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{ stdenv
, lib
, fetchFromGitHub
, makeDesktopItem
, python3
, python3Packages
, netcdf
, glew
, glm
, libpng
, libxml2
, freetype
, msgpack
, qt5
}:
let
pname = "pymol";
description = "A Python-enhanced molecular graphics tool";
desktopItem = makeDesktopItem {
name = pname;
exec = pname;
desktopName = "PyMol Molecular Graphics System";
genericName = "Molecular Modeler";
comment = description;
icon = pname;
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
python3Packages.buildPythonApplication rec {
inherit pname;
version = "3.0.0";
pyproject = true;
src = fetchFromGitHub {
owner = "schrodinger";
repo = "pymol-open-source";
rev = "v${version}";
hash = "sha256-GhTHxacjGN7XklZ6gileBMRZAGq4Pp4JknNL+qGqrVE=";
};
postPatch = ''
substituteInPlace setup.py \
--replace-fail "self.install_libbase" '"${placeholder "out"}/${python3.sitePackages}"'
'';
build-system = [
python3Packages.setuptools
];
nativeBuildInputs = [ qt5.wrapQtAppsHook ];
buildInputs = [ python3Packages.numpy python3Packages.pyqt5 glew glm libpng libxml2 freetype msgpack netcdf ];
env.NIX_CFLAGS_COMPILE = "-I ${libxml2.dev}/include/libxml2";
postInstall = with python3Packages; ''
wrapProgram $out/bin/pymol \
--prefix PYTHONPATH : ${lib.makeSearchPathOutput "lib" python3.sitePackages [ pyqt5 pyqt5.pyqt5-sip ]}
mkdir -p "$out/share/icons/"
ln -s $out/${python3.sitePackages}/pymol/pymol_path/data/pymol/icons/icon2.svg "$out/share/icons/pymol.svg"
'' + lib.optionalString stdenv.hostPlatform.isLinux ''
cp -r "${desktopItem}/share/applications/" "$out/share/"
'';
pythonImportsCheck = [
"pymol"
];
nativeCheckInputs = with python3Packages; [
python3Packages.msgpack
pillow
pytestCheckHook
];
# some tests hang for some reason
doCheck = !(stdenv.hostPlatform.isLinux && stdenv.hostPlatform.isAarch64);
disabledTestPaths = [
# require biopython which is broken as of 2024-04-20
"tests/api/seqalign.py"
];
disabledTests = [
# the output image does not exactly match
"test_commands"
# touch the network
"testFetch"
# requires collada2gltf which is not included in nixpkgs
"testglTF"
# require mmtf-cpp which does not support darwin
"testMMTF"
"testSave_symmetry__mmtf"
];
preCheck = ''
cd testing
'';
__darwinAllowLocalNetworking = true;
preFixup = ''
wrapQtApp "$out/bin/pymol"
'';
meta = with lib; {
inherit description;
mainProgram = "pymol";
homepage = "https://www.pymol.org/";
license = licenses.mit;
maintainers = with maintainers; [ natsukium samlich ];
};
}
|
