Coverage for biobb_model/model/fix_amides.py: 68%

1#!/usr/bin/env python3 

2 

3"""Module containing the FixAmides 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.file_utils import launchlogger 

11 

12 

13class FixAmides(BiobbObject): 

14 """ 

15 | biobb_model FixAmides 

16 | Fix amide groups from residues. 

17 | Flip the clashing amide groups to avoid clashes. 

18 

19 Args: 

20 input_pdb_path (str): Input PDB file path. File type: input. `Sample file <https://github.com/bioexcel/biobb_model/raw/master/biobb_model/test/data/model/5s2z.pdb>`_. Accepted formats: pdb (edam:format_1476). 

21 output_pdb_path (str): Output PDB file path. File type: output. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_model/master/biobb_model/test/reference/model/output_amide_pdb_path.pdb>`_. Accepted formats: pdb (edam:format_1476). 

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

23 * **modeller_key** (*str*) - (None) Modeller license key. 

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

28 

29 Examples: 

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

31 

32 from biobb_model.model.fix_amides import fix_amides 

33 prop = { 'restart': False } 

34 fix_amides(input_pdb_path='/path/to/myStructure.pdb', 

35 output_pdb_path='/path/to/newStructure.pdb', 

36 properties=prop) 

37 

38 Info: 

39 * wrapped_software: 

40 * name: In house 

41 * license: Apache-2.0 

42 * ontology: 

43 * name: EDAM 

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

45 """ 

46 

47 def __init__( 

48 self, 

49 input_pdb_path: str, 

50 output_pdb_path: str, 

51 properties: Optional[dict] = None, 

52 **kwargs, 

53 ) -> 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 = { 

62 "in": {"input_pdb_path": input_pdb_path}, 

63 "out": {"output_pdb_path": output_pdb_path}, 

64 } 

65 

66 # Properties specific for BB 

67 self.binary_path = properties.get("binary_path", "check_structure") 

68 self.modeller_key = properties.get("modeller_key") 

69 

70 # Check the properties 

71 self.check_properties(properties) 

72 self.check_arguments() 

73 

74 @launchlogger 

75 def launch(self) -> int: 

76 """Execute the :class:`FixAmides <model.fix_amides.FixAmides>` object.""" 

77 

78 # Setup Biobb 

79 if self.check_restart(): 

80 return 0 

81 self.stage_files() 

82 

83 self.cmd = [ 

84 self.binary_path, 

85 "-i", 

86 self.stage_io_dict["in"]["input_pdb_path"], 

87 "-o", 

88 self.stage_io_dict["out"]["output_pdb_path"], 

89 "--force_save", 

90 "amide", 

91 "--fix", 

92 "All", 

93 ] 

94 

95 if self.modeller_key: 

96 self.cmd.insert(1, self.modeller_key) 

97 self.cmd.insert(1, "--modeller_key") 

98 

99 # Run Biobb block 

100 self.run_biobb() 

101 

102 # Copy files to host 

103 self.copy_to_host() 

104 

105 # Remove temporal files 

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

107 self.remove_tmp_files() 

108 

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

110 return self.return_code 

111 

112 

113def fix_amides( 

114 input_pdb_path: str, 

115 output_pdb_path: str, 

116 properties: Optional[dict] = None, 

117 **kwargs, 

118) -> int: 

119 """Create :class:`FixAmides <model.fix_amides.FixAmides>` class and 

120 execute the :meth:`launch() <model.fix_amides.FixAmides.launch>` method.""" 

121 return FixAmides( 

122 input_pdb_path=input_pdb_path, 

123 output_pdb_path=output_pdb_path, 

124 properties=properties, 

125 **kwargs, 

126 ).launch() 

127 

128 fix_amides.__doc__ = FixAmides.__doc__ 

129 

130 

131def main(): 

132 parser = argparse.ArgumentParser( 

133 description="Flip the clashing amide groups to avoid clashes.", 

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

135 ) 

136 parser.add_argument( 

137 "-c", 

138 "--config", 

139 required=False, 

140 help="This file can be a YAML file, JSON file or JSON string", 

141 ) 

142 

143 # Specific args of each building block 

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

145 required_args.add_argument( 

146 "-i", "--input_pdb_path", required=True, help="Input PDB file name" 

147 ) 

148 required_args.add_argument( 

149 "-o", "--output_pdb_path", required=True, help="Output PDB file name" 

150 ) 

151 

152 args = parser.parse_args() 

153 config = args.config if args.config else None 

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

155 

156 # Specific call of each building block 

157 fix_amides( 

158 input_pdb_path=args.input_pdb_path, 

159 output_pdb_path=args.output_pdb_path, 

160 properties=properties, 

161 ) 

162 

163 

164if __name__ == "__main__": 

165 main()