Coverage for biobb_mem/fatslim/common.py: 88%

1from MDAnalysis.transformations.boxdimensions import set_dimensions 

2from biobb_common.tools import file_utils as fu 

3import glob 

4import shutil 

5import os 

6 

7 

8def set_box(u): 

9 # Calculate the dimensions of the box 

10 positions = u.atoms.positions 

11 box_dimensions = positions.max(axis=0) - positions.min(axis=0) 

12 # Set the box dimensions 

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

14 

15 

16def ignore_no_box(u, ignore_no_box, out_log, global_log): 

17 # FATSLiM ValueError: Box does not correspond to PBC=xyz 

18 if u.dimensions is None: 

19 if ignore_no_box: 

20 fu.log('Setting box dimensions using the minimum and maximum positions of the atoms.', 

21 out_log, global_log) 

22 set_box(u) 

23 else: 

24 fu.log('The trajectory does not contain box information. ' 

25 'Please set the ignore_no_box property to True to ignore this error.', 

26 out_log, global_log) 

27 raise ValueError("Box dimensions are required but not found in the trajectory.") 

28 

29 

30def move_output_file(file, out_file_path, out_log, global_log): 

31 # Add a wildcard to support multiples frames output (it adds 0000 suffix) 

32 base, ext = os.path.splitext(file) 

33 file_glob = base + '*' + ext 

34 files_to_move = glob.glob(file_glob) 

35 if files_to_move: 

36 fu.log(f"Renaming file {files_to_move[0]} to {out_file_path}", out_log, global_log) 

37 # Move the file to the output path 

38 shutil.move(files_to_move[0], out_file_path) 

39 else: 

40 fu.log(f"Warning: File {file} not found, APL calculation might have failed.", out_log, global_log)