File size: 8,104 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 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 | from __future__ import annotations
import argparse
import json
import sys
import tempfile
from pathlib import Path
from typing import Any, Dict, List
import yaml
ROOT_DIR = Path(__file__).resolve().parents[1]
if str(ROOT_DIR) not in sys.path:
sys.path.insert(0, str(ROOT_DIR))
from libs.benchmark.cleanup import execute_results_cleanup, plan_results_cleanup
from libs.benchmark.runtime import AUTO_MINUS_FOUR
from libs.utils.config import load_config
from pipeline.run_large_benchmark import run_large_benchmark
from pipeline.run_fixed_pocket_repair import run_fixed_pocket_repair
from pipeline.run_policy_repair_benchmark import run_policy_repair_benchmark
from pipeline.run_ppi_sanity_check import run_ppi_sanity_check
SUPPORTED_BENCHMARK_TYPES = {
"small_molecule",
"peptide_like",
"policy_repair",
"fixed_pocket_repair",
}
def _parse_bool(text: str) -> bool:
v = str(text).strip().lower()
if v in {"1", "true", "t", "yes", "y"}:
return True
if v in {"0", "false", "f", "no", "n"}:
return False
raise ValueError(f"Invalid boolean value: {text}")
def _build_large_config(args: argparse.Namespace) -> Dict[str, Any]:
cfg = load_config(args.config_template)
cfg.setdefault("run", {})
cfg.setdefault("target", {})
cfg.setdefault("reference", {})
cfg.setdefault("benchmark_dataset", {})
cfg.setdefault("backend", {})
cfg.setdefault("matrix", {})
if args.output_dir:
cfg["run"]["output_dir"] = args.output_dir
if args.pdb_id:
cfg["target"]["docking_reference_pdb"] = str(args.pdb_id)
cfg["reference"]["pdb_id"] = str(args.pdb_id)
if args.ligand_id:
cfg["reference"]["ligand_comp_id"] = str(args.ligand_id)
if args.reference_id:
cfg["reference"]["reference_id"] = str(args.reference_id)
if args.n_ligands is not None:
cfg["benchmark_dataset"]["target_size"] = int(args.n_ligands)
cfg["run"]["adaptive_budget"] = int(args.n_ligands)
cfg["run"]["baseline_budget"] = int(args.n_ligands)
cfg["run"]["max_batches"] = max(1, int(args.n_ligands) // max(1, int(cfg["run"].get("batch_size", 32))) + 10)
mode_map = {
"docking-only": ["docking_only"],
"full-feature": ["full_feature"],
"both": ["docking_only", "full_feature"],
}
cfg["matrix"]["modes"] = mode_map[args.mode]
strategies = {s.strip().lower() for s in args.strategies}
cfg["matrix"]["include_adaptive"] = "adaptive" in strategies
cfg["matrix"]["include_naive_random"] = "naive" in strategies
cfg["matrix"]["include_cluster_naive"] = "cluster-naive" in strategies
cfg["matrix"]["naive_random_seeds"] = [11 + i * 11 for i in range(max(0, int(args.naive_runs)))]
cfg["matrix"]["cluster_naive_seeds"] = [101 + i * 101 for i in range(max(0, int(args.cluster_runs)))]
if "docking_only" not in cfg["matrix"]["modes"]:
cfg["matrix"]["include_adaptive_top1_variant"] = False
cfg["backend"]["type"] = args.backend
cfg["backend"]["require_real_backend"] = bool(args.require_real_backend)
cfg["backend"]["parallel_jobs"] = args.threads
cfg["backend"]["pocket_mode"] = str(args.pocket_mode)
if args.pocket_center:
cfg["backend"]["pocket_center"] = str(args.pocket_center)
if args.pocket_box_size:
cfg["backend"]["pocket_box_size"] = str(args.pocket_box_size)
if args.pocket_radius is not None:
cfg["backend"]["pocket_radius"] = float(args.pocket_radius)
if args.pocket_reference_ligand_id:
cfg["backend"]["pocket_reference_ligand_id"] = str(args.pocket_reference_ligand_id)
if args.pocket_relaxation_margin is not None:
cfg["backend"]["pocket_relaxation_margin"] = float(args.pocket_relaxation_margin)
cfg["run"]["enable_adaptive_early_stop"] = bool(args.enable_early_stop)
cfg["run"]["allow_resume"] = bool(args.allow_resume)
return cfg
def _validate_runner_args(args: argparse.Namespace) -> None:
btype = str(args.benchmark_type).strip().lower()
if btype not in SUPPORTED_BENCHMARK_TYPES:
raise ValueError(f"Unsupported benchmark_type `{args.benchmark_type}`")
if btype == "peptide_like":
if args.backend != "rdock":
raise ValueError("peptide_like mode does not accept --backend overrides; use default architecture-level proxy path")
if args.mode != "full-feature":
raise ValueError("peptide_like mode does not use docking mode matrix; keep --mode full-feature")
if args.strategies != ["adaptive", "naive", "cluster-naive"]:
raise ValueError("peptide_like mode does not use small-molecule strategy matrix arguments")
def main() -> int:
parser = argparse.ArgumentParser(description="Unified production benchmark runner")
parser.add_argument("--benchmark-type", default="small_molecule", choices=sorted(SUPPORTED_BENCHMARK_TYPES))
parser.add_argument("--config-template", default="configs/large_benchmark.yaml")
parser.add_argument("--pdb-id", default="")
parser.add_argument("--ligand-id", default="")
parser.add_argument("--reference-id", default="")
parser.add_argument("--n-ligands", type=int, default=None)
parser.add_argument("--strategies", nargs="+", default=["adaptive", "naive", "cluster-naive"])
parser.add_argument("--naive-runs", type=int, default=5)
parser.add_argument("--cluster-runs", type=int, default=5)
parser.add_argument("--mode", choices=["docking-only", "full-feature", "both"], default="full-feature")
parser.add_argument("--backend", choices=["rdock"], default="rdock")
parser.add_argument(
"--pocket-mode",
choices=["user_fixed_pocket", "reference_complex_pocket", "reference_complex_pocket_relaxed"],
default="reference_complex_pocket",
)
parser.add_argument("--pocket-center", default="")
parser.add_argument("--pocket-box-size", default="")
parser.add_argument("--pocket-radius", type=float, default=None)
parser.add_argument("--pocket-reference-ligand-id", default="")
parser.add_argument("--pocket-relaxation-margin", type=float, default=0.0)
parser.add_argument("--require-real-backend", type=_parse_bool, default=True)
parser.add_argument("--threads", default=AUTO_MINUS_FOUR)
parser.add_argument("--enable-early-stop", type=_parse_bool, default=True)
parser.add_argument("--allow-resume", type=_parse_bool, default=True)
parser.add_argument("--output-dir", default="")
parser.add_argument("--ppi-config", default="configs/ppi_sanity_check.yaml")
parser.add_argument("--cleanup-legacy-results", type=_parse_bool, default=False)
parser.add_argument("--policy-repair-config", default="configs/policy_repair_benchmark.yaml")
args = parser.parse_args()
_validate_runner_args(args)
outputs: Dict[str, Any] = {}
if args.cleanup_legacy_results:
plan = plan_results_cleanup(ROOT_DIR / "results")
archive_dir = execute_results_cleanup(ROOT_DIR / "results", plan)
outputs["cleanup"] = {
"items": [str(x.path) for x in plan],
"archive_dir": str(archive_dir),
}
if args.benchmark_type == "small_molecule":
large_cfg = _build_large_config(args)
with tempfile.TemporaryDirectory() as tmp:
cfg_path = Path(tmp) / "run_benchmark.generated.yaml"
cfg_path.write_text(yaml.safe_dump(large_cfg, sort_keys=False), encoding="utf-8")
outputs["small_molecule"] = run_large_benchmark(cfg_path)
elif args.benchmark_type == "policy_repair":
outputs["policy_repair"] = run_policy_repair_benchmark(args.policy_repair_config)
elif args.benchmark_type == "fixed_pocket_repair":
outputs["fixed_pocket_repair"] = run_fixed_pocket_repair()
elif args.benchmark_type == "peptide_like":
outputs["ppi_sanity"] = run_ppi_sanity_check(args.ppi_config)
else:
raise NotImplementedError("Unreachable benchmark type state")
print(json.dumps(outputs, indent=2))
return 0
if __name__ == "__main__":
raise SystemExit(main())
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