pipeline/cluster_ligands.py

from __future__ import annotations

import argparse
import json
from pathlib import Path
import sys

ROOT_DIR = Path(__file__).resolve().parents[1]
if str(ROOT_DIR) not in sys.path:
    sys.path.insert(0, str(ROOT_DIR))

import numpy as np
import pandas as pd

from libs.adaptive.clustering import cluster_ligands_butina
from libs.adaptive.hyperclustering import hypercluster_representatives
from libs.encoders.ligand_encoder import LigandEncoder
from libs.utils.config import load_config
from libs.utils.io_smiles import read_smiles_table


def main() -> int:
    parser = argparse.ArgumentParser(description="Cluster ligands and derive hyperclusters")
    parser.add_argument("--config", default="configs/default.yaml")
    parser.add_argument("--output", default="results/clustering.csv")
    args = parser.parse_args()

    cfg = load_config(args.config)
    root = Path(__file__).resolve().parents[1]
    ligands = read_smiles_table(root / cfg["data"]["ligand_table"])
    enc = LigandEncoder().encode_table(ligands)

    ligand_ids = [e.ligand_id for e in enc]
    fps = [e.fingerprint for e in enc]
    vectors = np.vstack([e.vector for e in enc])
    id_to_idx = {lid: i for i, lid in enumerate(ligand_ids)}

    cluster_map = cluster_ligands_butina(ligand_ids, fps, cutoff=float(cfg["clustering"]["butina_cutoff"]))
    reps = {}
    for cid in sorted(set(cluster_map.values())):
        members = [lid for lid in ligand_ids if cluster_map[lid] == cid]
        reps[cid] = np.mean(np.vstack([vectors[id_to_idx[lid]] for lid in members]), axis=0)
    hyper = hypercluster_representatives(reps, int(cfg["clustering"]["n_hyperclusters"]))

    rows = [{"ligand_id": lid, "cluster_id": cluster_map[lid], "hypercluster_id": hyper.get(cluster_map[lid], -1)} for lid in ligand_ids]
    out = root / args.output
    out.parent.mkdir(parents=True, exist_ok=True)
    pd.DataFrame(rows).to_csv(out, index=False)
    print(json.dumps({"output": str(out), "n_clusters": len(set(cluster_map.values()))}, indent=2))
    return 0


if __name__ == "__main__":
    raise SystemExit(main())