Coverage for biobb_chemistry/ambertools/common.py: 70%

1""" Common functions for package biobb_chemistry.ambertools """ 

2from pathlib import Path, PurePath 

3from biobb_common.tools import file_utils as fu 

4 

5 

6def check_input_path(path, out_log, classname): 

7 """ Checks input file """ 

8 if not Path(path).exists(): 

9 fu.log(classname + ': Unexisting input file, exiting', out_log) 

10 raise SystemExit(classname + ': Unexisting input file') 

11 file_extension = PurePath(path).suffix 

12 if not is_valid_reduce(file_extension[1:]): 

13 fu.log(classname + ': Format %s in input file is not compatible' % file_extension[1:], out_log) 

14 raise SystemExit(classname + ': Format %s in input file is not compatible' % file_extension[1:]) 

15 if (PurePath(path).name == path or not PurePath(path).is_absolute()): 

16 path = str(PurePath(Path.cwd()).joinpath(path)) 

17 

18 return path 

19 

20 

21def check_output_path(path, out_log, classname): 

22 """ Checks output path """ 

23 if PurePath(path).parent and not Path(PurePath(path).parent).exists(): 

24 fu.log(classname + ': Unexisting output %s output folder, exiting' % type, out_log) 

25 raise SystemExit(classname + ': Unexisting %s output folder' % type) 

26 file_extension = PurePath(path).suffix 

27 if not is_valid_reduce(file_extension[1:]): 

28 fu.log(classname + ': Format %s in input file is not compatible' % file_extension[1:], out_log) 

29 raise SystemExit(classname + ': Format %s in output file is not compatible' % file_extension[1:]) 

30 

31 return path 

32 

33 

34def get_binary_path(properties, type): 

35 """ Gets binary path """ 

36 return properties.get(type, get_default_value(type)) 

37 

38 

39def get_default_value(key): 

40 """ Gives default values according to the given key """ 

41 default_values = { 

42 "binary_path": "reduce", 

43 } 

44 

45 return default_values[key] 

46 

47 

48def is_valid_reduce(ext): 

49 """ Checks if input file format is compatible with Reduce """ 

50 formats = ["pdb"] 

51 

52 return ext in formats