The LibraryMCS computes the maximum common substructure (MCS) of a set of compounds. Typical size of such set is a few thousand molecules. It is not only one common subgraph that the algorithm determines (since in most cases it would be not more than two single bonded carbon atoms), instead some of the most frequently occuring common substructures are found. The more diverse the set to be analysed is the larger the number of the frequent common substructures is, while in case of a more focused set with limited structural diversity, the number of frequent common substructures is smaller. The algorithm is capable of going one or more level further finding the MCS of the frequent common substructures - and again, this is not one single structure, but the most frequently occuring ones and so on. Thus a hierarchy of the common substructures is obtained. Practically speaking structures are clustered based on their MCS in a hierarchical clustering procedure. This class implements the ClusteredMolecules interface, which allows client to retieve the hierarchy found. The tree of clusters as well as data associated to nodes of this tree (in this case molecule sin the leaves and maximum common substructures in the higher level tree nodes) can be accessed via this interface. This class also provides a simple command line interface for batch processing of MCS search for a set of structures, as well as a simple graphical user interface for easy navigation through clusters of structures.
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