Coverage for biobb_model/model/fix_ssbonds.py: 70%
44 statements
« prev ^ index » next coverage.py v7.4.3, created at 2024-03-13 17:26 +0000
« prev ^ index » next coverage.py v7.4.3, created at 2024-03-13 17:26 +0000
1#!/usr/bin/env python3
3"""Module containing the FixSSBonds class and the command line interface."""
4import argparse
5from biobb_common.generic.biobb_object import BiobbObject
6from biobb_common.configuration import settings
7from biobb_common.tools.file_utils import launchlogger
10class FixSSBonds(BiobbObject):
11 """
12 | biobb_model FixSSBonds
13 | Fix SS bonds from residues.
15 Args:
16 input_pdb_path (str): Input PDB file path. File type: input. `Sample file <https://github.com/bioexcel/biobb_model/raw/master/biobb_model/test/data/model/1aki.pdb>`_. Accepted formats: pdb (edam:format_1476).
17 output_pdb_path (str): Output PDB file path. File type: output. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_model/master/biobb_model/test/reference/model/output_ssbonds.pdb>`_. Accepted formats: pdb (edam:format_1476).
18 properties (dict - Python dictionary object containing the tool parameters, not input/output files):
19 * **modeller_key** (*str*) - (None) Modeller license key.
20 * **binary_path** (*str*) - ("check_structure") Path to the check_structure executable binary.
21 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
22 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
24 Examples:
25 This is a use example of how to use the building block from Python::
27 from biobb_model.model.fix_ssbonds import fix_ssbonds
28 prop = { 'restart': False }
29 fix_ssbonds(input_pdb_path='/path/to/myStructure.pdb',
30 output_pdb_path='/path/to/newStructure.pdb',
31 properties=prop)
33 Info:
34 * wrapped_software:
35 * name: In house
36 * license: Apache-2.0
37 * ontology:
38 * name: EDAM
39 * schema: http://edamontology.org/EDAM.owl
40 """
42 def __init__(self, input_pdb_path: str, output_pdb_path: str, properties: dict = None, **kwargs) -> None:
43 properties = properties or {}
45 # Call parent class constructor
46 super().__init__(properties)
47 self.locals_var_dict = locals().copy()
49 # Input/Output files
50 self.io_dict = {
51 "in": {"input_pdb_path": input_pdb_path},
52 "out": {"output_pdb_path": output_pdb_path}
53 }
55 # Properties specific for BB
56 self.binary_path = properties.get('binary_path', 'check_structure')
57 self.modeller_key = properties.get('modeller_key')
59 # Check the properties
60 self.check_properties(properties)
61 self.check_arguments()
63 @launchlogger
64 def launch(self) -> int:
65 """Execute the :class:`FixSSBonds <model.fix_ssbonds.FixSSBonds>` object."""
67 # Setup Biobb
68 if self.check_restart():
69 return 0
70 self.stage_files()
72 self.cmd = [self.binary_path,
73 '-i', self.stage_io_dict["in"]["input_pdb_path"],
74 '-o', self.stage_io_dict["out"]["output_pdb_path"],
75 '--force_save',
76 '--non_interactive',
77 'getss', '--mark', 'All']
79 if self.modeller_key:
80 self.cmd.insert(1, self.modeller_key)
81 self.cmd.insert(1, '--modeller_key')
83 # Run Biobb block
84 self.run_biobb()
86 # Copy files to host
87 self.copy_to_host()
89 # Remove temporal files
90 self.tmp_files.extend([self.stage_io_dict.get("unique_dir")])
91 self.remove_tmp_files()
93 self.check_arguments(output_files_created=True, raise_exception=False)
94 return self.return_code
97def fix_ssbonds(input_pdb_path: str, output_pdb_path: str, properties: dict = None, **kwargs) -> int:
98 """Create :class:`FixSSBonds <model.fix_ssbonds.FixSSBonds>` class and
99 execute the :meth:`launch() <model.fix_ssbonds.FixSSBonds.launch>` method."""
100 return FixSSBonds(input_pdb_path=input_pdb_path,
101 output_pdb_path=output_pdb_path,
102 properties=properties, **kwargs).launch()
105def main():
106 parser = argparse.ArgumentParser(description="Fix SS bonds from residues",
107 formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
108 parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string")
110 # Specific args of each building block
111 required_args = parser.add_argument_group('required arguments')
112 required_args.add_argument('-i', '--input_pdb_path', required=True, help="Input PDB file name")
113 required_args.add_argument('-o', '--output_pdb_path', required=True, help="Output PDB file name")
115 args = parser.parse_args()
116 config = args.config if args.config else None
117 properties = settings.ConfReader(config=config).get_prop_dic()
119 # Specific call of each building block
120 fix_ssbonds(input_pdb_path=args.input_pdb_path,
121 output_pdb_path=args.output_pdb_path,
122 properties=properties)
125if __name__ == '__main__':
126 main()