rdkit

rdkit : Cheminformatics functionality for PostgreSQL.

Overview

Packages

Source

pig build pkg rdkit;		# build rpm/deb

Install

Make sure PGDG and PIGSTY repo available:

pig repo add pgsql -u   # add both repo and update cache

Install this extension with pig:

pig install rdkit;		# install via package name, for the active PG version

pig install rdkit -v 18;   # install for PG 18
pig install rdkit -v 17;   # install for PG 17
pig install rdkit -v 16;   # install for PG 16
pig install rdkit -v 15;   # install for PG 15
pig install rdkit -v 14;   # install for PG 14

Create this extension with:

CREATE EXTENSION rdkit;

Usage

Sources:

• Cartridge documentation
• Control
• SQL template
• Upgrade script

rdkit provides molecular types, substructure search, fingerprints and chemical descriptors. This page follows the PostgreSQL cartridge shipped in RDKit 2026.03.6.

Create The Extension

CREATE EXTENSION rdkit;

The cartridge adds chemistry-specific types including mol, bfp, and sfp.

Core Search Operators

The cartridge documentation covers:

• @> and <@ for substructure matching.
• @= for exact molecular equality.
• %, <%>, and <#> style fingerprint similarity and KNN operators for similarity search.

These are typically combined with GiST indexes over fingerprint columns.

Fingerprints And Similarity

Common fingerprint functions documented for SQL usage include morgan_fp, morganbv_fp, featmorgan_fp, rdkit_fp, atompair_fp, torsion_fp, layered_fp, and maccs_fp.

Example from the cartridge docs:

SELECT tanimoto_sml(
  morganbv_fp('c1ccccc1'::mol),
  morganbv_fp('c1ccccc1O'::mol)
);

Descriptors And Validation

The cartridge docs also expose validation and descriptor helpers such as:

• is_valid_smiles()
• is_valid_ctab()
• is_valid_smarts()
• mol_amw()
• mol_hba()
• mol_numrings()

These functions are the main user-facing surface for SQL analytics on molecular structures.

Version and Upgrade Boundary

The RDKit toolkit release 2026.03.6 contains SQL extension version 4.8.0; these are different version namespaces. The upstream 4.7.0 to 4.8.0 SQL template changes function costs, but its fmcs_smiles statement has a line comment that swallows the cost clause and terminator. Do not assume an unpatched ALTER EXTENSION rdkit UPDATE path works: verify the installed upgrade script and test the update on a restored copy first. A packaging patch is distinct from the upstream source.