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