Coverage for biobb_structure_utils/utils/sort_gro_residues.py: 74%

1#!/usr/bin/env python3 

2 

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

4import argparse 

5from biobb_common.configuration import settings 

6from biobb_common.generic.biobb_object import BiobbObject 

7from biobb_common.tools.file_utils import launchlogger 

8from biobb_structure_utils.gro_lib.gro import Gro 

9 

10 

11class SortGroResidues(BiobbObject): 

12 """ 

13 | biobb_structure_utils SortGroResidues 

14 | Class to sort the selected residues from a GRO 3D structure. 

15 | Sorts the selected residues from a GRO 3D structure. 

16 

17 Args: 

18 input_gro_path (str): Input GRO file path. File type: input. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/data/utils/WT_aq4_md_1.gro>`_. Accepted formats: gro (edam:format_2033). 

19 output_gro_path (str): Output sorted GRO file path. File type: output. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/reference/utils/WT_aq4_md_sorted.gro>`_. Accepted formats: gro (edam:format_2033). 

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

21 * **residue_name_list** (*list*) - (["NA", "CL", "SOL"]) Ordered residue name list. 

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

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

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

25 

26 Examples: 

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

28 

29 from biobb_structure_utils.utils.sort_gro_residues import sort_gro_residues 

30 prop = { 

31 'residue_name_list': ['NA', 'CL', 'SOL'] 

32 } 

33 sort_gro_residues(input_gro_path='/path/to/myInputStr.gro', 

34 output_gro_path='/path/to/newStructure.gro', 

35 properties=prop) 

36 

37 Info: 

38 * wrapped_software: 

39 * name: In house 

40 * license: Apache-2.0 

41 * ontology: 

42 * name: EDAM 

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

44 

45 """ 

46 

47 def __init__(self, input_gro_path, output_gro_path, properties=None, **kwargs) -> None: 

48 properties = properties or {} 

49 

50 # Call parent class constructor 

51 super().__init__(properties) 

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

53 

54 # Input/Output files 

55 self.io_dict = { 

56 "in": {"input_gro_path": input_gro_path}, 

57 "out": {"output_gro_path": output_gro_path} 

58 } 

59 

60 # Properties specific for BB 

61 self.residue_name_list = properties.get('residue_name_list', ["NA", "CL", "SOL"]) 

62 

63 # Check the properties 

64 self.check_properties(properties) 

65 self.check_arguments() 

66 

67 @launchlogger 

68 def launch(self) -> int: 

69 """Execute the :class:`SortGroResidues <utils.sort_gro_residues.SortGroResidues>` utils.sort_gro_residues.SortGroResidues object.""" 

70 

71 # Setup Biobb 

72 if self.check_restart(): 

73 return 0 

74 self.stage_files() 

75 

76 # Business code 

77 in_gro = Gro() 

78 in_gro.read_gro_file(self.stage_io_dict['in']['input_gro_path']) 

79 in_gro.sort_residues2(self.residue_name_list) 

80 in_gro.write_gro_file(self.stage_io_dict['out']['output_gro_path']) 

81 self.return_code = 0 

82 ########## 

83 

84 # Copy files to host 

85 self.copy_to_host() 

86 

87 # Remove temporal files 

88 self.tmp_files.append(self.stage_io_dict.get("unique_dir")) 

89 self.remove_tmp_files() 

90 

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

92 

93 return self.return_code 

94 

95 

96def sort_gro_residues(input_gro_path: str, output_gro_path: str, properties: dict = None, **kwargs) -> int: 

97 """Execute the :class:`SortGroResidues <utils.sort_gro_residues.SortGroResidues>` class and 

98 execute the :meth:`launch() <utils.sort_gro_residues.SortGroResidues.launch>` method.""" 

99 

100 return SortGroResidues(input_gro_path=input_gro_path, 

101 output_gro_path=output_gro_path, 

102 properties=properties, **kwargs).launch() 

103 

104 

105def main(): 

106 """Command line execution of this building block. Please check the command line documentation.""" 

107 parser = argparse.ArgumentParser(description="Renumber atoms and residues from a 3D structure.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999)) 

108 parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string") 

109 

110 # Specific args of each building block 

111 required_args = parser.add_argument_group('required arguments') 

112 required_args.add_argument('-i', '--input_gro_path', required=True, help="Input GRO file name") 

113 required_args.add_argument('-o', '--output_gro_path', required=True, help="Output sorted GRO file name") 

114 

115 args = parser.parse_args() 

116 config = args.config if args.config else None 

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

118 

119 # Specific call of each building block 

120 sort_gro_residues(input_gro_path=args.input_gro_path, 

121 output_gro_path=args.output_gro_path, 

122 properties=properties) 

123 

124 

125if __name__ == '__main__': 

126 main()