kelly1210 / clusfps

A Molecular cluster tools built on RDKit

clusfps

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

RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python. Detail information can be found at Github

RDKit on windows

1. cp the whole RDKit package to a folder like d:/RDKit_2015_03_1

2. Add environment variables RBASE=d:/RDKit_2015_03_1

3. Add environment variables PYTHONPATH:%RBASE%

4. Add environment variables PATH:%RDBASE%/lib

RDKit on Linux

Detail installation guild can be found at RDKit install guild

clusfps clustering process

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