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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 "bst"
19 "dune" {< "3.0"}
20 "batteries"
21 "dolog" {< "4.0.0"}
22 "minicli"
23 "conf-rdkit"
24 "conf-python-3"
25 "ocaml" {>= "4.04.0" & < "5.0"}
26]
27synopsis: "Molecular encoder/featurizer using rdkit and OCaml"
28description: """Chemical fingerprints are lossy encodings of molecules.
29molenc allows to encode molecules using unfolded-counted fingerprints
30(i.e. a potentially very long but sparse vector of positive integers).
31
32Currently, Faulon fingerprints are supported.
33In the future, atom pair fingerprints might be added.
34Currently, atom types are the quadruplet
35(#pi-electrons, element symbol, #HA neighbors, formal charge).
36In the future, pharmacophore features might be supported (a more abstract/fuzzy
37atom typing scheme).
38
39Bibliography:
40
41Carhart, 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.
42
43Kearsley, 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.
44
45Faulon, 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.
46
47OpenSMILES specification. Craig A. James et. al. v1.0 2016-05-15. http://opensmiles.org/opensmiles.html
48"""
49url {
50 src: "https://github.com/UnixJunkie/molenc/archive/v4.0.2.tar.gz"
51 checksum: [
52 "sha256=6933233e9418d5ae6f1c6bdf479909e8e6eb655e5203e4c5edb95e95d321f70b"
53 "md5=64a1e384cda925dfca2d0635ac64faaa"
54 ]
55}