Coverage for biobb_model / model / fix_altlocs.py: 87%

1#!/usr/bin/env python3 

2 

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

4 

5from typing import Optional 

6 

7from biobb_common.generic.biobb_object import BiobbObject 

8from biobb_common.tools.file_utils import launchlogger 

9 

10from biobb_model.model.common import _from_string_to_list 

11 

12 

13class FixAltLocs(BiobbObject): 

14 """ 

15 | biobb_model FixAltLocs 

16 | Fix alternate locations from residues. 

17 | Fix alternate locations using the altlocs list or occupancy. 

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/3ebp.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_altloc.pdb>`_. Accepted formats: pdb (edam:format_1476). 

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

23 * **altlocs** (*list*) - (None) List of alternate locations to fix. Format: ["A339:A", "A171:B", "A768:A"]; where for each residue the format is as follows: "<chain><residue id>:<chosen alternate location>". If empty, no action will be executed. 

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

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

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

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

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

29 

30 Examples: 

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

32 

33 from biobb_model.model.fix_altlocs import fix_altlocs 

34 prop = { 'altlocs': ['A339:A', 'A171:B', 'A768:A'] } 

35 fix_altlocs(input_pdb_path='/path/to/myStructure.pdb', 

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

37 properties=prop) 

38 

39 Info: 

40 * wrapped_software: 

41 * name: In house 

42 * license: Apache-2.0 

43 * ontology: 

44 * name: EDAM 

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

46 """ 

47 

48 def __init__( 

49 self, 

50 input_pdb_path: str, 

51 output_pdb_path: str, 

52 properties: Optional[dict] = None, 

53 **kwargs, 

54 ) -> None: 

55 properties = properties or {} 

56 

57 # Call parent class constructor 

58 super().__init__(properties) 

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

60 

61 # Input/Output files 

62 self.io_dict = { 

63 "in": {"input_pdb_path": input_pdb_path}, 

64 "out": {"output_pdb_path": output_pdb_path}, 

65 } 

66 

67 # Properties specific for BB 

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

69 self.altlocs = _from_string_to_list(properties.get("altlocs", None)) 

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

71 

72 # Check the properties 

73 self.check_properties(properties) 

74 self.check_arguments() 

75 

76 @launchlogger 

77 def launch(self) -> int: 

78 """Execute the :class:`FixAltLocs <model.fix_altlocs.FixAltLocs>` object.""" 

79 

80 # Setup Biobb 

81 if self.check_restart(): 

82 return 0 

83 self.stage_files() 

84 

85 self.cmd = [ 

86 self.binary_path, 

87 "-i", 

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

89 "-o", 

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

91 "--force_save", 

92 "--non_interactive", 

93 "altloc", 

94 "--select", 

95 ] 

96 

97 if self.altlocs: 

98 self.cmd.append(",".join(self.altlocs)) 

99 else: 

100 self.cmd.append("occupancy") 

101 

102 if self.modeller_key: 

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

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

105 

106 # Run Biobb block 

107 self.run_biobb() 

108 

109 # Copy files to host 

110 self.copy_to_host() 

111 

112 # Remove temporal files 

113 self.remove_tmp_files() 

114 

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

116 return self.return_code 

117 

118 

119def fix_altlocs( 

120 input_pdb_path: str, 

121 output_pdb_path: str, 

122 properties: Optional[dict] = None, 

123 **kwargs, 

124) -> int: 

125 """Create :class:`FixAltLocs <model.fix_altlocs.FixAltLocs>` class and 

126 execute the :meth:`launch() <model.fix_altlocs.FixAltLocs.launch>` method.""" 

127 return FixAltLocs(**dict(locals())).launch() 

128 

129 

130fix_altlocs.__doc__ = FixAltLocs.__doc__ 

131main = FixAltLocs.get_main(fix_altlocs, "Fix alternate locations from residues") 

132 

133if __name__ == "__main__": 

134 main()