portable_rdock_pipeline/libs/benchmark/ordering.py

from __future__ import annotations

import random
from typing import Dict, Iterable, List


def cluster_naive_order(
    ligand_ids: Iterable[str],
    cluster_map: Dict[str, int],
    seed: int,
) -> List[str]:
    """
    Static cluster baseline ordering:
    1) one representative per cluster (cluster round-robin),
    2) then remaining members cluster-by-cluster.
    """
    ids = [str(x) for x in ligand_ids]
    by_cluster: Dict[int, List[str]] = {}
    for lid in ids:
        by_cluster.setdefault(int(cluster_map.get(lid, -1)), []).append(lid)

    rng = random.Random(int(seed))
    cluster_ids = sorted(by_cluster.keys())
    rng.shuffle(cluster_ids)
    for cid in cluster_ids:
        rng.shuffle(by_cluster[cid])

    order: List[str] = []
    for cid in cluster_ids:
        if by_cluster[cid]:
            order.append(by_cluster[cid][0])

    for cid in cluster_ids:
        members = by_cluster[cid][1:]
        order.extend(members)

    seen = set()
    out: List[str] = []
    for lid in order:
        if lid in seen:
            continue
        seen.add(lid)
        out.append(lid)
    return out