SpaceCompare is a command line tool for the product overlap calculation of large, nonenumerable combinatorial fragment spaces. SpaceCompare utilizes the combinatorial character of fragment spaces. This way SpaceCompare is able to determine the overlap of chemical libraries containing billions or even trillions of compounds for the first time.
The SpaceCompare tool is available for Linux, MacOS and Windows as part of the NAOMI ChemBio Suite at htttps://uhh.de/naomi and is free for academic use and evaluation purposes.
To calculate the overlap of your custom space with the KnowledgeSpace, a publicly available combinatorial fragment space of over 1015 conpounds, access it at https://www.zbh.uni-hamburg.de/forschung/amd/datasets.html#knowledge