JKlustor

JKlustor is a Java software for diversity calculations and clustering. The module is integrated with JChem (its classes are included in jchem.jar).
Though the audience of the JChem system are chemists, JKlustor is not specific to molecules, it can be applied to other types of objects.

At present, JKlustor includes the following command-line tools:

• GenerateMD generates various molecular descriptors including chemical hashed fingerprints and pharmacophore fingerprints for molecules, which may be used for structural diversity computations and clustering.
• Compr compares two sets of objects (like compound libraries) using diversity and dissimilarity calculations.
  • Comparing all individual compounds of a set with a library.
  • Comparing two libraries.
  • Library self-dissimilarity test: comparing all individual compounds of a set with the rest of the compounds.
• Jarp performs variable-length Jarvis-Patrick clustering.
• Ward clusters molecules using Ward's hierarchic clustering method applying the RNN approach.
• LibMCS clusters molecules by maximum common substructures in a hierarchical manner. It can be applied to focused set profiling and diversity analisys.
• CreateView composes an SDfile that contains both structures and calculation results using the input SDfile of GenerateMD and a table containing the ordinal number of compounds from the SDfile and other data to be viewed. Such table can be created for example by Compr, Jarp, or Ward. The generated SDfiles can be displayed by the MarvinView application or other SDF viewer.