Coverage for biobb_model/model/mutate.py: 69%

1#!/usr/bin/env python3 

2 

3"""Module containing the Mutate 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 

13from biobb_model.model.common import modeller_installed 

14 

15 

16class Mutate(BiobbObject): 

17 """ 

18 | biobb_model Mutate 

19 | Class to mutate one amino acid by another in a 3d structure. 

20 | Mutate side chain with minimal atom replacement. if the use_modeller property is added the `Modeller suite <https://salilab.org/modeller/>`_ will be used to optimize the side chains. 

21 

22 Args: 

23 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/2ki5.pdb>`_. Accepted formats: pdb (edam:format_1476). 

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

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

26 * **mutation_list** (*str*) - (None) Mutation list in the format "Chain:WT_AA_ThreeLeterCode Resnum MUT_AA_ThreeLeterCode" (no spaces between the elements) separated by commas. If no chain is provided as chain code all the chains in the pdb file will be mutated. ie: "A:ALA15CYS" 

27 * **use_modeller** (*bool*) - (False) Use `Modeller suite <https://salilab.org/modeller/>`_ to optimize the side chains. 

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

29 * **binary_path** (*str*) - ("check_structure") Path to the check_structure executable binary. 

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

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

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

33 

34 Examples: 

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

36 

37 from biobb_model.model.mutate import mutate 

38 prop = { 'mutation_list': 'A:Val2Ala', 

39 'use_modeller': True } 

40 mutate(input_pdb_path='/path/to/myStructure.pdb', 

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

42 properties=prop) 

43 

44 Info: 

45 * wrapped_software: 

46 * name: In house 

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_pdb_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": {"input_pdb_path": input_pdb_path}, 

69 "out": {"output_pdb_path": output_pdb_path}, 

70 } 

71 

72 # Properties specific for BB 

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

74 self.mutation_list = properties.get("mutation_list", "").replace(" ", "") 

75 self.use_modeller = properties.get("use_modeller", False) 

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

77 

78 # Check the properties 

79 self.check_properties(properties) 

80 self.check_arguments() 

81 

82 @launchlogger 

83 def launch(self) -> int: 

84 """Execute the :class:`Mutate <model.mutate.Mutate>` object.""" 

85 

86 # Setup Biobb 

87 if self.check_restart(): 

88 return 0 

89 self.stage_files() 

90 

91 # Create command line 

92 self.cmd = [ 

93 self.binary_path, 

94 "-i", 

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

96 "-o", 

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

98 "--force_save", 

99 "--non_interactive", 

100 "mutateside", 

101 ] 

102 

103 if self.mutation_list: 

104 self.cmd.append("--mut") 

105 self.cmd.append(self.mutation_list) 

106 

107 if self.modeller_key: 

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

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

110 

111 if self.use_modeller: 

112 if modeller_installed(self.out_log, self.global_log): 

113 self.cmd.append("--rebuild") 

114 else: 

115 fu.log( 

116 "Modeller is not installed --rebuild option can not be used proceeding without using it", 

117 self.out_log, 

118 self.global_log, 

119 ) 

120 

121 # Run Biobb block 

122 self.run_biobb() 

123 

124 # Copy files to host 

125 self.copy_to_host() 

126 

127 # Remove temporal files 

128 # self.tmp_files.append(self.stage_io_dict.get("unique_dir", "")) 

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

130 self.remove_tmp_files() 

131 

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

133 return self.return_code 

134 

135 

136def mutate( 

137 input_pdb_path: str, 

138 output_pdb_path: str, 

139 properties: Optional[dict] = None, 

140 **kwargs, 

141) -> int: 

142 """Create :class:`Mutate <model.mutate.Mutate>` class and 

143 execute the :meth:`launch() <model.mutate.Mutate.launch>` method.""" 

144 return Mutate( 

145 input_pdb_path=input_pdb_path, 

146 output_pdb_path=output_pdb_path, 

147 properties=properties, 

148 **kwargs, 

149 ).launch() 

150 

151 mutate.__doc__ = Mutate.__doc__ 

152 

153 

154def main(): 

155 parser = argparse.ArgumentParser( 

156 description="Model the missing atoms in aminoacid side chains of a PDB.", 

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

158 ) 

159 parser.add_argument( 

160 "-c", 

161 "--config", 

162 required=False, 

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

164 ) 

165 

166 # Specific args of each building block 

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

168 required_args.add_argument( 

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

170 ) 

171 required_args.add_argument( 

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

173 ) 

174 

175 args = parser.parse_args() 

176 config = args.config if args.config else None 

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

178 

179 # Specific call of each building block 

180 mutate( 

181 input_pdb_path=args.input_pdb_path, 

182 output_pdb_path=args.output_pdb_path, 

183 properties=properties, 

184 ) 

185 

186 

187if __name__ == "__main__": 

188 main()