Installing CDK (Chemistry Development Kit) on Ubuntu (Linux)

CDK stands for chemistry development kit [1]. This is an open source kit for cheminformatics consisting of modular JAVA libraries. In this article, we will install CDK on Ubuntu.

Preparing system

Open a terminal by pressing Ctrl+Alt+T. Update and upgrade your system using the following commands:

$ sudo apt-get update

$ sudo apt-get upgrade

Installing prerequisites

You need to install the following packages to run CDK on your system. Paste the following command in the terminal.

$ sudo apt-get install -y maven

$ sudo apt-get install -y default-jdk

Downloading CDK

At first, change to the directory where you want to download the software. Let’s say ‘Downloads‘.

$ cd Downloads/

You can either manually download the latest version of the CDK from here or use the following command.

$ wget https://github.com/cdk/cdk/archive/refs/tags/cdk-2.5.tar.gz

It will take a moment to finish downloading.

Installing CDK

Extract the downloaded package.

$ tar xvzf cdk-2.5.tar.gz

A new directory would have been created namely, cdk-cdk-2.5. Change to this new directory to install.

$ cd cdk-cdk-2.5/

Now install using the following command.

$ mvn install

It will be finished in a few moments.

References

1. Steinbeck, C., Han, Y., Kuhn, S., Horlacher, O., Luttmann, E., & Willighagen, E. (2003). The Chemistry Development Kit (CDK): An open-source Java library for chemo-and bioinformatics. Journal of chemical information and computer sciences, 43(2), 493-500.