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Update dependency versions #4

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9555b26
updated dependencies in pyproject.toml and poetry.lock
Sep 17, 2025
97e9a00
version bump
Sep 17, 2025
8b1c825
updated dependencies in pyproject.toml and poetry.lock
Sep 17, 2025
41260d6
Merge branch 'PDBE-7869' of https://github.com/PDBeurope/rellig into …
Sep 17, 2025
49db722
update pdbe api url and chebi file url
Oct 20, 2025
0cb36a0
update chebi flat file column names
Oct 20, 2025
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4 changes: 2 additions & 2 deletions pdberellig/conf/conf.ini
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
reactants_threshold=0.7
similarities_threshold=0.6
minimal_ligand_size=5
api_base_url=https://wwwdev.ebi.ac.uk/pdbe/aggregated-api
api_base_url=https://www.ebi.ac.uk/pdbe/aggregated-api

[cofactor]
template_path=cofactors/templates
Expand All @@ -11,4 +11,4 @@ details=cofactors/cofactors_details.json
ec=cofactors/cofactor_ec.csv

[reactant]
chebi_structure_file=https://ftp.ebi.ac.uk/pub/databases/chebi/Flat_file_tab_delimited/structures.csv.gz
chebi_structure_file=https://ftp.ebi.ac.uk/pub/databases/chebi/flat_files/structures.tsv.gz
18 changes: 10 additions & 8 deletions pdberellig/core/reactants.py
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Expand Up @@ -162,25 +162,27 @@ def parse_chebi(self, chebi_ids: list[str]) -> list[CompareObj]:

self.chebi = pd.read_csv(chebi_structure_file, dtype=str)
self.chebi = self.chebi.loc[
(self.chebi["COMPOUND_ID"].isin(chebi_ids))
& (self.chebi["TYPE"] == "mol")
& (self.chebi["DEFAULT_STRUCTURE"] == "Y"),
["COMPOUND_ID", "STRUCTURE"],
(self.chebi["compound_id"].isin(chebi_ids))
& (self.chebi["status_id"] == 1) # include only ChEBI curated entires
& (
self.chebi["default_structure"] == "TRUE"
), # include only with structure
["compound_id", "molfile"],
]
for _, row in self.chebi.iterrows():
try:
chebi_mol = Chem.MolFromMolBlock(row["STRUCTURE"])
chebi_mol = Chem.MolFromMolBlock(row["molfile"])
chebi_mol_no_h = Chem.RemoveHs(chebi_mol)
if len(chebi_mol_no_h.GetAtoms()) < self.args.minimal_ligand_size:
# chebi is too small.
self.log.debug(f"""Number of atoms in {row["COMPOUND_ID"]} is less
self.log.debug(f"""Number of atoms in {row["compound_id"]} is less
than {self.args.minimal_ligand_size},
hence skipping""")
else:
templates.append(CompareObj(row["COMPOUND_ID"], chebi_mol_no_h))
templates.append(CompareObj(row["compound_id"], chebi_mol_no_h))

except Exception:
self.log.warn(f"Couldn't parse {row['COMPOUND_ID']} using RDKit")
self.log.warn(f"Couldn't parse {row['compound_id']} using RDKit")

return templates

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26 changes: 13 additions & 13 deletions poetry.lock
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8 changes: 4 additions & 4 deletions pyproject.toml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
[tool.poetry]
name = "pdberellig"
version = "1.0.1"
version = "1.0.2"
description = "A toolkit for functional annotation of ligands in the PDB"
authors = ["Ibrahim Roshan Kunnakkattu <roshan@ebi.ac.uk>"]
readme = "README.md"
Expand All @@ -19,11 +19,11 @@ classifiers = [


[tool.poetry.dependencies]
python = "^3.10"
python = ">=3.10,<4"
click = "8.1.7"
pdbeccdutils = "^0.8.6"
pdbeccdutils = ">=1.0.0"
sparqlwrapper = "^2.0.0"
pandas = "^2.2.3"
pandas = ">=2.2.3"



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