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Cheminformatics toolkit for DuckDB - SMILES, InChI, MOL/SDF, PDB, SELFIES, Wildman-Crippen LogP, Morgan/ECFP fingerprints, and Tanimoto similarity from SQL

Installing and Loading

INSTALL ducksmiles FROM community;
LOAD ducksmiles;

Example

-- Parse SMILES and get molecular formula
SELECT mol_formula('CCO');
-- C2H6O

-- Calculate molecular weight
SELECT round(mol_weight('c1ccccc1'), 2);
-- 78.11

-- Wildman-Crippen LogP (matches RDKit)
SELECT round(logp_crippen('CCO'), 4);
-- -0.0014

-- Morgan/ECFP fingerprint as 2048-bit BLOB (ECFP4 default)
SELECT bit_count(CAST(morgan_fp_bits('CC(=O)Oc1ccccc1C(=O)O') AS BIT));
-- 26   (aspirin popcount)

-- Tanimoto similarity between two fingerprint BLOBs (no CAST AS BIT needed)
SELECT round(tanimoto_bit(morgan_fp_bits('CCO'), morgan_fp_bits('CCN')), 4);
-- 0.3333

-- Validate and extract InChI layers
SELECT inchi_formula('InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)');
-- C2H4O2

-- Convert SMILES to SELFIES (ML-friendly notation)
SELECT smiles_to_selfies('CCO');

About ducksmiles

Cheminformatics toolkit for DuckDB - analyze molecular structures directly from SQL without leaving your database. Pure Rust implementation with no external chemistry library dependencies (no RDKit required).

Supported Formats:

• SMILES: Molecular validation, formula, weight, atom/bond counts, LogP
• InChI/InChIKey: Layer extraction, stereochemistry detection, skeleton matching
• MOL/SDF: V2000/V3000 block parsing, molecule counting
• PDB/CIF/XYZ: Protein structure analysis (atom, chain, residue, model counts)
• SELFIES: Bidirectional SMILES-SELFIES conversion for ML pipelines

39 scalar SQL functions for molecular property extraction, format conversion, structural comparison, and physicochemical property prediction. Ideal for cheminformatics datasets, drug discovery pipelines, and molecular ML feature engineering.

LogP: logp_crippen() implements the Wildman-Crippen atom-contribution method (110 SMARTS patterns, 68 atom types) and matches RDKit's Crippen.MolLogP exactly for small molecules.

Morgan / ECFP fingerprint: morgan_fp_bits() ports RDKit's MorganGenerator (layered BFS + hash_combine + dead-atom dedup) to Rust and returns a fixed-width bit vector as BLOB. Defaults to ECFP4 (radius=2, 2048 bit); 3-arg overload morgan_fp_bits(smi, radius, n_bits) exposes full control.

Tanimoto similarity: tanimoto_bit(BLOB, BLOB) -> DOUBLE computes popcount(a & b) / popcount(a | b) directly on raw BLOB bytes (no CAST AS BIT round-trip), processing 8 bytes at a time via count_ones() so it lowers to POPCNT on x86_64 / CNT on aarch64. Mismatched lengths raise a clear InvalidInputException; empty-vs-empty returns 0.0 (RDKit convention). The SQL-level bit_count(a & b)::DOUBLE / bit_count(a | b) is still available and produces bit-exact identical results.

Architecture: Rust (core logic, 5 crates) + C++ (DuckDB integration via FFI)

Added Functions

Overloaded Functions

This extension does not add any function overloads.

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