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

1#!/usr/bin/env python3 

2 

3"""Module containing the Pdbselchain 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 Pdbselchain(BiobbObject): 

12 """ 

13 | biobb_pdb_tools Pdbselchain 

14 | Extracts one or more chains from a PDB file. 

15 | This tool extracts a specific chain or list of chains from a PDB file, discarding all others. 

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_selchain.pdb>`_. Accepted formats: pdb (edam:format_1476). 

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

20 properties (dic): 

21 * **chains** (*str*) - ('A') Chain or list of chains (comma separated) to extract from the PDB file. 

22 * **binary_path** (*str*) - ("pdb_selchain") Path to the pdb_selchain 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_selchain import biobb_pdb_selchain 

30 

31 prop = { 

32 'chains': 'A,B' 

33 } 

34 biobb_pdb_selchain(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 

54 super().__init__(properties) 

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

56 

57 self.io_dict = { 

58 "in": {"input_file_path": input_file_path}, 

59 "out": {"output_file_path": output_file_path}, 

60 } 

61 

62 self.binary_path = properties.get("binary_path", "pdb_selchain") 

63 self.chains = properties.get("chains", "A") 

64 self.properties = properties 

65 self.check_init(properties) 

66 

67 @launchlogger 

68 def launch(self) -> int: 

69 """Execute the :class:`Pdbselchain <biobb_pdb_tools.pdb_tools.pdb_selchain>` object.""" 

70 

71 if self.check_restart(): 

72 return 0 

73 self.stage_files() 

74 

75 instructions = [] 

76 if self.chains: 

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

78 fu.log("Appending chains to select", self.out_log, self.global_log) 

79 

80 self.cmd = [ 

81 self.binary_path, 

82 " ".join(instructions), 

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

84 ">", 

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

86 ] 

87 

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

89 

90 fu.log( 

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

92 self.out_log, 

93 self.global_log, 

94 ) 

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_selchain( 

105 input_file_path: str, 

106 output_file_path: str, 

107 properties: Optional[dict] = None, 

108 **kwargs, 

109) -> int: 

110 """Create :class:`Pdbselchain <biobb_pdb_tools.pdb_tools.pdb_selchain>` class and 

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

112 

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

114 

115 

116biobb_pdb_selchain.__doc__ = Pdbselchain.__doc__ 

117main = Pdbselchain.get_main(biobb_pdb_selchain, "Extracts one or more chains from a PDB file.") 

118 

119if __name__ == "__main__": 

120 main()