Installation

To get up and running with ChemDataExtractor, you will need to install the python toolkit and then download the data files.

Installing the Toolkit

There are a few different ways to download and install the ChemDataExtractor toolkit.

Option 1: Use conda

This method is recommended for all Windows users, as well as beginners on all platforms who don't already have Python installed. Anaconda Python is a self-contained Python environment that is particularly useful for scientific applications.

Start by installing Miniconda, which includes a complete Python distribution and the conda package manager, or Anaconda, which additionally includes many pre-installed packages. Choose the Python 3.5 version, unless you have a particular reason why you must use Python 2.7.

Once installed, at the command line, run:

conda install -c chemdataextractor chemdataextractor

This command installs the chemdataextractor package from the chemdataextractor conda channel.

Option 2: Use pip

If you already have Python installed, it's easiest to install the ChemDataExtractor package using pip. At the command line, run:

pip install ChemDataExtractor

On Windows, this will require the Microsoft Visual C++ Build Tools to be installed. If you don't already have pip installed, you can install it using get-pip.py.

Option 3: Download the Latest Release

Alternatively, download the latest release manually and install yourself by running:

python setup.py install

The setup.py command will install ChemDataExtractor in your site-packages folder so it is automatically available to all your python scripts.

You can also get the unstable development version by cloning the git source code repository.

Getting the Data Files

In order to function, ChemDataExtractor requires a variety of data files, such as machine learning models, dictionaries, and word clusters. Get these by running:

cde data download

This will download all the necessary data files to the data directory. Run cde data where to see where this is.

Updating

Upgrade your installation to the latest version at any time using conda or pip, matching the method you used originally to install it. For conda, run:

conda update -c chemdataextractor chemdataextractor

For pip, run:

pip install --upgrade ChemDataExtractor

Either way, always remember to download any new data files after doing this:

cde data download