Coverage for biobb_chemistry / ambertools / reduce_remove_hydrogens.py: 95%

1#!/usr/bin/env python3 

2 

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

4from typing import Optional 

5from biobb_common.generic.biobb_object import BiobbObject 

6from biobb_common.tools.file_utils import launchlogger 

7from biobb_chemistry.ambertools.common import get_binary_path, check_input_path, check_output_path 

8 

9 

10class ReduceRemoveHydrogens(BiobbObject): 

11 """ 

12 | biobb_chemistry ReduceRemoveHydrogens 

13 | This class is a wrapper of the `Ambertools <http://ambermd.org/doc12/AmberTools12.pdf>`_ reduce module for removing hydrogens from a given structure. 

14 | Reduce is a program for `adding or removing hydrogens to a Protein DataBank (PDB) molecular structure file <http://ambermd.org/doc12/AmberTools12.pdf>`_. 

15 

16 Args: 

17 input_path (str): Path to the input file. File type: input. `Sample file <https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/data/ambertools/reduce.H.pdb>`_. Accepted formats: pdb (edam:format_1476). 

18 output_path (str): Path to the output file. File type: output. `Sample file <https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/reference/ambertools/ref_reduce.remove.pdb>`_. Accepted formats: pdb (edam:format_1476). 

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

20 * **binary_path** (*str*) - ("reduce") Path to the reduce executable binary. 

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

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

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

24 * **container_path** (*str*) - (None) Container path definition. 

25 * **container_image** (*str*) - ('afandiadib/ambertools:serial') Container image definition. 

26 * **container_volume_path** (*str*) - ('/tmp') Container volume path definition. 

27 * **container_working_dir** (*str*) - (None) Container working directory definition. 

28 * **container_user_id** (*str*) - (None) Container user_id definition. 

29 * **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container. 

30 

31 Examples: 

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

33 

34 from biobb_chemistry.ambertools.reduce_remove_hydrogens import reduce_remove_hydrogens 

35 prop = { } 

36 reduce_remove_hydrogens(input_path='/path/to/myStructure.pdb', 

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

38 properties=prop) 

39 

40 Info: 

41 * wrapped_software: 

42 * name: AmberTools Reduce 

43 * version: >=20.0 

44 * license: GNU 

45 * ontology: 

46 * name: EDAM 

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

48 

49 """ 

50 

51 def __init__(self, input_path, output_path, 

52 properties=None, **kwargs) -> None: 

53 properties = properties or {} 

54 

55 # Call parent class constructor 

56 super().__init__(properties) 

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

58 

59 # Input/Output files 

60 self.io_dict = { 

61 "in": {"input_path": input_path}, 

62 "out": {"output_path": output_path} 

63 } 

64 

65 # Properties specific for BB 

66 self.binary_path = get_binary_path(properties, 'binary_path') 

67 self.properties = properties 

68 

69 # Check the properties 

70 self.check_properties(properties) 

71 self.check_arguments() 

72 

73 def check_data_params(self, out_log, err_log): 

74 """ Checks all the input/output paths and parameters """ 

75 self.io_dict["in"]["input_path"] = check_input_path(self.io_dict["in"]["input_path"], out_log, self.__class__.__name__) 

76 self.io_dict["out"]["output_path"] = check_output_path(self.io_dict["out"]["output_path"], out_log, self.__class__.__name__) 

77 

78 def create_cmd(self, container_io_dict, out_log, err_log): 

79 """Creates the command line instruction using the properties file settings""" 

80 instructions_list = [] 

81 

82 # executable path 

83 instructions_list.append(self.binary_path) 

84 

85 instructions_list.append('-Trim') 

86 

87 instructions_list.append(container_io_dict["in"]["input_path"]) 

88 instructions_list.append('>') 

89 instructions_list.append(container_io_dict["out"]["output_path"]) 

90 

91 return instructions_list 

92 

93 @launchlogger 

94 def launch(self) -> int: 

95 """Execute the :class:`ReduceRemoveHydrogens <ambertools.reduce_remove_hydrogens.ReduceRemoveHydrogens>` ambertools.reduce_remove_hydrogens.ReduceRemoveHydrogens object.""" 

96 

97 # check input/output paths and parameters 

98 self.check_data_params(self.out_log, self.err_log) 

99 

100 # Setup Biobb 

101 if self.check_restart(): 

102 return 0 

103 self.stage_files() 

104 

105 # create command line instruction 

106 self.cmd = self.create_cmd(self.stage_io_dict, self.out_log, self.err_log) 

107 

108 # Run Biobb block 

109 self.run_biobb() 

110 

111 # Copy files to host 

112 self.copy_to_host() 

113 

114 # remove temporary folder(s) 

115 self.remove_tmp_files() 

116 

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

118 

119 return self.return_code 

120 

121 

122def reduce_remove_hydrogens(input_path: str, output_path: str, properties: Optional[dict] = None, **kwargs) -> int: 

123 """Create the :class:`ReduceRemoveHydrogens <ambertools.reduce_remove_hydrogens.ReduceRemoveHydrogens>` class and 

124 execute the :meth:`launch() <ambertools.reduce_remove_hydrogens.ReduceRemoveHydrogens.launch>` method.""" 

125 return ReduceRemoveHydrogens(**dict(locals())).launch() 

126 

127 

128reduce_remove_hydrogens.__doc__ = ReduceRemoveHydrogens.__doc__ 

129main = ReduceRemoveHydrogens.get_main(reduce_remove_hydrogens, "Removes hydrogen atoms to small molecules.") 

130 

131 

132if __name__ == '__main__': 

133 main()