Typing: Parameters, vector_algebra

- Parameters typing
- vector_algebra tests and refactoring
- Various pyright typing improvements

tests/test_basic_regression.py

@@ -68,11 +68,11 @@ def run_propka(options, pdb_path, tmp_path):
     """
     options += [str(pdb_path)]
     args = loadOptions(options)
+    cwd = Path.cwd()
     try:
         _LOGGER.warning(
             "Working in tmpdir {0:s} because of PROPKA file output; "
             "need to fix this.".format(str(tmp_path)))
-        cwd = Path.cwd()
         os.chdir(tmp_path)
         parameters = read_parameter_file(args.parameters, Parameters())
         molecule = MolecularContainer(parameters, args)
@@ -148,6 +148,7 @@ def compare_output(pdb, tmp_path, ref_path):
 def test_regression(pdb, options, tmp_path):
     """Basic regression test of PROPKA functionality."""
     path_dict = get_test_dirs()
+    ref_path = None
 
     for ext in ["json", "dat"]:
         ref_path = path_dict["results"] / f"{pdb}.{ext}"

tests/test_vector_algebra.py

@@ -0,0 +1,159 @@
+import propka.vector_algebra as m
+
+import math
+import pytest
+from pytest import approx
+
+RADIANS_90 = math.pi / 2
+
+
+def assert_vector_equal(v1: m.Vector, v2: m.Vector):
+    assert isinstance(v1, m.Vector)
+    assert isinstance(v2, m.Vector)
+    assert v1.x == approx(v2.x)
+    assert v1.y == approx(v2.y)
+    assert v1.z == approx(v2.z)
+
+
+def _matrix4x4_tolist(self: m.Matrix4x4) -> list:
+    return [
+        self.a11, self.a12, self.a13, self.a14, self.a21, self.a22, self.a23, self.a24,
+        self.a31, self.a32, self.a33, self.a34, self.a41, self.a42, self.a43, self.a44
+    ]
+
+def assert_matrix4x4_equal(m1: m.Matrix4x4, m2: m.Matrix4x4):
+    assert isinstance(m1, m.Matrix4x4)
+    assert isinstance(m2, m.Matrix4x4)
+    assert _matrix4x4_tolist(m1) == approx(_matrix4x4_tolist(m2))
+
+
+def test_Vector__init():
+    v = m.Vector()
+    assert v.x == 0.0
+    assert v.y == 0.0
+    assert v.z == 0.0
+    v = m.Vector(12, 34, 56)
+    assert v.x == 12
+    assert v.y == 34
+    assert v.z == 56
+    v1 = m.Vector(atom1=v)
+    assert v1.x == 12
+    assert v1.y == 34
+    assert v1.z == 56
+    v2 = m.Vector(5, 4, 3)
+    v3 = m.Vector(atom1=v2, atom2=v1)
+    assert v3.x == 7
+    assert v3.y == 30
+    assert v3.z == 53
+
+
+def test_Vector__plusminus():
+    v1 = m.Vector(1, 2, 3)
+    v2 = m.Vector(4, 5, 6)
+    v3 = v1 + v2
+    assert v3.x == 5
+    assert v3.y == 7
+    assert v3.z == 9
+    v3 = v1 - v2
+    assert v3.x == -3
+    assert v3.y == -3
+    assert v3.z == -3
+    v4 = -v1
+    assert v4.x == -1
+    assert v4.y == -2
+    assert v4.z == -3
+
+
+def test_Vector__mul__number():
+    v1 = m.Vector(1, 2, 3)
+    assert_vector_equal(v1 * 2, m.Vector(2, 4, 6))
+
+
+def test_Vector__mul__Vector():
+    v1 = m.Vector(1, 2, 3)
+    v2 = m.Vector(4, 5, 6)
+    assert v1 * v2 == 32
+    assert v1.dot(v2) == 32
+    with pytest.raises(TypeError):
+        v1 @ v2  # type: ignore
+
+
+def test_Vector__mul__Matrix4x4():
+    v1 = m.Vector(1, 2, 3)
+    assert_vector_equal(v1 * m.Matrix4x4(), m.Vector())
+    m2 = m.Matrix4x4(0, 1, 0, 0, 20, 0, 0, 0, 0, 0, 300, 0, 0, 0, 0, 1)
+    assert_vector_equal(v1 * m2, m.Vector(2, 20, 900))
+    assert_vector_equal(m2 * v1, m.Vector(2, 20, 900))
+    assert_vector_equal(m2 @ v1, m.Vector(2, 20, 900))
+    with pytest.raises(TypeError):
+        v1 @ m2  # type: ignore
+
+
+def test_Vector__cross():
+    v1 = m.Vector(1, 2, 3)
+    v2 = m.Vector(4, 5, 6)
+    assert_vector_equal(v1**v2, m.Vector(-3, 6, -3))  # TODO deprecate
+    assert_vector_equal(v1.cross(v2), m.Vector(-3, 6, -3))
+    assert_vector_equal(v2.cross(v1), m.Vector(3, -6, 3))
+
+
+def test_Vector__length():
+    v1 = m.Vector(1, 2, 3)
+    assert v1.length() == 14**0.5
+    assert v1.sq_length() == 14
+
+
+def test_Vector__orthogonal():
+    v1 = m.Vector(1, 2, 3)
+    assert v1.dot(v1.orthogonal()) == 0
+
+
+def test_Vector__rescale():
+    v1 = m.Vector(1, 2, 3)
+    v2 = v1.rescale(4)
+    assert v2.length() == 4
+    assert v2.x / v1.x == approx(4 / 14**0.5)
+    assert v2.y / v1.y == approx(4 / 14**0.5)
+    assert v2.z / v1.z == approx(4 / 14**0.5)
+
+
+def test_angle():
+    v1 = m.Vector(0, 0, 1)
+    v2 = m.Vector(0, 2, 0)
+    assert m.angle(v1, v2) == RADIANS_90
+
+
+def test_angle_degrees():
+    v1 = m.Vector(0, 0, 3)
+    v2 = m.Vector(5, 0, 0)
+    assert m.angle_degrees(v1, v2) == 90
+
+
+def test_signed_angle_around_axis():
+    v1 = m.Vector(0, 0, 3)
+    v2 = m.Vector(5, 0, 0)
+    v3 = m.Vector(0, 1, 0)
+    assert m.signed_angle_around_axis(v1, v2, v3) == -RADIANS_90
+    v1 = m.Vector(0, 2, 3)
+    v2 = m.Vector(5, 4, 0)
+    assert m.signed_angle_around_axis(v1, v2, v3) == -RADIANS_90
+
+
+def test_rotate_vector_around_an_axis():
+    v1 = m.Vector(0, 0, 3)
+    v2 = m.Vector(3, 0, 0)
+    v3 = m.Vector(0, -1, 0)
+    v4 = m.rotate_vector_around_an_axis(RADIANS_90, v3, v2)
+    assert_vector_equal(v4, v1)
+
+
+def test_rotate_atoms_around_z_axis():
+    m_rot = m.rotate_atoms_around_z_axis(-RADIANS_90)
+    assert_matrix4x4_equal(m_rot,
+                           m.Matrix4x4(0, 1, 0, 0, -1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1))
+
+
+def test_rotate_atoms_around_y_axis():
+    m_rot = m.rotate_atoms_around_y_axis(RADIANS_90)
+    assert_matrix4x4_equal(m_rot,
+                           m.Matrix4x4(0, 0, 1, 0, 0, 1, 0, 0, -1, 0, 0, 0, 0, 0, 0, 1))