Coverage for biobb_io/api/alphafold.py: 77%

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1#!/usr/bin/env python 

2 

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

4import argparse 

5from biobb_common.generic.biobb_object import BiobbObject 

6from biobb_common.configuration import settings 

7from biobb_common.tools.file_utils import launchlogger 

8from biobb_io.api.common import check_output_path, check_mandatory_property, check_uniprot_code, download_af, write_pdb 

9 

10 

11class AlphaFold(BiobbObject): 

12 """ 

13 | biobb_io AlphaFold 

14 | This class is a wrapper for downloading a PDB structure from the AlphaFold Protein Structure Database. 

15 | Wrapper for the `AlphaFold Protein Structure Database <https://alphafold.ebi.ac.uk/>`_ for downloading a single PDB structure from its corresponding Uniprot code. 

16 

17 Args: 

18 output_pdb_path (str): Path to the output PDB file. File type: output. `Sample file <https://github.com/bioexcel/biobb_io/raw/master/biobb_io/test/reference/api/output_alphafold.pdb>`_. Accepted formats: pdb (edam:format_1476). 

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

20 * **uniprot_code** (*str*) - (None) Uniprot code. 

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

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

23 

24 Examples: 

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

26 

27 from biobb_io.api.alphafold import alphafold 

28 prop = { 

29 'uniprot_code': 'P00489' 

30 } 

31 alphafold(output_pdb_path='/path/to/newStructure.pdb', 

32 properties=prop) 

33 

34 Info: 

35 * wrapped_software: 

36 * name: AlphaFold Protein Structure Database 

37 * license: Apache-2.0 

38 * ontology: 

39 * name: EDAM 

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

41 

42 """ 

43 

44 def __init__(self, output_pdb_path, 

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

46 properties = properties or {} 

47 

48 # Call parent class constructor 

49 super().__init__(properties) 

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

51 

52 # Input/Output files 

53 self.io_dict = { 

54 "out": {"output_pdb_path": output_pdb_path} 

55 } 

56 

57 # Properties specific for BB 

58 self.uniprot_code = properties.get('uniprot_code', None) 

59 self.properties = properties 

60 

61 # Check the properties 

62 self.check_properties(properties) 

63 self.check_arguments() 

64 

65 def check_data_params(self, out_log, err_log): 

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

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

68 

69 @launchlogger 

70 def launch(self) -> int: 

71 """Execute the :class:`AlphaFold <api.alphafold.AlphaFold>` api.alphafold.AlphaFold object.""" 

72 

73 # check input/output paths and parameters 

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

75 

76 # Setup Biobb 

77 if self.check_restart(): 

78 return 0 

79 

80 check_mandatory_property(self.uniprot_code, 'uniprot_code', self.out_log, self.__class__.__name__) 

81 

82 self.uniprot_code = self.uniprot_code.strip().upper() 

83 

84 check_uniprot_code(self.uniprot_code, self.out_log, self.__class__.__name__) 

85 

86 # Downloading PDB file 

87 pdb_string = download_af(self.uniprot_code, self.out_log, self.global_log, self.__class__.__name__) 

88 write_pdb(pdb_string, self.output_pdb_path, None, self.out_log, self.global_log) 

89 

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

91 

92 return 0 

93 

94 

95def alphafold(output_pdb_path: str, properties: dict = None, **kwargs) -> int: 

96 """Execute the :class:`AlphaFold <api.alphafold.AlphaFold>` class and 

97 execute the :meth:`launch() <api.alphafold.AlphaFold.launch>` method.""" 

98 

99 return AlphaFold(output_pdb_path=output_pdb_path, 

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

101 

102 

103def main(): 

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

105 parser = argparse.ArgumentParser(description="This class is a wrapper for downloading a PDB structure from the Protein Data Bank.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999)) 

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

107 

108 # Specific args of each building block 

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

110 required_args.add_argument('-o', '--output_pdb_path', required=True, help="Path to the output PDB file. Accepted formats: pdb.") 

111 

112 args = parser.parse_args() 

113 config = args.config if args.config else None 

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

115 

116 # Specific call of each building block 

117 alphafold(output_pdb_path=args.output_pdb_path, 

118 properties=properties) 

119 

120 

121if __name__ == '__main__': 

122 main()