Fix bug in PDB DataFrame (e.g. when using add_distance_threshold edges in construct_graph)

[kamurani]

fixes #418

Testing

uniprot_id = "P04629"

from functools import partial
from graphein.protein import construct_graph
from graphein.protein.config import ProteinGraphConfig
from graphein.protein.edges.distance import add_distance_threshold

threshold_distance = 6.0

new_edge_funcs = {"edge_construction_functions": [partial(add_distance_threshold, long_interaction_threshold=-1, threshold=threshold_distance)]}
config = ProteinGraphConfig(**new_edge_funcs)
g_dist_all = construct_graph(
    path = f"{uniprot_id}.pdb",
    config=config,
)

for edge in g_dist_all.edges(data=True):
    d = edge[-1]["distance"]
    assert d < threshold_distance

[kamurani]

@a-r-j

Added a 2nd graph construction test under protein.test_graphs.test_distance_edges (that actually checks the edges' distance values). Interestingly the test passes either way (i.e. without the rest_index fix) when you use the .pdb files that are already under test_data/, so I added the problematic structure that I was using when I first discovered the bug.

[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

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