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: [
  "batteries"
  "bst"
  "conf-python-3"
  "conf-rdkit"
  "cpm"
  "dokeysto"
  "dolog" {>= "4.0.0" & < "5.0.0"}
  "dune" {>= "1.11"}
  "minicli"
  "ocaml"
  "parany" {>= "9.0.0" & < "11.0.0"}
]
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 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).

Bibliography:
=============

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.
http://opensmiles.org/opensmiles.html
"""
url {
  src: "https://github.com/UnixJunkie/molenc/archive/v8.0.2.tar.gz"
  checksum: "md5=62e5c7ffff4227ab46c9e0134037f019"
}
