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use chebifier graph instead of chebai graph #14

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Merged
sfluegel05 merged 2 commits into from
Jul 30, 2025
Merged

use chebifier graph instead of chebai graph #14

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4cc3e9e
use chebifier graph instead of chebai graph
sfluegel05 Jul 30, 2025
75204a5
reformat with black
sfluegel05 Jul 30, 2025
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11 changes: 2 additions & 9 deletions chebifier/prediction_models/chebi_lookup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@
import networkx as nx
from rdkit import Chem
import json
from chebifier.utils import load_chebi_graph


class ChEBILookupPredictor(BasePredictor):
Expand All @@ -23,15 +24,7 @@ def __init__(
or "ChEBI Lookup: If the SMILES is equivalent to a ChEBI entry, retrieve the classification of that entry."
)
self.chebi_version = chebi_version
self.chebi_graph = kwargs.get("chebi_graph", None)
if self.chebi_graph is None:
from chebai.preprocessing.datasets.chebi import ChEBIOver50

self.chebi_dataset = ChEBIOver50(chebi_version=self.chebi_version)
self.chebi_dataset._download_required_data()
self.chebi_graph = self.chebi_dataset._extract_class_hierarchy(
os.path.join(self.chebi_dataset.raw_dir, "chebi.obo")
)
self.chebi_graph = kwargs.get("chebi_graph", load_chebi_graph())
self.lookup_table = self.get_smiles_lookup()

def get_smiles_lookup(self):
Expand Down