Coverage for biobb_mem/lipyphilic_biobb/common.py: 25%

1""" Common functions for package biobb_mem.lipyphilic_biobb """ 

2import numpy as np 

3from MDAnalysis.transformations.boxdimensions import set_dimensions 

4 

5 

6def calculate_box(u): 

7 print('Warning: trajectory probably has no box variable. Setting dimensions using the minimum and maximum positions of the atoms.') 

8 # Initialize min and max positions with extreme values 

9 min_pos = np.full(3, np.inf) 

10 max_pos = np.full(3, -np.inf) 

11 

12 # Iterate over all frames to find the overall min and max positions 

13 for ts in u.trajectory: 

14 positions = u.atoms.positions 

15 min_pos = np.minimum(min_pos, positions.min()) 

16 max_pos = np.maximum(max_pos, positions.max()) 

17 

18 # Calculate the dimensions of the box 

19 box_dimensions = max_pos - min_pos 

20 u.trajectory.add_transformations(set_dimensions([*box_dimensions, 90, 90, 90]))