Molecular encoder/featurizer using rdkit and OCaml

Chemical fingerprints are lossy encodings of molecules. molenc allows to encode molecules using unfolded-counted fingerprints (i.e. a potentially very long but sparse vector of positive integers).

Currently, Faulon fingerprints and atom pairs are supported.

Currently, atom types are the quadruplet (#pi-electrons, element symbol, #HA neighbors, formal charge). In the future, pharmacophore features might be supported (a more abstract/fuzzy atom typing scheme).


Faulon, J. L., Visco, D. P., & Pophale, R. S. (2003). The signature molecular descriptor.

  1. Using extended valence sequences in QSAR and QSPR studies. Journal of chemical information and computer sciences, 43(3), 707-720.

Carhart, R. E., Smith, D. H., & Venkataraghavan, R. (1985). Atom pairs as molecular features in structure-activity studies: definition and applications. Journal of Chemical Information and Computer Sciences, 25(2), 64-73.

Kearsley, S. K., Sallamack, S., Fluder, E. M., Andose, J. D., Mosley, R. T., & Sheridan, R. P. (1996). Chemical similarity using physiochemical property descriptors. Journal of Chemical Information and Computer Sciences, 36(1), 118-127.

OpenSMILES specification. Craig A. James et. al. v1.0 2016-05-15.

AuthorFrancois Berenger
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