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



Installing cdk on Ubuntu

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

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.


  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 sciences43(2), 493-500.

Dr. Muniba is a Bioinformatician based in New Delhi, India. She has completed her PhD in Bioinformatics from South China University of Technology, Guangzhou, China. She has cutting edge knowledge of bioinformatics tools, algorithms, and drug designing. When she is not reading she is found enjoying with the family. Know more about Muniba

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