commit a19eadd80f4fb74ba2c03ed518d14fe033354892 · anil.recoil.org/opam-repository

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packages/molenc/molenc.17.0.1/opam
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       opam-version: "2.0"

     

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       authors: "Francois Berenger"

     

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       maintainer: "unixjunkie@sdf.org"

     

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       homepage: "https://github.com/UnixJunkie/molenc"

     

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       bug-reports: "https://github.com/UnixJunkie/molenc/issues"

     

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       dev-repo: "git+https://github.com/UnixJunkie/molenc.git"

     

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       license: "BSD-3-Clause"

     

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       build: ["dune" "build" "-p" name "-j" jobs]

     

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       install: [

     

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         ["cp" "bin/molenc_diam.py" "%{bin}%/molenc_diam.py"]

     

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         ["cp" "bin/molenc_ph4.py" "%{bin}%/molenc_ph4.py"]

     

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         ["cp" "bin/molenc.sh" "%{bin}%/molenc.sh"]

     

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         ["cp" "bin/molenc_ligprep.sh" "%{bin}%/molenc_ligprep.sh"]

     

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         ["cp" "bin/molenc_common.py" "%{bin}%/molenc_common.py"]

     

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         ["cp" "bin/molenc_lean.py" "%{bin}%/molenc_lean.py"]

     

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         ["cp" "bin/molenc_lizard.py" "%{bin}%/molenc_lizard.py"]

     

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         ["cp" "bin/molenc_scan.py" "%{bin}%/molenc_scan.py"]

     

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         ["cp" "bin/molenc_scan.sh" "%{bin}%/molenc_scan.sh"]

     

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         ["cp" "bin/molenc_type_atoms.py" "%{bin}%/molenc_type_atoms.py"]

     

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         ["cp" "bin/smi2png.py" "%{bin}%/molenc_smi2png.py"]

     

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         ["cp" "bin/molenc_smisur.py" "%{bin}%/molenc_smisur.py"]

     

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         ["cp" "bin/molenc_panascan.py" "%{bin}%/molenc_panascan.py"]

     

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         ["cp" "bin/molenc_scaffold.py" "%{bin}%/molenc_scaffold.py"]

     

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         ["cp" "bin/molenc_deepsmi.py" "%{bin}%/molenc_deepsmi.py"]

     

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         ["cp" "bin/molenc_lead.py" "%{bin}%/molenc_lead.py"]

     

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         ["cp" "bin/molenc_drug.py" "%{bin}%/molenc_drug.py"]

     

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         ["cp" "bin/molenc_smi2cansmi.py" "%{bin}%/molenc_smi2cansmi.py"]

     

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         ["cp" "bin/molenc_std.py" "%{bin}%/molenc_std.py"]

     

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         ["cp" "bin/molenc_padel.py" "%{bin}%/molenc_padel.py"]

     

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         ["cp" "bin/molenc_rotbond.py" "%{bin}%/molenc_rotbond.py"]

     

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         ["cp" "bin/molenc_mview.py" "%{bin}%/molenc_mview.py"]

     

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         ["cp" "bin/molenc_HA.py" "%{bin}%/molenc_HA.py"]

     

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         ["cp" "bin/molenc_sdf2smi.py" "%{bin}%/molenc_sdf2smi.py"]

     

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         ["cp" "bin/molenc_atoms_filter.py" "%{bin}%/molenc_atoms_filter.py"]

     

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         ["cp" "bin/molenc_gpr.py" "%{bin}%/molenc_gpr.py"]

     

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         ["cp" "bin/molenc_stable.py" "%{bin}%/molenc_stable.py"]

     

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         ["cp" "bin/molenc_thash.py" "%{bin}%/molenc_thash.py"]

     

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         ["cp" "bin/molenc_SA.py" "%{bin}%/molenc_SA.py"]

     

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         ["cp" "bin/fpscores.pkl.gz" "%{bin}%/fpscores.pkl.gz"] # molenc_SA.py's data

     

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       ]

     

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       depends: [

     

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         "batteries" {>= "3.5.0"}

     

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         "bst" {>= "2.0.0"}

     

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         "conf-graphviz"

     

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         "conf-python-3"

     

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         "conf-rdkit"

     

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         "cpm" {>= "9.0.0"}

     

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         "dokeysto"

     

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         "dolog" {>= "5.0.0"}

     

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         "dune" {>= "1.11"}

     

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         "line_oriented" {>= "1.2.0"}

     

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         "minicli" {>= "5.0.0"}

     

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         "ocaml" {>= "5.1.0"}

     

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         "ocamlgraph"

     

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         "parany" {>= "12.1.1"}

     

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         "vector3"

     

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         "pyml" {>= "20211015"}

     

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       ]

     

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       available: arch != "arm32" & arch != "x86_32"

     

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       synopsis: "Molecular encoder/featurizer using rdkit and OCaml"

     

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       description: """Chemical fingerprints are lossy encodings of molecules.

     

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       molenc allows to encode molecules using unfolded-counted fingerprints

     

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       (i.e. a potentially very long but sparse vector of positive integers).

     

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       Currently, Faulon fingerprints and atom pairs are supported.

     

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       Currently, atom types are the quadruplet

     

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       (#pi-electrons, element symbol, #HA neighbors, formal charge).

     

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       In the future, pharmacophore features might be supported (a more abstract/fuzzy

     

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       atom typing scheme).

     

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       Bibliography:

     

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       =============

     

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       Faulon, J. L., Visco, D. P., & Pophale, R. S. (2003).

     

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       The signature molecular descriptor.

     

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       1. Using extended valence sequences in QSAR and QSPR studies.

     

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       Journal of chemical information and computer sciences, 43(3), 707-720.

     

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       Carhart, R. E., Smith, D. H., & Venkataraghavan, R. (1985).

     

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       Atom pairs as molecular features in structure-activity studies:

     

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       definition and applications.

     

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       Journal of Chemical Information and Computer Sciences, 25(2), 64-73.

     

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       Kearsley, S. K., Sallamack, S., Fluder, E. M., Andose, J. D., Mosley, R. T., &

     

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       Sheridan, R. P. (1996).

     

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       Chemical similarity using physiochemical property descriptors.

     

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       Journal of Chemical Information and Computer Sciences, 36(1), 118-127.

     

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       OpenSMILES specification. Craig A. James et. al. v1.0 2016-05-15.

     

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       http://opensmiles.org/opensmiles.html

     

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       """

     

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       url {

     

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         src:

     

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           "https://github.com/UnixJunkie/molenc/archive/refs/tags/v17.0.1.tar.gz"

     

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         checksum: [

     

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           "sha256=dee16015c4088cc4a690bfeb5afc4fe4869540bf7e2a998ae3ca8094023728ae"

     

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         ]

     

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       }