#!/usr/bin/env python
"""PdbClusterZip Module"""
import os
import argparse
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.configuration import settings
from biobb_common.tools import file_utils as fu
from biobb_common.tools.file_utils import launchlogger
from biobb_io.api.common import check_mandatory_property, check_output_path, get_cluster_pdb_codes, download_pdb, write_pdb
[docs]class PdbClusterZip(BiobbObject):
"""
| biobb_io PdbClusterZip
| This class is a wrapper for downloading a PDB cluster from the Protein Data Bank.
| 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 PDB cluster.
Args:
output_pdb_zip_path (str): Path to the ZIP file containing the output PDB files. File type: output. `Sample file <https://github.com/bioexcel/biobb_io/raw/master/biobb_io/test/reference/api/output_pdb_cluster.zip>`_. Accepted formats: zip (edam:format_3987).
properties (dic - Python dictionary object containing the tool parameters, not input/output files):
* **pdb_code** (*str*) - (None) RSCB PDB code.
* **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)
* **cluster** (*int*) - (90) Sequence Similarity Cutoff. Values: 50 (structures having less than 50% sequence identity to each other), 70 (structures having less than 70% sequence identity to each other), 90 (structures having less than 90% sequence identity to each other), 95 (structures having less than 95% sequence identity to each other).
* **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/>`_).
* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
Examples:
This is a use example of how to use the building block from Python::
from biobb_io.api.pdb_cluster_zip import pdb_cluster_zip
prop = {
'pdb_code': '2VGB',
'filter': ['ATOM', 'MODEL', 'ENDMDL'],
'cluster': 90,
'api_id': 'pdbe'
}
pdb_cluster_zip(output_pdb_zip_path='/path/to/newStructures.zip',
properties=prop)
Info:
* wrapped_software:
* name: Protein Data Bank
* license: Apache-2.0
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(self, output_pdb_zip_path,
properties=None, **kwargs) -> None:
properties = properties or {}
# Call parent class constructor
super().__init__(properties)
self.locals_var_dict = locals().copy()
# Input/Output files
self.io_dict = {
"out": {"output_pdb_zip_path": output_pdb_zip_path}
}
# Properties specific for BB
self.api_id = properties.get('api_id', 'pdbe')
self.pdb_code = properties.get('pdb_code', None)
self.filter = properties.get('filter', ['ATOM', 'MODEL', 'ENDMDL'])
self.cluster = properties.get('cluster', 90)
self.properties = properties
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs] def check_data_params(self, out_log, err_log):
""" Checks all the input/output paths and parameters """
self.output_pdb_zip_path = check_output_path(self.io_dict["out"]["output_pdb_zip_path"], "output_pdb_zip_path", False, out_log, self.__class__.__name__)
[docs] @launchlogger
def launch(self) -> int:
"""Execute the :class:`PdbClusterZip <api.pdb_cluster_zip.PdbClusterZip>` api.pdb_cluster_zip.PdbClusterZip object."""
# check input/output paths and parameters
self.check_data_params(self.out_log, self.err_log)
# Setup Biobb
if self.check_restart():
return 0
check_mandatory_property(self.pdb_code, 'pdb_code', self.out_log, self.__class__.__name__)
self.pdb_code = self.pdb_code.strip().lower()
file_list = []
# Downloading PDB_files
pdb_code_list = get_cluster_pdb_codes(pdb_code=self.pdb_code, cluster=self.cluster, out_log=self.out_log, global_log=self.global_log)
unique_dir = fu.create_unique_dir()
for pdb_code in pdb_code_list:
pdb_file = os.path.join(unique_dir, pdb_code+".pdb")
pdb_string = download_pdb(pdb_code=pdb_code, api_id=self.api_id, out_log=self.out_log, global_log=self.global_log)
write_pdb(pdb_string, pdb_file, self.filter, self.out_log, self.global_log)
file_list.append(os.path.abspath(pdb_file))
# Zipping files
fu.log("Zipping the pdb files to: %s" % self.output_pdb_zip_path)
fu.zip_list(self.output_pdb_zip_path, file_list, out_log=self.out_log)
self.tmp_files.extend([
self.stage_io_dict.get("unique_dir"),
unique_dir
])
self.remove_tmp_files()
self.check_arguments(output_files_created=True, raise_exception=False)
return 0
[docs]def pdb_cluster_zip(output_pdb_zip_path: str, properties: dict = None, **kwargs) -> int:
"""Execute the :class:`PdbClusterZip <api.pdb_cluster_zip.PdbClusterZip>` class and
execute the :meth:`launch() <api.pdb_cluster_zip.PdbClusterZip.launch>` method."""
return PdbClusterZip(output_pdb_zip_path=output_pdb_zip_path,
properties=properties, **kwargs).launch()
[docs]def main():
"""Command line execution of this building block. Please check the command line documentation."""
parser = argparse.ArgumentParser(description="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 PDB cluster.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string")
# Specific args of each building block
required_args = parser.add_argument_group('required arguments')
required_args.add_argument('-o', '--output_pdb_zip_path', required=True, help="Path to the ZIP or PDB file containing the output PDB files. Accepted formats: pdb, zip.")
args = parser.parse_args()
config = args.config if args.config else None
properties = settings.ConfReader(config=config).get_prop_dic()
# Specific call of each building block
pdb_cluster_zip(output_pdb_zip_path=args.output_pdb_zip_path,
properties=properties)
if __name__ == '__main__':
main()