/
opam
66 lines (59 loc) · 2.38 KB
/
opam
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
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-Clause"
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" {>= "2.0.0"}
"conf-python-3"
"conf-rdkit"
"cpm" {>= "9.0.0"}
"dokeysto"
"dolog" {>= "4.0.0" & < "5.0.0"}
"dune" {>= "1.11"}
"minicli" {>= "5.0.0"}
"ocaml" {< "5.0"}
"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"
}