| """Select the compounds that extend the shared spectral library (2026-10-14 expansion, 95 -> ~200). |
| |
| Phases (all idempotent; downloads are cached): |
| rank scan every template library (same discovery as ``build_crosswalk.py``) for CAS numbers and rank the CAS that |
| are not yet in ``compounds_list.py`` by the number of distinct instruments (asset_type_id) whose libraries |
| contain them (shared spectral_library files excluded); |
| probe for every candidate with >= 2 instruments plus every molecular substances.json species: PubChem properties |
| (identity, formula, SMILES) and the NIST WebBook Mask=2000 page (GC retention tables + the list of other |
| data NIST holds: IR, mass spectrum, UV/Vis, phase change). These are exactly the requests |
| ``fetch_sources.py`` makes for ``pubchem_props.json`` / ``gc.html``, cached under |
| ``outputs/spectral_library_expansion/probe_raw/<cas>/`` and later copied into ``references/spectral_raw/<id>/``; |
| select classify (molecular vs salt / hydrate / metal / element / network solid), apply the selection rules and write |
| ``outputs/spectral_library_expansion/selection.json``. |
| |
| Selection rules (in this order; new ids and Chinese names come from ``EXPANSION_META`` below): |
| 1. every molecular (non-salt, non-mineral, non-metal) species of substances.json that is not yet in the table; |
| 2. every curated common lab solvent / reagent (``COMMON_LAB``) found in >= 2 instruments' libraries; |
| 3. remaining molecular candidates ranked by (instruments desc, NIST data types desc, libraries desc, records desc) |
| until the table holds ``--target`` compounds. |
| Rules 2-3 require NIST WebBook data of at least one spectral kind (GC retention index, IR, EI-MS or UV/Vis). |
| |
| Usage: python -I select_expansion.py [--phase rank|probe|select|all] [--delay 1.0] [--target 200] |
| """ |
| from __future__ import annotations |
|
|
| import argparse |
| import json |
| import re |
| import shutil |
| import sys |
| import time |
| from collections import Counter, defaultdict |
| from pathlib import Path |
|
|
| sys.path.insert(0, str(Path(__file__).resolve().parent)) |
| import build_crosswalk as bc |
| from compounds_list import COMPOUNDS |
|
|
| ROOT = Path(__file__).resolve().parents[2] |
| OUTDIR = ROOT / "outputs" / "spectral_library_expansion" |
| PROBE = OUTDIR / "probe_raw" |
| RANK_FILE = OUTDIR / "candidates_ranked.json" |
| SELECTION = OUTDIR / "selection.json" |
| RAW = ROOT / "references" / "spectral_raw" |
|
|
| |
| NON_MOLECULAR_SUBSTANCES = { |
| "calcium_carbonate", "calcium_oxide", "sodium_hydroxide", "sodium_chloride", "sodium_bicarbonate", "sodium_carbonate", |
| "silver_nitrate", "silver_chloride", "sodium_nitrate", "sodium_acetate", "manganese_dioxide", "copper_sulfate_pentahydrate", |
| "copper_sulfate_trihydrate", "copper_sulfate_monohydrate", "copper_sulfate", "copper_oxide", "copper", "basic_copper_carbonate", |
| "zinc_carbonate", "zinc_oxide", "nickel_oxide", "nickel", "iron_oxide_hematite", "iron_oxide_magnetite", "iron", |
| "magnesium_hydroxide", "magnesium_oxide", "magnesium_carbonate", "calcium_oxalate_monohydrate", "calcium_oxalate", |
| "calcium_sulfate_dihydrate", "calcium_sulfate_hemihydrate", "potassium_chlorate", "potassium_chloride", "palladium", |
| } |
| |
| PHASE_VARIANTS = {"water_vapor", "ethanol_vapor", "methanol_vapor", "acetone_vapor", "ethyl_acetate_vapor"} |
| |
| SUBSTANCE_CAS = {"sulfuric_acid": "7664-93-9", "hydrochloric_acid": "7647-01-0", "oxygen": "7782-44-7", "hydrogen": "1333-74-0", |
| "carbon_monoxide": "630-08-0", "maleic_acid": "110-16-7", "succinic_acid": "110-15-6"} |
| NETWORK_SOLIDS = {"7631-86-9", "1344-28-1", "13463-67-7", "1317-33-5", "1306-06-5"} |
|
|
| |
| COMMON_LAB = { |
| "121-44-8": "base (Et3N)", "110-71-4": "solvent (DME)", "108-87-2": "solvent", "109-86-4": "solvent", "109-89-7": "base", |
| "127-18-4": "solvent", "540-84-1": "solvent / octane standard", "57-55-6": "solvent / humectant", "79-01-6": "solvent", |
| "107-83-5": "solvent (isohexane)", "78-78-4": "solvent", "872-50-4": "solvent (NMP)", "75-52-5": "solvent", |
| "108-32-7": "solvent / electrolyte", "105-58-8": "solvent / electrolyte", "120-92-3": "solvent", "96-22-0": "solvent", |
| "287-92-3": "solvent", "98-82-8": "solvent", "108-67-8": "solvent", "108-86-1": "solvent / reagent", "110-80-5": "solvent", |
| "111-96-6": "solvent (diglyme)", "108-65-6": "solvent (PGMEA)", "110-63-4": "solvent / monomer", "96-48-0": "solvent (GBL)", |
| "107-18-6": "reagent", "108-05-4": "monomer", "98-00-0": "reagent", "141-97-9": "reagent", "149-73-5": "reagent", |
| "122-51-0": "reagent", "56-40-6": "buffer / reagent", "77-92-9": "buffer / reagent", "10043-35-3": "buffer / reagent", |
| "288-32-4": "buffer / reagent", "302-01-2": "reagent", "123-31-9": "reagent", "7697-37-2": "acid", "7664-39-3": "acid", |
| "7664-38-2": "acid", "57-13-6": "reagent", "57-50-1": "reagent", "50-00-0": "reagent", "144-62-7": "acid / standard", |
| "88-99-3": "acid", "77-86-1": "buffer (Tris)", "141-43-5": "base", "111-42-2": "base", "102-71-6": "base", |
| "107-15-3": "base / ligand", "109-73-9": "base", "60-24-2": "reducing agent", "106-51-4": "oxidant", |
| "109-52-4": "acid", "79-31-2": "acid", "74-82-8": "gas", "7446-09-5": "gas", "7783-06-4": "gas", |
| "106-97-8": "gas", "74-98-6": "gas", "74-84-0": "gas", "10024-97-2": "gas", "7727-37-9": "gas", "2551-62-4": "gas", |
| "60-00-4": "chelator (EDTA)", "108-89-4": "base / solvent", "109-06-8": "base / solvent", "108-99-6": "base / solvent", |
| "124-40-3": "base", "74-89-5": "base", "75-50-3": "base", |
| } |
|
|
| |
| EXPANSION_META: dict[str, tuple[str, str, str, str]] = { |
| |
| "7664-93-9": ("sulfuric_acid", "sulfuric acid", "硫酸", "inorganic_acid"), |
| "7647-01-0": ("hydrochloric_acid", "hydrogen chloride (hydrochloric acid solute)", "氯化氢（盐酸溶质）", "inorganic_acid"), |
| "7782-44-7": ("oxygen", "oxygen", "氧气", "gas"), |
| "1333-74-0": ("hydrogen", "hydrogen", "氢气", "gas"), |
| "630-08-0": ("carbon_monoxide", "carbon monoxide", "一氧化碳", "gas"), |
| "110-16-7": ("maleic_acid", "maleic acid", "马来酸（顺丁烯二酸）", "carboxylic_acid"), |
| "110-15-6": ("succinic_acid", "succinic acid", "琥珀酸（丁二酸）", "carboxylic_acid"), |
| |
| "121-44-8": ("triethylamine", "triethylamine", "三乙胺", "amine"), |
| "110-71-4": ("dimethoxyethane_1_2", "1,2-dimethoxyethane", "乙二醇二甲醚（DME）", "ether"), |
| "108-87-2": ("methylcyclohexane", "methylcyclohexane", "甲基环己烷", "alkane"), |
| "109-86-4": ("methoxyethanol_2", "2-methoxyethanol", "乙二醇单甲醚（2-甲氧基乙醇）", "glycol_ether"), |
| "109-89-7": ("diethylamine", "diethylamine", "二乙胺", "amine"), |
| "127-18-4": ("tetrachloroethylene", "tetrachloroethylene", "四氯乙烯", "halogenated"), |
| "540-84-1": ("isooctane", "2,2,4-trimethylpentane", "异辛烷（2,2,4-三甲基戊烷）", "alkane"), |
| "57-55-6": ("propylene_glycol", "1,2-propanediol", "1,2-丙二醇", "polyol"), |
| "79-01-6": ("trichloroethylene", "trichloroethylene", "三氯乙烯", "halogenated"), |
| "107-83-5": ("methylpentane_2", "2-methylpentane", "2-甲基戊烷", "alkane"), |
| "78-78-4": ("isopentane", "2-methylbutane", "异戊烷（2-甲基丁烷）", "alkane"), |
| "872-50-4": ("nmp", "N-methyl-2-pyrrolidone", "N-甲基吡咯烷酮", "amide"), |
| "75-52-5": ("nitromethane", "nitromethane", "硝基甲烷", "nitro"), |
| "108-32-7": ("propylene_carbonate", "propylene carbonate", "碳酸丙烯酯", "ester"), |
| "105-58-8": ("diethyl_carbonate", "diethyl carbonate", "碳酸二乙酯", "ester"), |
| "120-92-3": ("cyclopentanone", "cyclopentanone", "环戊酮", "ketone"), |
| "96-22-0": ("pentan_3_one", "3-pentanone", "3-戊酮（二乙基酮）", "ketone"), |
| "287-92-3": ("cyclopentane", "cyclopentane", "环戊烷", "alkane"), |
| "98-82-8": ("cumene", "isopropylbenzene", "异丙苯", "aromatic"), |
| "108-67-8": ("mesitylene", "1,3,5-trimethylbenzene", "均三甲苯", "aromatic"), |
| "108-86-1": ("bromobenzene", "bromobenzene", "溴苯", "halogenated"), |
| "110-80-5": ("ethoxyethanol_2", "2-ethoxyethanol", "乙二醇单乙醚（2-乙氧基乙醇）", "glycol_ether"), |
| "111-96-6": ("diglyme", "bis(2-methoxyethyl) ether", "二乙二醇二甲醚（二甘醇二甲醚）", "ether"), |
| "108-65-6": ("pgmea", "propylene glycol methyl ether acetate", "丙二醇甲醚醋酸酯（PGMEA）", "ester"), |
| "110-63-4": ("butanediol_1_4", "1,4-butanediol", "1,4-丁二醇", "polyol"), |
| "96-48-0": ("gamma_butyrolactone", "gamma-butyrolactone", "γ-丁内酯", "ester"), |
| "107-18-6": ("allyl_alcohol", "allyl alcohol", "烯丙醇", "alcohol"), |
| "108-05-4": ("vinyl_acetate", "vinyl acetate", "乙酸乙烯酯", "ester"), |
| "98-00-0": ("furfuryl_alcohol", "furfuryl alcohol", "糠醇", "alcohol"), |
| "141-97-9": ("ethyl_acetoacetate", "ethyl acetoacetate", "乙酰乙酸乙酯", "ester"), |
| "149-73-5": ("trimethyl_orthoformate", "trimethyl orthoformate", "原甲酸三甲酯", "ester"), |
| "122-51-0": ("triethyl_orthoformate", "triethyl orthoformate", "原甲酸三乙酯", "ester"), |
| "56-40-6": ("glycine", "glycine", "甘氨酸", "amino_acid"), |
| "77-92-9": ("citric_acid", "citric acid", "柠檬酸", "carboxylic_acid"), |
| "10043-35-3": ("boric_acid", "boric acid", "硼酸", "inorganic_acid"), |
| "288-32-4": ("imidazole", "imidazole", "咪唑", "heterocycle"), |
| "302-01-2": ("hydrazine", "hydrazine", "肼", "inorganic"), |
| "123-31-9": ("hydroquinone", "hydroquinone", "对苯二酚", "phenol"), |
| "7697-37-2": ("nitric_acid", "nitric acid", "硝酸", "inorganic_acid"), |
| "57-13-6": ("urea", "urea", "尿素", "amide"), |
| "57-50-1": ("sucrose", "sucrose", "蔗糖", "carbohydrate"), |
| "50-00-0": ("formaldehyde", "formaldehyde", "甲醛", "aldehyde"), |
| "144-62-7": ("oxalic_acid", "oxalic acid", "草酸", "carboxylic_acid"), |
| "88-99-3": ("phthalic_acid", "phthalic acid", "邻苯二甲酸", "carboxylic_acid"), |
| "77-86-1": ("tris", "tris(hydroxymethyl)aminomethane", "三羟甲基氨基甲烷（Tris）", "amine"), |
| "141-43-5": ("ethanolamine", "ethanolamine", "乙醇胺", "amine"), |
| "111-42-2": ("diethanolamine", "diethanolamine", "二乙醇胺", "amine"), |
| "102-71-6": ("triethanolamine", "triethanolamine", "三乙醇胺", "amine"), |
| "107-15-3": ("ethylenediamine", "ethylenediamine", "乙二胺", "amine"), |
| "109-73-9": ("butylamine", "n-butylamine", "正丁胺", "amine"), |
| "60-24-2": ("mercaptoethanol_2", "2-mercaptoethanol", "2-巯基乙醇", "thiol"), |
| "106-51-4": ("benzoquinone_1_4", "1,4-benzoquinone", "对苯醌", "quinone"), |
| "109-52-4": ("pentanoic_acid", "pentanoic acid", "戊酸", "carboxylic_acid"), |
| "79-31-2": ("isobutyric_acid", "isobutyric acid", "异丁酸", "carboxylic_acid"), |
| "74-82-8": ("methane", "methane", "甲烷", "alkane"), |
| "7446-09-5": ("sulfur_dioxide", "sulfur dioxide", "二氧化硫", "gas"), |
| "7783-06-4": ("hydrogen_sulfide", "hydrogen sulfide", "硫化氢", "gas"), |
| "106-97-8": ("butane", "butane", "正丁烷", "alkane"), |
| "74-98-6": ("propane", "propane", "丙烷", "alkane"), |
| "74-84-0": ("ethane", "ethane", "乙烷", "alkane"), |
| "10024-97-2": ("nitrous_oxide", "nitrous oxide", "一氧化二氮", "gas"), |
| "7727-37-9": ("nitrogen", "nitrogen", "氮气", "gas"), |
| "2551-62-4": ("sulfur_hexafluoride", "sulfur hexafluoride", "六氟化硫", "gas"), |
| "60-00-4": ("edta", "ethylenediaminetetraacetic acid", "乙二胺四乙酸（EDTA）", "carboxylic_acid"), |
| "108-89-4": ("picoline_4", "4-methylpyridine", "4-甲基吡啶", "heterocycle"), |
| "109-06-8": ("picoline_2", "2-methylpyridine", "2-甲基吡啶", "heterocycle"), |
| "108-99-6": ("picoline_3", "3-methylpyridine", "3-甲基吡啶", "heterocycle"), |
| "124-40-3": ("dimethylamine", "dimethylamine", "二甲胺", "amine"), |
| "74-89-5": ("methylamine", "methylamine", "甲胺", "amine"), |
| "75-50-3": ("trimethylamine", "trimethylamine", "三甲胺", "amine"), |
| "7664-39-3": ("hydrogen_fluoride", "hydrogen fluoride", "氟化氢", "inorganic_acid"), |
| "7664-38-2": ("phosphoric_acid", "phosphoric acid", "磷酸", "inorganic_acid"), |
| |
| "115-25-3": ("octafluorocyclobutane", "octafluorocyclobutane (RC318)", "八氟环丁烷（RC318）", "halogenated"), |
| "75-43-4": ("dichlorofluoromethane", "dichlorofluoromethane (R21)", "二氯一氟甲烷（R21）", "halogenated"), |
| "75-68-3": ("chlorodifluoroethane_r142b", "1-chloro-1,1-difluoroethane (R142b)", "1-氯-1,1-二氟乙烷（R142b）", "halogenated"), |
| "75-69-4": ("trichlorofluoromethane", "trichlorofluoromethane (R11)", "三氯一氟甲烷（R11）", "halogenated"), |
| "76-14-2": ("dichlorotetrafluoroethane_r114", "1,2-dichloro-1,1,2,2-tetrafluoroethane (R114)", "1,2-二氯四氟乙烷（R114）", "halogenated"), |
| "431-63-0": ("hexafluoropropane_r236ea", "1,1,1,2,3,3-hexafluoropropane (R236ea)", "1,1,1,2,3,3-六氟丙烷（R236ea）", "halogenated"), |
| "690-39-1": ("hexafluoropropane_r236fa", "1,1,1,3,3,3-hexafluoropropane (R236fa)", "1,1,1,3,3,3-六氟丙烷（R236fa）", "halogenated"), |
| "110-87-2": ("dihydropyran", "3,4-dihydro-2H-pyran", "3,4-二氢-2H-吡喃", "ether"), |
| "137-18-8": ("dimethylbenzoquinone_2_5", "2,5-dimethyl-1,4-benzoquinone", "2,5-二甲基对苯醌", "quinone"), |
| "59-47-2": ("mephenesin", "mephenesin", "美芬新（甲苯丙醇）", "pharmaceutical"), |
| "83-72-7": ("lawsone", "2-hydroxy-1,4-naphthoquinone (lawsone)", "2-羟基-1,4-萘醌（指甲花醌）", "quinone"), |
| "92-82-0": ("phenazine", "phenazine", "吩嗪", "heterocycle"), |
| "103-82-2": ("phenylacetic_acid", "phenylacetic acid", "苯乙酸", "carboxylic_acid"), |
| "57-44-3": ("barbital", "barbital", "巴比妥", "pharmaceutical"), |
| "103-79-7": ("phenylacetone", "1-phenyl-2-propanone", "苯基丙酮（1-苯基-2-丙酮）", "ketone"), |
| "106-62-7": ("dipropylene_glycol", "2-(2-hydroxypropoxy)-1-propanol (dipropylene glycol isomer)", "二丙二醇（2-(2-羟丙氧基)-1-丙醇）", "polyol"), |
| "106-65-0": ("dimethyl_succinate", "dimethyl succinate", "丁二酸二甲酯", "ester"), |
| "107-19-7": ("propargyl_alcohol", "propargyl alcohol", "炔丙醇", "alcohol"), |
| "108-59-8": ("dimethyl_malonate", "dimethyl malonate", "丙二酸二甲酯", "ester"), |
| "109-49-9": ("hex_5_en_2_one", "5-hexen-2-one", "5-己烯-2-酮", "ketone"), |
| "110-13-4": ("hexanedione_2_5", "2,5-hexanedione", "2,5-己二酮", "ketone"), |
| "110-64-5": ("but_2_ene_1_4_diol", "2-butene-1,4-diol", "2-丁烯-1,4-二醇", "polyol"), |
| "111-45-5": ("allyloxyethanol", "2-(allyloxy)ethanol", "乙二醇单烯丙基醚", "glycol_ether"), |
| "111-90-0": ("ethoxyethoxyethanol", "2-(2-ethoxyethoxy)ethanol", "二乙二醇单乙醚", "glycol_ether"), |
| "112-34-5": ("butoxyethoxyethanol", "2-(2-butoxyethoxy)ethanol", "二乙二醇单丁醚", "glycol_ether"), |
| "112-36-7": ("diethylene_glycol_diethyl_ether", "diethylene glycol diethyl ether", "二乙二醇二乙醚", "ether"), |
| "115-07-1": ("propene", "propene", "丙烯", "alkene"), |
| "115-19-5": ("methylbutynol", "2-methyl-3-butyn-2-ol", "2-甲基-3-丁炔-2-醇", "alcohol"), |
| "123-63-7": ("paraldehyde", "paraldehyde", "三聚乙醛", "ether"), |
| "137-32-6": ("methylbutan_2_1_ol", "2-methyl-1-butanol", "2-甲基-1-丁醇", "alcohol"), |
| "144-19-4": ("trimethylpentanediol", "2,2,4-trimethyl-1,3-pentanediol", "2,2,4-三甲基-1,3-戊二醇", "polyol"), |
| "462-95-3": ("diethoxymethane", "diethoxymethane", "二乙氧基甲烷", "ether"), |
| } |
|
|
|
|
| def log(msg: str) -> None: |
| print(msg, flush=True) |
|
|
|
|
| |
| def rank() -> dict: |
| libs = bc.scan_all() |
| spectral = {rel for rel in libs if rel.startswith("assets/reactions/spectral_library/")} |
| have = {row[3] for row in COMPOUNDS} |
| inst, libsets, names, recs, prim_inst = defaultdict(set), defaultdict(set), defaultdict(Counter), defaultdict(list), defaultdict(set) |
| for rel, info in libs.items(): |
| if rel in spectral: |
| continue |
| for r in info["records"]: |
| for kind in ("primary", "components"): |
| for cas in r[kind]["cas"]: |
| inst[cas].update(info["asset_type_ids"]) |
| libsets[cas].add(rel) |
| if kind == "primary": |
| prim_inst[cas].update(info["asset_type_ids"]) |
| names[cas][r["name"] or r["record_id"]] += 1 |
| if len(recs[cas]) < 12: |
| recs[cas].append({"library": rel, "record_id": r["record_id"], "role": kind}) |
| rows = [] |
| for cas, aids in inst.items(): |
| rows.append({"cas": cas, "in_table": cas in have, "n_instruments": len(aids), "n_instruments_as_primary": len(prim_inst[cas]), |
| "n_libraries": len(libsets[cas]), "n_records": sum(names[cas].values()), "instruments": sorted(aids), |
| "libraries": sorted(libsets[cas]), "names_seen": [n for n, _ in names[cas].most_common(4)], "example_records": recs[cas]}) |
| rows.sort(key=lambda r: (-r["n_instruments"], -r["n_libraries"], -r["n_records"], r["cas"])) |
| out = {"built_by": "scripts/spectral_library/select_expansion.py --phase rank", "built_at": time.strftime("%Y-%m-%dT%H:%M:%S%z"), |
| "n_libraries_scanned": len(libs) - len(spectral), "n_cas_total": len(rows), "n_cas_new": sum(1 for r in rows if not r["in_table"]), |
| "candidates": rows} |
| OUTDIR.mkdir(parents=True, exist_ok=True) |
| RANK_FILE.write_text(json.dumps(out, ensure_ascii=False, indent=1) + "\n", encoding="utf-8") |
| log(f"ranked {len(rows)} CAS ({out['n_cas_new']} new) from {out['n_libraries_scanned']} libraries -> {RANK_FILE.relative_to(ROOT)}") |
| return out |
|
|
|
|
| |
| def probe_targets(ranked: dict) -> list[str]: |
| cas = [r["cas"] for r in ranked["candidates"] if not r["in_table"] and r["n_instruments"] >= 2] |
| for sid, c in SUBSTANCE_CAS.items(): |
| if c not in cas: |
| cas.append(c) |
| return cas |
|
|
|
|
| def probe(ranked: dict, delay: float) -> None: |
| import requests |
| import fetch_sources as fs |
| targets = probe_targets(ranked) |
| PROBE.mkdir(parents=True, exist_ok=True) |
| props = "MolecularFormula,MolecularWeight,SMILES,ConnectivitySMILES,XLogP,IUPACName,Title" |
| with requests.Session() as session: |
| |
| for cas in targets: |
| d = PROBE / cas |
| d.mkdir(exist_ok=True) |
| fs.get(session, f"{fs.PUBCHEM}/pug/compound/name/{cas}/property/{props}/JSON", None, d / "pubchem_props.json", 0.25, False, log) |
| |
| pending = [] |
| for cas in targets: |
| try: |
| p = json.loads((PROBE / cas / "pubchem_props.json").read_text())["PropertyTable"]["Properties"][0] |
| except Exception: |
| p = {} |
| if classify(cas, p) in ("molecular", "unresolved"): |
| pending.append(cas) |
| log(f" NIST probe for {len(pending)} molecular/unresolved of {len(targets)} candidates") |
| for attempt in range(3): |
| failed = [] |
| for i, cas in enumerate(pending, 1): |
| a = fs.get(session, fs.NIST, {"ID": fs.nist_id(cas), "Mask": "2000", "Units": "SI"}, PROBE / cas / "gc.html", delay, False, log) |
| if a is None: |
| failed.append(cas) |
| if i % 25 == 0: |
| log(f" NIST probe pass {attempt + 1}: {i}/{len(pending)}") |
| if not failed: |
| break |
| log(f" {len(failed)} NIST probes failed (HTTP 429/5xx / network); waiting 60 s before retrying") |
| time.sleep(60) |
| pending = failed |
| log(f"probe done: {len(targets)} CAS") |
|
|
|
|
| def nist_availability(html: str) -> dict: |
| if not html: |
| return {"found": False} |
| found = "Registry Number Not Found" not in html and "<h1 id=\"Top\">" in html |
| tables = re.findall(r"<h3[^>]*>\s*(Kovats|Van Den Dool|Normal alkane)[^<]*</h3>", html) |
| return {"found": found, "gc_ri_tables": len(tables), "ir": "Mask=80#IR-Spec" in html, "ms": "Mask=200#Mass-Spec" in html, |
| "uv": "Mask=400#UV-Vis-Spec" in html, "phase_change": "Mask=4#Thermo-Phase" in html, |
| "nist_name": (re.search(r'<h1 id="Top">(.*?)</h1>', html) or [None, None])[1]} |
|
|
|
|
| def classify(cas: str, props: dict) -> str: |
| if cas in NETWORK_SOLIDS: |
| return "network_solid" |
| smi = props.get("SMILES") or props.get("ConnectivitySMILES") |
| if not smi: |
| return "unresolved" |
| from rdkit import Chem, RDLogger |
| RDLogger.DisableLog("rdApp.*") |
| mol = Chem.MolFromSmiles(smi) |
| if mol is None: |
| return "unresolved" |
| nonmetals = {"H", "B", "C", "N", "O", "F", "Si", "P", "S", "Cl", "Se", "Br", "I", "As"} |
| symbols = [a.GetSymbol() for a in mol.GetAtoms()] |
| if any(s not in nonmetals and s not in {"He", "Ne", "Ar", "Kr", "Xe"} for s in symbols): |
| return "metal_or_salt" |
| if "." in smi: |
| return "salt_hydrate_or_mixture" |
| if mol.GetNumAtoms() + sum(a.GetTotalNumHs() for a in mol.GetAtoms()) == 1: |
| return "element_atomic" |
| return "molecular" |
|
|
|
|
| |
| def select(ranked: dict, target: int) -> dict: |
| subs = json.loads((ROOT / "assets" / "reactions" / "substances.json").read_text(encoding="utf-8"))["substances"] |
| have_ids = {row[0] for row in COMPOUNDS} |
| have_cas = {row[3] for row in COMPOUNDS} |
| by_cas = {r["cas"]: r for r in ranked["candidates"]} |
| info = {} |
| for cas in probe_targets(ranked): |
| d = PROBE / cas |
| html = (d / "gc.html").read_text(encoding="utf-8", errors="replace") if (d / "gc.html").exists() else "" |
| try: |
| props = json.loads((d / "pubchem_props.json").read_text())["PropertyTable"]["Properties"][0] |
| except Exception: |
| props = {} |
| nist = nist_availability(html) |
| cls = classify(cas, props) |
| r = by_cas.get(cas, {"cas": cas, "n_instruments": 0, "n_instruments_as_primary": 0, "n_libraries": 0, "n_records": 0, |
| "instruments": [], "libraries": [], "names_seen": [], "example_records": []}) |
| spectral_kinds = [k for k in ("gc_ri", "ir", "ms", "uv") if (nist.get("gc_ri_tables") if k == "gc_ri" else nist.get(k))] |
| info[cas] = {**{k: r[k] for k in ("cas", "n_instruments", "n_instruments_as_primary", "n_libraries", "n_records", "instruments", "names_seen")}, |
| "pubchem": {"cid": props.get("CID"), "title": props.get("Title"), "formula": props.get("MolecularFormula"), "smiles": props.get("SMILES")}, |
| "classification": cls, "nist": nist, "nist_spectral_kinds": spectral_kinds} |
| selected, rejected = [], [] |
|
|
| def add(cas, rule, why): |
| meta = EXPANSION_META.get(cas) |
| selected.append({"cas": cas, "id": meta[0] if meta else None, "name_en": meta[1] if meta else None, "name_zh": meta[2] if meta else None, |
| "class": meta[3] if meta else None, "rule": rule, "why": why, **info[cas]}) |
|
|
| |
| rule1 = [] |
| for sid, row in subs.items(): |
| if sid in have_ids or sid in NON_MOLECULAR_SUBSTANCES or sid in PHASE_VARIANTS: |
| continue |
| cas = SUBSTANCE_CAS.get(sid) or row.get("cas") |
| if cas and cas not in have_cas: |
| rule1.append(cas) |
| add(cas, "1_substances_molecular_species", f"substances.json species '{sid}' ({row.get('name_zh')}) used by the reaction templates") |
| chosen = set(rule1) |
| |
| for cas, why in COMMON_LAB.items(): |
| i = info.get(cas) |
| if not i or cas in chosen or cas in have_cas: |
| continue |
| if i["n_instruments"] >= 2 and i["classification"] == "molecular" and i["nist_spectral_kinds"]: |
| chosen.add(cas) |
| add(cas, "2_common_lab_solvent_or_reagent", f"{why}; in {i['n_instruments']} instruments' libraries") |
| else: |
| rejected.append({"cas": cas, "rule": "2", "reason": f"classification={i['classification']}, instruments={i['n_instruments']}, nist={i['nist_spectral_kinds']}"}) |
| |
| pool = [i for c, i in info.items() if c not in chosen and c not in have_cas] |
| pool.sort(key=lambda i: (-i["n_instruments"], -len(i["nist_spectral_kinds"]), -i["n_libraries"], -i["n_records"], i["cas"])) |
| for i in pool: |
| if len(have_cas) + len(chosen) >= target: |
| rejected.append({"cas": i["cas"], "rule": "3", "reason": "below the cut (target reached)", "n_instruments": i["n_instruments"], |
| "classification": i["classification"], "nist": i["nist_spectral_kinds"], "names_seen": i["names_seen"][:2]}) |
| continue |
| if i["classification"] != "molecular": |
| rejected.append({"cas": i["cas"], "rule": "3", "reason": f"not molecular ({i['classification']})", "names_seen": i["names_seen"][:2]}) |
| continue |
| if not i["nist_spectral_kinds"]: |
| rejected.append({"cas": i["cas"], "rule": "3", "reason": "NIST WebBook has no GC/IR/MS/UV data", "names_seen": i["names_seen"][:2]}) |
| continue |
| chosen.add(i["cas"]) |
| add(i["cas"], "3_ranked_by_instrument_linkage", f"in {i['n_instruments']} instruments' libraries; NIST {i['nist_spectral_kinds']}") |
| missing_meta = [s["cas"] for s in selected if not s["id"]] |
| out = { |
| "built_by": "scripts/spectral_library/select_expansion.py --phase select", "built_at": time.strftime("%Y-%m-%dT%H:%M:%S%z"), |
| "target_total": target, "n_existing": len(have_cas), "n_selected": len(selected), |
| "rules": __doc__.split("Selection rules")[1].split("Usage:")[0].strip(), |
| "ranking_source": str(RANK_FILE.relative_to(ROOT)), "n_libraries_scanned": ranked["n_libraries_scanned"], |
| "by_rule": dict(Counter(s["rule"] for s in selected)), "missing_metadata": missing_meta, |
| "selected": selected, "not_selected": rejected, |
| } |
| SELECTION.write_text(json.dumps(out, ensure_ascii=False, indent=1) + "\n", encoding="utf-8") |
| log(f"selected {len(selected)} ({out['by_rule']}); missing metadata for {len(missing_meta)} -> {SELECTION.relative_to(ROOT)}") |
| return out |
|
|
|
|
| def seed_raw_cache(selection: dict) -> None: |
| """Copy the probe downloads (same requests as fetch_sources.py) into references/spectral_raw/<id>/.""" |
| for s in selection["selected"]: |
| if not s["id"]: |
| continue |
| d = RAW / s["id"] |
| d.mkdir(parents=True, exist_ok=True) |
| for name in ("gc.html", "pubchem_props.json"): |
| src = PROBE / s["cas"] / name |
| if src.exists() and not (d / name).exists(): |
| shutil.copy2(src, d / name) |
|
|
|
|
| def main() -> None: |
| ap = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter) |
| ap.add_argument("--phase", default="all", choices=["rank", "probe", "select", "seed", "all"]) |
| ap.add_argument("--delay", type=float, default=1.0) |
| ap.add_argument("--target", type=int, default=200) |
| args = ap.parse_args() |
| ranked = rank() if args.phase in ("rank", "all") or not RANK_FILE.exists() else json.loads(RANK_FILE.read_text(encoding="utf-8")) |
| if args.phase in ("probe", "all"): |
| probe(ranked, args.delay) |
| if args.phase in ("select", "all"): |
| select(ranked, args.target) |
| if args.phase == "seed": |
| seed_raw_cache(json.loads(SELECTION.read_text(encoding="utf-8"))) |
|
|
|
|
| if __name__ == "__main__": |
| main() |
|
|
