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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_diam.py" "%{bin}%/molenc_diam.py"]
11 ["cp" "bin/molenc_ph4.py" "%{bin}%/molenc_ph4.py"]
12 ["cp" "bin/molenc.sh" "%{bin}%/molenc.sh"]
13 ["cp" "bin/molenc_ligprep.sh" "%{bin}%/molenc_ligprep.sh"]
14 ["cp" "bin/molenc_common.py" "%{bin}%/molenc_common.py"]
15 ["cp" "bin/molenc_lean.py" "%{bin}%/molenc_lean.py"]
16 ["cp" "bin/molenc_lizard.py" "%{bin}%/molenc_lizard.py"]
17 ["cp" "bin/molenc_scan.py" "%{bin}%/molenc_scan.py"]
18 ["cp" "bin/molenc_scan.sh" "%{bin}%/molenc_scan.sh"]
19 ["cp" "bin/molenc_standardize.py" "%{bin}%/molenc_standardize.py"]
20 ["cp" "bin/molenc_type_atoms.py" "%{bin}%/molenc_type_atoms.py"]
21 ["cp" "bin/smi2png.py" "%{bin}%/molenc_smi2png.py"]
22 ["cp" "bin/molenc_smisur.py" "%{bin}%/molenc_smisur.py"]
23 ["cp" "bin/molenc_panascan.py" "%{bin}%/molenc_panascan.py"]
24 ["cp" "bin/molenc_scaffold.py" "%{bin}%/molenc_scaffold.py"]
25 ["cp" "bin/molenc_deepsmi.py" "%{bin}%/molenc_deepsmi.py"]
26 ["cp" "bin/molenc_lead.py" "%{bin}%/molenc_lead.py"]
27 ["cp" "bin/molenc_smi2cansmi.py" "%{bin}%/molenc_smi2cansmi.py"]
28 ["cp" "bin/molenc_std.py" "%{bin}%/molenc_std.py"]
29 ["cp" "bin/molenc_padel.py" "%{bin}%/molenc_padel.py"]
30]
31depends: [
32 "batteries" {>= "3.5.0"}
33 "bst" {>= "2.0.0"}
34 "conf-graphviz"
35 "conf-python-3"
36 "conf-rdkit"
37 "cpm" {>= "9.0.0"}
38 "dokeysto"
39 "dolog" {>= "5.0.0"}
40 "dune" {>= "1.11"}
41 "line_oriented"
42 "minicli" {>= "5.0.0"}
43 "ocaml" {>= "5.0"}
44 "ocamlgraph"
45 "parany" {>= "12.1.1"}
46 "vector3"
47 "pyml" {>= "20211015"}
48]
49synopsis: "Molecular encoder/featurizer using rdkit and OCaml"
50description: """Chemical fingerprints are lossy encodings of molecules.
51molenc allows to encode molecules using unfolded-counted fingerprints
52(i.e. a potentially very long but sparse vector of positive integers).
53
54Currently, Faulon fingerprints and atom pairs are supported.
55
56Currently, atom types are the quadruplet
57(#pi-electrons, element symbol, #HA neighbors, formal charge).
58In the future, pharmacophore features might be supported (a more abstract/fuzzy
59atom typing scheme).
60
61Bibliography:
62=============
63
64Faulon, J. L., Visco, D. P., & Pophale, R. S. (2003).
65The signature molecular descriptor.
661. Using extended valence sequences in QSAR and QSPR studies.
67Journal of chemical information and computer sciences, 43(3), 707-720.
68
69Carhart, R. E., Smith, D. H., & Venkataraghavan, R. (1985).
70Atom pairs as molecular features in structure-activity studies:
71definition and applications.
72Journal of Chemical Information and Computer Sciences, 25(2), 64-73.
73
74Kearsley, S. K., Sallamack, S., Fluder, E. M., Andose, J. D., Mosley, R. T., &
75Sheridan, R. P. (1996).
76Chemical similarity using physiochemical property descriptors.
77Journal of Chemical Information and Computer Sciences, 36(1), 118-127.
78
79OpenSMILES specification. Craig A. James et. al. v1.0 2016-05-15.
80http://opensmiles.org/opensmiles.html
81"""
82url {
83 src:
84 "https://github.com/UnixJunkie/molenc/archive/refs/tags/v16.15.0.tar.gz"
85 checksum: [
86 "sha256=2ac72993ac8d285656f20599962f97e1d41b5a9ad4755e370afad457cc99ff34"
87 "md5=4cdc1ba94834f4e463f1b55cfa816611"
88 ]
89}