Chemistry Development Kit (CDK)

Introduction to CDK

The Chemistry Development Kit (CDK) is a Java library for cheminformatics and bioinformatics, developed at the University of Notre Dame. It's an open-source toolkit, available for Windows, Linux, Unix, and macOS, and distributed under the GNU Lesser General Public License (LGPL) 2.0. CDK is used extensively in drug discovery, metabolomics, and toxicology. Explore more at CDK GitHub

Key Features of CDK

• Diverse Chemical Data Structures: Provides data structures for chemical concepts and methods for computations on these structures.
• Cheminformatics Algorithms: Implements algorithms for chemical structure normalization, molecular descriptor computation, and pharmacophore sensing.
• Bioinformatics Applications: Includes protein active site detection, cognate ligand detection, and metabolite identification.

Capabilities and Services

• Bioinformatics Services: Protein descriptors, pathway database analysis.
• Cheminformatics Services: QSAR descriptor calculations, coordinate generation, substructure searches.
• File Format Support: Reads and writes various formats like SMILES, SDF, InChI, Mol2, CML.
• Molecular Processing Algorithms: Efficient algorithms for ring search, kekulisation, and aromaticity detection.

Advanced Features

• 2D Graphics Drawing: Controller2D for model changes and Renderer2D for 2D graphics.
• Aromaticity Detection: Based on the Hückel rule, labeling atoms and bonds in aromatic rings.
• Isomorphism Detection: Essential for determining structural similarities or differences.
• Structure Generators: For computer-aided structure interpretation.

How to Run a Case:

This example demonstrates how to generate a SMILES string for a molecule using the CDK library. To run the example, you will need the CDKTest.java program and the run_script.sh script.

Downloading the Files

You can download the required files using the following links:

• CDKTest.java - The Java program file.
• run_script.sh - The shell script to compile and run the Java program.

Steps to Execute on Our Platform

1. Upload Files: On the Volume line, click on the folder icon and upload both CDKTest.java and run_script.sh to the working directory of the project.
2. Set Project Directory: Ensure the Project Directory is set to /volume.
3. Configure Run Script: In the Run Script line, add run_script.sh as the input.
4. Create the Project: Click on Create to set up your project.
5. Run the Container: Navigate to the project tab and initiate the container to execute the script.

By following these steps, the platform will compile and run CDKTest.java, outputting a SMILES string for a simple molecule to the console. Ensure you have uploaded the correct files and set the appropriate configurations as outlined above.

Tags for CDK

1. Cheminformatics
2. Bioinformatics
3. Molecular Descriptor Computation
4. Drug Discovery
5. Structure Analysis

Explore CDK Documentation