depot/third_party/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix

{ stdenv
, lib
, fetchurl
, unzip
, makeDesktopItem
, jre
}:

let
  desktopItem = makeDesktopItem {
    name = "jmol";
    exec = "jmol";
    desktopName = "JMol";
    genericName = "Molecular Modeler";
    mimeTypes = [
      "chemical/x-pdb"
      "chemical/x-mdl-molfile"
      "chemical/x-mol2"
      "chemical/seq-aa-fasta"
      "chemical/seq-na-fasta"
      "chemical/x-xyz"
      "chemical/x-mdl-sdf"
    ];
    categories = [ "Graphics" "Education" "Science" "Chemistry" ];
  };
in
stdenv.mkDerivation rec {
  version = "16.1.33";
  pname = "jmol";

  src = let
    baseVersion = "${lib.versions.major version}.${lib.versions.minor version}";
  in fetchurl {
    url = "mirror://sourceforge/jmol/Jmol/Version%20${baseVersion}/Jmol%20${version}/Jmol-${version}-binary.tar.gz";
    hash = "sha256-vOFGmLsCQNYRBMuDRVrdjWE6/MxY7IucB1OpV4cdZrs=";
  };

  patchPhase = ''
    sed -i -e "4s:.*:command=${jre}/bin/java:" -e "10s:.*:jarpath=$out/share/jmol/Jmol.jar:" -e "11,21d" jmol
  '';

  installPhase = ''
    mkdir -p "$out/share/jmol" "$out/bin"

    ${unzip}/bin/unzip jsmol.zip -d "$out/share/"

    cp *.jar jmol.sh "$out/share/jmol"
    cp -r ${desktopItem}/share/applications $out/share
    cp jmol $out/bin
  '';

  enableParallelBuilding = true;

  meta = with lib; {
     description = "A Java 3D viewer for chemical structures";
     homepage = "https://sourceforge.net/projects/jmol";
     sourceProvenance = with sourceTypes; [ binaryBytecode ];
     license = licenses.lgpl2;
     platforms = platforms.all;
     maintainers = with maintainers; [ mounium ] ++ teams.sage.members;
  };
}