Broke maths.lattices into submodules

polymerist/maths/lattices/__init__.py

@@ -0,0 +1 @@
+'''Tools for representing and manipulating coordinate lattices'''

polymerist/maths/lattices/coordops.py

@@ -0,0 +1,39 @@
+'''Distance geometry methods for arrays of coordinates'''
+
+'''Utilities for generating periodic unit lattices'''
+
+from typing import Optional
+import numpy as np
+from itertools import product as cartesian_product
+
+from ...genutils.typetools.numpytypes import Shape, N, M, DType
+
+
+def mean_coord(coords : np.ndarray[Shape[M, N], DType]) -> np.ndarray[Shape[N], DType]:
+    '''The average (center-of-mass) coordinate of a vector of coordinates'''
+    return coords.mean(axis=0)
+center_of_mass = COM = mean_coord
+
+def dists_to_point(coords : np.ndarray[Shape[M, N], DType], point : np.ndarray[Shape[N], DType], norm_order : Optional[int]=None) -> np.ndarray[Shape[M], DType]:
+    '''The distance between each point in a coordinate array and a single arbitrary point'''
+    return np.linalg.norm(coords - point, ord=norm_order, axis=1)
+
+def dists_to_centroid(coords : np.ndarray[Shape[M, N], DType], norm_order : Optional[int]=None) -> np.ndarray[Shape[M], DType]:
+    '''The distance of each coordinate in an array of coordinates to the coordinates' centroid'''
+    return dists_to_point(coords, point=mean_coord(coords), norm_order=norm_order)
+
+
+def bounding_box_dims(coords : np.ndarray[Shape[M, N], DType]) -> np.ndarray[Shape[N], DType]:
+    '''The N-dimensional tight bounding box side lengths around an array of coordinates'''
+    return coords.ptp(axis=0)
+
+def bounding_box_extrema(coords : np.ndarray[Shape[M, N], DType]) -> tuple[np.ndarray[Shape[N], DType], np.ndarray[Shape[N], DType]]:
+    '''The minimal and maximal coordinates of the N-dimensional tight bounding box around an array of coordinate'''
+    return coords.min(axis=0), coords.max(axis=0)
+
+def bounding_box_points(coords : np.ndarray[Shape[M, N], DType]) -> np.ndarray[Shape[M, N], DType]: # TOSELF : first axis of returned array is actually of size 2**N (haven't implemented typing yet)
+    '''The corner points the N-dimensional tight bounding box around an array of coordinate'''
+    return np.array([
+        corner_point
+            for corner_point in cartesian_product(*np.vstack(bounding_box_extrema(coords)).T)
+    ])