Coverage for model_workflow/tools/get_box_size.py: 90%

1# This script is used to find out the box size (x, y and z) in a pdb topology 

2# This process is carried by Gromacs 

3 

4import os 

5from subprocess import run, PIPE, Popen 

6 

7from model_workflow.utils.constants import GROMACS_EXECUTABLE 

8 

9# Set the box analysis filename 

10# This analysis is used here to mine the box size data 

11# It is never used further 

12box_analysis = 'box.xvg' 

13 

14# input_topology_filename - The name string of the input topology file (path) 

15# Tested supported formats are .pdb and .tpr 

16# input_trajectory_filename - The name string of the input trajectory file (path) 

17# Tested supported formats are .trr and .xtc 

18 

19 

20def get_box_size( 

21 input_topology_filename: str, 

22 input_trajectory_filename: str, 

23) -> tuple: 

24 

25 # Generate the box analysis 

26 # WARNING: Do not use the first_frame here instead of the trajectory 

27 # In modified topologies the first frame pdb may have lost box size data 

28 p = Popen([ 

29 "echo", 

30 "System", 

31 ], stdout=PIPE) 

32 logs = run([ 

33 GROMACS_EXECUTABLE, 

34 "traj", 

35 "-s", 

36 input_topology_filename, 

37 "-f", 

38 input_trajectory_filename, 

39 '-ob', 

40 box_analysis, 

41 '-b', 

42 '0', 

43 '-e', 

44 '0', 

45 '-quiet' 

46 ], stdin=p.stdout, stdout=PIPE, stderr=PIPE).stdout.decode() 

47 p.stdout.close() 

48 

49 if not os.path.exists(box_analysis): 

50 print(logs) 

51 raise SystemExit('ERROR: Something went wrong with Gromacs') 

52 

53 # Read the box analysis and get the desired data 

54 boxsizex, boxsizey, boxsizez = "", "", "" 

55 with open(box_analysis, 'r') as file: 

56 for line in file: 

57 if line.startswith(("#", "@")) == False: 

58 

59 # Simulation box 'x' size 

60 boxsizex = float(line.split()[1]) 

61 

62 # Simulation box 'y' size 

63 boxsizey = float(line.split()[2]) 

64 

65 # Simulation box 'z' size 

66 boxsizez = float(line.split()[3]) 

67 

68 # Display it 

69 print('Box size: (' + str(boxsizex) + ',' + 

70 str(boxsizey) + ',' + str(boxsizez) + ')') 

71 

72 # Remove the box analysis 

73 os.remove(box_analysis) 

74 

75 # Return gromacs logs 

76 return (boxsizex, boxsizey, boxsizez)