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CGRdb

Chemical cartridge for reactions and molecules.

INSTALL

Stable version

pip install CGRdb

Stable version with index support

pip install CGRdb[index]

DEV version

pip install -U git+https://github.com/stsouko/CGRdb.git@master#egg=CGRdb

INDEX GENERATION

Index stored in RAM and implemented as http service. Index can be hosted on a different machine.

cgrdb index -c '{"host": "localhost", "password": "your password", "user": "postgres"}'
    -n 'schema_name'
    -p '{"check_threshold": null or positive float in range 0-1,
         "threshold": float in range 0-1 (approximate treshold for MinHashLSH),
         "num_perm": MinHashLSH parameter,
         "n_workers": number of workers for index creation,
         "chunk_size": 10000}'
    -d path/to/index.dump

default parameters : check_threshold=.7, threshold=.6, num_perm=64, n_workers=1, chunk_size=10000

INDEX LOADING

cgrdb daemon -p '{parameters of aiohttp run_app}' -d path/to/index.dump

For each schema separate daemons should be used.

SETUP

initialize CGRdb [after postgres setup only] [need only once]

cgrdb init -c '{"host": "localhost", "password": "your password", "user": "postgres"}'

Note: connection config is JSON string with arguments acceptable by psycopg2

create database

cgrdb create -c '{"host": "localhost", "password": "your password", "user": "postgres"}'
    -n 'schema_name'
    -f 'path/to/cartridge.parameters. see example config.json}'

Note: database admin rights required (postgres user by default)
Note: schema 'schema_name' will be dropped if exists and not proper CGRdb schema.

POSTGRES SETUP (Ubuntu example)

install postgresql (required version 10 or newer):

sudo apt install postgresql postgresql-plpython3-10

edit user:

sudo -u postgres psql
ALTER USER postgres WITH PASSWORD 'your password';
\q

uncomment and change next line in /etc/postgresql/10/main/postgresql.conf

deadlock_timeout = 10s

restart postgres

sudo systemctl restart postgresql

install CGRtools, StructureFingerprint into system or virtual environment accessible for postgres user.

sudo pip3 install CGRtools StructureFingerprint

Note: virtual environment should contain in bin directory activate_this.py script.

COPYRIGHT

2017-2021 Ramil Nugmanov nougmanoff@protonmail.com

CONTRIBUTORS