update: restrucutre

src/py/mat3ra/made/tools/analyze.py

@@ -483,23 +483,6 @@ def get_undercoordinated_atom_indices(
     return undercoordinated_atoms_indices
 
 
-def calculate_norm_of_distances_between_coordinates(coords1: np.ndarray, coords2: np.ndarray) -> float:
-    """
-    Calculate the norm of distances between two sets of coordinates.
-
-    Args:
-        coords1 (np.ndarray): The first set of coordinates.
-        coords2 (np.ndarray): The second set of coordinates.
-
-    Returns:
-        float: The calculated norm.
-    """
-    tree = cKDTree(coords2)
-    distances, _ = tree.query(coords1)
-    distances = distances[~np.isinf(distances)]
-    return float(np.linalg.norm(distances))
-
-
 def get_optimal_displacements(
     material: Material, grid_size: Tuple[int, int] = (10, 10), search_range: float = 1.0
 ) -> List[List[float]]:

src/py/mat3ra/made/tools/calculate.py

@@ -2,11 +2,11 @@
 
 import numpy as np
 from mat3ra.made.tools.convert.utils import InterfacePartsEnum
-from scipy.spatial import cKDTree
 
 from .build.passivation.enums import SurfaceTypes
+from .utils import calculate_norm_of_distances_between_coordinates
 from ..material import Material
-from .analyze import get_surface_area, get_surface_atom_indices, calculate_norm_of_distances_between_coordinates
+from .analyze import get_surface_area, get_surface_atom_indices
 from .build.interface.utils import get_slab
 from .convert import decorator_convert_material_args_kwargs_to_atoms
 from .third_party import ASEAtoms, ASECalculator, ASECalculatorEMT

src/py/mat3ra/made/tools/utils/__init__.py

@@ -5,6 +5,7 @@
 from mat3ra.made.material import Material
 from mat3ra.made.utils import ArrayWithIds
 from mat3ra.utils.matrix import convert_2x2_to_3x3
+from scipy.spatial import cKDTree
 
 from ..third_party import PymatgenStructure
 from .coordinate import (
@@ -64,6 +65,23 @@ def get_distance_between_coordinates(coordinate1: List[float], coordinate2: List
     return float(np.linalg.norm(np.array(coordinate1) - np.array(coordinate2)))
 
 
+def calculate_norm_of_distances_between_coordinates(coords1: np.ndarray, coords2: np.ndarray) -> float:
+    """
+    Calculate the norm of distances between two sets of coordinates.
+
+    Args:
+        coords1 (np.ndarray): The first set of coordinates.
+        coords2 (np.ndarray): The second set of coordinates.
+
+    Returns:
+        float: The calculated norm.
+    """
+    tree = cKDTree(coords2)
+    distances, _ = tree.query(coords1)
+    distances = distances[~np.isinf(distances)]
+    return float(np.linalg.norm(distances))
+
+
 def get_norm(vector: List[float]) -> float:
     """
     Get the norm of a vector.