depot/third_party/nixpkgs/pkgs/development/python-modules/pdb2pqr/default.nix

{ lib
, buildPythonPackage
, fetchPypi
, pythonOlder
, pythonRelaxDepsHook
, mmcif-pdbx
, numpy
, propka
, requests
, docutils
, pytestCheckHook
, pandas
, testfixtures
}:

buildPythonPackage rec {
  pname = "pdb2pqr";
  version = "3.6.2";
  format = "setuptools";

  disabled = pythonOlder "3.7";

  src = fetchPypi {
    inherit pname version;
    hash = "sha256-He301TJ1bzWub0DZ6Ro/Xc+JMtJBbyygVpWjPY6RMbA=";
  };

  nativeBuildInputs = [
    pythonRelaxDepsHook
  ];

  pythonRelaxDeps = [
    "docutils"
  ];

  propagatedBuildInputs = [
    mmcif-pdbx
    numpy
    propka
    requests
    docutils
  ];

  nativeCheckInputs = [
    pytestCheckHook
    pandas
    testfixtures
  ];

  disabledTests = [
    # these tests have network access
    "test_short_pdb"
    "test_basic_cif"
    "test_long_pdb"
    "test_ligand_biomolecule"
    "test_log_output_in_pqr_location"
    "test_propka_apo"
    "test_propka_pka"
    "test_basic"
  ];

  pythonImportsCheck = [
    "pdb2pqr"
  ];

  meta = with lib; {
    description = "Software for determining titration states, adding missing atoms, and assigning charges/radii to biomolecules";
    homepage = "https://www.poissonboltzmann.org/";
    changelog = "https://github.com/Electrostatics/pdb2pqr/releases/tag/v${version}";
    license = licenses.bsd3;
    maintainers = with maintainers; [ natsukium ];
  };
}