Coverage for biobb_io/api/pdb.py: 77%
44 statements
« prev ^ index » next coverage.py v7.6.9, created at 2024-12-10 15:33 +0000
« prev ^ index » next coverage.py v7.6.9, created at 2024-12-10 15:33 +0000
1#!/usr/bin/env python
3"""Module containing the Pdb 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.file_utils import launchlogger
12from biobb_io.api.common import (
13 check_mandatory_property,
14 check_output_path,
15 download_pdb,
16 write_pdb,
17)
20class Pdb(BiobbObject):
21 """
22 | biobb_io Pdb
23 | This class is a wrapper for downloading a PDB structure from the Protein Data Bank.
24 | Wrapper for the `Protein Data Bank in Europe <https://www.ebi.ac.uk/pdbe/>`_, the `Protein Data Bank <https://www.rcsb.org/>`_ and the `MMB PDB mirror <http://mmb.irbbarcelona.org/api/>`_ for downloading a single PDB structure.
26 Args:
27 output_pdb_path (str): Path to the output PDB file. File type: output. `Sample file <https://github.com/bioexcel/biobb_io/raw/master/biobb_io/test/reference/api/output_pdb.pdb>`_. Accepted formats: pdb (edam:format_1476).
28 properties (dic - Python dictionary object containing the tool parameters, not input/output files):
29 * **pdb_code** (*str*) - (None) RSCB PDB code.
30 * **filter** (*str*) - (["ATOM", "MODEL", "ENDMDL"]) Array of groups to be kept. If value is None or False no filter will be applied. All the possible values are defined in the `official PDB specification <http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html)>`_.
31 * **api_id** (*str*) - ("pdbe") Identifier of the PDB REST API from which the PDB structure will be downloaded. Values: pdbe (`PDB in Europe REST API <https://www.ebi.ac.uk/pdbe/pdbe-rest-api>`_), pdb (`RCSB PDB REST API <https://data.rcsb.org/>`_), mmb (`MMB PDB mirror API <http://mmb.irbbarcelona.org/api/>`_).
32 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
33 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
34 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
36 Examples:
37 This is a use example of how to use the building block from Python::
39 from biobb_io.api.pdb import pdb
40 prop = {
41 'pdb_code': '2VGB',
42 'filter': ['ATOM', 'MODEL', 'ENDMDL'],
43 'api_id': 'pdbe'
44 }
45 pdb(output_pdb_path='/path/to/newStructure.pdb',
46 properties=prop)
48 Info:
49 * wrapped_software:
50 * name: Protein Data Bank
51 * license: Apache-2.0
52 * ontology:
53 * name: EDAM
54 * schema: http://edamontology.org/EDAM.owl
56 """
58 def __init__(self, output_pdb_path, properties=None, **kwargs) -> None:
59 properties = properties or {}
61 # Call parent class constructor
62 super().__init__(properties)
63 self.locals_var_dict = locals().copy()
65 # Input/Output files
66 self.io_dict = {"out": {"output_pdb_path": output_pdb_path}}
68 # Properties specific for BB
69 self.api_id = properties.get("api_id", "pdbe")
70 self.pdb_code = properties.get("pdb_code", None)
71 self.filter = properties.get("filter", ["ATOM", "MODEL", "ENDMDL"])
72 self.properties = properties
74 # Check the properties
75 self.check_properties(properties)
76 self.check_arguments()
78 def check_data_params(self, out_log, err_log):
79 """Checks all the input/output paths and parameters"""
80 self.output_pdb_path = check_output_path(
81 self.io_dict["out"]["output_pdb_path"],
82 "output_pdb_path",
83 False,
84 out_log,
85 self.__class__.__name__,
86 )
88 @launchlogger
89 def launch(self) -> int:
90 """Execute the :class:`Pdb <api.pdb.Pdb>` api.pdb.Pdb object."""
92 # check input/output paths and parameters
93 self.check_data_params(self.out_log, self.err_log)
95 # Setup Biobb
96 if self.check_restart():
97 return 0
99 check_mandatory_property(
100 self.pdb_code, "pdb_code", self.out_log, self.__class__.__name__
101 )
103 self.pdb_code = self.pdb_code.strip().lower()
105 # Downloading PDB file
106 pdb_string = download_pdb(
107 self.pdb_code, self.api_id, self.out_log, self.global_log
108 )
109 write_pdb(
110 pdb_string, self.output_pdb_path, self.filter, self.out_log, self.global_log
111 )
113 self.check_arguments(output_files_created=True, raise_exception=False)
115 return 0
118def pdb(output_pdb_path: str, properties: Optional[dict] = None, **kwargs) -> int:
119 """Execute the :class:`Pdb <api.pdb.Pdb>` class and
120 execute the :meth:`launch() <api.pdb.Pdb.launch>` method."""
122 return Pdb(
123 output_pdb_path=output_pdb_path, properties=properties, **kwargs
124 ).launch()
127def main():
128 """Command line execution of this building block. Please check the command line documentation."""
129 parser = argparse.ArgumentParser(
130 description="This class is a wrapper for downloading a PDB structure from the Protein Data Bank.",
131 formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999),
132 )
133 parser.add_argument(
134 "-c",
135 "--config",
136 required=False,
137 help="This file can be a YAML file, JSON file or JSON string",
138 )
140 # Specific args of each building block
141 required_args = parser.add_argument_group("required arguments")
142 required_args.add_argument(
143 "-o",
144 "--output_pdb_path",
145 required=True,
146 help="Path to the output PDB file. Accepted formats: pdb.",
147 )
149 args = parser.parse_args()
150 config = args.config if args.config else None
151 properties = settings.ConfReader(config=config).get_prop_dic()
153 # Specific call of each building block
154 pdb(output_pdb_path=args.output_pdb_path, properties=properties)
157if __name__ == "__main__":
158 main()