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{
lib,
buildPythonPackage,
fetchFromGitHub,
setuptools,
wheel,
numpy,
openmm,
pytestCheckHook,
}:
buildPythonPackage rec {
pname = "pdbfixer";
version = "1.11";
pyproject = true;
src = fetchFromGitHub {
owner = "openmm";
repo = "pdbfixer";
tag = "v${version}";
hash = "sha256-Xk3m2w1p3Wu4g6qKGOH679wkKT0LKZLgGn/ARn219fQ=";
};
nativeBuildInputs = [
setuptools
wheel
];
propagatedBuildInputs = [
numpy
openmm
];
nativeCheckInputs = [ pytestCheckHook ];
preCheck = ''
export PATH=$out/bin:$PATH
'';
disabledTests = [
# require network access
"test_build_and_simulate"
"test_mutate_1"
"test_mutate_2"
"test_mutate_3_fails"
"test_mutate_4_fails"
"test_mutate_5_fails"
"test_mutate_multiple_copies_of_chain_A"
"test_pdbid"
"test_url"
"test_charge_and_solvate"
"test_download_template"
"test_nonstandard"
"test_leaving_atoms"
];
pythonImportsCheck = [ "pdbfixer" ];
meta = {
description = "PDBFixer fixes problems in PDB files";
homepage = "https://github.com/openmm/pdbfixer";
changelog = "https://github.com/openmm/pdbfixer/releases/tag/${src.tag}";
license = lib.licenses.mit;
maintainers = with lib.maintainers; [ natsukium ];
mainProgram = "pdbfixer";
};
}
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