opam-version: "2.0"
authors: "Francois Berenger"
maintainer: "unixjunkie@sdf.org"
homepage: "https://github.com/UnixJunkie/molenc"
bug-reports: "https://github.com/UnixJunkie/molenc/issues"
dev-repo: "git+https://github.com/UnixJunkie/molenc.git"
license: "BSD-3"
build: ["dune" "build" "-p" name "-j" jobs]
install: [
  # ["cp" "bin/molenc_ph4_type_atoms.py" "%{bin}%/molenc_ph4_type_atoms.py"]
  ["cp" "bin/molenc_common.py" "%{bin}%/molenc_common.py"]
  ["cp" "bin/molenc_type_atoms.py" "%{bin}%/molenc_type_atoms.py"]
  ["cp" "bin/molenc_scan.py" "%{bin}%/molenc_scan.py"]
  ["cp" "bin/molenc.sh" "%{bin}%/molenc.sh"]
  ["cp" "bin/molenc_scan.sh" "%{bin}%/molenc_scan.sh"]
]
depends: [
  "bst"
  "dune" {>= "1.11"}
  "batteries"
  "dolog" {>= "4.0.0" & < "5.0.0"}
  "minicli"
  "conf-rdkit"
  "conf-python-3"
  "ocaml" {>= "4.04.0"}
  "parmap"
]
synopsis: "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
"""
url {
  src: "https://github.com/UnixJunkie/molenc/archive/v5.0.0.tar.gz"
  checksum: "md5=b1624a02bc9d75d003a2b63e3bf65804"
}
