Coverage for biobb_io/api/api_binding_site.py: 78%

1#!/usr/bin/env python 

2 

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

4import argparse 

5import json 

6from biobb_common.generic.biobb_object import BiobbObject 

7from biobb_common.configuration import settings 

8from biobb_common.tools import file_utils as fu 

9from biobb_common.tools.file_utils import launchlogger 

10from biobb_io.api.common import check_output_path, check_mandatory_property, download_binding_site, write_json 

11 

12 

13class ApiBindingSite(BiobbObject): 

14 """ 

15 | biobb_io ApiBindingSite 

16 | 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. 

17 | 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. 

18 

19 Args: 

20 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). 

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

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

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

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

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

26 

27 Examples: 

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

29 

30 from biobb_io.api.api_binding_site import api_binding_site 

31 prop = { 

32 'pdb_code': '4i23' 

33 } 

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

35 properties=prop) 

36 

37 Info: 

38 * wrapped_software: 

39 * name: PDBe REST API 

40 * license: Apache-2.0 

41 * ontology: 

42 * name: EDAM 

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

44 

45 """ 

46 

47 def __init__(self, output_json_path, 

48 properties=None, **kwargs) -> None: 

49 properties = properties or {} 

50 

51 # Call parent class constructor 

52 super().__init__(properties) 

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

54 

55 # Input/Output files 

56 self.io_dict = { 

57 "out": {"output_json_path": output_json_path} 

58 } 

59 

60 # Properties specific for BB 

61 self.pdb_code = properties.get('pdb_code', None) 

62 self.properties = properties 

63 

64 # Check the properties 

65 self.check_properties(properties) 

66 self.check_arguments() 

67 

68 def check_data_params(self, out_log, err_log): 

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

70 self.output_json_path = check_output_path(self.io_dict["out"]["output_json_path"], "output_json_path", False, out_log, self.__class__.__name__) 

71 

72 @launchlogger 

73 def launch(self) -> int: 

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

75 

76 # check input/output paths and parameters 

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

78 

79 # Setup Biobb 

80 if self.check_restart(): 

81 return 0 

82 # self.stage_files() 

83 

84 check_mandatory_property(self.pdb_code, 'pdb_code', self.out_log, self.__class__.__name__) 

85 

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

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

88 

89 # get JSON object 

90 json_string = download_binding_site(self.pdb_code, url, self.out_log, self.global_log) 

91 

92 # get number of binding sites 

93 fu.log('%d binding sites found' % (len(json.loads(json_string)[self.pdb_code])), self.out_log, self.global_log) 

94 

95 # write JSON file 

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

97 

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

99 

100 return 0 

101 

102 

103def api_binding_site(output_json_path: str, properties: dict = None, **kwargs) -> int: 

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

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

106 

107 return ApiBindingSite(output_json_path=output_json_path, 

108 properties=properties, **kwargs).launch() 

109 

110 

111def main(): 

112 """Command line execution of this building block. Please check the command line documentation.""" 

113 parser = argparse.ArgumentParser(description="This class is a wrapper for the PDBe REST API Binding Sites endpoint", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999)) 

114 parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string") 

115 

116 # Specific args of each building block 

117 required_args = parser.add_argument_group('required arguments') 

118 required_args.add_argument('-o', '--output_json_path', required=True, help="Path to the JSON file with the binding sites for the requested structure. Accepted formats: json.") 

119 

120 args = parser.parse_args() 

121 config = args.config if args.config else None 

122 properties = settings.ConfReader(config=config).get_prop_dic() 

123 

124 # Specific call of each building block 

125 api_binding_site(output_json_path=args.output_json_path, 

126 properties=properties) 

127 

128 

129if __name__ == '__main__': 

130 main()