molenc

Molecular encoder/featurizer using rdkit and OCaml
Description

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 are supported. In the future, atom pair fingerprints might be added. 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).

Bibliography:

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.

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.

OpenSMILES specification. Craig A. James et. al. v1.0 2016-05-15. http://opensmiles.org/opensmiles.html

Install
Published
21 Nov 2019
Authors
Maintainers
Sources
v5.0.1.tar.gz
md5=c665b8e27de72f2b7ccf5f54d758ed28
Dependencies
ocaml >= "4.04.0" & < "5.0"
dune >= "1.11"
dolog >= "4.0.0" & < "5.0.0"
bst >= "2.0.0"
Reverse Dependencies
linwrap >= "9.0.3"
rankers < "2.0.9"