Coverage for biobb_model / model / fix_side_chain.py: 82%

1#!/usr/bin/env python3 

2 

3"""Module containing the FixSideChain 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 FixSideChain(BiobbObject): 

15 """ 

16 | biobb_model FixSideChain 

17 | Class to model the missing atoms in amino acid side chains of a PDB. 

18 | Model the missing atoms in amino acid side chains of a PDB using `biobb_structure_checking <https://anaconda.org/bioconda/biobb_structure_checking>`_ if the use_modeller property is added the `Modeller suite <https://salilab.org/modeller/>`_ will also be used to rebuild the missing atoms. 

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_pdb_path.pdb>`_. Accepted formats: pdb (edam:format_1476). 

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

24 * **use_modeller** (*bool*) - (False) Use `Modeller suite <https://salilab.org/modeller/>`_ to rebuild the missing side chain atoms. 

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

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

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

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

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

30 

31 Examples: 

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

33 

34 from biobb_model.model.fix_side_chain import fix_side_chain 

35 prop = { 'use_modeller': True } 

36 fix_side_chain(input_pdb_path='/path/to/myStructure.pdb', 

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

38 properties=prop) 

39 

40 Info: 

41 * wrapped_software: 

42 * name: In house 

43 * license: Apache-2.0 

44 * ontology: 

45 * name: EDAM 

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

47 """ 

48 

49 def __init__( 

50 self, 

51 input_pdb_path: str, 

52 output_pdb_path: str, 

53 properties: Optional[dict] = None, 

54 **kwargs, 

55 ) -> None: 

56 properties = properties or {} 

57 

58 # Call parent class constructor 

59 super().__init__(properties) 

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

61 

62 # Input/Output files 

63 self.io_dict = { 

64 "in": {"input_pdb_path": input_pdb_path}, 

65 "out": {"output_pdb_path": output_pdb_path}, 

66 } 

67 

68 # Properties specific for BB 

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

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

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

72 

73 # Check the properties 

74 self.check_properties(properties) 

75 self.check_arguments() 

76 

77 @launchlogger 

78 def launch(self) -> int: 

79 """Execute the :class:`FixSideChain <model.fix_side_chain.FixSideChain>` object.""" 

80 

81 # Setup Biobb 

82 if self.check_restart(): 

83 return 0 

84 self.stage_files() 

85 

86 # Create command line 

87 self.cmd = [ 

88 self.binary_path, 

89 "-i", 

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

91 "-o", 

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

93 "--force_save", 

94 "fixside", 

95 "--fix", 

96 "ALL", 

97 ] 

98 

99 if self.modeller_key: 

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

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

102 

103 if self.use_modeller: 

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

105 self.cmd.append("--rebuild") 

106 else: 

107 fu.log( 

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

109 self.out_log, 

110 self.global_log, 

111 ) 

112 

113 # Run Biobb block 

114 self.run_biobb() 

115 

116 # Copy files to host 

117 self.copy_to_host() 

118 

119 # Remove temporal files 

120 self.remove_tmp_files() 

121 

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

123 return self.return_code 

124 

125 

126def fix_side_chain( 

127 input_pdb_path: str, 

128 output_pdb_path: str, 

129 properties: Optional[dict] = None, 

130 **kwargs, 

131) -> int: 

132 """Create :class:`FixSideChain <model.fix_side_chain.FixSideChain>` class and 

133 execute the :meth:`launch() <model.fix_side_chain.FixSideChain.launch>` method.""" 

134 return FixSideChain(**dict(locals())).launch() 

135 

136 

137fix_side_chain.__doc__ = FixSideChain.__doc__ 

138main = FixSideChain.get_main(fix_side_chain, "Model the missing atoms in amino acid side chains of a PDB.") 

139 

140if __name__ == "__main__": 

141 main()