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{
lib,
stdenv,
buildPythonPackage,
fetchFromGitHub,
# build-system
setuptools,
# dependencies
gemmi,
numpy,
rdkit,
scipy,
# tests
pytestCheckHook,
}:
buildPythonPackage rec {
pname = "meeko";
version = "0.7.1";
pyproject = true;
src = fetchFromGitHub {
owner = "forlilab";
repo = "Meeko";
tag = "v${version}";
hash = "sha256-ObGUUNzfK2k37uJ/aY3DHf9BlJ1nzqTe6tHvV2rj1og=";
};
build-system = [
setuptools
];
dependencies = [
gemmi
numpy
rdkit
scipy
];
nativeCheckInputs = [ pytestCheckHook ];
disabledTests = [
# Require internet connection
"test_add_variants"
"test_build_noncovalent_CC"
# AssertionError: assert {'chosen_by_d...ond': [], ...} == {'chosen_by_d...ond': [], ...}
"test_polymer_encoding_decoding"
]
++ lib.optionals stdenv.hostPlatform.isDarwin [
# AssertionError: assert 'altloc' in 'updated 1 h positions but deleted 11
"test_AHHY_all_static_residues"
"test_AHHY_flex_residues"
"test_AHHY_flexibilize_then_parameterize"
"test_AHHY_mk_prep_and_export"
"test_AHHY_mutate_residues"
"test_AHHY_padding"
"test_disulfide_adjacent"
"test_disulfides"
"test_export_sidechains_no_idxmap"
"test_insertion_code"
"test_just_three_padded_mol"
"test_monomer_encoding_decoding"
"test_pdbqt_writing_from_decoded_polymer"
"test_rdkit_molsetup_encoding_decoding"
"test_residue_chem_templates_encoding_decoding"
"test_residue_padder_encoding_decoding"
"test_residue_template_encoding_decoding"
"test_stitch_polymer"
"test_write_pdb_1igy"
"test_write_pdb_AHHY"
# RuntimeError: Updated 1 H positions but deleted 10
"test_altloc"
];
pythonImportsCheck = [ "meeko" ];
meta = {
description = "Python package for preparing small molecule for docking";
homepage = "https://github.com/forlilab/Meeko";
changelog = "https://github.com/forlilab/Meeko/releases/tag/${src.tag}";
license = lib.licenses.lgpl21Only;
maintainers = with lib.maintainers; [ natsukium ];
};
}
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