Coverage for biobb_cmip/cmip/cmip_ignore_residues.py: 70%

1#!/usr/bin/env python3 

2 

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

4import argparse 

5from typing import Optional 

6import shutil 

7from biobb_cmip.cmip.common import mark_residues 

8from biobb_common.generic.biobb_object import BiobbObject 

9from biobb_common.configuration import settings 

10from biobb_common.tools.file_utils import launchlogger 

11import biobb_common.tools.file_utils as fu 

12 

13 

14class CmipIgnoreResidues(BiobbObject): 

15 """ 

16 | biobb_cmip CmipIgnoreResidues 

17 | Class to ignore residues in CMIP potential calculations. 

18 | Mark residues which will be ignored in the CMIP potential calculations except for dielectric definition. 

19 

20 Args: 

21 input_cmip_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/input_ignore_res.pdb>`_. Accepted formats: pdb (edam:format_1476). 

22 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/ignore_res_gln3.pdb>`_. Accepted formats: pdb (edam:format_1476). 

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

24 * **residue_list** (*str*) - (None) Residue list in the format "Chain:Resnum" (no spaces between the elements) separated by commas. If no chain is provided all the residues in the pdb file will be market. ie: "A:3". 

25 * **ignore_all** (*bool*) - (False) Mark all the residues in the PDB file. 

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_ignore_residues import cmip_ignore_residues 

35 prop = { 'residue_list': "A:3" } 

36 cmip_ignore_residues(input_cmip_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_cmip_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_cmip_pdb_path": input_cmip_pdb_path}, 

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

61 } 

62 

63 # Properties specific for BB 

64 self.residue_list = properties.get('residue_list', None) 

65 self.ignore_all = properties.get('ignore_all', False) 

66 

67 # Check the properties 

68 self.check_properties(properties) 

69 self.check_arguments() 

70 

71 @launchlogger 

72 def launch(self) -> int: 

73 """Execute the :class:`IgnoreResidues <cmip.ignore_residues.IgnoreResidues>` object.""" 

74 

75 # Setup Biobb 

76 if self.check_restart(): 

77 return 0 

78 

79 if not self.ignore_all and not self.residue_list: 

80 fu.log("Residue_list is empty and ignore_all is false nothing will be done.", self.out_log, self.global_log) 

81 shutil.copyfile(self.io_dict["in"]["input_cmip_pdb_path"], self.io_dict["out"]["output_cmip_pdb_path"]) 

82 return self.return_code 

83 

84 if self.ignore_all: 

85 self.residue_list = None 

86 

87 if self.residue_list: 

88 if not isinstance(self.residue_list, list): 

89 self.residue_list = str(self.residue_list).split(",") 

90 for i in range(len(self.residue_list)): 

91 residue_code_list = str(self.residue_list[i]).split(":") 

92 if len(residue_code_list) < 2: 

93 resnum = residue_code_list[0] 

94 chain = '' 

95 else: 

96 chain, resnum = residue_code_list 

97 self.residue_list[i] = chain.strip().upper()+":"+str(resnum).strip() 

98 

99 mark_residues(residue_list=self.residue_list or [], input_cmip_pdb_path=self.io_dict["in"]["input_cmip_pdb_path"], output_cmip_pdb_path=self.io_dict["out"]["output_cmip_pdb_path"], out_log=self.out_log, global_log=self.global_log) 

100 

101 # remove temporary 

102 self.remove_tmp_files() 

103 

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

105 

106 return self.return_code 

107 

108 

109def cmip_ignore_residues(input_cmip_pdb_path: str, output_cmip_pdb_path: str, properties: Optional[dict] = None, **kwargs) -> int: 

110 """Create :class:`IgnoreResidues <cmip.ignore_residues.IgnoreResidues>` class and 

111 execute the :meth:`launch() <cmip.ignore_residues.IgnoreResidues.launch>` method.""" 

112 return CmipIgnoreResidues(input_cmip_pdb_path=input_cmip_pdb_path, 

113 output_cmip_pdb_path=output_cmip_pdb_path, 

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

115 

116 cmip_ignore_residues.__doc__ = CmipIgnoreResidues.__doc__ 

117 

118 

119def main(): 

120 parser = argparse.ArgumentParser(description="Mark residues which charges will be ignored in the CMIP potential calculations.", 

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

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

123 

124 # Specific args of each building block 

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

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

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

128 

129 args = parser.parse_args() 

130 config = args.config if args.config else None 

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

132 

133 # Specific call of each building block 

134 cmip_ignore_residues(input_cmip_pdb_path=args.input_cmip_pdb_path, 

135 output_cmip_pdb_path=args.output_cmip_pdb_path, 

136 properties=properties) 

137 

138 

139if __name__ == '__main__': 

140 main()