/aita130/lm/zerobind/test.py", line 27, in
g = construct_graph(config=config, path=str(protein_path)+str(pdb_ID)+".pdb")
File "/media/aita130/anaconda_space/envs/ZeroBind/lib/python3.9/site-packages/graphein/protein/graphs.py", line 855, in construct_graph
g = compute_edges(
File "/media/aita130/anaconda_space/envs/ZeroBind/lib/python3.9/site-packages/graphein/protein/graphs.py", line 682, in compute_edges
func(G)
File "/media/aita130/anaconda_space/envs/ZeroBind/lib/python3.9/site-packages/graphein/protein/edges/distance.py", line 968, in add_distance_threshold
n2 = G.graph["pdb_df"].loc[a2, "node_id"]
File "/media/aita130/anaconda_space/envs/ZeroBind/lib/python3.9/site-packages/pandas/core/indexing.py", line 1066, in getitem
return self.obj._get_value(*key, takeable=self._takeable)
File "/media/aita130/anaconda_space/envs/ZeroBind/lib/python3.9/site-packages/pandas/core/frame.py", line 3921, in _get_value
row = self.index.get_loc(index)
File "/media/aita130/anaconda_space/envs/ZeroBind/lib/python3.9/site-packages/pandas/core/indexes/base.py", line 3805, in get_loc
raise KeyError(key) from err
KeyError: 230

[a-r-j]

Hi @1412140736 can you share a snippet and the pdb id to reproduce this?

[1412140736]

yes,this is the snippet :
(Here are the IDs of some problematic PDB files that I downloaded from RCSB:
P55211 4RHW
P29597 3NZ0
Q6V1X1 6EOO
)
from graphein.protein.config import ProteinGraphConfig
from graphein.protein.graphs import construct_graph
from functools import partial
from graphein.protein.edges.distance import add_distance_threshold,add_peptide_bonds
import esm
import networkx as nx
import os
import torch
import pandas
import warnings
import pickle
from torch_geometric.data import Data
from tqdm import tqdm

pandas.set_option('mode.chained_assignment', None)
protein_model, alphabet = esm.pretrained.esm2_t33_650M_UR50D()
batch_converter = alphabet.get_batch_converter()
protein_model.eval()
new_edge_funcs = {"edge_construction_functions": [partial(add_distance_threshold, long_interaction_threshold=0, threshold=8)]}
config = ProteinGraphConfig(**new_edge_funcs)

pdb_ID="P55211"
protein_path = os.getcwd() + "/tmp/"
g = construct_graph(config=config, path=str(protein_path)+str(pdb_ID)+".pdb")

[a-r-j]

Thanks! I could reproduce it.

It looks like removing altlocs throws off the indexing order in the dataframe.

Quick fix first: replace .loc with .iloc in add_distance_threshold:

def add_distance_threshold(
    G: nx.Graph, long_interaction_threshold: int, threshold: float = 5.0
):
    """
    Adds edges to any nodes within a given distance of each other.
    Long interaction threshold is used to specify minimum separation in sequence
    to add an edge between networkx nodes within the distance threshold

    :param G: Protein Structure graph to add distance edges to
    :type G: nx.Graph
    :param long_interaction_threshold: minimum distance in sequence for two
        nodes to be connected
    :type long_interaction_threshold: int
    :param threshold: Distance in angstroms, below which two nodes are connected
    :type threshold: float
    :return: Graph with distance-based edges added
    """
    pdb_df = filter_dataframe(
        G.graph["pdb_df"], "node_id", list(G.nodes()), True
    )
    dist_mat = compute_distmat(pdb_df)
    interacting_nodes = get_interacting_atoms(threshold, distmat=dist_mat)
    interacting_nodes = list(zip(interacting_nodes[0], interacting_nodes[1]))

    log.info(f"Found: {len(interacting_nodes)} distance edges")
    count = 0
    for a1, a2 in interacting_nodes:
        n1 = G.graph["pdb_df"].iloc[a1]["node_id"]
        n2 = G.graph["pdb_df"].iloc[a2]["node_id"]
        n1_chain = G.graph["pdb_df"].iloc[a1]["chain_id"]
        n2_chain = G.graph["pdb_df"].iloc[a2]["chain_id"]
        n1_position = G.graph["pdb_df"].iloc[a1]["residue_number"]
        n2_position = G.graph["pdb_df"].iloc[a2]["residue_number"]

        condition_1 = n1_chain == n2_chain
        condition_2 = (
            abs(n1_position - n2_position) < long_interaction_threshold
        )

        if not (condition_1 and condition_2):
            count += 1
            add_edge(G, n1, n2, "distance_threshold")

    log.info(
        f"Added {count} distance edges. ({len(list(interacting_nodes)) - count}\
            removed by LIN)"
    )

Longer term fix: resetting the index after removing altlocs.

[1412140736]

Thank you for your prompt response. I have followed your advice to change .loc to .iloc in add_distance_threshold. However, a new error has occurred, and the error message is as follows (thanks again for your response):
File "/media/aita130/anaconda_space/envs/ZeroBind/lib/python3.9/site-packages/pandas/core/indexing.py", line 873, in _validate_tuple_indexer
self._validate_key(k, i)
File "/media/aita130/anaconda_space/envs/ZeroBind/lib/python3.9/site-packages/pandas/core/indexing.py", line 1483, in _validate_key
raise ValueError(f"Can only index by location with a [{self._valid_types}]")
ValueError: Can only index by location with a [integer, integer slice (START point is INCLUDED, END point is EXCLUDED), listlike of integers, boolean array]

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/home/aita130/lm/zerobind/test.py", line 98, in
g = construct_graph(config=config, path=str(protein_path)+str(pdb_ID)+".pdb")
File "/media/aita130/anaconda_space/envs/ZeroBind/lib/python3.9/site-packages/graphein/protein/graphs.py", line 855, in construct_graph
g = compute_edges(
File "/media/aita130/anaconda_space/envs/ZeroBind/lib/python3.9/site-packages/graphein/protein/graphs.py", line 682, in compute_edges
func(G)
File "/home/aita130/lm/zerobind/test.py", line 64, in modified_add_distance_threshold
n1 = G.graph["pdb_df"].iloc[a1, "node_id"]
File "/media/aita130/anaconda_space/envs/ZeroBind/lib/python3.9/site-packages/pandas/core/indexing.py", line 1067, in getitem
return self._getitem_tuple(key)
File "/media/aita130/anaconda_space/envs/ZeroBind/lib/python3.9/site-packages/pandas/core/indexing.py", line 1563, in _getitem_tuple
tup = self._validate_tuple_indexer(tup)
File "/media/aita130/anaconda_space/envs/ZeroBind/lib/python3.9/site-packages/pandas/core/indexing.py", line 875, in _validate_tuple_indexer
raise ValueError(
ValueError: Location based indexing can only have [integer, integer slice (START point is INCLUDED, END point is EXCLUDED), listlike of integers, boolean array] types

[a-r-j]

Apologies, syntax error on my part. I've updated the codeblock above.

[1412140736]

The issue has been resolved. Thank you!

[Runinthenight]

The issue has been resolved. Thank you!

Hello, I'm facing the same problem you encountered. Could you tell me how you overcame it?