- GenerateMD generates various molecular descriptors including chemical hashed and pharmacophore fingerprints for molecules, which may be used for structural diversity computations and clustering.
- 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 analysis.
- 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 or Ward. The generated SDfiles can be displayed by MarvinView or other SDF viewer.