Molecule Set Comparator (MSC)

Molecule Set Comparator (MSC) is designed as an application that enables a user to do a versatile and fast comparison of large molecule sets with a unique inter-set, molecule-to-molecule comparison, for the original set and a predicted set of molecules obtained by machine learning approaches.
The molecule-to-molecule comparison is based on chemical descriptors, which are included in the Chemistry Development Kit (CDK), such as Tanimoto similarities, atom/bond/ring counts, and physicochemical properties like logP. The results are presented graphically and summarized by interactive histograms that can be exported in publication quality

Contents of subfolders

Tutorials - a comprehensive step-by-step guide for the installation of MSC (MSC_Installation_Guide.pdf), a short introductory tutorial for MSC usage (MSC_1.0_Tutorial.pdf) and an application example (MSC_Application_Example.pdf)
src - all Java source files and resources
lib - open libraries used by MSC
installation - contains the installation folder MSC_1.0 to be copied to a local machine for MSC execution.
- Note, that an additional JDK download is necessary (see instructions in subdirectory JDK-11.0.2).
- For a guided installation look at the installation guide in the Tutorials folder
Gradle Project for Netbeans - a Gradle project that can be compiled and run with Gradle, the Netbeans IDE or any other IDE that supports Gradle (JDK 11 or higher is needed)

A precompiled fat jar file (that includes all dependent libraries) is already provided in this repository. To directly use it, please have a look at the steps provided under the installation directory.
Alternatively, the MSC can be compiled using Gradle. For this, have a look at the Gradle Project for Netbeans folder where additional information is provided

K. Rajan, J.-M. Hein, C. Steinbeck and A. Zielesny, Molecule Set Comparator (MSC) – A CDK-based open rich-client tool for molecule set similarity evaluations, Journal of Cheminformatics (2021), 13:5