clusfps is just a script that I wrote on the top of RDKit (2015_03_1) to do compound structure clustering. This script is under the terms of the WTFPL(Do What the Fuck You Want to Public License).
RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python. Detail information can be found at Github
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cp the whole RDKit package to a folder like d:/RDKit_2015_03_1
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Add environment variables RBASE=d:/RDKit_2015_03_1
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Add environment variables PYTHONPATH:%RBASE%
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Add environment variables PATH:%RDBASE%/lib
Detail installation guild can be found at RDKit install guild
Two steps are included in clusfps: fingerprint generation and cluster calculation. Three type of fingerprint can be calculated: Topological Fingerprints, MACCS Keys and Morgan Fingerprints. Morgan Fingerprints generation needs users to define radius through command-line. Cluster algorithm include Butina and Murtagh. When using Butina, a cutoff is needed , which means elements within this range of each other are considered to be neighbors. When using Murtagh, the number of clusters should be pre-defined. Example can be found at Example
