Read and write protein structure mmcif files using SQL
Installing and Loading
INSTALL mmcif FROM community;
LOAD mmcif;
Example
sql
-- single table SELECT count(*) FROM mmcif_scan('https://files.rcsb.org/download/1AMB.cif.gz', 'atom_site'); -- 438
-- All tables in file ATTACH 'https://files.rcsb.org/download/1AMB.cif.gz' AS mmcifdb (TYPE mmcif); USE mmcifdb;
SELECT count(*) FROM information_schema.tables WHERE table_catalog = 'mmcifdb'; -- 43
SELECT count(*) FROM atom_site; -- 438
-- Positions of Zinc atoms SELECT Cartn_x, Cartn_y, Cartn_z FROM atom_site WHERE type_symbol = 'ZN';
-- Write mode 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; -- writes the mutated tables back to the attached file
Added Functions
| function_name | function_type | description | comment | examples |
|---|---|---|---|---|
| mmcif_relationships | table | NULL | NULL | |
| mmcif_scan | table | NULL | NULL | |
| mmcif_tables | table | NULL | NULL |
Overloaded Functions
This extension does not add any function overloads.
Added Types
This extension does not add any types.
Added Settings
This extension does not add any settings.