ipbhalle/crimsydb repository overview

⁠CRIMSy Container Images

This project provides a collection of container images for use with CRIMSy⁠:

• An PostgreSQL image augmented with an extension for chemical structure handling (currently used: Bingo https://github.com/epam/Indigo⁠)
• An Apache HTTP Server image containing a selection of JavaScript libraries for chemical drawing and spectra display

Additionally, this project provides Dockerfiles for experimenting with additional PostgreSQL releases and database extensions: (RDKit⁠ and pgchem::tigress⁠

⁠Getting started

To set up a fresh database container, usually the following sequence of commands is needed:

cd crimsydb/$FLAVOUR
docker build -t crimsydb:$FLAVOUR .
docker run -e POSTGRES_PASSWORD="your-OWN-password" -v /path/to/your/storage:/var/lib/postgresql/data crimsydb:$FLAVOUR

$FLAVOUR currently can be one of bingo_pg11, bingo_pg12, ccdbc_pg11 or rdkit_pg13. If you want to avoid building yourself, please use either ipbhalle/crimsydb:bingo_pg12 or ipbhalle/ccdbc (outdated) from the docker registry. For smaller experiments, you can omit -v option and store the data in your container.

A newly set up database requires activation of the database extensions. See the following example commands for reference:

// Bingo
/*
    GRANT USAGE ON SCHEMA bingo TO %ROLE%;
    GRANT SELECT ON bingo.bingo_config TO %ROLE%;
    GRANT SELECT ON bingo.bingo_tau_config TO %ROLE%;
 */
CREATE TABLE example_bingo (
    id SERIAL NOT NULL PRIMARY KEY,
    mol TEXT);
CREATE INDEX i_example_bingo_mol_idx ON example_bingo USING bingo_idx (mol bingo.molecule);
SELECT * from example_bingo WHERE mol @ ('CCOCC', '')::bingo.sub;


// pgchem::tigress
CREATE EXTENSION IF NOT EXISTS "pgchem_tigress";
CREATE TABLE example_pgchem (
    id SERIAL NOT NULL PRIMARY KEY,
    mol MOLECULE);
CREATE INDEX i_example_pgchem_mol_idx ON example_pgchem USING gist(mol);
SELECT * from example_pgchem WHERE mol >= 'CCOCC';

// RDKit
CREATE EXTENSION IF NOT EXISTS "rdkit";
CREATE TABLE example_rdkit (
    id SERIAL NOT NULL PRIMARY KEY,
    mol MOL);
CREATE INDEX i_example_rdkit_mol_idx ON example_rdkit USING gist(mol);
SELECT * from example_rdkit WHERE mol @> 'CCOCC';

⁠More docs

The containers are based on the official Apache httpd and PostgreSQL containers, respectively. For reference see

• Apache httpd: https://hub.docker.com/_/httpd⁠ and https://github.com/docker-library/docs/blob/master/httpd/README.md⁠
• PostgreSQL: https://hub.docker.com/_/postgres⁠ and https://github.com/docker-library/docs/blob/master/postgres/README.md⁠
• Bingo: https://github.com/epam/Indigo⁠ and https://lifescience.opensource.epam.com/bingo/user-manual-postgres.html⁠
• RDKit: https://www.rdkit.org/docs/Cartridge.html⁠ and [
• pgchem::tigress: https://github.com/ergo70/pgchem_tigress/⁠ Please note that pgchem::tigress builds on GPL licensed OpenBabel⁠.

Have fun!