Merge pull request #260460 from natsukium/pdbfixer/init

python311Packages.pdbfixer: init at 1.9

pkgs/development/python-modules/pdbfixer/default.nix

@@ -0,0 +1,64 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, setuptools
+, wheel
+, numpy
+, openmm
+, pytestCheckHook
+}:
+
+buildPythonPackage rec {
+  pname = "pdbfixer";
+  version = "1.9";
+  pyproject = true;
+
+  src = fetchFromGitHub {
+    owner = "openmm";
+    repo = "pdbfixer";
+    rev = version;
+    hash = "sha256-ZXQWdNQyoVgjpZj/Wimcfwcbxk3CIvg3n5S1glNYUP4=";
+  };
+
+  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"
+  ];
+
+  pythonImportsCheck = [ "pdbfixer" ];
+
+  meta = with lib; {
+    description = "PDBFixer fixes problems in PDB files";
+    homepage = "https://github.com/openmm/pdbfixer";
+    changelog = "https://github.com/openmm/pdbfixer/releases/tag/${src.rev}";
+    license = licenses.mit;
+    maintainers = with maintainers; [ natsukium ];
+    mainProgram = "pdbfixer";
+  };
+}

pkgs/top-level/python-packages.nix

@@ -8757,6 +8757,8 @@ self: super: with self; {
 
   pdb2pqr = callPackage ../development/python-modules/pdb2pqr { };
 
+  pdbfixer = callPackage ../development/python-modules/pdbfixer { };
+
   pdf2docx = callPackage ../development/python-modules/pdf2docx { };
 
   pdf2image = callPackage ../development/python-modules/pdf2image { };