Coverage for biobb_io/api/api_binding_site.py: 95%

1#!/usr/bin/env python 

2 

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

4 

5import json 

6from typing import Optional 

7from biobb_common.generic.biobb_object import BiobbObject 

8from biobb_common.tools import file_utils as fu 

9from biobb_common.tools.file_utils import launchlogger 

10 

11from biobb_io.api.common import ( 

12 check_mandatory_property, 

13 check_output_path, 

14 download_binding_site, 

15 write_json, 

16) 

17 

18 

19class ApiBindingSite(BiobbObject): 

20 """ 

21 | biobb_io ApiBindingSite 

22 | This class is a wrapper for the `PDBe REST API <https://www.ebi.ac.uk/pdbe/api/doc/#pdb_apidiv_call_16_calltitle>`_ Binding Sites endpoint. 

23 | This call provides details on binding sites in the entry as per STRUCT_SITE records in PDB files, such as ligand, residues in the site, description of the site, etc. 

24 

25 Args: 

26 output_json_path (str): Path to the JSON file with the binding sites for the requested structure. File type: output. `Sample file <https://github.com/bioexcel/biobb_io/raw/master/biobb_io/test/reference/api/output_binding_site.json>`_. Accepted formats: json (edam:format_3464). 

27 properties (dic - Python dictionary object containing the tool parameters, not input/output files): 

28 * **pdb_code** (*str*) - (None) RSCB PDB code. 

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

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

31 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory. 

32 

33 Examples: 

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

35 

36 from biobb_io.api.api_binding_site import api_binding_site 

37 prop = { 

38 'pdb_code': '4i23' 

39 } 

40 api_binding_site(output_json_path='/path/to/newBindingSites.json', 

41 properties=prop) 

42 

43 Info: 

44 * wrapped_software: 

45 * name: PDBe REST API 

46 * license: Apache-2.0 

47 * ontology: 

48 * name: EDAM 

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

50 

51 """ 

52 

53 def __init__(self, output_json_path, properties=None, **kwargs) -> None: 

54 properties = properties or {} 

55 

56 # Call parent class constructor 

57 super().__init__(properties) 

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

59 

60 # Input/Output files 

61 self.io_dict = {"out": {"output_json_path": output_json_path}} 

62 

63 # Properties specific for BB 

64 self.pdb_code = properties.get("pdb_code", None) 

65 self.properties = properties 

66 

67 # Check the properties 

68 self.check_properties(properties) 

69 self.check_arguments() 

70 

71 def check_data_params(self, out_log, err_log): 

72 """Checks all the input/output paths and parameters""" 

73 self.output_json_path = check_output_path( 

74 self.io_dict["out"]["output_json_path"], 

75 "output_json_path", 

76 False, 

77 out_log, 

78 self.__class__.__name__, 

79 ) 

80 

81 @launchlogger 

82 def launch(self) -> int: 

83 """Execute the :class:`ApiBindingSite <api.api_binding_site.ApiBindingSite>` api.api_binding_site.ApiBindingSite object.""" 

84 

85 # check input/output paths and parameters 

86 self.check_data_params(self.out_log, self.err_log) 

87 

88 # Setup Biobb 

89 if self.check_restart(): 

90 return 0 

91 # self.stage_files() 

92 

93 check_mandatory_property( 

94 self.pdb_code, "pdb_code", self.out_log, self.__class__.__name__ 

95 ) 

96 

97 self.pdb_code = self.pdb_code.strip().lower() 

98 url = "https://www.ebi.ac.uk/pdbe/api/pdb/entry/binding_sites/%s" 

99 

100 # get JSON object 

101 json_string = download_binding_site( 

102 self.pdb_code, url, self.out_log, self.global_log 

103 ) 

104 

105 # get number of binding sites 

106 fu.log( 

107 "%d binding sites found" % (len(json.loads(json_string)[self.pdb_code])), 

108 self.out_log, 

109 self.global_log, 

110 ) 

111 

112 # write JSON file 

113 write_json(json_string, self.output_json_path, self.out_log, self.global_log) 

114 

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

116 

117 return 0 

118 

119 

120def api_binding_site( 

121 output_json_path: str, properties: Optional[dict] = None, **kwargs 

122) -> int: 

123 """Execute the :class:`ApiBindingSite <api.api_binding_site.ApiBindingSite>` class and 

124 execute the :meth:`launch() <api.api_binding_site.ApiBindingSite.launch>` method.""" 

125 return ApiBindingSite(**dict(locals())).launch() 

126 

127 

128api_binding_site.__doc__ = ApiBindingSite.__doc__ 

129main = ApiBindingSite.get_main(api_binding_site, "This class is a wrapper for the PDBe REST API Binding Sites endpoint") 

130 

131if __name__ == "__main__": 

132 main()