Merge pull request #231095 from natsukium/pdb2pqr/init

pkgs/development/python-modules/mmcif-pdbx/default.nix

@@ -0,0 +1,42 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, pythonOlder
+, setuptools
+, pytestCheckHook
+}:
+
+buildPythonPackage rec {
+  pname = "mmcif-pdbx";
+  version = "2.0.1";
+  format = "pyproject";
+
+  disabled = pythonOlder "3.5";
+
+  src = fetchFromGitHub {
+    owner = "Electrostatics";
+    repo = "mmcif_pdbx";
+    rev = "refs/tags/v${version}";
+    hash = "sha256-ymMQ/q4IMoq+B8RvIdL0aqolKxyE/4rnVfd4bUV5OUY=";
+  };
+
+  nativeBuildInputs = [
+    setuptools
+  ];
+
+  nativeCheckInputs = [
+    pytestCheckHook
+  ];
+
+  pythonImportsCheck = [
+    "pdbx"
+  ];
+
+  meta = with lib; {
+    description = "Yet another version of PDBx/mmCIF Python implementation";
+    homepage = "https://github.com/Electrostatics/mmcif_pdbx";
+    changelog = "https://github.com/Electrostatics/mmcif_pdbx/releases/tag/v${version}";
+    license = licenses.cc0;
+    maintainers = with maintainers; [ natsukium ];
+  };
+}

pkgs/development/python-modules/pdb2pqr/default.nix

@@ -0,0 +1,73 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, pythonOlder
+, pythonRelaxDepsHook
+, mmcif-pdbx
+, numpy
+, propka
+, requests
+, docutils
+, pytestCheckHook
+, pandas
+, testfixtures
+}:
+
+buildPythonPackage rec {
+  pname = "pdb2pqr";
+  version = "3.6.1";
+  format = "setuptools";
+
+  disabled = pythonOlder "3.7";
+
+  src = fetchPypi {
+    inherit pname version;
+    hash = "sha256-wFak5tKOsPYRflBW8viWEjM6Cku5JkWB6mWVyINYh1g=";
+  };
+
+  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 ];
+  };
+}

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

@@ -0,0 +1,42 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, pythonOlder
+, setuptools
+, pytestCheckHook
+}:
+
+buildPythonPackage rec {
+  pname = "propka";
+  version = "3.5.0";
+  format = "setuptools";
+
+  disabled = pythonOlder "3.7";
+
+  src = fetchFromGitHub {
+    owner = "jensengroup";
+    repo = "propka";
+    rev = "refs/tags/v${version}";
+    hash = "sha256-NbvrlapBALGbUyBqdqDcDG/igDf/xqxC35DzVUrbHlo=";
+  };
+
+  propagatedBuildInputs = [
+    setuptools
+  ];
+
+  nativeCheckInputs = [
+    pytestCheckHook
+  ];
+
+  pythonImportsCheck = [
+    "propka"
+  ];
+
+  meta = with lib; {
+    description = "A predictor of the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure";
+    homepage = "https://github.com/jensengroup/propka";
+    changelog = "https://github.com/jensengroup/propka/releases/tag/v${version}";
+    license = licenses.lgpl21Only;
+    maintainers = with maintainers; [ natsukium ];
+  };
+}

pkgs/top-level/all-packages.nix

@@ -37700,6 +37700,8 @@ with pkgs;
 
   openmolcas = callPackage ../applications/science/chemistry/openmolcas { };
 
+  pdb2pqr = with python3Packages; toPythonApplication pdb2pqr;
+
   pymol = callPackage ../applications/science/chemistry/pymol { };
 
   quantum-espresso = callPackage ../applications/science/chemistry/quantum-espresso { };

pkgs/top-level/python-packages.nix

@@ -6339,6 +6339,8 @@ self: super: with self; {
     enablePython = true;
   });
 
+  mmcif-pdbx = callPackage ../development/python-modules/mmcif-pdbx { };
+
   mmcv = callPackage ../development/python-modules/mmcv { };
 
   mmengine = callPackage ../development/python-modules/mmengine { };
@@ -7428,6 +7430,8 @@ self: super: with self; {
 
   pcpp = callPackage ../development/python-modules/pcpp { };
 
+  pdb2pqr = callPackage ../development/python-modules/pdb2pqr { };
+
   pdf2image = callPackage ../development/python-modules/pdf2image { };
 
   pdfkit = callPackage ../development/python-modules/pdfkit { };
@@ -7687,6 +7691,8 @@ self: super: with self; {
 
   prodict = callPackage ../development/python-modules/prodict { };
 
+  propka = callPackage ../development/python-modules/propka { };
+
   proxy_tools = callPackage ../development/python-modules/proxy_tools { };
 
   py-nextbusnext = callPackage ../development/python-modules/py-nextbusnext { };