biobb_pdb_tools/pdb_tools/biobb_pdb_tidy.py source
1 #!/usr/bin/env python3
2
3 """Module containing the Pdbtidy 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 class Pdbtidy(BiobbObject):
15 """
16 | biobb_pdb_tools Pdbtidy
17 | Modifies the file to adhere (as much as possible) to the format specifications.
18 | This tool modifies the file to adhere (as much as possible) to the format specifications. It can be used to fix a PDB file that does not adhere to the format specifications.
19
20 Args:
21 input_file_path (str): PDB file. File type: input. `Sample file <https://github.com/bioexcel/biobb_pdb_tools/blob/master/biobb_pdb_tools/test/data/pdb_tools/1AKI.pdb>`_. Accepted formats: pdb (edam:format_1476).
22 output_file_path (str): PDB file modified according to the specifications. File type: output. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_pdb_tools/master/biobb_pdb_tools/test/reference/pdb_tools/ref_pdb_tidy.pdb>`_. Accepted formats: pdb (edam:format_1476).
23 properties (dic):
24 * **strict** (*bool*) - (False) Does not add TER on chain breaks.
25 * **binary_path** (*str*) - ("pdb_tidy") Path to the pdb_tidy 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_tidy import biobb_pdb_tidy
33
34 prop = {
35 'strict': False
36 }
37 biobb_pdb_tidy(input_file_path='/path/to/input.pdb',
38 output_file_path='/path/to/output.pdb',
39 properties=prop)
40
41 Info:
42 * wrapped_software:
43 * name: pdb_tools
44 * version: >=2.5.0
45 * license: Apache-2.0
46 * ontology:
47 * name: EDAM
48 * schema: http://edamontology.org/EDAM.owl
49
50 """
51
52 def __init__(
53 self, input_file_path, output_file_path, properties=None, **kwargs
54 ) -> None:
55 properties = properties or {}
56
57 super().__init__(properties)
58 self.locals_var_dict = locals().copy()
59
60 self.io_dict = {
61 "in": {"input_file_path": input_file_path},
62 "out": {"output_file_path": output_file_path},
63 }
64
65 self.binary_path = properties.get("binary_path", "pdb_tidy")
66 self.strict = properties.get("strict", False)
67 self.properties = properties
68
69 self.check_properties(properties)
70 self.check_arguments()
71
72 @launchlogger
73 def launch(self) -> int:
74 """Execute the :class:`Pdbtidy <biobb_pdb_tools.pdb_tools.pdb_tidy>` object."""
75
76 if self.check_restart():
77 return 0
78 self.stage_files()
79
80 instructions = []
81 if self.strict:
82 instructions.append("-strict")
83 fu.log("Appending optional boolean property", self.out_log, self.global_log)
84
85 self.cmd = [
86 self.binary_path,
87 " ".join(instructions),
88 self.io_dict["in"]["input_file_path"],
89 ">",
90 self.io_dict["out"]["output_file_path"],
91 ]
92
93 fu.log(" ".join(self.cmd), self.out_log, self.global_log)
94
95 fu.log(
96 "Creating command line with instructions and required arguments",
97 self.out_log,
98 self.global_log,
99 )
100
101 self.run_biobb()
102 self.copy_to_host()
103
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_tidy(
112 input_file_path: str,
113 output_file_path: str,
114 properties: Optional[dict] = None,
115 **kwargs,
116 ) -> int:
117 """Create :class:`Pdbtidy <biobb_pdb_tools.pdb_tools.pdb_tidy>` class and
118 execute the :meth:`launch() <biobb_pdb_tools.pdb_tools.pdb_tidy.launch>` method."""
119
120 return Pdbtidy(
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 file to adhere (as much as possible) to the format specifications.",
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_tidy(
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()