Coverage for biobb_cmip/cmip/cmip_prepare_pdb.py: 76%

1#!/usr/bin/env python3 

2 

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

4import argparse 

5from typing import Optional 

6from biobb_common.generic.biobb_object import BiobbObject 

7from biobb_common.configuration import settings 

8from biobb_common.tools.file_utils import launchlogger 

9 

10 

11class CmipPreparePDB(BiobbObject): 

12 """ 

13 | biobb_cmip CmipPreparePDB 

14 | Class to add CMIP charges and atom types. 

15 | Add CMIP charges and atom types to a PDB structure using `biobb_structure_checking <https://anaconda.org/bioconda/biobb_structure_checking>`_. 

16 

17 Args: 

18 input_pdb_path (str): Input PDB file path. File type: input. `Sample file <https://github.com/bioexcel/biobb_cmip/raw/master/biobb_cmip/test/data/cmip/1aki.pdb>`_. Accepted formats: pdb (edam:format_1476). 

19 output_cmip_pdb_path (str): Output PDB file path. File type: output. `Sample file <https://github.com/bioexcel/biobb_cmip/raw/master/biobb_cmip/test/reference/cmip/egfr_cmip.pdb>`_. Accepted formats: pdb (edam:format_1476). 

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

21 * **remove_water** (*bool*) - (True) Remove Water molecules. 

22 * **add_hydrogen** (*bool*) - (True) Add Hydrogen atoms to the structure. 

23 * **keep_hydrogen** (*bool*) - (False) If **add_hydrogen** is True. All hydrogen atoms will be removed before adding the new ones unless this option is set True. 

24 * **fix_sidechains** (*bool*) - (True) Complete side chains (heavy atoms, protein only). 

25 * **fix_backbone_atoms** (*bool*) - (True) Add missing O, OXT backbone atoms. 

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

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

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

29 

30 

31 Examples: 

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

33 

34 from biobb_cmip.cmip.cmip_prepare_pdb import cmip_prepare_pdb 

35 prop = { 'restart': False } 

36 cmip_prepare_pdb(input_pdb_path='/path/to/myStructure.pdb', 

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

38 properties=prop) 

39 

40 Info: 

41 * wrapped_software: 

42 * name: CMIP cmip 

43 * version: 2.7.0 

44 * license: Apache-2.0 

45 * ontology: 

46 * name: EDAM 

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

48 """ 

49 

50 def __init__(self, input_pdb_path: str, output_cmip_pdb_path: str, properties: Optional[dict] = None, **kwargs) -> None: 

51 properties = properties or {} 

52 

53 # Call parent class constructor 

54 super().__init__(properties) 

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

56 

57 # Input/Output files 

58 self.io_dict = { 

59 "in": {"input_pdb_path": input_pdb_path}, 

60 "out": {"output_cmip_pdb_path": output_cmip_pdb_path} 

61 } 

62 

63 # Properties specific for BB 

64 self.check_structure_path = properties.get('check_structure_path', 'check_structure') 

65 self.remove_water = properties.get('remove_water', True) 

66 self.keep_hydrogen = properties.get('keep_hydrogen', False) 

67 self.fix_sidechains = properties.get('fix_sidechains', True) 

68 self.fix_backbone_atoms = properties.get('fix_backbone_atoms', True) 

69 

70 # Check the properties 

71 self.check_properties(properties) 

72 self.check_arguments() 

73 

74 @launchlogger 

75 def launch(self) -> int: 

76 """Execute the :class:`PreparePDB <cmip.prepare_pdb.PreparePDB>` object.""" 

77 

78 # Setup Biobb 

79 if self.check_restart(): 

80 return 0 

81 self.stage_files() 

82 

83 command_list = "" 

84 if self.remove_water: 

85 command_list += 'water --remove yes; ' 

86 

87 if self.fix_backbone_atoms: 

88 command_list += 'backbone --add_caps none; ' 

89 

90 if self.fix_sidechains: 

91 command_list += 'fixside --fix All; ' 

92 

93 command_list += 'add_hydrogen --add_mode auto ' 

94 if self.keep_hydrogen: 

95 command_list += ' -keep_h ' 

96 command_list += '--add_charges CMIP' 

97 

98 self.cmd = [self.check_structure_path, 

99 '-v', 

100 '-i', self.stage_io_dict["in"]["input_pdb_path"], 

101 '-o', self.stage_io_dict["out"]["output_cmip_pdb_path"], 

102 '--output_format', 'cmip', 

103 '--non_interactive', 

104 'command_list', 

105 '--list', "'"+command_list+"'"] 

106 

107 # Run Biobb block 

108 self.run_biobb() 

109 

110 # Copy files to host 

111 self.copy_to_host() 

112 

113 # remove temporary folder(s) 

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

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 cmip_prepare_pdb(input_pdb_path: str, output_cmip_pdb_path: str, properties: Optional[dict] = None, **kwargs) -> int: 

123 """Create :class:`PreparePDB <cmip.prepare_pdb.PreparePDB>` class and 

124 execute the :meth:`launch() <cmip.prepare_pdb.PreparePDB.launch>` method.""" 

125 return CmipPreparePDB(input_pdb_path=input_pdb_path, 

126 output_cmip_pdb_path=output_cmip_pdb_path, 

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

128 

129 cmip_prepare_pdb.__doc__ = CmipPreparePDB.__doc__ 

130 

131 

132def main(): 

133 parser = argparse.ArgumentParser(description="Model the missing atoms in the backbone of a PDB structure.", 

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

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

136 

137 # Specific args of each building block 

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

139 required_args.add_argument('-i', '--input_pdb_path', required=True, help="Input PDB file name") 

140 required_args.add_argument('-o', '--output_cmip_pdb_path', required=True, help="Output PDB file name") 

141 

142 args = parser.parse_args() 

143 config = args.config if args.config else None 

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

145 

146 # Specific call of each building block 

147 cmip_prepare_pdb(input_pdb_path=args.input_pdb_path, 

148 output_cmip_pdb_path=args.output_cmip_pdb_path, 

149 properties=properties) 

150 

151 

152if __name__ == '__main__': 

153 main()