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openchemlib-sqlite

library2.0.0jsnpmunverified

SQLite-backed molecular database for substructure, exact, and similarity search using OpenChemLib (OCL). Current version: 2.0.0, released September 2025. Uses Node.js built-in node:sqlite (requires Node >=22.5). Does not own the molecules table — you provide it. Key differentiator: works alongside your existing table, uses OCL 512-bit fingerprints, supports stereo-insensitive exact search via optional id_code_no_stereo column. Released as needed; mature library with active maintenance.

npm install openchemlib-sqlite

github ↗package ↗homepage ↗

INSTALL

IMPORT

SIG · OPENCHEMLIB-SQLITE

openchemlib-sqlite

searchjavascriptv2.0.0

harness data pending

Install & Compatibility

Where this runs

No compatibility data collected yet for this library.

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

MoleculesDBSQLite

✓ import { MoleculesDBSQLite } from 'openchemlib-sqlite'

✗ const { MoleculesDBSQLite } = require('openchemlib-sqlite')

Package is ESM-only. CommonJS require will fail with ERR_REQUIRE_ESM.

SearchMode

✓ import { SearchMode } from 'openchemlib-sqlite'

SearchMode is an enum-like object with keys EXACT, SUBSTRUCTURE, SIMILARITY. Available since v2.0.0.

SearchResponse

✓ import type { SearchResponse } from 'openchemlib-sqlite'

✗ import { SearchResponse } from 'openchemlib-sqlite'

SearchResponse is a TypeScript type/interface, not a runtime value. Use import type to avoid bundling issues.

Set up an in-memory SQLite database, create molecules table, insert a molecule (caffeine), then substructure-search for benzene ring.

import { DatabaseSync } from 'node:sqlite'; import * as OCL from 'openchemlib'; import { MoleculesDBSQLite, SearchMode } from 'openchemlib-sqlite'; const db = new DatabaseSync(':memory:'); db.exec(` CREATE TABLE molecules ( id INTEGER PRIMARY KEY, id_code TEXT NOT NULL UNIQUE, id_code_no_stereo TEXT NOT NULL ) `); const molDB = new MoleculesDBSQLite(db, OCL, { entriesTable: 'molecules', idCodeNoStereoColumn: 'id_code_no_stereo', }); molDB.migrate(); const mol = OCL.Molecule.fromText('Cn1c(=O)c2c(ncn2C)n(C)c1=O'); if (!mol) throw new Error('Parse failed'); const idCode = mol.getIDCode(); const molNoStereo = mol.getCompactCopy(); molNoStereo.stripStereoInformation(); const idCodeNoStereo = molNoStereo.getIDCode(); const { lastInsertRowid } = db .prepare('INSERT INTO molecules (id_code, id_code_no_stereo) VALUES (?, ?)') .run(idCode, idCodeNoStereo); molDB.insert(Number(lastInsertRowid), mol); const query = OCL.Molecule.fromText('C1=CC=CC=C1'); const results = molDB.search(query, SearchMode.SUBSTRUCTURE); console.log(results.total);

Debug

Known issues

breakingNode.js version requirement: >=22.5.0. Using built-in node:sqlite module.

fix

Upgrade Node.js to v22.5.0 or later, or use older openchemlib-sqlite v1.x which did not require node:sqlite.

affects: >=2.0.0

breakingPackage is ESM-only since v2.0.0. No CommonJS support.

fix

Use import instead of require(). Ensure your project is configured for ESM (type: module in package.json).

affects: >=2.0.0

breakingPeer dependency openchemlib must be >=9.20.1.

fix

Install openchemlib@^9.20.1 alongside this package.

affects: >=2.0.0

gotchamigrate() must be called after constructor and before any insert/search. It creates the ocl_ss_index table.

fix

Ensure molDB.migrate() is called. It is idempotent.

affects: >=1.0.0

gotchaThe molecules table must be created by you before instantiating MoleculesDBSQLite. The library does not create it.

fix

Create your molecules table with appropriate columns before constructing MoleculesDBSQLite.

affects: >=1.0.0

gotchainsert() expects the entry ID as a number, not a BigInt. Using lastInsertRowid may return a BigInt in newer sqlite3 versions.

fix

Always convert lastInsertRowid to Number: molDB.insert(Number(lastInsertRowid), mol);

affects: >=2.0.0

gotchaSearch results do not include any data from your molecules table, only entryId and idCode. You must join yourself.

fix

After search, use the entryId to fetch additional columns from your table.

affects: >=1.0.0

Errors

Common errors & fixes

ERR_REQUIRE_ESM: require() of ES Module

Using CommonJS require() on an ESM-only package (v2.x).

fix

Replace require() with import, and set type: module in package.json, or rename file to .mjs.

TypeError: db.prepare is not a function

Using a DatabaseSync instance (from node:sqlite) incorrectly. The library expects node:sqlite's DatabaseSync, not better-sqlite3 or other libraries.

fix

Use import { DatabaseSync } from 'node:sqlite' and create db = new DatabaseSync('path').

Error: entriesTable is required

Missing entriesTable in config options when constructing MoleculesDBSQLite.

fix

Provide entriesTable: 'your_table_name' in the config object.

Error: No such table: ocl_ss_index

migrate() was not called before attempting search or insert.

fix

Call molDB.migrate() after constructing MoleculesDBSQLite and before any operations.

Upgrade

Version history

2.0.0latest on npm

Audit

Dependencies

openchemlibrequiredPeer dependency: provides OCL molecule parsing, idCode generation, and fingerprint computation

Agent activity

28 hits · last 30 days

node

Resources

githubhttps://github.com/cheminfo/openchemlib-sqlite ↗

packageopenchemlib-sqlite ↗

homepagehttps://github.com/cheminfo/openchemlib-sqlite#readme ↗