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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: [
10 # ["cp" "bin/molenc_ph4_type_atoms.py" "%{bin}%/molenc_ph4_type_atoms.py"]
11 ["cp" "bin/molenc_common.py" "%{bin}%/molenc_common.py"]
12 ["cp" "bin/molenc_type_atoms.py" "%{bin}%/molenc_type_atoms.py"]
13 ["cp" "bin/molenc_scan.py" "%{bin}%/molenc_scan.py"]
14 ["cp" "bin/molenc.sh" "%{bin}%/molenc.sh"]
15 ["cp" "bin/molenc_scan.sh" "%{bin}%/molenc_scan.sh"]
16]
17depends: [
18 "batteries"
19 "bst" {>= "2.0.0"}
20 "conf-python-3"
21 "conf-rdkit"
22 "dolog" {>= "4.0.0" & < "5.0.0"}
23 "dune" {>= "1.11"}
24 "minicli" {>= "5.0.0"}
25 "ocaml" {>= "4.04.0" & < "5.0"}
26 "parmap"
27]
28synopsis: "Molecular encoder/featurizer using rdkit and OCaml"
29description: """Chemical fingerprints are lossy encodings of molecules.
30molenc allows to encode molecules using unfolded-counted fingerprints
31(i.e. a potentially very long but sparse vector of positive integers).
32
33Currently, Faulon fingerprints are supported.
34In the future, atom pair fingerprints might be added.
35Currently, atom types are the quadruplet
36(#pi-electrons, element symbol, #HA neighbors, formal charge).
37In the future, pharmacophore features might be supported (a more abstract/fuzzy
38atom typing scheme).
39
40Bibliography:
41
42Carhart, 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.
43
44Kearsley, 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.
45
46Faulon, 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.
47
48OpenSMILES specification. Craig A. James et. al. v1.0 2016-05-15. http://opensmiles.org/opensmiles.html
49"""
50url {
51 src: "https://github.com/UnixJunkie/molenc/archive/v5.0.1.tar.gz"
52 checksum: [
53 "sha256=e5e665156ce7a4bf7cea63d95f753ef328f9fbc0bce02170bc60ed10c0a3642a"
54 "md5=c665b8e27de72f2b7ccf5f54d758ed28"
55 ]
56}