Coverage for model_workflow/tools/get_summarized_trajectory.py: 0%

1# This script is used to get a reduced version of a given trajectory 

2# The summarized trajectory frames are frames selected along the whole trajectory 

3# This process is carried by Gromacs 

4 

5from subprocess import run, PIPE, Popen 

6 

7from model_workflow.utils.constants import GROMACS_EXECUTABLE 

8 

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

10# Tested supported formats are .pdb and .tpr 

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

12# Tested supported formats are .trr and .xtc 

13# summarized_trajectory_filename - The name string of the output summarized trajectory file (path) 

14# Tested supported format is .pdb  

15def get_summarized_trajectory ( 

16 input_topology_filename : str, 

17 input_trajectory_filename : str, 

18 summarized_trajectory_filename : str 

19 ) -> str: 

20 

21 # Run Gromacs 

22 p = Popen([ 

23 "echo", 

24 "System", 

25 ], stdout=PIPE) 

26 # Run Gromacs 

27 logs = run([ 

28 GROMACS_EXECUTABLE, 

29 "trjconv", 

30 "-s", 

31 input_topology_filename, 

32 "-f", 

33 input_trajectory_filename, 

34 '-o', 

35 summarized_trajectory_filename, 

36 '-dt', 

37 '10', 

38 '-quiet' 

39 ], stdin=p.stdout, stdout=PIPE).stdout.decode() 

40 p.stdout.close() 

41 

42 # Return gromacs logs 

43 return logs