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. We recommended using conda.

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. Either way, choose the Python 3 version.

Once installed, at the command line, run:

conda config --add channels conda-forge
conda install chemdataextractor

The first command adds the conda-forge channel as a package source, then the second command installs the chemdataextractor package from this channel.

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.


Upgrade your installation to the latest version at any time using conda:

conda update chemdataextractor

Remember to download any new data files after doing this:

cde data download