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opam
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opam
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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_diam.py" "%{bin}%/molenc_diam.py"]
["cp" "bin/molenc_ph4.py" "%{bin}%/molenc_ph4.py"]
["cp" "bin/molenc.sh" "%{bin}%/molenc.sh"]
["cp" "bin/molenc_ligprep.sh" "%{bin}%/molenc_ligprep.sh"]
["cp" "bin/molenc_common.py" "%{bin}%/molenc_common.py"]
["cp" "bin/molenc_lean.py" "%{bin}%/molenc_lean.py"]
["cp" "bin/molenc_lizard.py" "%{bin}%/molenc_lizard.py"]
["cp" "bin/molenc_scan.py" "%{bin}%/molenc_scan.py"]
["cp" "bin/molenc_scan.sh" "%{bin}%/molenc_scan.sh"]
["cp" "bin/molenc_type_atoms.py" "%{bin}%/molenc_type_atoms.py"]
["cp" "bin/smi2png.py" "%{bin}%/molenc_smi2png.py"]
["cp" "bin/molenc_smisur.py" "%{bin}%/molenc_smisur.py"]
["cp" "bin/molenc_panascan.py" "%{bin}%/molenc_panascan.py"]
["cp" "bin/molenc_scaffold.py" "%{bin}%/molenc_scaffold.py"]
["cp" "bin/molenc_deepsmi.py" "%{bin}%/molenc_deepsmi.py"]
["cp" "bin/molenc_lead.py" "%{bin}%/molenc_lead.py"]
["cp" "bin/molenc_drug.py" "%{bin}%/molenc_drug.py"]
["cp" "bin/molenc_smi2cansmi.py" "%{bin}%/molenc_smi2cansmi.py"]
["cp" "bin/molenc_std.py" "%{bin}%/molenc_std.py"]
["cp" "bin/molenc_padel.py" "%{bin}%/molenc_padel.py"]
["cp" "bin/molenc_rotbond.py" "%{bin}%/molenc_rotbond.py"]
["cp" "bin/molenc_mview.py" "%{bin}%/molenc_mview.py"]
["cp" "bin/molenc_HA.py" "%{bin}%/molenc_HA.py"]
["cp" "bin/molenc_sdf2smi.py" "%{bin}%/molenc_sdf2smi.py"]
["cp" "bin/molenc_atoms_filter.py" "%{bin}%/molenc_atoms_filter.py"]
]
depends: [
"batteries" {>= "3.5.0"}
"bst" {>= "2.0.0"}
"conf-graphviz"
"conf-python-3"
"conf-rdkit"
"cpm" {>= "9.0.0"}
"dokeysto"
"dolog" {>= "5.0.0"}
"dune" {>= "1.11"}
"line_oriented" {>= "1.2.0"}
"minicli" {>= "5.0.0"}
"ocaml" {>= "5.1.0"}
"ocamlgraph"
"parany" {>= "12.1.1"}
"vector3"
"pyml" {>= "20211015"}
]
available: arch != "arm32" & arch != "x86_32"
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/refs/tags/v16.23.0.tar.gz"
checksum: "md5=cab545a0a8b78f78d54c33750349022c"
}