Coverage for biobb_structure_utils / utils / str_check_add_hydrogens.py: 91%

1#!/usr/bin/env python3 

2 

3"""Module containing the StrCheckAddHydrogens 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_structure_utils.utils.common import ( 

11 check_input_path, 

12 check_output_end, 

13 check_output_path_pdbqt, 

14) 

15 

16 

17class StrCheckAddHydrogens(BiobbObject): 

18 """ 

19 | biobb_structure_utils StrCheckAddHydrogens 

20 | This class is a wrapper of the Structure Checking tool to add hydrogens to a 3D structure. 

21 | Wrapper for the `Structure Checking <https://github.com/bioexcel/biobb_structure_checking>`_ tool to add hydrogens to a 3D structure. 

22 

23 Args: 

24 input_structure_path (str): Input structure file path. File type: input. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/data/utils/str_no_H.pdb>`_. Accepted formats: pdb (edam:format_1476). 

25 output_structure_path (str): Output structure file path. File type: output. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/reference/utils/ref_str_H.pdbqt>`_. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476). 

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

27 * **charges** (*bool*) - (False) Whether or not to add charges to the output file. If True the output is in PDBQT format. 

28 * **mode** (*string*) - (auto) Selection mode. Values: auto, list, ph 

29 * **ph** (*float*) - (7.4) [0~14|0.1] Add hydrogens appropriate for pH. Only in case mode ph selected. 

30 * **list** (*string*) - ("") List of residues to modify separated by commas (i.e HISA234HID,HISB33HIE). Only in case mode list selected. 

31 * **keep_canonical_resnames** (*bool*) - (False) Whether or not keep canonical residue names 

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

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

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

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

36 

37 Examples: 

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

39 

40 from biobb_structure_utils.utils.str_check_add_hydrogens import str_check_add_hydrogens 

41 prop = { 

42 'charges': False, 

43 'mode': 'auto' 

44 } 

45 str_check_add_hydrogens(input_structure_path='/path/to/myInputStr.pdb', 

46 output_structure_path='/path/to/newStructure.pdb', 

47 properties=prop) 

48 

49 Info: 

50 * wrapped_software: 

51 * name: Structure Checking from MDWeb 

52 * version: >=3.0.3 

53 * license: Apache-2.0 

54 * ontology: 

55 * name: EDAM 

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

57 

58 """ 

59 

60 def __init__( 

61 self, input_structure_path, output_structure_path, properties=None, **kwargs 

62 ) -> None: 

63 properties = properties or {} 

64 

65 # Call parent class constructor 

66 super().__init__(properties) 

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

68 

69 # Input/Output files 

70 self.io_dict = { 

71 "in": {"input_structure_path": input_structure_path}, 

72 "out": {"output_structure_path": output_structure_path}, 

73 } 

74 

75 # Properties specific for BB 

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

77 self.charges = properties.get("charges", False) 

78 self.mode = properties.get("mode", "auto") 

79 self.ph = properties.get("ph", 7.4) 

80 self.list = properties.get("list", "") 

81 self.keep_canonical_resnames = properties.get("keep_canonical_resnames", False) 

82 self.properties = properties 

83 

84 # Check the properties 

85 self.check_properties(properties) 

86 self.check_arguments() 

87 

88 @launchlogger 

89 def launch(self) -> int: 

90 """Execute the :class:`StrCheckAddHydrogens <utils.str_check_add_hydrogens.StrCheckAddHydrogens>` utils.str_check_add_hydrogens.StrCheckAddHydrogens object.""" 

91 

92 self.io_dict["in"]["input_structure_path"] = check_input_path( 

93 self.io_dict["in"]["input_structure_path"], 

94 self.out_log, 

95 self.__class__.__name__, 

96 ) 

97 self.io_dict["out"]["output_structure_path"] = check_output_path_pdbqt( 

98 self.io_dict["out"]["output_structure_path"], 

99 self.out_log, 

100 self.__class__.__name__, 

101 ) 

102 

103 # Setup Biobb 

104 if self.check_restart(): 

105 return 0 

106 self.stage_files() 

107 

108 self.cmd = [ 

109 self.binary_path, 

110 "-i", 

111 self.stage_io_dict["in"]["input_structure_path"], 

112 "-o", 

113 self.stage_io_dict["out"]["output_structure_path"], 

114 "--non_interactive", 

115 "--force_save", 

116 ] 

117 

118 if self.keep_canonical_resnames: 

119 self.cmd.append("--keep_canonical_resnames") 

120 

121 self.cmd.extend(["command_list", "--list", "'add_hydrogen"]) 

122 

123 if self.charges: 

124 self.cmd.append("--add_charges") 

125 self.cmd.append("ADT") 

126 

127 if self.mode: 

128 self.cmd.extend(["--add_mode", self.mode]) 

129 if self.mode == "ph": 

130 self.cmd.extend(["--pH", self.ph]) 

131 if self.mode == "list": 

132 self.cmd.extend(["--list", self.list]) 

133 else: 

134 self.cmd.extend(["--add_mode", "None"]) 

135 

136 self.cmd.append("'") 

137 # Run Biobb block 

138 self.run_biobb() 

139 

140 # Copy files to host 

141 self.copy_to_host() 

142 

143 check_output_end(self.io_dict["out"]["output_structure_path"], self.out_log) 

144 

145 # Remove temporal files 

146 self.remove_tmp_files() 

147 

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

149 

150 return self.return_code 

151 

152 

153def str_check_add_hydrogens( 

154 input_structure_path: str, 

155 output_structure_path: str, 

156 properties: Optional[dict] = None, 

157 **kwargs, 

158) -> int: 

159 """Create the :class:`StrCheckAddHydrogens <utils.str_check_add_hydrogens.StrCheckAddHydrogens>` class and 

160 execute the :meth:`launch() <utils.str_check_add_hydrogens.StrCheckAddHydrogens.launch>` method.""" 

161 return StrCheckAddHydrogens(**dict(locals())).launch() 

162 

163 

164str_check_add_hydrogens.__doc__ = StrCheckAddHydrogens.__doc__ 

165main = StrCheckAddHydrogens.get_main(str_check_add_hydrogens, "Class to add hydrogens to a 3D structure.") 

166 

167if __name__ == "__main__": 

168 main()