Coverage for biobb_pdb_tools/pdb_tools/biobb_pdb_reres.py: 78%
50 statements
« prev ^ index » next coverage.py v7.9.1, created at 2025-06-20 08:28 +0000
1#!/usr/bin/env python3
3"""Module containing the Pdbreres class and the command line interface."""
5import argparse
6from typing import Optional
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
14# 1. Rename class as required
15class Pdbreres(BiobbObject):
16 """
17 | biobb_pdb_tools Pdbreres
18 | Renumbers the residues of the PDB file starting from a given number (default 1).
19 | This tool renumbers the residues of the PDB file starting from a given number (default 1). It can be used to renumber the residues of a PDB file starting from a given number.
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): Renumbered PDB file by number of redisue selected. File type: output. `Sample file <https://github.com/bioexcel/biobb_pdb_tools/blob/master/biobb_pdb_tools/test/reference/pdb_tools/ref_pdb_reres.pdb>`_. Accepted formats: pdb (edam:format_1476).
24 properties (dic):
25 * **number** (*int*) - (4) Number of the protein residue.
26 * **binary_path** (*str*) - ("pdb_reres") Path to the pdb_reres 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.
30 Examples:
31 This is a use example of how to use the building block from Python::
33 from biobb_pdb_tools.pdb_tools.biobb_pdb_reres import biobb_pdb_reres
35 prop = {
36 'number': 4
37 }
38 biobb_pdb_reres(input_file_path='/path/to/input.pdb',
39 output_file_path='/path/to/output.pdb',
40 properties=prop)
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
51 """
53 def __init__(
54 self, input_file_path, output_file_path, properties=None, **kwargs
55 ) -> None:
56 properties = properties or {}
58 super().__init__(properties)
59 self.locals_var_dict = locals().copy()
60 self.io_dict = {
61 "in": {"input_file_path": input_file_path},
62 "out": {"output_file_path": output_file_path},
63 }
65 self.binary_path = properties.get("binary_path", "pdb_reres")
66 self.number = properties.get("number", False)
67 self.properties = properties
69 self.check_properties(properties)
70 self.check_arguments()
72 @launchlogger
73 def launch(self) -> int:
74 """Execute the :class:`Pdbreres <biobb_pdb_tools.pdb_tools.pdb_reres>` object."""
76 if self.check_restart():
77 return 0
78 self.stage_files()
80 instructions = []
81 if self.number:
82 instructions.append("-" + str(self.number))
83 fu.log("Appending optional boolean property",
84 self.out_log, self.global_log)
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 ]
94 fu.log(" ".join(self.cmd), self.out_log, self.global_log)
96 fu.log(
97 "Creating command line with instructions and required arguments",
98 self.out_log,
99 self.global_log,
100 )
102 self.run_biobb()
103 self.copy_to_host()
105 self.tmp_files.extend([self.stage_io_dict.get("unique_dir", "")])
106 self.remove_tmp_files()
107 self.check_arguments(output_files_created=True, raise_exception=False)
109 return self.return_code
112def biobb_pdb_reres(
113 input_file_path: str,
114 output_file_path: str,
115 properties: Optional[dict] = None,
116 **kwargs,
117) -> int:
118 """Create :class:`Pdbreres <biobb_pdb_tools.pdb_tools.pdb_reres>` class and
119 execute the :meth:`launch() <biobb_pdb_tools.pdb_tools.pdb_reres.launch>` method."""
121 return Pdbreres(
122 input_file_path=input_file_path,
123 output_file_path=output_file_path,
124 properties=properties,
125 **kwargs,
126 ).launch()
129biobb_pdb_reres.__doc__ = Pdbreres.__doc__
132def main():
133 """Command line execution of this building block. Please check the command line documentation."""
134 parser = argparse.ArgumentParser(
135 description="Renumbers the residues of the PDB file starting from a given number (default 1).",
136 formatter_class=lambda prog: argparse.RawTextHelpFormatter(
137 prog, width=99999),
138 )
139 parser.add_argument("--config", required=True, help="Configuration file")
141 required_args = parser.add_argument_group("required arguments")
142 required_args.add_argument(
143 "--input_file_path",
144 required=True,
145 help="Description for the first input file path. Accepted formats: pdb.",
146 )
147 required_args.add_argument(
148 "--output_file_path",
149 required=True,
150 help="Description for the output file path. Accepted formats: pdb.",
151 )
153 args = parser.parse_args()
154 args.config = args.config or "{}"
155 properties = settings.ConfReader(config=args.config).get_prop_dic()
156 biobb_pdb_reres(
157 input_file_path=args.input_file_path,
158 output_file_path=args.output_file_path,
159 properties=properties,
160 )
163if __name__ == "__main__":
164 main()