120 lines
2.9 KiB
Nix
120 lines
2.9 KiB
Nix
{ stdenv
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, lib
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, fetchFromGitHub
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, makeDesktopItem
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, python3Packages
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, netcdf
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, glew
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, glm
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, libpng
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, libxml2
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, freetype
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, msgpack
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, qt5
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}:
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let
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pname = "pymol";
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description = "A Python-enhanced molecular graphics tool";
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desktopItem = makeDesktopItem {
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name = pname;
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exec = pname;
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desktopName = "PyMol Molecular Graphics System";
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genericName = "Molecular Modeler";
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comment = description;
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icon = pname;
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mimeTypes = [
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"chemical/x-pdb"
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"chemical/x-mdl-molfile"
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"chemical/x-mol2"
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"chemical/seq-aa-fasta"
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"chemical/seq-na-fasta"
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"chemical/x-xyz"
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"chemical/x-mdl-sdf"
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];
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categories = [ "Graphics" "Education" "Science" "Chemistry" ];
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};
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in
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python3Packages.buildPythonApplication rec {
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inherit pname;
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version = "3.0.0";
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pyproject = true;
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src = fetchFromGitHub {
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owner = "schrodinger";
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repo = "pymol-open-source";
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rev = "v${version}";
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hash = "sha256-GhTHxacjGN7XklZ6gileBMRZAGq4Pp4JknNL+qGqrVE=";
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};
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postPatch = ''
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substituteInPlace setup.py \
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--replace-fail "self.install_libbase" '"${placeholder "out"}/${python3Packages.python.sitePackages}"'
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'';
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build-system = [
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python3Packages.setuptools
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];
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nativeBuildInputs = [ qt5.wrapQtAppsHook ];
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buildInputs = [ python3Packages.numpy python3Packages.pyqt5 glew glm libpng libxml2 freetype msgpack netcdf ];
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env.NIX_CFLAGS_COMPILE = "-I ${libxml2.dev}/include/libxml2";
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postInstall = with python3Packages; ''
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wrapProgram $out/bin/pymol \
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--prefix PYTHONPATH : ${lib.makeSearchPathOutput "lib" python3Packages.python.sitePackages [ pyqt5 pyqt5.pyqt5-sip ]}
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mkdir -p "$out/share/icons/"
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ln -s $out/${python3Packages.python.sitePackages}/pymol/pymol_path/data/pymol/icons/icon2.svg "$out/share/icons/pymol.svg"
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'' + lib.optionalString stdenv.hostPlatform.isLinux ''
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cp -r "${desktopItem}/share/applications/" "$out/share/"
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'';
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pythonImportsCheck = [
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"pymol"
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];
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nativeCheckInputs = with python3Packages; [
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python3Packages.msgpack
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pillow
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pytestCheckHook
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];
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# some tests hang for some reason
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doCheck = !(stdenv.hostPlatform.isLinux && stdenv.hostPlatform.isAarch64);
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disabledTestPaths = [
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# require biopython which is broken as of 2024-04-20
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"tests/api/seqalign.py"
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];
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disabledTests = [
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# the output image does not exactly match
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"test_commands"
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# touch the network
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"testFetch"
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# requires collada2gltf which is not included in nixpkgs
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"testglTF"
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# require mmtf-cpp which does not support darwin
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"testMMTF"
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"testSave_symmetry__mmtf"
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];
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preCheck = ''
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cd testing
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'';
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__darwinAllowLocalNetworking = true;
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preFixup = ''
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wrapQtApp "$out/bin/pymol"
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'';
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meta = with lib; {
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inherit description;
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mainProgram = "pymol";
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homepage = "https://www.pymol.org/";
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license = licenses.mit;
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maintainers = with maintainers; [ natsukium samlich ];
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};
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}
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