wip

examples/gulp_test_example.py

@@ -1,6 +1,6 @@
 # ruff: noqa: S101
+import argparse
 import logging
-import sys
 from pathlib import Path
 
 import numpy as np
@@ -10,12 +10,7 @@
 
 def main() -> None:
     """Run the example."""
-    first_line = f"Usage: {__file__}.py"
-    if len(sys.argv) != 2:
-        logging.info("%s gulp_path", first_line)
-        sys.exit()
-    else:
-        gulp_path = sys.argv[1]
+    args = _parse_args()
 
     iron_atom = stk.BuildingBlock(
         smiles="[Fe+2]",
@@ -72,7 +67,7 @@ def main() -> None:
     # Use conjugate gradient method for a slower, but more stable
     # optimisation.
     gulp_opt = stko.GulpUFFOptimizer(
-        gulp_path=gulp_path,
+        gulp_path=args.gulp_path,
         output_dir="gulp_test_output",
         metal_FF={26: "Fe4+2"},
         conjugate_gradient=True,
@@ -86,7 +81,7 @@ def main() -> None:
 
     target_num_confs = 40
     gulp_md = stko.GulpUFFMDOptimizer(
-        gulp_path=gulp_path,
+        gulp_path=args.gulp_path,
         metal_FF={26: "Fe4+2"},
         output_dir="gulp_test_output_MD",
         temperature=300,
@@ -104,6 +99,12 @@ def main() -> None:
     assert len(confs_gen) == target_num_confs
 
 
+def _parse_args() -> argparse.Namespace:
+    parser = argparse.ArgumentParser()
+    parser.add_argument("gulp_path", type=str)
+    return parser.parse_args()
+
+
 if __name__ == "__main__":
     logging.basicConfig(
         level=logging.INFO,

pyproject.toml

@@ -58,6 +58,7 @@ select = ["ALL"]
 ignore = [
   "ANN101",
   "ANN102",
+  "ANN401",
   "COM812",
   "ISC001",
   "FBT001",

src/stko/_internal/calculators/geometry_analysis/geometry.py

@@ -28,7 +28,7 @@ class GeometryAnalyser:
     def _get_metal_atom_ids(
         self,
         molecule: stk.Molecule,
-        metal_atom_nos: tuple[int],
+        metal_atom_nos: tuple[int, ...],
     ) -> list[int]:
         return [
             i.get_id()
@@ -39,7 +39,7 @@ def _get_metal_atom_ids(
     def get_metal_distances(
         self,
         molecule: stk.Molecule,
-        metal_atom_nos: tuple[int],
+        metal_atom_nos: tuple[int, ...],
     ) -> dict[tuple[int, int], float]:
         """Get all metal atom pair distances.
 
@@ -71,7 +71,7 @@ def get_metal_distances(
     def get_metal_centroid_metal_angle(
         self,
         molecule: stk.Molecule,
-        metal_atom_nos: tuple[int],
+        metal_atom_nos: tuple[int, ...],
     ) -> dict[tuple[int, int], float]:
         """Get all metal-centroid-metal angles.
 
@@ -206,7 +206,7 @@ def get_max_diameter(self, molecule: stk.Molecule) -> float:
     def calculate_bonds(
         self,
         molecule: stk.Molecule,
-    ) -> dict[tuple[str, ...], list[float]]:
+    ) -> dict[tuple[str, str], list[float]]:
         """Calculate bond lengths for all `stk.Molecule.get_bonds()`.
 
         Parameters:
@@ -218,19 +218,17 @@ def calculate_bonds(
 
         """
         position_matrix = molecule.get_position_matrix()
-        lengths = defaultdict(list)
+        lengths: dict[tuple[str, str], list[float]] = defaultdict(list)
         for bond in molecule.get_bonds():
             a1id = bond.get_atom1().get_id()
             a2id = bond.get_atom2().get_id()
-            length_type = tuple(
-                sorted(
-                    (
-                        bond.get_atom1().__class__.__name__,
-                        bond.get_atom2().__class__.__name__,
-                    )
+            a, b = sorted(
+                (
+                    bond.get_atom1().__class__.__name__,
+                    bond.get_atom2().__class__.__name__,
                 )
             )
-            lengths[length_type].append(
+            lengths[(a, b)].append(
                 get_atom_distance(position_matrix, a1id, a2id)
             )
 
@@ -239,7 +237,7 @@ def calculate_bonds(
     def calculate_angles(
         self,
         molecule: stk.Molecule,
-    ) -> dict[tuple[str, ...], list[float]]:
+    ) -> dict[tuple[str, str, str], list[float]]:
         """Calculate angles for all angles defined by molecule bonding.
 
         Parameters:
@@ -251,7 +249,7 @@ def calculate_angles(
 
         """
         position_matrix = molecule.get_position_matrix()
-        angles: dict[tuple[str, ...], list[float]] = defaultdict(list)
+        angles: dict[tuple[str, str, str], list[float]] = defaultdict(list)
         for a_ids in self._get_paths(molecule, 3):
             atoms = list(molecule.get_atoms(atom_ids=a_ids))
             atom1 = atoms[0]

src/stko/_internal/molecular/conversion/md_analysis.py

@@ -1,4 +1,5 @@
 import logging
+from typing import Any
 
 import stk
 
@@ -45,7 +46,7 @@ def __init__(self) -> None:
             )
             raise WrapperNotInstalledError(msg)
 
-    def get_universe(self, mol: stk.Molecule):  # type: ignore[no-untyped-def]
+    def get_universe(self, mol: stk.Molecule) -> Any:  # type: ignore[no-untyped-def]
         """Get an MDAnalysis object.
 
         Parameters:

src/stko/_internal/molecular/molecule_modifiers/molecule_splitter.py

@@ -1,5 +1,4 @@
 import logging
-from collections import abc
 from itertools import combinations
 
 import stk

tests/calculators/geometry/case_data.py

@@ -1,31 +1,19 @@
+from dataclasses import dataclass
+
 import stk
 
 
+@dataclass(frozen=True, slots=True)
 class CaseData:
-    def __init__(
-        self,
-        molecule: stk.Molecule,
-        metal_atom_distances: dict[tuple[int, int], float],
-        metal_centroid_angles: dict[tuple[int, int], float],
-        min_centoid_distance: float,
-        avg_centoid_distance: tuple[float, float],
-        radius_gyration: float,
-        min_atom_atom_distance: float,
-        max_diameter: float,
-        bonds: dict[tuple[str, str], list[float]],
-        angles: dict[tuple[str, str, str], list[float]],
-        torsions: dict[tuple[str, str, str, str], list[float]],
-        name: str,
-    ) -> None:
-        self.molecule = molecule
-        self.metal_atom_distances = metal_atom_distances
-        self.metal_centroid_angles = metal_centroid_angles
-        self.min_centoid_distance = min_centoid_distance
-        self.avg_centoid_distance = avg_centoid_distance
-        self.radius_gyration = radius_gyration
-        self.min_atom_atom_distance = min_atom_atom_distance
-        self.max_diameter = max_diameter
-        self.bonds = bonds
-        self.angles = angles
-        self.torsions = torsions
-        self.name = name
+    molecule: stk.Molecule
+    metal_atom_distances: dict[tuple[int, int], float]
+    metal_centroid_angles: dict[tuple[int, int], float]
+    min_centoid_distance: float
+    avg_centoid_distance: tuple[float, float]
+    radius_gyration: float
+    min_atom_atom_distance: float
+    max_diameter: float
+    bonds: dict[tuple[str, str], list[float]]
+    angles: dict[tuple[str, str, str], list[float]]
+    torsions: dict[tuple[str, str, str, str], list[float]]
+    name: str

tests/calculators/geometry/conftest.py

@@ -1,3 +1,4 @@
+import numpy as np
 import pytest
 import stk
 
@@ -8,9 +9,9 @@
         metals=stk.BuildingBlock(
             smiles="[Fe+2]",
             functional_groups=(
-                stk.SingleAtom(stk.Fe(0, charge=2)) for i in range(6)
+                stk.SingleAtom(stk.Fe(0, charge=2)) for _ in range(6)
             ),
-            position_matrix=[[0, 0, 0]],
+            position_matrix=np.array([[0, 0, 0]]),
         ),
         ligands=stk.BuildingBlock(
             smiles="C1=NC(C=NBr)=CC=C1",
@@ -2321,9 +2322,9 @@
                             smiles="[Pd+2]",
                             functional_groups=(
                                 stk.SingleAtom(stk.Pd(0, charge=2))
-                                for i in range(4)
+                                for _ in range(4)
                             ),
-                            position_matrix=[[0, 0, 0]],
+                            position_matrix=np.array([[0, 0, 0]]),
                         ),
                         stk.BuildingBlock(
                             smiles=(
@@ -2926,7 +2927,7 @@
         ),
     ),
 )
-def case_data(request) -> CaseData:
+def case_data(request: pytest.FixtureRequest) -> CaseData:
     return request.param(
         f"{request.fixturename}{request.param_index}",
     )

tests/calculators/geometry/test_calculate_angles.py

@@ -1,20 +1,13 @@
 import numpy as np
 import stko
 
+from .case_data import CaseData
 
-def test_calculate_angles(case_data):
-    """Test :class:`.GeometryAnalyser.calculate_angles`.
 
-    Parameters
-    ----------
-        case_data:
-            A test case.
-
-    """
+def test_calculate_angles(case_data: CaseData) -> None:
     analyser = stko.molecule_analysis.GeometryAnalyser()
 
     result = analyser.calculate_angles(case_data.molecule)
-    print(result)
     for triple in result:
         if triple == ("C", "C", "C"):
             continue

tests/calculators/geometry/test_calculate_bonds.py

@@ -1,20 +1,13 @@
 import numpy as np
 import stko
 
+from .case_data import CaseData
 
-def test_calculate_bonds(case_data):
-    """Test :class:`.GeometryAnalyser.calculate_bonds`.
 
-    Parameters
-    ----------
-        case_data:
-            A test case.
-
-    """
+def test_calculate_bonds(case_data: CaseData) -> None:
     analyser = stko.molecule_analysis.GeometryAnalyser()
 
     result = analyser.calculate_bonds(case_data.molecule)
-    print(result)
     for pair in result:
         if pair == ("C", "C"):
             continue

tests/calculators/geometry/test_calculate_torsions.py

@@ -1,20 +1,13 @@
 import numpy as np
 import stko
 
+from .case_data import CaseData
 
-def test_calculate_torsions(case_data):
-    """Test :class:`.GeometryAnalyser.calculate_torsions`.
 
-    Parameters
-    ----------
-        case_data:
-            A test case.
-
-    """
+def test_calculate_torsions(case_data: CaseData) -> None:
     analyser = stko.molecule_analysis.GeometryAnalyser()
 
     result = analyser.calculate_torsions(case_data.molecule)
-    print(result)
     for four in result:
         if four == ("C", "C", "C", "C"):
             continue

tests/calculators/geometry/test_get_avg_centroid_distance.py

@@ -1,20 +1,13 @@
 import numpy as np
 import stko
 
+from .case_data import CaseData
 
-def test_get_avg_centroid_distance(case_data):
-    """Test :class:`.GeometryAnalyser.get_avg_centroid_distance`.
 
-    Parameters
-    ----------
-        case_data:
-            A test case.
-
-    """
+def test_get_avg_centroid_distance(case_data: CaseData) -> None:
     analyser = stko.molecule_analysis.GeometryAnalyser()
 
     result = analyser.get_avg_centroid_distance(case_data.molecule)
-    print(result)
     assert np.isclose(
         result[0], case_data.avg_centoid_distance[0], atol=1e-3, rtol=0
     )

tests/calculators/geometry/test_get_max_diamter.py

@@ -1,18 +1,11 @@
 import numpy as np
 import stko
 
+from .case_data import CaseData
 
-def test_get_max_diameter(case_data):
-    """Test :class:`.GeometryAnalyser.get_max_diameter`.
 
-    Parameters
-    ----------
-        case_data:
-            A test case.
-
-    """
+def test_get_max_diameter(case_data: CaseData) -> None:
     analyser = stko.molecule_analysis.GeometryAnalyser()
 
     result = analyser.get_max_diameter(case_data.molecule)
-    print(result)
     assert np.isclose(result, case_data.max_diameter, atol=1e-3, rtol=0)

tests/calculators/geometry/test_get_metal_centroid_metal_angle.py

@@ -1,26 +1,18 @@
 import numpy as np
 import stko
 
+from .case_data import CaseData
 
-def test_get_metal_centroid_metal_angle(case_data):
-    """Test :class:`.GeometryAnalyser.get_metal_centroid_metal_angle`.
 
-    Parameters
-    ----------
-        case_data:
-            A test case.
-
-    """
+def test_get_metal_centroid_metal_angle(case_data: CaseData) -> None:
     analyser = stko.molecule_analysis.GeometryAnalyser()
 
     result = analyser.get_metal_centroid_metal_angle(
         case_data.molecule,
         metal_atom_nos=(26, 46),
     )
-    print(result)
     assert len(result) == len(case_data.metal_centroid_angles)
     for i in result:
-        print(i, result[i])
         assert np.isclose(
             result[i], case_data.metal_centroid_angles[i], atol=1e-3, rtol=0
         )