Coverage for biobb_io/api/mmcif.py: 76%
42 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 Mmcif 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_output_path, check_mandatory_property, download_mmcif, write_mmcif
11class Mmcif(BiobbObject):
12 """
13 | biobb_io Mmcif
14 | This class is a wrapper for downloading a MMCIF 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 MMCIF structure.
17 Args:
18 output_mmcif_path (str): Path to the output MMCIF file. File type: output. `Sample file <https://github.com/bioexcel/biobb_io/raw/master/biobb_io/test/reference/api/ref_output.mmcif>`_. Accepted formats: cif (edam:format_1477), mmcif (edam:format_1477).
19 properties (dic - Python dictionary object containing the tool parameters, not input/output files):
20 * **pdb_code** (*str*) - (None) RSCB PDB code.
21 * **api_id** (*str*) - ("pdbe") Identifier of the PDB REST API from which the MMCIF 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/>`_).
22 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
23 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
24 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
26 Examples:
27 This is a use example of how to use the building block from Python::
29 from biobb_io.api.mmcif import mmcif
30 prop = {
31 'pdb_code': '2VGB',
32 'api_id': 'pdbe'
33 }
34 mmcif(output_mmcif_path='/path/to/newStructure.mmcif',
35 properties=prop)
37 Info:
38 * wrapped_software:
39 * name: Protein Data Bank
40 * license: Apache-2.0
41 * ontology:
42 * name: EDAM
43 * schema: http://edamontology.org/EDAM.owl
45 """
47 def __init__(self, output_mmcif_path,
48 properties=None, **kwargs) -> None:
49 properties = properties or {}
51 # Call parent class constructor
52 super().__init__(properties)
53 self.locals_var_dict = locals().copy()
55 # Input/Output files
56 self.io_dict = {
57 "out": {"output_mmcif_path": output_mmcif_path}
58 }
60 # Properties specific for BB
61 self.api_id = properties.get('api_id', 'pdbe')
62 self.pdb_code = properties.get('pdb_code', None)
63 self.properties = properties
65 # Check the properties
66 self.check_properties(properties)
67 self.check_arguments()
69 def check_data_params(self, out_log, err_log):
70 """ Checks all the input/output paths and parameters """
71 self.output_mmcif_path = check_output_path(self.io_dict["out"]["output_mmcif_path"], "output_mmcif_path", False, out_log, self.__class__.__name__)
73 @launchlogger
74 def launch(self) -> int:
75 """Execute the :class:`Mmcif <api.mmcif.Mmcif>` api.mmcif.Mmcif object."""
77 # check input/output paths and parameters
78 self.check_data_params(self.out_log, self.err_log)
80 # Setup Biobb
81 if self.check_restart():
82 return 0
84 check_mandatory_property(self.pdb_code, 'pdb_code', self.out_log, self.__class__.__name__)
86 self.pdb_code = self.pdb_code.strip().lower()
88 # Downloading PDB file
89 mmcif_string = download_mmcif(self.pdb_code, self.api_id, self.out_log, self.global_log)
90 write_mmcif(mmcif_string, self.output_mmcif_path, self.out_log, self.global_log)
92 self.check_arguments(output_files_created=True, raise_exception=False)
94 return 0
97def mmcif(output_mmcif_path: str, properties: dict = None, **kwargs) -> int:
98 """Execute the :class:`Mmcif <api.mmcif.Mmcif>` class and
99 execute the :meth:`launch() <api.mmcif.Mmcif.launch>` method."""
101 return Mmcif(output_mmcif_path=output_mmcif_path,
102 properties=properties, **kwargs).launch()
105def main():
106 """Command line execution of this building block. Please check the command line documentation."""
107 parser = argparse.ArgumentParser(description="This class is a wrapper for downloading a MMCIF structure from the Protein Data Bank.", 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('-o', '--output_mmcif_path', required=True, help="Path to the output MMCIF file. Accepted formats: cif, mmcif.")
114 args = parser.parse_args()
115 config = args.config if args.config else None
116 properties = settings.ConfReader(config=config).get_prop_dic()
118 # Specific call of each building block
119 mmcif(output_mmcif_path=args.output_mmcif_path,
120 properties=properties)
123if __name__ == '__main__':
124 main()