| """Add derived ``gc_7890b_fid`` fingerprints from the spectral library to ``assets/reactions/substances.json`` -- ADD ONLY. |
| |
| Since 2026-10-14 this script never changes an existing value: it only adds a ``gc_7890b_fid`` block to species that do |
| not have one yet and whose id has a fingerprint in ``spectral_library/gc_retention.json`` (non-polar column by |
| default). Species that already carry a fingerprint (derived or assumed), and every other field, are left untouched; |
| the file is rewritten only when something was added, with the serializer of scripts/substances/apply_storage_hazard.py |
| (``json.dumps(indent=1)`` + newline, the file's format since 2026-10-22; it was indent=2 without a newline before) so |
| unchanged content stays byte-identical. ``--only`` limits the additions to the given ids (2026-10-23: the C8-C20 n-alkane |
| standard and its hexane solvent). The Matterix reaction tests read this file. |
| |
| ``--refresh`` (with ``--only``) also replaces a fingerprint that this script wrote earlier (evidence ``derived`` and source |
| ``spectral_library/gc_retention.json ...``), e.g. after a library rule changed (2026-10-23 D-2: the C8-C20 alkane dvapH series); |
| assumed or hand-made fingerprints are never replaced. |
| |
| Usage: python apply_to_substances.py [--dry-run] [--column nonpolar|polar] [--only id ...] [--refresh] |
| """ |
| from __future__ import annotations |
|
|
| import argparse |
| import json |
| from pathlib import Path |
|
|
| ROOT = Path(__file__).resolve().parents[2] |
| SUBS = ROOT / "assets" / "reactions" / "substances.json" |
| LIB = ROOT / "assets" / "reactions" / "spectral_library" / "gc_retention.json" |
|
|
|
|
| def fingerprint_block(fp: dict, fid_visible: bool, column: str) -> dict: |
| return { |
| "k_ref": fp["k_ref"], "delta_h_J_mol": fp["delta_h_J_mol"], |
| "response_C_kg": fp["response_C_kg"] if fid_visible else 0.0, |
| "reference_temperature_K": fp["reference_temperature_K"], |
| "evidence": "derived", "source": f"spectral_library/gc_retention.json ({column}): NIST retention index {fp['retention_index_used']} " |
| f"({fp['retention_index_class']}) + enthalpy of vaporization + ECN response; column calibration is an assumption", |
| } |
|
|
|
|
| def main(): |
| ap = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter) |
| ap.add_argument("--dry-run", action="store_true") |
| ap.add_argument("--column", default="nonpolar", choices=["nonpolar", "polar"]) |
| ap.add_argument("--only", nargs="*", help="add fingerprints only for these substance ids") |
| ap.add_argument("--refresh", action="store_true", help="with --only: replace fingerprints this script derived earlier") |
| args = ap.parse_args() |
| raw = SUBS.read_text(encoding="utf-8") |
| subs = json.loads(raw) |
| lib = json.load(open(LIB, encoding="utf-8"))["compounds"] |
| if args.refresh and not args.only: |
| ap.error("--refresh needs --only") |
| added, kept, refreshed = [], [], [] |
| for sid, rec in subs["substances"].items(): |
| fp = lib.get(sid, {}).get("model_fingerprint", {}).get(args.column) |
| if not fp or (args.only and sid not in args.only): |
| continue |
| if "gc_7890b_fid" in rec: |
| old = rec["gc_7890b_fid"] |
| ours = old.get("evidence") == "derived" and str(old.get("source", "")).startswith("spectral_library/gc_retention.json") |
| new = fingerprint_block(fp, rec.get("fid_visible", True), args.column) |
| if args.refresh and ours and new != old: |
| rec["gc_7890b_fid"] = new |
| refreshed.append(sid) |
| else: |
| kept.append(sid) |
| continue |
| rec["gc_7890b_fid"] = fingerprint_block(fp, rec.get("fid_visible", True), args.column) |
| added.append(sid) |
| for sid in added + refreshed: |
| f = subs["substances"][sid]["gc_7890b_fid"] |
| print(f"{'add' if sid in added else 'refresh'} {sid:18} k_ref {f['k_ref']} dH {f['delta_h_J_mol']} resp {f['response_C_kg']}") |
| print(f"{len(added)} added, {len(refreshed)} refreshed, {len(kept)} species already had a fingerprint (unchanged)") |
| if (added or refreshed) and not args.dry_run: |
| text = json.dumps(subs, ensure_ascii=False, indent=1) + "\n" |
| |
| before = json.loads(raw) |
| after = json.loads(text) |
| for sid, rec in before["substances"].items(): |
| assert {k: v for k, v in after["substances"][sid].items() if not (sid in added + refreshed and k == "gc_7890b_fid")} == \ |
| {k: v for k, v in rec.items() if not (sid in refreshed and k == "gc_7890b_fid")}, sid |
| assert {k: v for k, v in after.items() if k != "substances"} == {k: v for k, v in before.items() if k != "substances"} |
| SUBS.write_text(text, encoding="utf-8") |
| print(f"updated {len(added) + len(refreshed)} substances in {SUBS.relative_to(ROOT)}") |
|
|
|
|
| if __name__ == "__main__": |
| main() |
|
|
