Coverage for biobb_pdb_tools/pdb_tools/biobb_pdb_delhetatm.py: 76%

1#!/usr/bin/env python3 

2 

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

4 

5import argparse 

6from typing import Optional 

7 

8from biobb_common.configuration import settings 

9from biobb_common.generic.biobb_object import BiobbObject 

10from biobb_common.tools import file_utils as fu 

11from biobb_common.tools.file_utils import launchlogger 

12 

13 

14class Delhetatm(BiobbObject): 

15 """ 

16 | biobb_pdb_tools Delhetatm 

17 | Removes all HETATM records in the PDB file. 

18 | This tool removes all HETATM records in the PDB file. It can be used to remove all HETATM records from a PDB file. 

19 

20 Args: 

21 input_file_path (str): PDB file. File type: input. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_pdb_tools/master/biobb_pdb_tools/test/data/pdb_tools/1AKI.pdb>`_. Accepted formats: pdb (edam:format_1476). 

22 output_file_path (str): PDB file with all HETATM records removed. File type: output. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_pdb_tools/master/biobb_pdb_tools/test/reference/pdb_tools/ref_pdb_delhetatm.pdb>`_. Accepted formats: pdb (edam:format_1476). 

23 properties (dic): 

24 * **binary_path** (*str*) - ("pdb_delhetatm") Path to the pdb_delhetatm executable binary. 

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

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

27 

28 Examples: 

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

30 

31 from biobb_pdb_tools.pdb_tools.biobb_pdb_delhetatm import biobb_pdb_delhetatm 

32 

33 biobb_pdb_delhetatm(input_file_path='/path/to/input.pdb', 

34 output_file_path='/path/to/output.pdb') 

35 

36 Info: 

37 * wrapped_software: 

38 * name: pdb_tools 

39 * version: >=2.5.0 

40 * license: Apache-2.0 

41 * ontology: 

42 * name: EDAM 

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

44 

45 """ 

46 

47 def __init__( 

48 self, input_file_path, output_file_path, properties=None, **kwargs 

49 ) -> None: 

50 properties = properties or {} 

51 

52 super().__init__(properties) 

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

54 

55 self.io_dict = { 

56 "in": {"input_file_path": input_file_path}, 

57 "out": {"output_file_path": output_file_path}, 

58 } 

59 

60 self.binary_path = properties.get("binary_path", "pdb_delhetatm") 

61 self.properties = properties 

62 

63 self.check_properties(properties) 

64 self.check_arguments() 

65 

66 @launchlogger 

67 def launch(self) -> int: 

68 """Execute the :class:`Delhetatm <biobb_pdb_tools.pdb_tools.pdb_delhetatm>` object.""" 

69 

70 if self.check_restart(): 

71 return 0 

72 self.stage_files() 

73 

74 self.cmd = [ 

75 self.binary_path, 

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

77 ">", 

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

79 ] 

80 

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

82 

83 fu.log( 

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

85 self.out_log, 

86 self.global_log, 

87 ) 

88 

89 self.run_biobb() 

90 self.copy_to_host() 

91 

92 self.tmp_files.extend([self.stage_io_dict.get("unique_dir", "")]) 

93 self.remove_tmp_files() 

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

95 

96 return self.return_code 

97 

98 

99def biobb_pdb_delhetatm( 

100 input_file_path: str, 

101 output_file_path: str, 

102 properties: Optional[dict] = None, 

103 **kwargs, 

104) -> int: 

105 """Create :class:`Delhetatm <biobb_pdb_tools.pdb_tools.pdb_delhetatm>` class and 

106 execute the :meth:`launch() <biobb_pdb_tools.pdb_tools.pdb_delhetatm.launch>` method.""" 

107 return Delhetatm( 

108 input_file_path=input_file_path, 

109 output_file_path=output_file_path, 

110 properties=properties, 

111 **kwargs, 

112 ).launch() 

113 

114biobb_pdb_delhetatm.__doc__ = Delhetatm.__doc__ 

115 

116 

117def main(): 

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

119 parser = argparse.ArgumentParser( 

120 description="Removes all HETATM records in the PDB file.", 

121 formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999), 

122 ) 

123 parser.add_argument("--config", required=True, help="Configuration file") 

124 required_args = parser.add_argument_group("required arguments") 

125 required_args.add_argument( 

126 "--input_file_path", 

127 required=True, 

128 help="Description for the first input file path. Accepted formats: pdb.", 

129 ) 

130 required_args.add_argument( 

131 "--output_file_path", 

132 required=True, 

133 help="Description for the output file path. Accepted formats: pdb.", 

134 ) 

135 

136 args = parser.parse_args() 

137 args.config = args.config or "{}" 

138 properties = settings.ConfReader(config=args.config).get_prop_dic() 

139 

140 biobb_pdb_delhetatm( 

141 input_file_path=args.input_file_path, 

142 output_file_path=args.output_file_path, 

143 properties=properties, 

144 ) 

145 

146 

147if __name__ == "__main__": 

148 main()