{"id":2784,"date":"2025-10-09T13:54:34","date_gmt":"2025-10-09T04:54:34","guid":{"rendered":"https:\/\/www.insilico.jp\/blog\/?p=2784"},"modified":"2025-10-09T13:54:36","modified_gmt":"2025-10-09T04:54:36","slug":"moleculeresolver","status":"publish","type":"post","link":"https:\/\/www.insilico.jp\/blog\/2025\/10\/09\/moleculeresolver\/","title":{"rendered":"MoleculeResolver\u306b\u3088\u308b\u7269\u8cea\u540d\u304b\u3089\u306eSMILES\u691c\u7d22"},"content":{"rendered":"\n

\u7406\u8ad6\u5275\u85ac\u7814\u7a76\u6240\u306e\u91d1\u5b50\u4fe1\u4eba\u3067\u3059\u3002
\u4eca\u56de\u306f\u7269\u8cea\u540d\u304b\u3089\u5316\u5408\u7269\u60c5\u5831\u3092\u53d6\u5f97\u3059\u308bMoleculeResolver\u3092\u7d39\u4ecb\u3057\u307e\u3059\u3002<\/p>\n\n\n\n

\u53c2\u8003\u8ad6\u6587
How to crack a SMILES: automatic crosschecked chemical structure resolution across multiple services using MoleculeResolver
\uff08Simon M\u00fcller, Journal of Cheminformatics<\/em> 2025<\/strong>, 17<\/em>, 117.\uff09
https:\/\/doi.org\/10.1186\/s13321-025-01064-7<\/a><\/p>\n\n\n\n

SMILES\uff08simplified molecular input line entry system\uff09\u306f\u5206\u5b50\u69cb\u9020\u3092\u82f1\u6570\u5b57\u8a18\u53f7\u306e\u6587\u5b57\u5217\u3067\u8868\u8a18\u3057\u305f\u3082\u306e\u3067\u3001\u5c11\u306a\u3044\u30c7\u30fc\u30bf\u91cf\u3067\u5206\u5b50\u3092\u6271\u3046\u3053\u3068\u304c\u3067\u304d\u308b\u305f\u3081\u30c7\u30fc\u30bf\u30b5\u30a4\u30a8\u30f3\u30b9\u3067\u306f\u5e83\u304f\u7528\u3044\u3089\u308c\u3066\u3044\u307e\u3059\u3002\u4e00\u65b9\u3067\u7269\u8cea\u540d\u304b\u3089SMILES\u60c5\u5831\u3092\u53d6\u5f97\u3059\u308b\u305f\u3081\u306b\u306fCAS\u203b1<\/sup>\u3084PubChem\u203b2<\/sup>\u306a\u3069\u306e\u5316\u5408\u7269\u30c7\u30fc\u30bf\u30d9\u30fc\u30b9\u3092\u691c\u7d22\u3059\u308b\u306e\u304c\u4e00\u822c\u7684\u3067\u3059\u304c\u3001\u30c7\u30fc\u30bf\u30d9\u30fc\u30b9\u306b\u3088\u3063\u3066\u60c5\u5831\u306e\u6709\u7121\u306e\u5dee\u304c\u3042\u3063\u305f\u308a\u3001\u8907\u6570\u306e\u540d\u79f0\u304c\u3042\u308b\u7269\u8cea\u3067\u306f\u66f8\u304d\u65b9\u306b\u3088\u3063\u3066\u306f\u30d2\u30c3\u30c8\u3057\u306a\u3044\u306a\u3069\u306e\u554f\u984c\u304c\u3042\u308a\u307e\u3057\u305f\u3002\u4eca\u56de\u7d39\u4ecb\u3059\u308bMoleculeResolver\u306f\u8907\u6570\u306e\u30c7\u30fc\u30bf\u30d9\u30fc\u30b9\u304b\u3089\u30af\u30ed\u30b9\u30c1\u30a7\u30c3\u30af\u3059\u308b\u3053\u3068\u306b\u3088\u308a\u9ad8\u7cbe\u5ea6\u3067\u5316\u5408\u7269\u60c5\u5831\u3092\u53d6\u5f97\u3059\u308b\u3053\u3068\u3092\u53ef\u80fd\u306b\u3057\u305f\u3082\u306e\u306b\u306a\u308a\u307e\u3059\u3002<\/p>\n\n\n\n

\u52d5\u4f5c\u74b0\u5883
Intel Core i7-1265U
Windows 11 Pro
conda 25.7.0
pip 25.2<\/p>\n\n\n\n

Chem\u00e9o\u306eAPI\u53d6\u5f97<\/h2>\n\n\n\n

\u30c7\u30fc\u30bf\u30d9\u30fc\u30b9\u306e\u4e00\u3064\u3067\u3042\u308bChem\u00e9o\u304b\u3089\u306fAPI\u3092\u7d4c\u7531\u3057\u3066\u60c5\u5831\u3092\u53d6\u5f97\u3057\u3066\u3044\u307e\u3059\u306e\u3067\u3001\u5148\u306bAPI\u3092\u53d6\u5f97\u3057\u307e\u3059\u3002https:\/\/www.chemeo.com\/<\/a> \u306b\u30a2\u30af\u30bb\u30b9\u3057\u3001\u53f3\u4e0a\u306e\u30e1\u30cb\u30e5\u30fc\u304b\u3089Register\u3092\u30af\u30ea\u30c3\u30af\u3057\u767b\u9332\u3057\u307e\u3059\u3002<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n
\"\"<\/figure>\n\n\n\n

\u540d\u524d\u30fb\u56fd\u30fb\u30e1\u30fc\u30eb\u30a2\u30c9\u30ec\u30b9\u30fb\u30d1\u30b9\u30ef\u30fc\u30c9\u3092\u5165\u529b\u3057\u3066\u767b\u9332\u3059\u308b\u3068\u3001\u8a18\u5165\u3057\u305f\u30e1\u30fc\u30eb\u30a2\u30c9\u30ec\u30b9\u306b\u30e1\u30fc\u30eb\u304c\u5c4a\u304d\u307e\u3059\u306e\u3067\u3001\u30e1\u30fc\u30eb\u306b\u8a18\u8f09\u3055\u308c\u305f\u30ea\u30f3\u30af\u304b\u3089\u30ed\u30b0\u30a4\u30f3\u3057\u307e\u3059\u3002\u30ed\u30b0\u30a4\u30f3\u5f8c\u53f3\u4e0a\u306e\u30e1\u30cb\u30e5\u30fc\u304b\u3089Profile\u3092\u9078\u629e\u3059\u308b\u3068\u4e2d\u592e\u306bAPI Key\u304c\u8868\u793a\u3055\u308c\u307e\u3059\u306e\u3067\u30b3\u30d4\u30fc\u3057\u3066\u304a\u304d\u307e\u3059\u3002<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n
\"\"<\/figure>\n\n\n\n

MoleculeResolver\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb<\/h2>\n\n\n\n

Python\u306e\u4eee\u60f3\u74b0\u5883\u3092\u4f5c\u6210\u3057\u3001MoleculeResolver\u3092\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3057\u307e\u3059\u3002<\/p>\n\n\n\n

$ conda create -n MoleculeResolver python=3.12 -y\n$ conda activate MoleculeResolver\n$ pip install molecule-resolver<\/code><\/pre>\n\n\n\n
numpy, pillow, rdkit\u306a\u3069\u306e\u4f9d\u5b58\u30d1\u30c3\u30b1\u30fc\u30b8\u304c\u81ea\u52d5\u3067\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3055\u308c\u307e\u3057\u305f\u3002<\/p>\n\n\n\n
MoleculeResolver\u306e\u5b9f\u884c<\/h2>\n\n\n\n
Python\u306e\u5bfe\u8a71\u30e2\u30fc\u30c9\u3067MoleculeResolver\u3092\u5b9f\u884c\u3057\u3066\u307f\u307e\u3057\u3087\u3046\u3002
YOUR_API_KEY\u306e\u90e8\u5206\u306b\u5148\u307b\u3069\u53d6\u5f97\u3057\u305fAPI Key\u3092\u5165\u529b\u3057\u307e\u3059\u3002<\/p>\n\n\n\n
>>> from rdkit import Chem\n>>> from moleculeresolver import MoleculeResolver\n>>> with MoleculeResolver(available_service_API_keys={\"chemeo\": \"YOUR_API_KEY\"}) as mr:\n...     molecule_name = mr.find_single_molecule([\"aspirin\"], [\"name\"])\n...\n>>> print(molecule_name)\nMolecule(SMILES='CC(=O)Oc1ccccc1C(=O)O', synonyms=['aspirin', '2-acetyloxybenzoic acid', '2-Acetoxybenzoic acid', '2-(Acetyloxy)benzoic acid', '2-Carboxyphenyl acetate'], CAS=[], additional_information='cir', mode='name', service='cir', number_of_crosschecks=1, identifier='aspirin', found_molecules=[])<\/code><\/pre>\n\n\n\n
\u5206\u5b50\u540d\u691c\u7d22\u3067\u5165\u529b\u3057\u305faspirin\u306b\u5bfe\u3057\u3001SMILES\u3068\u5225\u79f0\u30fb\u4ed8\u968f\u60c5\u5831\u304c\u51fa\u529b\u3055\u308c\u307e\u3059\u3002
\u8907\u6570\u306e\u5206\u5b50\u3092\u540c\u6642\u306b\u691c\u7d22\u3059\u308b\u3053\u3068\u3082\u53ef\u80fd\u3067\u3001GitHub\u3067\u63d0\u793a\u3055\u308c\u3066\u3044\u308bPython\u30b9\u30af\u30ea\u30d7\u30c8\u3092\u5b9f\u884c\u3057\u3066\u307f\u307e\u3057\u3087\u3046\u3002<\/p>\n\n\n\n
import json\nfrom moleculeresolver import MoleculeResolver\n\nmolecule_names = [\"aspirin\", \"propanol\", \"ibuprofen\", \"non-exixtent-name\"]\nnot_found_molecules = []\nmolecules_dicts = {}\n\nwith MoleculeResolver(available_service_API_keys={\"chemeo\": \"YOUR_API_KEY\"}) as mr:\n    molecules = mr.find_multiple_molecules_parallelized(molecule_names, [[\"name\"]] * len(molecule_names))\n    for name, molecule in zip(molecule_names, molecules):\n        if molecule:\n            molecules_dicts[name] = molecule.to_dict(found_molecules='remove')\n        else:\n            not_found_molecules.append(name)\n\nwith open(\"molecules.json\", \"w\") as json_file:\n    json.dump(molecules_dicts, json_file, indent=4)\n\nprint(f\"Molecules not found: {not_found_molecules}\")<\/code><\/pre>\n\n\n\n
\u5b9f\u884c\u3059\u308b\u3068\u30b3\u30f3\u30bd\u30fc\u30eb\u306b\u306f\u4ee5\u4e0b\u306e\u3088\u3046\u306b\u8868\u793a\u3055\u308c\u3001’non-exixtent-name’ \u3068\u3044\u3046\u540d\u524d\u306e\u5206\u5b50\u306f\u5b58\u5728\u3057\u306a\u3044\u3068\u3044\u3046\u3088\u3046\u306b\u5206\u5225\u3055\u308c\u307e\u3059\u3002<\/p>\n\n\n\n
Getting data from services\n100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4\/4 [00:10<00:00,  2.59s\/it]\nMolecules not found: ['non-exixtent-name']<\/code><\/pre>\n\n\n\n
\u5b9f\u884c\u7d50\u679c\u306fmolecules.json\u306b\u4fdd\u5b58\u3055\u308c\u3001\u691c\u7d22\u3057\u305f\u5206\u5b50\u306eSMILES\u30fb\u5225\u79f0\u30fbCAS\u767b\u9332\u756a\u53f7\u3068\u3044\u304f\u3064\u306e\u30c7\u30fc\u30bf\u30d9\u30fc\u30b9\u3067\u30af\u30ed\u30b9\u30c1\u30a7\u30c3\u30af\u3055\u308c\u305f\u304b\u7b49\u304c\u51fa\u529b\u3055\u308c\u307e\u3059\u3002<\/p>\n\n\n\n
{\n    \"aspirin\": {\n        \"SMILES\": \"CC(=O)Oc1ccccc1C(=O)O\",\n        \"synonyms\": [\n            \"aspirin\",\n            \"2-(acetyloxy)-Benzoic acid\",\n            \"2-acetyloxybenzoic acid\",\n            \"acetylsalicylic acid\",\n            \"2-Acetoxybenzoic acid\"\n        ],\n        \"CAS\": [\n            \"50-78-2\"\n        ],\n        \"additional_information\": \"cir; nist id: C50782; pubchem id: 2244; srs id: 1198\",\n        \"mode\": \"name; name; name; name\",\n        \"service\": \"cir; nist; pubchem; srs\",\n        \"number_of_crosschecks\": 4,\n        \"identifier\": \"aspirin\"\n    },\n    \"propanol\": {\n        \"SMILES\": \"CCCO\",\n        \"synonyms\": [\n            \"propanol\",\n            \"1-Propanol\",\n            \"Alcohol, propyl\",\n            \"Propan-1-ol\",\n            \"Propyl alcohol\"\n        ],\n        \"CAS\": [\n            \"71-23-8\"\n        ],\n        \"additional_information\": \"chemeo id: 15-582-9; cir; nist id: C71238; ; pubchem id: 1031; srs id: 17121898\",\n        \"mode\": \"name; name; name; name; name; name\",\n        \"service\": \"chemeo; cir; nist; opsin; pubchem; srs\",\n        \"number_of_crosschecks\": 6,\n        \"identifier\": \"propanol\"\n    },\n    \"ibuprofen\": {\n        \"SMILES\": \"CC(C)Cc1ccc(C(C)C(=O)O)cc1\",\n        \"synonyms\": [\n            \"ibuprofen\",\n            \"2-[4-(2-methylpropyl)phenyl]propanoic acid\",\n            \"2-(4-Isobutylphenyl)propanoic acid\",\n            \"(.+\/-.)-2-(p-Isobutylphenyl)propionic acid\",\n            \"(.+\/-.)-p-Isobutylhydratropic acid\"\n        ],\n        \"CAS\": [\n            \"15687-27-1\"\n        ],\n        \"additional_information\": \"chemeo id: 20-897-4; cir; nist id: T999947192; ; pubchem id: 3672; srs id: 200931\",\n        \"mode\": \"name; name; name; name; name; name\",\n        \"service\": \"chemeo; cir; nist; opsin; pubchem; srs\",\n        \"number_of_crosschecks\": 6,\n        \"identifier\": \"ibuprofen\"\n    }\n}<\/code><\/pre>\n\n\n\n
\u3088\u308a\u4f7f\u3044\u3084\u3059\u3044\u3088\u3046\u306bCSV\u30d5\u30a1\u30a4\u30eb\u3092\u8aad\u307f\u8fbc\u3093\u3067\u3001\u4e00\u5217\u76ee\u306b\u3042\u308b\u5316\u5408\u7269\u540d\u3092\u691c\u7d22\u3057\u3066\u4e8c\u5217\u76ee\u306bSMILES\u3092\u66f8\u304d\u8fbc\u3080\u30b3\u30fc\u30c9\u3092\u4f5c\u6210\u3057\u3066\u307f\u307e\u3059\u3002\u540c\u69d8\u306bYOUR_API_KEY\u306e\u90e8\u5206\u306b\u53d6\u5f97\u3057\u305fAPI Key\u3092\u5165\u529b\u3057\u3066\u304f\u3060\u3055\u3044\u3002<\/p>\n\n\n\n
import csv\nfrom moleculeresolver import MoleculeResolver\n\n# Input and output file names\ninput_filename = 'molecule.csv'\noutput_filename = 'molecule_resolved.csv'\n\n# Read molecule names from the CSV\nmolecule_names = []\ntry:\n    with open(input_filename, 'r', newline='', encoding='utf-8') as infile:\n        reader = csv.reader(infile)\n        header = next(reader)\n        for row in reader:\n            if row:\n                molecule_names.append(row[0])\nexcept FileNotFoundError:\n    print(f\"Error: Input file '{input_filename}' not found.\")\n\nnot_found_molecules = []\noutput_data = [['name', 'SMILES']]\n\nwith MoleculeResolver(available_service_API_keys={\"chemeo\": \"YOUR_API_KEY\"}) as mr:\n    molecules = mr.find_multiple_molecules_parallelized(\n        molecule_names,\n        [[\"name\"]] * len(molecule_names)\n    )\n    \n    for name, molecule in zip(molecule_names, molecules):\n        if molecule and molecule.SMILES:\n            output_data.append([name, molecule.SMILES])\n        else:\n            output_data.append([name, ''])\n            not_found_molecules.append(name)\n\nwith open(output_filename, 'w', newline='', encoding='utf-8') as outfile:\n    writer = csv.writer(outfile)\n    writer.writerows(output_data)\n\nprint(f\"Processing complete. Results are saved in '{output_filename}'.\")\nif not_found_molecules:\n    print(f\"Molecules not found: {not_found_molecules}\")<\/code><\/pre>\n\n\n\n
\u5b9f\u884c\u3059\u308b\u3068molecule.csv\u3092\u8aad\u307f\u8fbc\u3093\u3067SMILES\u306e\u66f8\u304d\u8fbc\u307e\u308c\u305fmolecule_resolved.csv\u3092\u51fa\u529b\u3057\u307e\u3059\u3002<\/p>\n\n\n\n
name<\/td>SMILES<\/td><\/tr>
imatinib<\/td>Cc1ccc(NC(=O)c2ccc(CN3CCN(C)CC3)cc2)cc1Nc1nccc(-c2cccnc2)n1<\/td><\/tr>
gefitinib<\/td>COc1cc2ncnc(Nc3ccc(F)c(Cl)c3)c2cc1OCCCN1CCOCC1<\/td><\/tr>
ibrutinib<\/td>C=CC(=O)N1CCCC@@Hc3c(N)ncnc32)C1<\/td><\/tr>
tetrodotoxin<\/td>N=C1NC(O)C2C3OC4(O)OC(C(O)C2(N1)C4O)C3(O)CO<\/td><\/tr>
paclitaxel<\/td>CC(=O)OC1C(=O)C2(C)C(O)CC3OCC3(OC(C)=O)C2C(OC(=O)c2ccccc2)C2(O)CC(OC(=O)C(O)C(N=C(O)c3ccccc3)c3ccccc3)C(C)=C1C2(C)C<\/td><\/tr>
manzamine a<\/td>O[C@]12C=C(c3nccc4c3[nH]c3ccccc34)[C@@H]3CCN(CCCC\/C=C\\CC1)C[C@@]31CC3\/C=C\\CCCCN3[C@H]12.[Cl-].[H+]<\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n
\u533b\u85ac\u54c1\u5316\u5408\u7269\u3084\u5929\u7136\u7269\u306a\u3069\u3082\u304d\u3061\u3093\u3068\u691c\u7d22\u3067\u304d\u307e\u3059\u306e\u3067\u3001\u7cbe\u5ea6\u304c\u9ad8\u3044\u3053\u3068\u304c\u308f\u304b\u308a\u307e\u3059\u3002<\/p>\n\n\n\n
\u304a\u308f\u308a\u306b<\/h2>\n\n\n\n
\u69cb\u9020\u60c5\u5831\u3068SMILES\u306f\u5bfe\u5fdc\u95a2\u4fc2\u304c\u3042\u308b\u306e\u3067\u5909\u63db\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2\u3092\u4f7f\u7528\u3059\u308b\u3053\u3068\u3067\u7c21\u5358\u306b\u30a2\u30af\u30bb\u30b9\u3059\u308b\u3053\u3068\u304c\u3067\u304d\u308b\u4e00\u65b9\u3067\u3001\u5316\u5408\u7269\u540d\u306f\u8907\u6570\u306e\u540d\u79f0\u304c\u6df7\u5728\u3057\u3066\u3044\u308b\u305f\u3081\u30c7\u30fc\u30bf\u30d9\u30fc\u30b9\u304b\u3089\u306e\u691c\u7d22\u304c\u56f0\u96e3\u3067\u3057\u305f\u3002\u4eca\u56de\u7d39\u4ecb\u3057\u305fMoleculeResolver\u306f\u30af\u30ed\u30b9\u30c1\u30a7\u30c3\u30af\u6a5f\u80fd\u306b\u3088\u308a\u9ad8\u7cbe\u5ea6\u3067SMILES\u60c5\u5831\u3092\u53d6\u5f97\u3067\u304d\u307e\u3059\u3002\u5316\u5408\u7269\u540d\u306e\u307f\u306e\u30c7\u30fc\u30bf\u30d9\u30fc\u30b9\u304b\u3089\u30d0\u30fc\u30c1\u30e3\u30eb\u30b9\u30af\u30ea\u30fc\u30cb\u30f3\u30b0\u7528\u306bSMILES\u60c5\u5831\u3092\u53d6\u5f97\u3057\u305f\u3044\u3068\u304d\u306b\u6709\u7528\u306b\u306a\u308b\u304b\u3068\u601d\u3044\u307e\u3059\u3002<\/p>\n\n\n\n
\u203b1 CAS\uff08Chemical Abstracts Service\uff09\u30a2\u30e1\u30ea\u30ab\u5316\u5b66\u4f1a\u306e\u904b\u55b6\u3059\u308b\u5316\u5408\u7269\u30c7\u30fc\u30bf\u30d9\u30fc\u30b9
https:\/\/www.cas.org\/ja<\/a>
\u203b2 PubChem \u30a2\u30e1\u30ea\u30ab\u56fd\u7acb\u885b\u751f\u7814\u7a76\u6240\u306e\u904b\u55b6\u3059\u308b\u5316\u5408\u7269\u30c7\u30fc\u30bf\u30d9\u30fc\u30b9
https:\/\/pubchem.ncbi.nlm.nih.gov\/<\/a><\/p>\n\n\n\n
\u524d\u56de\u8a18\u4e8b
Chemprop\u3092\u6d3b\u7528\u3057\u305f\u6a5f\u68b0\u5b66\u7fd2\u306b\u3088\u308b\u5316\u5b66\u7279\u6027\u4e88\u6e2c
https:\/\/www.insilico.jp\/blog\/2025\/09\/11\/chemprop\/<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"
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