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  • Poster presentation
  • Open Access

The FPS fingerprint format and chemfp toolkit

Journal of Cheminformatics20135 (Suppl 1) :P36

  • Published:


  • Similarity Search
  • Performance Requirement
  • Poster Session
  • Draft Version
  • Careful Indexing

During GCC 2010 poster session I presented a draft version of the FPS format for storing dense binary fingerprints. That format is now stable, and supported by RDKit [1], CACTVS [2], and other software. The chemfp package is a set of command-line tools and a Python library for fingerprint generation and high-speed Tanimoto search. It can extract pre-computed fingerprints from an SD tag or use OpenEye's OEChem [3], Open Babel [4], or RDKit to generate fingerprints. Search uses a combination of careful indexing [5], CPU-specific instructions (if available), and OpenMP. Nearest-100 similarity searches of PubChem-sized take less than a second on a laptop, and Butina clustering [6] of 2 million compounds takes about 6 hours on a 15 CPU node. In my poster I present the FPS format and chemfp package, and describe how the memory and performance requirements lead to the internal search architecture.

Authors’ Affiliations

Andrew Dalke Scientific, 41134 Göteborg, Sweden


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  5. Swamidass SJ, Baldi P: Bounds and Algorithms for Fast Exact Searches of Chemical Fingerprints in Linear and Sublinear Time. J Chem Inf Model. 2007, 47: 302-317. 10.1021/ci600358f.View ArticleGoogle Scholar
  6. Butina D: Unsupervised Data Base Clustering Based on Daylight's Fingerprint and Tanimoto Similarity: A Fast and Automated Way To Cluster Small and Large Data Sets. J Chem Inf Model. 1999, 39: 747-750. 10.1021/ci9803381.View ArticleGoogle Scholar


© Dalke; licensee BioMed Central Ltd. 2013

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.