biobb_pdb_tools/pdb_tools/biobb_pdb_chain.py source
1 #!/usr/bin/env python3
2
3 """Module containing the Pdbchain class and the command line interface."""
4
5 import argparse
6 from typing import Optional
7
8 from biobb_common.configuration import settings
9 from biobb_common.generic.biobb_object import BiobbObject
10 from biobb_common.tools import file_utils as fu
11 from biobb_common.tools.file_utils import launchlogger
12
13
14 # 1. Rename class as required
15 class Pdbchain(BiobbObject):
16 """
17 | biobb_pdb_tools Pdbchain
18 | Modifies the chain identifier column of a PDB file.
19 | This tool modifies the chain identifier column of a PDB file. It can be used to change the chain identifier of a PDB file or to remove the chain identifier from a PDB file.
20
21 Args:
22 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/1AKI.pdb>`_. Accepted formats: pdb (edam:format_1476).
23 output_file_path (str): PDB file with selected modified chain. File type: output. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_pdb_tools/master/biobb_pdb_tools/test/reference/pdb_tools/ref_pdb_chain.pdb>`_. Accepted formats: pdb (edam:format_1476).
24 properties (dic):
25 * **chain** (*string*) - ('A') Modifies the chain identifier column of a PDB file.
26 * **binary_path** (*str*) - ("pdb_chain") Path to the pdb_chain executable binary.
27 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
28 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
29
30 Examples:
31 This is a use example of how to use the building block from Python::
32
33 from biobb_pdb_tools.pdb_tools.biobb_pdb_chain import biobb_pdb_chain
34
35 prop = {
36 'chain': 'A'
37 }
38 biobb_pdb_chain(input_file_path='/path/to/input.pdb',
39 output_file_path='/path/to/output.pdb',
40 properties=prop)
41
42 Info:
43 * wrapped_software:
44 * name: pdb_tools
45 * version: >=2.5.0
46 * license: Apache-2.0
47 * ontology:
48 * name: EDAM
49 * schema: http://edamontology.org/EDAM.owl
50
51 """
52
53 def __init__(
54 self, input_file_path, output_file_path, properties=None, **kwargs
55 ) -> None:
56 properties = properties or {}
57
58 super().__init__(properties)
59 self.locals_var_dict = locals().copy()
60
61 self.io_dict = {
62 "in": {"input_file_path": input_file_path},
63 "out": {"output_file_path": output_file_path},
64 }
65
66 self.binary_path = properties.get("binary_path", "pdb_chain")
67 self.chain = properties.get("chain", False)
68 self.properties = properties
69
70 self.check_properties(properties)
71 self.check_arguments()
72
73 @launchlogger
74 def launch(self) -> int:
75 """Execute the :class:`Pdbchain <biobb_pdb_tools.pdb_tools.pdb_chain>` object."""
76
77 if self.check_restart():
78 return 0
79 self.stage_files()
80
81 instructions = []
82 if self.chain:
83 instructions.append("-" + str(self.chain))
84 fu.log("Appending optional boolean property", self.out_log, self.global_log)
85
86 self.cmd = [
87 self.binary_path,
88 " ".join(instructions),
89 self.stage_io_dict["in"]["input_file_path"],
90 ">",
91 self.io_dict["out"]["output_file_path"],
92 ]
93
94 fu.log(" ".join(self.cmd), self.out_log, self.global_log)
95
96 fu.log(
97 "Creating command line with instructions and required arguments",
98 self.out_log,
99 self.global_log,
100 )
101
102 self.run_biobb()
103 self.copy_to_host()
104 self.tmp_files.extend([self.stage_io_dict.get("unique_dir", "")])
105 self.remove_tmp_files()
106 self.check_arguments(output_files_created=True, raise_exception=False)
107
108 return self.return_code
109
110
111 def biobb_pdb_chain(
112 input_file_path: str,
113 output_file_path: str,
114 properties: Optional[dict] = None,
115 **kwargs,
116 ) -> int:
117 """Create :class:`Pdbchain <biobb_pdb_tools.pdb_tools.pdb_chain>` class and
118 execute the :meth:`launch() <biobb_pdb_tools.pdb_tools.pdb_chain.launch>` method."""
119
120 return Pdbchain(
121 input_file_path=input_file_path,
122 output_file_path=output_file_path,
123 properties=properties,
124 **kwargs,
125 ).launch()
126
- E305 Expected 2 blank lines after class or function definition, found 1
128
129
130 def main():
131 """Command line execution of this building block. Please check the command line documentation."""
132 parser = argparse.ArgumentParser(
133 description="Modifies the chain identifier column of a PDB file.",
134 formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999),
135 )
136 parser.add_argument("--config", required=True, help="Configuration file")
137
138 required_args = parser.add_argument_group("required arguments")
139 required_args.add_argument(
140 "--input_file_path",
141 required=True,
142 help="Description for the first input file path. Accepted formats: pdb.",
143 )
144 required_args.add_argument(
145 "--output_file_path",
146 required=True,
147 help="Description for the output file path. Accepted formats: pdb.",
148 )
149
150 args = parser.parse_args()
151 args.config = args.config or "{}"
152 properties = settings.ConfReader(config=args.config).get_prop_dic()
153
154 biobb_pdb_chain(
155 input_file_path=args.input_file_path,
156 output_file_path=args.output_file_path,
157 properties=properties,
158 )
159
160
161 if __name__ == "__main__":
162 main()