anil.recoil.org / opam-repository
this repo has no description
0
fork

Configure Feed

Select the types of activity you want to include in your feed.

new file: molenc/molenc.16.5.0/opam (#20615)

* new file: molenc/molenc.16.5.0/opam

New exe:
$ molenc_bbad
usage:
molenc_bbad
[-i <filename>]: SMILES input file
-o <filename>: output file
[-np <int>]: nprocs (default=1)
[--bbad <fn1[,fn2[,...]]>]: previously computed BBAD
to apply as filter
will compute the union of ADs if several filenames
[-v]: verbose/debug mode

An Atom-Pairs (AP) based Bounding Box Applicability Domain (BBAD)

* added pyml in the opam file

* Update packages/molenc/molenc.16.5.0/opam

Co-authored-by: Marcello Seri <mseri@users.noreply.github.com>

authored by

Francois Berenger
Marcello Seri and committed by
GitHub 7e2b667d 0a5a17f8

+79
+79
packages/molenc/molenc.16.5.0/opam
··· 1 + opam-version: "2.0" 2 + authors: "Francois Berenger" 3 + maintainer: "unixjunkie@sdf.org" 4 + homepage: "https://github.com/UnixJunkie/molenc" 5 + bug-reports: "https://github.com/UnixJunkie/molenc/issues" 6 + dev-repo: "git+https://github.com/UnixJunkie/molenc.git" 7 + license: "BSD-3-Clause" 8 + build: ["dune" "build" "-p" name "-j" jobs] 9 + install: [ 10 + # ["cp" "bin/molenc_ph4_type_atoms.py" "%{bin}%/molenc_ph4_type_atoms.py"] 11 + ["cp" "bin/molenc.sh" "%{bin}%/molenc.sh"] 12 + ["cp" "bin/molenc_common.py" "%{bin}%/molenc_common.py"] 13 + ["cp" "bin/molenc_lean.py" "%{bin}%/molenc_lean.py"] 14 + ["cp" "bin/molenc_lizard.py" "%{bin}%/molenc_lizard.py"] 15 + ["cp" "bin/molenc_scan.py" "%{bin}%/molenc_scan.py"] 16 + ["cp" "bin/molenc_scan.sh" "%{bin}%/molenc_scan.sh"] 17 + ["cp" "bin/molenc_standardize.py" "%{bin}%/molenc_standardize.py"] 18 + ["cp" "bin/molenc_type_atoms.py" "%{bin}%/molenc_type_atoms.py"] 19 + ["cp" "bin/smi2png.py" "%{bin}%/molenc_smi2png.py"] 20 + ["cp" "bin/molenc_smisur.py" "%{bin}%/molenc_smisur.py"] 21 + ["cp" "bin/molenc_panascan.py" "%{bin}%/molenc_panascan.py"] 22 + ["cp" "bin/molenc_scaffold.py" "%{bin}%/molenc_scaffold.py"] 23 + ["cp" "bin/molenc_deepsmi.py" "%{bin}%/molenc_deepsmi.py"] 24 + ] 25 + depends: [ 26 + "batteries" {>= "3.5.0"} 27 + "bst" {>= "2.0.0"} 28 + "conf-graphviz" 29 + "conf-python-3" 30 + "conf-rdkit" 31 + "cpm" {>= "9.0.0"} 32 + "dokeysto_camltc" 33 + "dolog" {>= "5.0.0"} 34 + "dune" {>= "1.11"} 35 + "minicli" {>= "5.0.0"} 36 + "ocaml" {>= "4.08"} 37 + "ocamlgraph" 38 + "parany" {>= "12.1.1"} 39 + "vector3" 40 + "line_oriented" 41 + "pyml" {>= "20211015"} 42 + ] 43 + synopsis: "Molecular encoder/featurizer using rdkit and OCaml" 44 + description: """Chemical fingerprints are lossy encodings of molecules. 45 + molenc allows to encode molecules using unfolded-counted fingerprints 46 + (i.e. a potentially very long but sparse vector of positive integers). 47 + 48 + Currently, Faulon fingerprints and atom pairs are supported. 49 + 50 + Currently, atom types are the quadruplet 51 + (#pi-electrons, element symbol, #HA neighbors, formal charge). 52 + In the future, pharmacophore features might be supported (a more abstract/fuzzy 53 + atom typing scheme). 54 + 55 + Bibliography: 56 + ============= 57 + 58 + Faulon, J. L., Visco, D. P., & Pophale, R. S. (2003). 59 + The signature molecular descriptor. 60 + 1. Using extended valence sequences in QSAR and QSPR studies. 61 + Journal of chemical information and computer sciences, 43(3), 707-720. 62 + 63 + Carhart, R. E., Smith, D. H., & Venkataraghavan, R. (1985). 64 + Atom pairs as molecular features in structure-activity studies: 65 + definition and applications. 66 + Journal of Chemical Information and Computer Sciences, 25(2), 64-73. 67 + 68 + Kearsley, S. K., Sallamack, S., Fluder, E. M., Andose, J. D., Mosley, R. T., & 69 + Sheridan, R. P. (1996). 70 + Chemical similarity using physiochemical property descriptors. 71 + Journal of Chemical Information and Computer Sciences, 36(1), 118-127. 72 + 73 + OpenSMILES specification. Craig A. James et. al. v1.0 2016-05-15. 74 + http://opensmiles.org/opensmiles.html 75 + """ 76 + url { 77 + src: "https://github.com/UnixJunkie/molenc/archive/v16.5.0.tar.gz" 78 + checksum: "md5=bf3c6328d3cf768f34b17d2c242138b6" 79 + }