Op Module¶

The op module provides geometric operations for manipulating molecular coordinates.

Available Operations¶

• Rotation: Rodrigues rotation, quaternion rotation
• Translation: Coordinate translation
• Matrix operations: Rotation matrix from vectors

In [1]:

import numpy as np

from molpy.op.geometry import (
    rotate_by_rodrigues,
    translate,
)

# Rotate coordinates using Rodrigues formula
coords = np.array([[1.0, 0.0, 0.0], [0.0, 1.0, 0.0]])
axis = np.array([0.0, 0.0, 1.0])
theta = np.pi / 2  # 90 degrees

rotated = rotate_by_rodrigues(coords, axis, theta)
print(f"Rotated coordinates:\n{rotated}")

# Translate coordinates
vector = np.array([1.0, 1.0, 1.0])
translated = translate(coords, vector)
print(f"Translated coordinates:\n{translated}")

import numpy as np from molpy.op.geometry import ( rotate_by_rodrigues, translate, ) # Rotate coordinates using Rodrigues formula coords = np.array([[1.0, 0.0, 0.0], [0.0, 1.0, 0.0]]) axis = np.array([0.0, 0.0, 1.0]) theta = np.pi / 2 # 90 degrees rotated = rotate_by_rodrigues(coords, axis, theta) print(f"Rotated coordinates:\n{rotated}") # Translate coordinates vector = np.array([1.0, 1.0, 1.0]) translated = translate(coords, vector) print(f"Translated coordinates:\n{translated}")

Rotated coordinates:
[[ 6.123234e-17  1.000000e+00  0.000000e+00]
 [-1.000000e+00  6.123234e-17  0.000000e+00]]
Translated coordinates:
[[2. 1. 1.]
 [1. 2. 1.]]