Coverage for biobb_haddock/haddock_restraints/haddock_interface.py: 0%

1#!/usr/bin/env python3 

2 

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

4 

5from typing import Optional 

6from biobb_common.generic.biobb_object import BiobbObject 

7from biobb_common.tools.file_utils import launchlogger 

8 

9 

10class HaddockRestrainInterface(BiobbObject): 

11 """ 

12 | biobb_haddock HaddockRestrainInterface 

13 | Wrapper class for the Haddock-Restraints interface module. 

14 | `Haddock-Restraints interface <https://www.bonvinlab.org/haddock-restraints/interface.html>`_ lists residues in the interface based on a cutoff distance. 

15 

16 Args: 

17 input_pdb_path (str): Path to the input PDB structure to analyze. File type: input. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock_restraints/4G6K_clean.pdb>`_. Accepted formats: pdb (edam:format_1476). 

18 output_txt_path (str): Path to the output text file with the list of interface residues. File type: output. Accepted formats: txt (edam:format_2330). 

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

20 * **cutoff** (*float*) - (4.0) Cutoff distance in Angstroms for interface residues calculation. 

21 * **binary_path** (*str*) - ("haddock3-restraints") Path to the HADDOCK3 restraints executable binary. 

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

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

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

25 * **container_path** (*str*) - (None) Path to the binary executable of your container. 

26 * **container_image** (*str*) - (None) Container Image identifier. 

27 * **container_volume_path** (*str*) - ("/data") Path to an internal directory in the container. 

28 * **container_working_dir** (*str*) - (None) Path to the internal CWD in the container. 

29 * **container_user_id** (*str*) - (None) User number id to be mapped inside the container. 

30 * **container_shell_path** (*str*) - ("/bin/bash") Path to the binary executable of the container shell. 

31 

32 

33 Examples: 

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

35 

36 from biobb_haddock.haddock_restraints.haddock_interface import haddock_interface 

37 haddock_interface( 

38 input_pdb_path='/path/to/structure.pdb', 

39 output_txt_path='/path/to/interface_residues.txt', 

40 properties={'cutoff': 5.0} 

41 ) 

42 

43 Info: 

44 * wrapped_software: 

45 * name: Haddock3-restraints 

46 * version: 2025.5 

47 * license: Apache-2.0 

48 * ontology: 

49 * name: EDAM 

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

51 """ 

52 

53 def __init__( 

54 self, 

55 input_pdb_path: str, 

56 output_txt_path: str, 

57 properties: Optional[dict] = None, 

58 **kwargs, 

59 ) -> None: 

60 properties = properties or {} 

61 

62 # Call parent class constructor 

63 super().__init__(properties) 

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

65 

66 # Input/Output files 

67 self.io_dict = { 

68 "in": { 

69 "input_pdb_path": input_pdb_path 

70 }, 

71 "out": { 

72 "output_txt_path": output_txt_path, 

73 }, 

74 } 

75 

76 # Properties specific for BB 

77 self.binary_path = properties.get("binary_path", "haddock-restraints") 

78 self.cutoff = properties.get("cutoff", 4.0) 

79 

80 # Check the properties 

81 self.check_init(properties) 

82 

83 @launchlogger 

84 def launch(self) -> int: 

85 """Execute the :class:`Haddock3RestrainInterface <biobb_haddock.haddock_restraints.haddock_interface>` object.""" 

86 

87 # Setup Biobb 

88 if self.check_restart(): 

89 return 0 

90 self.stage_files() 

91 

92 # haddock3-restraints interface <structure> <cutoff> 

93 self.cmd = [self.binary_path, "interface", 

94 self.stage_io_dict['in']['input_pdb_path'], 

95 str(self.cutoff)] 

96 

97 self.cmd.append(">") 

98 self.cmd.append(self.stage_io_dict['out']['output_txt_path']) 

99 self.cmd.append("2>&1") 

100 

101 # Run Biobb block 

102 self.run_biobb() 

103 

104 # Open the file and sort the lines so the output is always the same 

105 with open(self.stage_io_dict['out']['output_txt_path'], 'r') as f: 

106 lines = f.readlines() 

107 lines.sort() 

108 with open(self.stage_io_dict['out']['output_txt_path'], 'w') as f: 

109 f.writelines(lines) 

110 

111 # Copy files to host 

112 self.copy_to_host() 

113 

114 # Remove temporal files 

115 self.remove_tmp_files() 

116 

117 return self.return_code 

118 

119 

120def haddock_interface( 

121 input_pdb_path: str, 

122 output_txt_path: str, 

123 properties: Optional[dict] = None, 

124 **kwargs, 

125) -> int: 

126 """Create :class:`Haddock3RestrainInterface <biobb_haddock.haddock_restraints.haddock_interface>` class and 

127 execute the :meth:`launch() <biobb_haddock.haddock_restraints.haddock_interface.launch>` method.""" 

128 return HaddockRestrainInterface(**dict(locals())).launch() 

129 

130 

131haddock_interface.__doc__ = HaddockRestrainInterface.__doc__ 

132main = HaddockRestrainInterface.get_main(haddock_interface, "Wrapper of the HADDOCK3 interface module.") 

133 

134 

135if __name__ == "__main__": 

136 main()