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: GitHub README, Cartridge docs, project site RDKit provides a PostgreSQL cartridge for cheminformatics storage, search, fingerprints, and descriptors.

CREATE EXTENSION rdkit;

The cartridge adds molecular types and operators for substructure search, exact match, similarity search, fingerprint generation, and many descriptor functions.

Core Types

• mol for molecule and query molecule values.
• bfp for bit-vector fingerprints.
• sfp for sparse count fingerprints.

Search Operators

• @> checks whether the right-hand molecule is a substructure of the left-hand molecule.
• <@ performs the reverse substructure check.
• @= checks exact molecular equality.
• # is the Dice similarity threshold operator.
• <%> supports Tanimoto KNN searches.
• <#> supports Dice KNN searches.

Fingerprints

• morgan_fp and morganbv_fp for Morgan fingerprints.
• featmorgan_fp and featmorganbv_fp for feature-based Morgan fingerprints.
• rdkit_fp for hashed RDKit fingerprints.
• atompair_fp, atompairbv_fp, torsion_fp, and torsionbv_fp.
• layered_fp and maccs_fp.

Descriptor Examples

SELECT is_valid_smiles('c1ccccc1');
SELECT tanimoto_sml(morganbv_fp('c1ccccc1'::mol), morganbv_fp('c1ccccc1O'::mol));
SELECT mol_amw('c1ccccc1'::mol);
SELECT mol_hba('c1ccccc1O'::mol);
SELECT mol_numrings('c1ccccc1'::mol);

Notes

• The docs describe additional molecule-validation helpers such as is_valid_smiles, is_valid_ctab, and is_valid_smarts.
• The cartridge also exposes many additional descriptor and fingerprint size GUCs, but the stub keeps only the core user-facing entry points.