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Colibri

About colibri

colibri is your Lightweight and Gregarious Chemistry Explorer. Use it to create new molecules, to construct chemical networks, and to compute their properties in a distributed fashion. colibri is written in Python.

Prerequisites

  • RDKit: open-source cheminformatics toolkit.
  • OpenBabel: chemistry format converter.
  • MOPAC: semiempirical quantum chemistry program maintained by J. Stewart.
  • ORCA: modern electronic structure program by F. Neese and co-workers.
  • MongoDB: high-performance document database and Python driver pymongo.
  • Memcached and pure-Python client pymemcache.
  • Neo4J: modern graph database (v3) and Python driver (v3) py2neo.

Working with colibri

 usage: colib [-h] [--version] [--no-config] [--no-site-config]
             [--site-config-path PATH] [--no-user-config] [--no-env-config]
             [--no-proj-config] [--config-file FILE] [-d HOST]
             [--db-port PORT] [--write-attempts N] [--write-interval T]
             [-t DB] [-k COLL] [-T DB] [-K COLL] [--with-raw-write]
             [--no-raw-write] [--raw-database DB] [--raw-collection COLL] [-H]
             [--no-cache] [--cache-hostname URL] [--cache-port PORT]
             [--cache-expire T] [--scratch-path PATH] [--executable-path PATH]
             [-n N] [-N N] [--count-idle-tasks] [--save-completed-tasks]
             [--polling-interval T] [--idle-interval T] [-L LEVEL] [-v] [-q]
             [--action-delay N] [-p] [-P] [-!] [--no-shutdown]
             [--idle-tasks-per-calc N] [--shutdown-quorum N]
             {init,add,fetch,delete,run,stat,suspend,resume,load,dump,graph,clean,config,doctor,key,network,proton}
             ...

colibri is your lightweight and gregarious chemistry explorer

optional arguments:
  -h, --help            show this help message and exit

execution arguments:
  --version             show program's version number and exit
  --no-config           ignore all configuration files
  --no-site-config      skip site configuration file
  --site-config-path PATH
                        location of site configuration. Default:
                        /usr/local/etc
  --no-user-config      skip user configuration file
  --no-env-config       skip configuration environment variables
  --no-proj-config      skip project configuration file
  --config-file FILE    colibri configuration file name. Default: colibri.json

configuration arguments:
  -d HOST, --db-hostname HOST
                        MongoDB database hostname
  --db-port PORT        MongoDB database port
  --write-attempts N    number of database write attempts before warning is
                        issued
  --write-interval T    interval in s between database write attempts
  -t DB, --mol-database DB
                        MongoDB molecule database name
  -k COLL, --mol-collection COLL
                        MongoDB molecule collection name
  -T DB, --flask-database DB
                        MongoDB flask database name
  -K COLL, --flask-collection COLL
                        MongoDB flask collection name
  --with-raw-write      write raw output files
  --no-raw-write        do not write raw output files
  --raw-database DB     MongoDB raw file database name
  --raw-collection COLL
                        MongoDB raw collection prefix
  -H, --with-cache      use Memcached cache
  --no-cache            do not use Memcached cache
  --cache-hostname URL  Memcached cache server location
  --cache-port PORT     Memcached cache port
  --cache-expire T      Memcached key expiration time in s
  --scratch-path PATH   scratch directory for task execution
  --executable-path PATH
                        search path for external executables
  -n N, --tasks-per-calc N
                        number of tasks per calculator
  -N N, --tasks-per-cycle N
                        number of tasks per calculator cycle
  --count-idle-tasks    count idle tasks as completed
  --save-completed-tasks
                        save completed tasks in calculator for debugging
  --polling-interval T  interval for calculator polling in s
  --idle-interval T     wait interval for database queries by idle tasks in s
  -L LEVEL, --logging-level LEVEL
                        logging level
  -v, --verbose         set logging level to DEBUG
  -q, --quiet           set logging level to ERROR
  --action-delay N      delay in s before shutdown or calculator restart
  -p, --with-persistent-pool
                        maintain a persistent calculator pool
  -P, --no-persistent-pool
                        do not maintain a persistent calculator pool
  -!, --with-shutdown   shut down calculators after being idle
  --no-shutdown         do not shut down calculators
  --idle-tasks-per-calc N
                        number of idle tasks before calculator declared idle
  --shutdown-quorum N   number of idle calculators before shutdown

colibri subcommands:
  {init,add,fetch,delete,run,stat,suspend,resume,load,dump,graph,clean,config,doctor,key,network,proton}
    init                initialize database
    add                 add data to database
    fetch               fetch data from database
    delete              delete data from database
    run                 run computation on database
    stat                retrieve database statistics
    suspend             suspend computation
    resume              resume computation
    load                load graph file into database
    dump                dump database as graph file
    graph               export database to graph storage
    clean               clean database
    config              configure colibri
    doctor              check database for potential issues
    key                 return flask or molecule keys
    network             run task suite for creating networks
    proton              compute the energy of a proton

Authors

colibri is maintained by Dmitrij Rappoport, email Dmitrij