File size: 2,082 Bytes
504d922 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 | 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())
|