Installation

Installing this software involves the following general steps: installing Python version 3.5, the commongroups Python package, and all of its software dependencies; initializing a PostgreSQL database and installing the RDKit extension; building a structure-searchable database.

The recommended way to install Python is with the Anaconda Python distribution, or the light-weight Miniconda distribution. This has the benefits of allowing installation of RDKit using the conda package manager, and simultanously creating a separate Python environment for Common Groups (which is highly recommended).

On Linux systems, parts of the installation process can be done automatically using a shell script that we provide.

Step by step

Any system

  1. Install Miniconda.

  2. Create a new conda environment and install RDKit, then activate the new environment:

    conda create -n <name> -c rdkit rdkit cairocffi
source activate <name>

    Where <name> is the name of the new conda environment to create (for example, cmg_env).

  3. Install the commongroups Python package and the rest of its software dependencies:

    pip install commongroups

  4. Install PostgreSQL. Initialize a PostgreSQL database and install the RDKit extension. See specific installation instructions for RDKit/PostgreSQL on your operating system.

Linux systems

  1. Install Miniconda.

  2. Clone or download the Common Groups repository.

  3. Run the provided shell script to install all software dependencies and initialize a PostgreSQL database with the RDKit extension:

    bash tools/install_deps.sh -n <name> -d <datadir>

    Where <name> is the name of the new conda environment to create (for example, cmg_env), and <datadir> is the path to a directory which shall be used as the PostgreSQL data directory.

    Make note of the database URL and instructions for starting/stopping the database server, which will be displayed if the install is successful.

Automated database instantiation

If you have already installed Common Groups software and dependencies, and have a PostgreSQL server running with the RDKit extension installed, then you can use some tools included with Common Groups to automatically download data and set up a database.

  • Clone or download the Common Groups repository.

  • First, download the data:

    bash tools/download_epa.sh <source_data_dir>

    Where <source_data_dir> is a directory where you want to store EPA data files (not the PostgreSQL data directory). If you do not have the bash shell on your system (i.e., Windows), it’s probably easier to just download using the links above.

  • Process the data to create a structure-searchable database:

    python tools/construct_database.py -u <db_url> -d <source_data_dir>

    Where <db_url> is the database URL and <source_data_dir> is the same directory where EPA data was downloaded. Note: This will take a long time and consume significant computational resources!

Next steps

After installing, configure Common Groups on your system to use the proper database, preferred file locations, and a Google Service Account (optional).