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anil.recoil.org
1opam-version: "2.0"
2authors: "Francois Berenger"
3maintainer: "unixjunkie@sdf.org"
4homepage: "https://github.com/UnixJunkie/molenc"
5bug-reports: "https://github.com/UnixJunkie/molenc/issues"
6dev-repo: "git+https://github.com/UnixJunkie/molenc.git"
7license: "BSD-3-Clause"
8build: ["dune" "build" "-p" name "-j" jobs]
9install: ["cp" "bin/molenc_type_atoms.py" "%{bin}%/molenc_type_atoms.py"]
10depends: [
11 "dune" {< "3.0"}
12 "batteries"
13 "dolog" {< "4.0.0"}
14 "parmap"
15 "minicli"
16 "conf-rdkit"
17 "ocaml" {>= "4.04.0" & < "5.0"}
18]
19synopsis: "Molecular encoder/featurizer using rdkit and OCaml"
20description: """Chemical fingerprints are lossy encodings of molecules.
21molenc allows to encode molecules using unfolded and counted fingerprints
22(i.e. potentially very long, but sparse, integer vectors).
23
24Currently, Faulon fingerprints are supported.
25In the future, atom pair fingerprints might be added.
26Currently, atom types are the quadruplet
27(#pi-electrons, element symbol, #HA neighbors, formal charge).
28In the future, pharmacophore features might be supported (a more abstract/fuzzy
29atom typing scheme).
30In the future, the stereo-chemistry information that can be encoded
31into SMILES strings might be taken into account.
32
33Bibliography:
34
35Carhart, 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.
36
37Kearsley, 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.
38
39Faulon, 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.
40
41OpenSMILES specification. Craig A. James et. al. v1.0 2016-05-15. http://opensmiles.org/opensmiles.html
42"""
43url {
44 src: "https://github.com/UnixJunkie/molenc/archive/v0.0.1.tar.gz"
45 checksum: [
46 "sha256=bc1c12eae7f335ae90868f8e0ff5c42a876385ac09170d41ee6714b4434e68a8"
47 "md5=9de5d3bb892267d5d2fb913532cb1d59"
48 ]
49}