Coverage for biobb_io/api/pdb.py: 77%
43 statements
« prev ^ index » next coverage.py v7.5.3, created at 2024-06-14 18:20 +0000
« prev ^ index » next coverage.py v7.5.3, created at 2024-06-14 18:20 +0000
1#!/usr/bin/env python
3"""Module containing the Pdb 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
8from biobb_io.api.common import check_mandatory_property, check_output_path, download_pdb, write_pdb
11class Pdb(BiobbObject):
12 """
13 | biobb_io Pdb
14 | This class is a wrapper for downloading a PDB structure from the Protein Data Bank.
15 | 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.
17 Args:
18 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).
19 properties (dic - Python dictionary object containing the tool parameters, not input/output files):
20 * **pdb_code** (*str*) - (None) RSCB PDB code.
21 * **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)>`_.
22 * **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/>`_).
23 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
24 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
25 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
27 Examples:
28 This is a use example of how to use the building block from Python::
30 from biobb_io.api.pdb import pdb
31 prop = {
32 'pdb_code': '2VGB',
33 'filter': ['ATOM', 'MODEL', 'ENDMDL'],
34 'api_id': 'pdbe'
35 }
36 pdb(output_pdb_path='/path/to/newStructure.pdb',
37 properties=prop)
39 Info:
40 * wrapped_software:
41 * name: Protein Data Bank
42 * license: Apache-2.0
43 * ontology:
44 * name: EDAM
45 * schema: http://edamontology.org/EDAM.owl
47 """
49 def __init__(self, output_pdb_path,
50 properties=None, **kwargs) -> None:
51 properties = properties or {}
53 # Call parent class constructor
54 super().__init__(properties)
55 self.locals_var_dict = locals().copy()
57 # Input/Output files
58 self.io_dict = {
59 "out": {"output_pdb_path": output_pdb_path}
60 }
62 # Properties specific for BB
63 self.api_id = properties.get('api_id', 'pdbe')
64 self.pdb_code = properties.get('pdb_code', None)
65 self.filter = properties.get('filter', ['ATOM', 'MODEL', 'ENDMDL'])
66 self.properties = properties
68 # Check the properties
69 self.check_properties(properties)
70 self.check_arguments()
72 def check_data_params(self, out_log, err_log):
73 """ Checks all the input/output paths and parameters """
74 self.output_pdb_path = check_output_path(self.io_dict["out"]["output_pdb_path"], "output_pdb_path", False, out_log, self.__class__.__name__)
76 @launchlogger
77 def launch(self) -> int:
78 """Execute the :class:`Pdb <api.pdb.Pdb>` api.pdb.Pdb object."""
80 # check input/output paths and parameters
81 self.check_data_params(self.out_log, self.err_log)
83 # Setup Biobb
84 if self.check_restart():
85 return 0
87 check_mandatory_property(self.pdb_code, 'pdb_code', self.out_log, self.__class__.__name__)
89 self.pdb_code = self.pdb_code.strip().lower()
91 # Downloading PDB file
92 pdb_string = download_pdb(self.pdb_code, self.api_id, self.out_log, self.global_log)
93 write_pdb(pdb_string, self.output_pdb_path, self.filter, self.out_log, self.global_log)
95 self.check_arguments(output_files_created=True, raise_exception=False)
97 return 0
100def pdb(output_pdb_path: str, properties: dict = None, **kwargs) -> int:
101 """Execute the :class:`Pdb <api.pdb.Pdb>` class and
102 execute the :meth:`launch() <api.pdb.Pdb.launch>` method."""
104 return Pdb(output_pdb_path=output_pdb_path,
105 properties=properties, **kwargs).launch()
108def main():
109 """Command line execution of this building block. Please check the command line documentation."""
110 parser = argparse.ArgumentParser(description="This class is a wrapper for downloading a PDB structure from the Protein Data Bank.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
111 parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string")
113 # Specific args of each building block
114 required_args = parser.add_argument_group('required arguments')
115 required_args.add_argument('-o', '--output_pdb_path', required=True, help="Path to the output PDB file. Accepted formats: pdb.")
117 args = parser.parse_args()
118 config = args.config if args.config else None
119 properties = settings.ConfReader(config=config).get_prop_dic()
121 # Specific call of each building block
122 pdb(output_pdb_path=args.output_pdb_path,
123 properties=properties)
126if __name__ == '__main__':
127 main()