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

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{ stdenv
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, lib
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, fetchurl
, unzip
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, makeDesktopItem
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, jre
}:
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let
desktopItem = makeDesktopItem {
name = "jmol";
exec = "jmol";
desktopName = "JMol";
genericName = "Molecular Modeler";
mimeType = "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
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stdenv.mkDerivation rec {
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version = "14.31.49";
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pname = "jmol";
src = let
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baseVersion = "${lib.versions.major version}.${lib.versions.minor version}";
in fetchurl {
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url = "mirror://sourceforge/jmol/Jmol/Version%20${baseVersion}/Jmol%20${version}/Jmol-${version}-binary.tar.gz";
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sha256 = "sha256-P+bzimBVammX5LxE6Yd6CmvmBeG8WdyA1T9bHXd+ifI=";
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};
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patchPhase = ''
sed -i -e "4s:.*:command=${jre}/bin/java:" -e "10s:.*:jarpath=$out/share/jmol/Jmol.jar:" -e "11,21d" jmol
'';
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installPhase = ''
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mkdir -p "$out/share/jmol" "$out/bin"
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${unzip}/bin/unzip jsmol.zip -d "$out/share/"
cp *.jar jmol.sh "$out/share/jmol"
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cp -r ${desktopItem}/share/applications $out/share
cp jmol $out/bin
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'';
enableParallelBuilding = true;
meta = with lib; {
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description = "A Java 3D viewer for chemical structures";
homepage = "https://sourceforge.net/projects/jmol";
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license = licenses.lgpl2;
platforms = platforms.all;
maintainers = with maintainers; [ mounium ] ++ teams.sage.members;
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};
}