Coverage for biobb_pdb_tools/pdb_tools/biobb_pdb_seg.py: 95%

1#!/usr/bin/env python3 

2 

3"""Module containing the Pdbseg class and the command line interface.""" 

4 

5from typing import Optional 

6from biobb_common.generic.biobb_object import BiobbObject 

7from biobb_common.tools import file_utils as fu 

8from biobb_common.tools.file_utils import launchlogger 

9 

10 

11class Pdbseg(BiobbObject): 

12 """ 

13 | biobb_pdb_tools Pdbseg 

14 | Modifies the segment identifier column of a PDB file. 

15 | This tool modifies the segment identifier column of a PDB file. It can be used to change the segment identifier of a PDB file or to remove the segment identifier from a PDB file. 

16 

17 Args: 

18 input_file_path (str): Input PDB file. File type: input. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_pdb_tools/master/biobb_pdb_tools/test/data/pdb_tools/input_pdb_seg.pdb>`_. Accepted formats: pdb (edam:format_1476). 

19 output_file_path (str): PDB file with segment identifier column modified. File type: output. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_pdb_tools/master/biobb_pdb_tools/test/reference/pdb_tools/ref_pdb_seg.pdb>`_. Accepted formats: pdb (edam:format_1476). 

20 properties (dic): 

21 * **segment** (*str*) - ('B') Default is an empty segment. 

22 * **binary_path** (*str*) - ("pdb_seg") Path to the pdb_seg executable binary. 

23 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files. 

24 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist. 

25 

26 Examples: 

27 This is a use example of how to use the building block from Python:: 

28 

29 from biobb_pdb_tools.pdb_tools.biobb_pdb_seg import biobb_pdb_seg 

30 

31 prop = { 

32 'segment': 'A' 

33 } 

34 biobb_pdb_seg(input_file_path='/path/to/input.pdb', 

35 output_file_path='/path/to/output.pdb', 

36 properties=prop) 

37 

38 Info: 

39 * wrapped_software: 

40 * name: pdb_tools 

41 * version: >=2.5.0 

42 * license: Apache-2.0 

43 * ontology: 

44 * name: EDAM 

45 * schema: http://edamontology.org/EDAM.owl 

46 

47 """ 

48 

49 def __init__( 

50 self, input_file_path, output_file_path, properties=None, **kwargs 

51 ) -> None: 

52 properties = properties or {} 

53 super().__init__(properties) 

54 self.locals_var_dict = locals().copy() 

55 self.io_dict = { 

56 "in": {"input_file_path": input_file_path}, 

57 "out": {"output_file_path": output_file_path}, 

58 } 

59 

60 self.binary_path = properties.get("binary_path", "pdb_seg") 

61 self.segment = properties.get("segment", False) 

62 self.properties = properties 

63 

64 self.check_properties(properties) 

65 self.check_arguments() 

66 

67 @launchlogger 

68 def launch(self) -> int: 

69 """Execute the :class:`Pdbseg <biobb_pdb_tools.pdb_tools.pdb_seg>` object.""" 

70 

71 if self.check_restart(): 

72 return 0 

73 self.stage_files() 

74 

75 instructions = [] 

76 if self.segment: 

77 instructions.append("-" + str(self.segment)) 

78 fu.log("Appending optional boolean property", 

79 self.out_log, self.global_log) 

80 

81 self.cmd = [ 

82 self.binary_path, 

83 " ".join(instructions), 

84 self.stage_io_dict["in"]["input_file_path"], 

85 ">", 

86 self.io_dict["out"]["output_file_path"], 

87 ] 

88 

89 fu.log(" ".join(self.cmd), self.out_log, self.global_log) 

90 

91 fu.log( 

92 "Creating command line with instructions and required arguments", 

93 self.out_log, 

94 self.global_log, 

95 ) 

96 self.run_biobb() 

97 self.copy_to_host() 

98 self.remove_tmp_files() 

99 self.check_arguments(output_files_created=True, raise_exception=False) 

100 

101 return self.return_code 

102 

103 

104def biobb_pdb_seg( 

105 input_file_path: str, 

106 output_file_path: str, 

107 properties: Optional[dict] = None, 

108 **kwargs, 

109) -> int: 

110 """Create :class:`Pdbseg <biobb_pdb_tools.pdb_tools.pdb_seg>` class and 

111 execute the :meth:`launch() <biobb_pdb_tools.pdb_tools.pdb_seg.launch>` method.""" 

112 

113 return Pdbseg(**dict(locals())).launch() 

114 

115 

116biobb_pdb_seg.__doc__ = Pdbseg.__doc__ 

117main = Pdbseg.get_main(biobb_pdb_seg, "Modifies the segment identifier column of a PDB file.") 

118 

119if __name__ == "__main__": 

120 main()