Coverage for biobb_model / model / mutate.py: 84%

1#!/usr/bin/env python3 

2 

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

4 

5from typing import Optional 

6 

7from biobb_common.generic.biobb_object import BiobbObject 

8from biobb_common.tools import file_utils as fu 

9from biobb_common.tools.file_utils import launchlogger 

10 

11from biobb_model.model.common import modeller_installed 

12 

13 

14class Mutate(BiobbObject): 

15 """ 

16 | biobb_model Mutate 

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

18 | 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. 

19 

20 Args: 

21 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). 

22 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). 

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

24 * **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" 

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

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

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

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

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

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

31 

32 Examples: 

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

34 

35 from biobb_model.model.mutate import mutate 

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

37 'use_modeller': True } 

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

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

40 properties=prop) 

41 

42 Info: 

43 * wrapped_software: 

44 * name: In house 

45 * license: Apache-2.0 

46 * ontology: 

47 * name: EDAM 

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

49 """ 

50 

51 def __init__( 

52 self, 

53 input_pdb_path: str, 

54 output_pdb_path: str, 

55 properties: Optional[dict] = None, 

56 **kwargs, 

57 ) -> None: 

58 properties = properties or {} 

59 

60 # Call parent class constructor 

61 super().__init__(properties) 

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

63 

64 # Input/Output files 

65 self.io_dict = { 

66 "in": {"input_pdb_path": input_pdb_path}, 

67 "out": {"output_pdb_path": output_pdb_path}, 

68 } 

69 

70 # Properties specific for BB 

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

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

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

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

75 

76 # Check the properties 

77 self.check_properties(properties) 

78 self.check_arguments() 

79 

80 @launchlogger 

81 def launch(self) -> int: 

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

83 

84 # Setup Biobb 

85 if self.check_restart(): 

86 return 0 

87 self.stage_files() 

88 

89 # Create command line 

90 self.cmd = [ 

91 self.binary_path, 

92 "-i", 

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

94 "-o", 

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

96 "--force_save", 

97 "--non_interactive", 

98 "mutateside", 

99 ] 

100 

101 if self.mutation_list: 

102 self.cmd.append("--mut") 

103 self.cmd.append(self.mutation_list) 

104 

105 if self.modeller_key: 

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

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

108 

109 if self.use_modeller: 

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

111 self.cmd.append("--rebuild") 

112 else: 

113 fu.log( 

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

115 self.out_log, 

116 self.global_log, 

117 ) 

118 

119 # Run Biobb block 

120 self.run_biobb() 

121 

122 # Copy files to host 

123 self.copy_to_host() 

124 

125 # Remove temporal files 

126 self.remove_tmp_files() 

127 

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

129 return self.return_code 

130 

131 

132def mutate( 

133 input_pdb_path: str, 

134 output_pdb_path: str, 

135 properties: Optional[dict] = None, 

136 **kwargs, 

137) -> int: 

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

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

140 return Mutate(**dict(locals())).launch() 

141 

142 

143mutate.__doc__ = Mutate.__doc__ 

144main = Mutate.get_main(mutate, "Model the missing atoms in aminoacid side chains of a PDB.") 

145 

146if __name__ == "__main__": 

147 main()