Coverage for biobb_vs/vina/common.py: 58%

1"""Common functions for package biobb_vs.vina""" 

2 

3from pathlib import Path, PurePath 

4 

5from biobb_common.tools import file_utils as fu 

6 

7# CHECK PARAMETERS 

8 

9 

10def check_input_path(path, argument, out_log, classname): 

11 """Checks input file""" 

12 if not Path(path).exists(): 

13 fu.log(classname + ": Unexisting %s file, exiting" % argument, out_log) 

14 raise SystemExit(classname + ": Unexisting %s file" % argument) 

15 file_extension = PurePath(path).suffix 

16 if not is_valid_file(file_extension[1:], argument): 

17 fu.log( 

18 classname + ": Format %s in %s file is not compatible" 

19 % (file_extension[1:], argument), 

20 out_log, 

21 ) 

22 raise SystemExit( 

23 classname + ": Format %s in %s file is not compatible" 

24 % (file_extension[1:], argument) 

25 ) 

26 return path 

27 

28 

29def check_output_path(path, argument, optional, out_log, classname): 

30 """Checks output file""" 

31 if optional and not path: 

32 return None 

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

34 fu.log(classname + ": Unexisting %s folder, exiting" % argument, out_log) 

35 raise SystemExit(classname + ": Unexisting %s folder" % argument) 

36 file_extension = PurePath(path).suffix 

37 if not is_valid_file(file_extension[1:], argument): 

38 fu.log( 

39 classname + ": Format %s in %s file is not compatible" 

40 % (file_extension[1:], argument), 

41 out_log, 

42 ) 

43 raise SystemExit( 

44 classname + ": Format %s in %s file is not compatible" 

45 % (file_extension[1:], argument) 

46 ) 

47 return path 

48 

49 

50def is_valid_file(ext, argument): 

51 """Checks if file format is compatible""" 

52 formats = { 

53 "input_ligand_path": ["pdb"], 

54 "output_ligand_path": ["pdbqt"], 

55 "input_receptor_path": ["pdb"], 

56 "output_receptor_path": ["pdbqt"], 

57 "input_ligand_pdbqt_path": ["pdbqt"], 

58 "input_receptor_pdbqt_path": ["pdbqt"], 

59 "input_box_path": ["pdb"], 

60 "output_pdbqt_path": ["pdbqt"], 

61 "output_log_path": ["log"], 

62 } 

63 return ext in formats[argument] 

64 

65 

66def check_mgltools_path(mgltools_path, out_log, classname): 

67 """Checks the path of mgltools""" 

68 if not Path(mgltools_path).exists(): 

69 fu.log(classname + ": Unexisting mgltools_path, exiting", out_log) 

70 raise SystemExit(classname + ": Unexisting mgltools_path, exiting") 

71 return mgltools_path 

72 

73 

74'''def check_input_autodock(structure, out_log): 

75 """ if structure ends with END, remove last line """ 

76 lines_new = [] 

77 with open(structure, 'r') as f: 

78 lines = f.read().splitlines() 

79 for item in lines: 

80 #if not item.startswith('END'): 

81 if not item.strip() == 'END': 

82 lines_new.append(item) 

83 else: 

84 fu.log('%s file ends with END, cleaning' % structure, out_log) 

85 

86 with open(structure, 'w') as f: 

87 for item in lines_new: 

88 f.write("%s\n" % item)'''