Coverage for biobb_pdb_tools/pdb_tools/biobb_pdb_selaltloc.py: 74%

1#!/usr/bin/env python3 

2 

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

4 

5import argparse 

6from typing import Optional 

7 

8from biobb_common.configuration import settings 

9from biobb_common.generic.biobb_object import BiobbObject 

10from biobb_common.tools import file_utils as fu 

11from biobb_common.tools.file_utils import launchlogger 

12 

13 

14class Pdbselaltloc(BiobbObject): 

15 """ 

16 | biobb_pdb_tools Pdbselaltloc 

17 | Selects alternative locations from a PDB file. 

18 | By default, selects the label with the highest occupancy value for each atom, but the user can define a specific altloc label to select. Selecting by highest occupancy removes all altloc labels for all atoms. If the user provides an option (e.g. -A), only atoms with conformers with an altloc A are processed by the script. 

19 

20 Args: 

21 input_file_path (str): PDB file. File type: input. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_pdb_tools/master/biobb_pdb_tools/test/data/pdb_tools/9INS.pdb>`_. Accepted formats: pdb (edam:format_1476). 

22 output_file_path (str): PDB file with selected alternative locations. File type: output. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_pdb_tools/master/biobb_pdb_tools/test/reference/pdb_tools/ref_pdb_selaltloc.pdb>`_. Accepted formats: pdb (edam:format_1476). 

23 properties (dic): 

24 * **altloc** (*string*) - (None) Specific alternative location label to select (e.g. "A"). 

25 * **binary_path** (*str*) - ("pdb_selaltloc") Path to the pdb_selaltloc 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 

29 Examples: 

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

31 

32 from biobb_pdb_tools.pdb_tools.biobb_pdb_selaltloc import biobb_pdb_selaltloc 

33 

34 # Select the highest occupancy alternative locations 

35 biobb_pdb_selaltloc(input_file_path='/path/to/input.pdb', 

36 output_file_path='/path/to/output.pdb') 

37 

38 # Select a specific alternative location label 

39 prop = { 

40 'altloc': 'A' 

41 } 

42 biobb_pdb_selaltloc(input_file_path='/path/to/input.pdb', 

43 output_file_path='/path/to/output.pdb', 

44 properties=prop) 

45 

46 Info: 

47 * wrapped_software: 

48 * name: pdb_tools 

49 * version: >=2.5.0 

50 * license: Apache-2.0 

51 * ontology: 

52 * name: EDAM 

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

54 

55 """ 

56 

57 def __init__( 

58 self, input_file_path, output_file_path, properties=None, **kwargs 

59 ) -> None: 

60 properties = properties or {} 

61 

62 super().__init__(properties) 

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

64 

65 self.io_dict = { 

66 "in": {"input_file_path": input_file_path}, 

67 "out": {"output_file_path": output_file_path}, 

68 } 

69 

70 self.binary_path = properties.get("binary_path", "pdb_selaltloc") 

71 self.altloc = properties.get("altloc", None) 

72 self.properties = properties 

73 

74 self.check_properties(properties) 

75 self.check_arguments() 

76 

77 @launchlogger 

78 def launch(self) -> int: 

79 """Execute the :class:`Pdbselaltloc <biobb_pdb_tools.pdb_tools.pdb_selaltloc>` object.""" 

80 

81 if self.check_restart(): 

82 return 0 

83 self.stage_files() 

84 

85 instructions = [] 

86 if self.altloc: 

87 instructions.append("-" + str(self.altloc)) 

88 fu.log("Selecting alternative location label: " + self.altloc, self.out_log, self.global_log) 

89 

90 self.cmd = [ 

91 self.binary_path, 

92 " ".join(instructions), 

93 self.stage_io_dict["in"]["input_file_path"], 

94 ">", 

95 self.io_dict["out"]["output_file_path"], 

96 ] 

97 

98 fu.log(" ".join(self.cmd), self.out_log, self.global_log) 

99 

100 fu.log( 

101 "Creating command line with instructions and required arguments", 

102 self.out_log, 

103 self.global_log, 

104 ) 

105 

106 self.run_biobb() 

107 self.copy_to_host() 

108 self.tmp_files.extend([self.stage_io_dict.get("unique_dir", "")]) 

109 self.remove_tmp_files() 

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

111 

112 return self.return_code 

113 

114 

115def biobb_pdb_selaltloc( 

116 input_file_path: str, 

117 output_file_path: str, 

118 properties: Optional[dict] = None, 

119 **kwargs, 

120) -> int: 

121 """Create :class:`Pdbselaltloc <biobb_pdb_tools.pdb_tools.pdb_selaltloc>` class and 

122 execute the :meth:`launch() <biobb_pdb_tools.pdb_tools.pdb_selaltloc.launch>` method.""" 

123 

124 return Pdbselaltloc( 

125 input_file_path=input_file_path, 

126 output_file_path=output_file_path, 

127 properties=properties, 

128 **kwargs, 

129 ).launch() 

130 

131biobb_pdb_selaltloc.__doc__ = Pdbselaltloc.__doc__ 

132 

133 

134def main(): 

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

136 parser = argparse.ArgumentParser( 

137 description="Selects alternative locations from a PDB file.", 

138 formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999), 

139 ) 

140 parser.add_argument("--config", required=True, help="Configuration file") 

141 

142 required_args = parser.add_argument_group("required arguments") 

143 required_args.add_argument( 

144 "--input_file_path", 

145 required=True, 

146 help="PDB file. Accepted formats: pdb.", 

147 ) 

148 required_args.add_argument( 

149 "--output_file_path", 

150 required=True, 

151 help="PDB file with selected alternative locations. Accepted formats: pdb.", 

152 ) 

153 

154 args = parser.parse_args() 

155 args.config = args.config or "{}" 

156 properties = settings.ConfReader(config=args.config).get_prop_dic() 

157 

158 biobb_pdb_selaltloc( 

159 input_file_path=args.input_file_path, 

160 output_file_path=args.output_file_path, 

161 properties=properties, 

162 ) 

163 

164 

165if __name__ == "__main__": 

166 main()