Checkpoint

notebooks/coord_funcs.py

@@ -2,10 +2,10 @@
 from numpy import ndarray
 
 
-def rotation_matrix(sigma: float) -> ndarray:
+def get_rotation_matrix(degrees: float) -> ndarray:
     """https://en.wikipedia.org/wiki/Rotation_matrix"""
 
-    radians = sigma * np.pi / 180.0
+    radians = degrees * np.pi / 180.0
 
     r11 = np.cos(radians)
     r12 = -np.sin(radians)
@@ -21,27 +21,9 @@ def degree2radiant(degrees):
     return degrees * np.pi / 180.0
 
 
-# def find_best_inertia(
-#     atoms_a,
-#     coord_a,
-#     atoms_b,
-#     coord_b,
-#     reorder_method=rmsdlib.hungarian,
-#     rotation_method=rmsdlib.kabsch,
-# ):
-#     """Expect coord are centered"""
-
-#     inertia_a = rmsdlib.get_inertia_tensor(atoms_a, coord_a)
-#     eigval_a, eigvec_a = np.linalg.eig(inertia_a)
-#     inertia_b = rmsdlib.get_inertia_tensor(atoms_b, coord_b)
-#     eigval_b, eigvec_b = np.linalg.eig(inertia_b)
-
-#     # Align by eignval
-
-#     # Enumerate permutation
-#     U = rmsdlib.kabsch(eigvec_a, eigvec_b)
-
-#     # U1 = rotation_matrix_vectors(p_axis, q_axis)
-#     # U2 = rotation_matrix_vectors(p_axis, -q_axis)
-
-#     return
+def rotate_coord(angle, coord, axis=[0, 1]):
+    U = get_rotation_matrix(angle)
+    _xy = np.dot(coord[:, axis], U)
+    _coord = np.array(coord, copy=True)
+    _coord[:, :2] = _xy
+    return _coord