code/scripts/generate_synthetic_thoughts.py

#!/usr/bin/env python
"""
Generate synthetic "Ground Truth Thought" for CoT training.

Two modes:
- **System 2 (default when formula/precursor_mz available):** Deductive trace:
  precursor analysis (formula, DoU, Nitrogen rule) → fragment logic (peak → substructure)
  → neutral loss analysis → core reconstruction → assembly. Uses RDKit for
  substructure matching and formula.
- **Fallback:** Short peak-based hints (m/z 91 → tropylium, etc.) when data or RDKit missing.
"""
from __future__ import annotations

import argparse
import json
import sys
from pathlib import Path

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

# Fallback fragment hints (no RDKit required)
FRAGMENT_HINTS = [
    (91, "m/z 91 (tropylium) suggests benzyl or aromatic ring"),
    (77, "m/z 77 suggests benzene ring"),
    (65, "m/z 65 suggests cyclopentadienyl or aromatic fragment"),
    (43, "m/z 43 often indicates acetyl or C3H7+"),
    (57, "m/z 57 suggests butyl or C4H9+"),
    (41, "m/z 41 suggests allyl or C3H5+"),
    (130, "m/z 130 is diagnostic for indole / 3-alkyl-indole cation"),
    (18, "loss of 18 Da suggests water (e.g. -OH)"),
    (17, "loss of 17 Da suggests ammonia or -OH"),
    (28, "loss of 28 Da suggests CO or C2H4"),
    (44, "loss of 44 Da suggests CO2"),
    (15, "loss of 15 Da suggests methyl"),
]


def get_top_peaks(peaks: list, top_k: int = 10) -> list[tuple[float, float]]:
    """Return top-k peaks by intensity."""
    sorted_peaks = sorted(peaks, key=lambda x: float(x[1]), reverse=True)
    return [(float(p[0]), float(p[1])) for p in sorted_peaks[:top_k]]


def generate_thought_fallback(peaks: list, precursor_mz: float | None = None) -> str:
    """Simple peak-based hints when System 2 is not used."""
    top = get_top_peaks(peaks, top_k=8)
    parts = []
    seen = set()
    for mz, _ in top:
        mz_round = round(mz)
        for frag_mz, hint in FRAGMENT_HINTS:
            if abs(mz_round - frag_mz) <= 2 and frag_mz not in seen:
                parts.append(hint)
                seen.add(frag_mz)
    if precursor_mz is not None and precursor_mz > 0:
        parts.insert(0, f"Precursor m/z {precursor_mz:.1f}.")
    if not parts:
        parts = [f"Key peaks at m/z {', '.join(f'{m:.0f}' for m, _ in top[:5])}."]
    return " ".join(parts)


def _load_cot_system2():
    """Load cot_system2 module without importing full spec_rag (avoids numpy etc)."""
    import importlib.util
    p = ROOT / "spec_rag" / "cot_system2.py"
    spec = importlib.util.spec_from_file_location("cot_system2", p)
    mod = importlib.util.module_from_spec(spec)
    spec.loader.exec_module(mod)
    return mod


def generate_thought_for_record(
    obj: dict, use_system2: bool = True, _system2_mod=None, output_format: str = "text"
) -> str:
    """
    Generate thought for one JSONL record. Prefer System 2 when formula or
    precursor_mz present and use_system2 is True.
    """
    peaks = obj.get("peaks", [])
    smiles = obj.get("smiles", "")
    formula = obj.get("formula") or None
    precursor_mz = obj.get("precursor_mz")
    if precursor_mz is not None:
        try:
            precursor_mz = float(precursor_mz)
        except (TypeError, ValueError):
            precursor_mz = None

    if use_system2 and (formula or precursor_mz or smiles):
        try:
            if _system2_mod is None:
                _system2_mod = _load_cot_system2()
            thought = _system2_mod.build_system2_thought(
                smiles=smiles,
                peaks=peaks if peaks else [[0, 0]],
                precursor_mz=precursor_mz,
                formula=formula,
                max_peaks=10,
                output_format=output_format,
            )
            if thought and len(thought.strip()) > 50:
                return thought.strip()
            print(f"Short thought ({len(thought)}): {thought}")
        except Exception as e:
            print(f"System 2 failed: {e}")
            pass
    if peaks:
        return generate_thought_fallback(peaks, precursor_mz)
    return "Analyzing spectrum for structural features."


def parse_args() -> argparse.Namespace:
    p = argparse.ArgumentParser(
        description="Generate synthetic thoughts for CoT (System 2 or fallback)."
    )
    p.add_argument("--input-jsonl", required=True, help="JSONL with peaks, smiles, optional formula, precursor_mz")
    p.add_argument("--output-jsonl", required=True, help="Same + 'thought' field")
    p.add_argument("--no-system2", action="store_true", help="Use only simple peak hints, no RDKit/System 2")
    p.add_argument("--format", choices=("text", "json"), default="text", help="System 2 thought format: sectioned text or JSON")
    p.add_argument("--precursor-col", default="precursor_mz", help="Column name for precursor m/z if any")
    return p.parse_args()


def main() -> None:
    args = parse_args()
    use_system2 = not args.no_system2
    try:
        system2_mod = _load_cot_system2() if use_system2 else None
    except Exception as e:
        print(f"Failed to load System 2 module: {e}")
        system2_mod = None
        use_system2 = False
    out_lines = []
    with open(args.input_jsonl) as f:
        for line in f:
            line = line.strip()
            if not line:
                continue
            obj = json.loads(line)
            thought = generate_thought_for_record(
                obj,
                use_system2=use_system2,
                _system2_mod=system2_mod,
                output_format=getattr(args, "format", "text"),
            )
            obj["thought"] = thought
            out_lines.append(json.dumps(obj) + "\n")
    Path(args.output_jsonl).parent.mkdir(parents=True, exist_ok=True)
    with open(args.output_jsonl, "w") as f:
        f.writelines(out_lines)
    print(f"Wrote {len(out_lines)} records to {args.output_jsonl}")


if __name__ == "__main__":
    main()