duckdb-mmcif

Query mmCIF (PDBx) structural-biology files with SQL, right inside DuckDB.

ATTACH a .cif file and every mmCIF category shows up as a normal DuckDB table — with column types inferred from the PDBx/mmCIF dictionary. No ETL, no schema design, no Python parsing loop: just SQL over macromolecular structure data.

LOAD 'mmcif.duckdb_extension';

-- Read only
ATTACH 'https://files.rcsb.org/download/1AMB.cif.gz' AS mmcifdb (TYPE mmcif);

SELECT count(*) FROM mmcifdb.atom_site;

-- Write
ATTACH '1amb_updated.cif' AS wdb (TYPE mmcif, READ_WRITE TRUE);
USE wdb;

BEGIN;
INSERT INTO atom_site (label_atom_id, Cartn_x, type_symbol) VALUES ('O1', 3.5, 'O');
UPDATE atom_site SET type_symbol='ZZ' WHERE label_atom_id='O1';
DELETE FROM atom_site WHERE label_atom_id='O1';
COMMIT;   -- updates 1amb_updated.cif file