Coverage for biobb_structure_utils/utils/remove_pdb_water.py: 72%

1#!/usr/bin/env python3 

2 

3"""Module containing the RemovePdbWater 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 

8 

9 

10class RemovePdbWater(BiobbObject): 

11 """ 

12 | biobb_structure_utils RemovePdbWater 

13 | This class is a wrapper of the Structure Checking tool to remove water molecules from PDB 3D structures. 

14 | Wrapper for the `Structure Checking <https://github.com/bioexcel/biobb_structure_checking>`_ tool to remove water molecules from PDB 3D structures. 

15 

16 Args: 

17 input_pdb_path (str): Input PDB 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_WAT.pdb>`_. Accepted formats: pdb (edam:format_1476). 

18 output_pdb_path (str): Output PDB file path. File type: output. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/reference/utils/WT_apo_no_wat.pdb>`_. Accepted formats: pdb (edam:format_1476). 

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

20 * **binary_path** (*string*) - ("check_structure") path to the check_structure application 

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 

25 Examples: 

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

27 

28 from biobb_structure_utils.utils.remove_pdb_water import remove_pdb_water 

29 prop = { } 

30 remove_pdb_water(input_pdb_path='/path/to/myStructure.pdb', 

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

32 properties=prop) 

33 

34 Info: 

35 * wrapped_software: 

36 * name: Structure Checking from MDWeb 

37 * version: >=3.0.3 

38 * license: Apache-2.0 

39 * ontology: 

40 * name: EDAM 

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

42 

43 """ 

44 

45 def __init__(self, input_pdb_path, output_pdb_path, properties=None, **kwargs) -> None: 

46 properties = properties or {} 

47 

48 # Call parent class constructor 

49 super().__init__(properties) 

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

51 

52 # Input/Output files 

53 self.io_dict = { 

54 "in": {"input_pdb_path": input_pdb_path}, 

55 "out": {"output_pdb_path": output_pdb_path} 

56 } 

57 

58 # Properties specific for BB 

59 self.binary_path = properties.get('binary_path', 'check_structure') 

60 

61 # Check the properties 

62 self.check_properties(properties) 

63 self.check_arguments() 

64 

65 @launchlogger 

66 def launch(self) -> int: 

67 """Execute the :class:`RemovePdbWater <utils.remove_pdb_water.RemovePdbWater>` utils.remove_pdb_water.RemovePdbWater object.""" 

68 

69 # Setup Biobb 

70 if self.check_restart(): 

71 return 0 

72 self.stage_files() 

73 

74 self.cmd = [self.binary_path, 

75 '-i', self.stage_io_dict['in']['input_pdb_path'], 

76 '-o', self.stage_io_dict['out']['output_pdb_path'], 

77 '--force_save', 

78 'water', '--remove', 'yes'] 

79 

80 # Run Biobb block 

81 self.run_biobb() 

82 

83 # Copy files to host 

84 self.copy_to_host() 

85 

86 # Remove temporal files 

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

88 self.remove_tmp_files() 

89 

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

91 

92 return self.return_code 

93 

94 

95def remove_pdb_water(input_pdb_path: str, output_pdb_path: str, properties: dict = None, **kwargs) -> int: 

96 """Execute the :class:`RemovePdbWater <utils.remove_pdb_water.RemovePdbWater>` class and 

97 execute the :meth:`launch() <utils.remove_pdb_water.RemovePdbWater.launch>` method.""" 

98 

99 return RemovePdbWater(input_pdb_path=input_pdb_path, 

100 output_pdb_path=output_pdb_path, 

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

102 

103 

104def main(): 

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

106 parser = argparse.ArgumentParser(description="Remove the water molecules from a PDB 3D structure.", 

107 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_pdb_path', required=True, help="Input pdb file name") 

113 required_args.add_argument('-o', '--output_pdb_path', required=True, help="Output pdb 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 remove_pdb_water(input_pdb_path=args.input_pdb_path, 

121 output_pdb_path=args.output_pdb_path, 

122 properties=properties) 

123 

124 

125if __name__ == '__main__': 

126 main()