Source code for utils.extract_chain
#!/usr/bin/env python3
"""Module containing the ExtractChain class and the command line interface."""
import argparse
import shutil
from biobb_common.configuration import settings
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.tools import file_utils as fu
from biobb_common.tools.file_utils import launchlogger
from biobb_structure_utils.utils.common import check_input_path, check_output_path
[docs]class ExtractChain(BiobbObject):
"""
| biobb_structure_utils ExtractAtoms
| This class is a wrapper of the Structure Checking tool to extract a chain from a 3D structure.
| Wrapper for the `Structure Checking <https://github.com/bioexcel/biobb_structure_checking>`_ tool to extract a chain from a 3D structure.
Args:
input_structure_path (str): Input structure file path. File type: input. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/data/utils/extract_chain.pdb>`_. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).
output_structure_path (str): Output structure file path. File type: output. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/reference/utils/ref_extract_chain.pdb>`_. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).
properties (dic - Python dictionary object containing the tool parameters, not input/output files):
* **chains** (*list*) - (None) List of chains to be extracted from the input_structure_path file. If empty, all the chains of the structure will be returned.
* **permissive** (*bool*) - (False) Use non standard PDB files.
* **binary_path** (*string*) - ("check_structure") path to the check_structure application
* **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_structure_utils.utils.extract_chain import extract_chain
prop = {
'chains': [ 'A', 'B' ]
}
extract_chain(input_structure_path='/path/to/myStructure.pdb',
output_structure_path='/path/to/newStructure.pdb',
properties=prop)
Info:
* wrapped_software:
* name: Structure Checking from MDWeb
* version: >=3.0.3
* license: Apache-2.0
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(self, input_structure_path, output_structure_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 = {
"in": {"input_structure_path": input_structure_path},
"out": {"output_structure_path": output_structure_path}
}
# Properties specific for BB
self.binary_path = properties.get('binary_path', 'check_structure')
self.chains = properties.get('chains', [])
self.permissive = properties.get('permissive', False)
self.properties = properties
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs] @launchlogger
def launch(self) -> int:
"""Execute the :class:`ExtractChain <utils.extract_chain.ExtractChain>` utils.extract_chain.ExtractChain object."""
self.io_dict['in']['input_structure_path'] = check_input_path(self.io_dict['in']['input_structure_path'],
self.out_log, self.__class__.__name__)
self.io_dict['out']['output_structure_path'] = check_output_path(self.io_dict['out']['output_structure_path'],
self.out_log, self.__class__.__name__)
# Setup Biobb
if self.check_restart():
return 0
self.stage_files()
# check if user has passed chains properly
chains = check_format_chains(self.chains, self.out_log)
fu.log(f"Selected Chains: {chains}", self.out_log, self.global_log)
if self.permissive:
fu.log('Warning: Use permissive=True is a risky option use it under your own responsability', self.out_log, self.global_log)
if chains.upper() == 'ALL':
shutil.copyfile(self.io_dict['in']['input_structure_path'], self.io_dict['out']['output_structure_path'])
else:
chain_list = chains.upper().replace(" ", "").split(",")
with open(self.io_dict['in']['input_structure_path']) as structure_in, open(self.io_dict['out']['output_structure_path'], 'w') as structure_out:
for line in structure_in:
if line.strip().upper().startswith(('ATOM', 'HETATM')) and line.strip().upper()[21] in chain_list:
structure_out.write(line)
else:
# run command line
self.cmd = [self.binary_path,
'-i', self.io_dict['in']['input_structure_path'],
'-o', self.io_dict['out']['output_structure_path'],
'--force_save',
'chains', '--select', chains]
# Run Biobb block
self.run_biobb()
# Copy files to host
self.copy_to_host()
# Remove temporal files
self.tmp_files.append(self.stage_io_dict.get("unique_dir"))
self.remove_tmp_files()
self.check_arguments(output_files_created=True, raise_exception=False)
return self.return_code
[docs]def check_format_chains(chains, out_log):
""" Check format of chains list """
if not chains:
fu.log('Empty chains parameter, all chains will be returned.', out_log)
return 'All'
if not isinstance(chains, list):
fu.log('Incorrect format of chains parameter, all chains will be returned.', out_log)
return 'All'
return ','.join(chains)
[docs]def extract_chain(input_structure_path: str, output_structure_path: str, properties: dict = None, **kwargs) -> int:
"""Execute the :class:`ExtractChain <utils.extract_chain.ExtractChain>` class and
execute the :meth:`launch() <utils.extract_chain.ExtractChain.launch>` method."""
return ExtractChain(input_structure_path=input_structure_path,
output_structure_path=output_structure_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="Extract a chain from a 3D structure.", 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('-i', '--input_structure_path', required=True, help="Input structure file path. Accepted formats: pdb.")
required_args.add_argument('-o', '--output_structure_path', required=True, help="Output structure file path. Accepted formats: pdb.")
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
extract_chain(input_structure_path=args.input_structure_path,
output_structure_path=args.output_structure_path,
properties=properties)
if __name__ == '__main__':
main()