Source code for utils.extract_model_pdbqt
#!/usr/bin/env python3
"""Module containing the ExtractModelPDBQT class and the command line interface."""
import argparse
from pathlib import PurePath
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_vs.utils.common import check_input_path, check_output_path
from Bio import BiopythonDeprecationWarning
import warnings
with warnings.catch_warnings():
warnings.simplefilter("ignore", BiopythonDeprecationWarning)
import Bio.PDB
import Bio.pairwise2
# try:
# import Bio.SubsMat.MatrixInfo
# except ImportError:
import Bio.Align.substitution_matrices
[docs]class ExtractModelPDBQT(BiobbObject):
"""
| biobb_vs ExtractModelPDBQT
| Extracts a model from a PDBQT file with several models.
Args:
input_pdbqt_path (str): Input PDBQT file. File type: input. `Sample file <https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/utils/models.pdbqt>`_. Accepted formats: pdbqt (edam:format_1476).
output_pdbqt_path (str): Output PDBQT file. File type: output. `Sample file <https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/utils/ref_extract_model.pdbqt>`_. Accepted formats: pdbqt (edam:format_1476).
properties (dic - Python dictionary object containing the tool parameters, not input/output files):
* **model** (*int*) - (1) [0~1000|1] Model number to extract from input_pdbqt_path.
* **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_vs.utils.extract_model_pdbqt import extract_model_pdbqt
prop = {
'model': 1
}
extract_model_pdbqt(input_pdbqt_path='/path/to/myStructure.pdbqt',
output_pdbqt_path='/path/to/newStructure.pdbqt',
properties=prop)
Info:
* wrapped_software:
* name: In house using Biopython
* version: >=1.76
* license: Apache-2.0
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(self, input_pdbqt_path, output_pdbqt_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_pdbqt_path": input_pdbqt_path},
"out": {"output_pdbqt_path": output_pdbqt_path}
}
# Properties specific for BB
self.model = properties.get('model', 1)
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.io_dict["in"]["input_pdbqt_path"] = check_input_path(self.io_dict["in"]["input_pdbqt_path"], "input_pdbqt_path", out_log, self.__class__.__name__)
self.io_dict["out"]["output_pdbqt_path"] = check_output_path(self.io_dict["out"]["output_pdbqt_path"], "output_pdbqt_path", False, out_log, self.__class__.__name__)
[docs] @launchlogger
def launch(self) -> int:
"""Execute the :class:`ExtractModelPDBQT <utils.extract_model_pdbqt.ExtractModelPDBQT>` utils.extract_model_pdbqt.ExtractModelPDBQT 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
self.stage_files()
if self.restart:
output_file_list = [self.io_dict["out"]["output_pdbqt_path"]]
if fu.check_complete_files(output_file_list):
fu.log('Restart is enabled, this step: %s will the skipped' % self.step, self.out_log, self.global_log)
return 0
structure_name = PurePath(self.io_dict["in"]["input_pdbqt_path"]).name
parser = Bio.PDB.PDBParser(QUIET=True)
structPDB = parser.get_structure(structure_name, self.io_dict["in"]["input_pdbqt_path"])
models = []
for model in structPDB.get_models():
models.append(model.id + 1)
if self.model not in models:
fu.log(self.__class__.__name__ + ': Selected model %d not found in %s structure.' % (self.model, self.io_dict["in"]["input_pdbqt_path"]), self.out_log)
raise SystemExit(self.__class__.__name__ + ': Selected model %d not found in %s structure.' % (self.model, self.io_dict["in"]["input_pdbqt_path"]))
save = False
lines = 0
with open(self.io_dict["in"]["input_pdbqt_path"], "r") as input_pdb, open(self.io_dict["out"]["output_pdbqt_path"], "w") as output_pdb:
for line in input_pdb:
if line.startswith('MODEL') and line.split()[1] == str(self.model):
save = True
if line.startswith('ENDMDL'):
save = False
if save and not line.startswith('MODEL'):
lines = lines + 1
output_pdb.write(line)
fu.log('Saving model %d to %s' % (self.model, self.io_dict["out"]["output_pdbqt_path"]), self.out_log)
# Copy files to host
self.copy_to_host()
self.tmp_files.extend([
self.stage_io_dict.get("unique_dir")
])
self.remove_tmp_files()
self.check_arguments(output_files_created=True, raise_exception=False)
return 0
[docs]def extract_model_pdbqt(input_pdbqt_path: str, output_pdbqt_path: str, properties: dict = None, **kwargs) -> int:
"""Execute the :class:`ExtractModelPDBQT <utils.extract_model_pdbqt.ExtractModelPDBQT>` class and
execute the :meth:`launch() <utils.extract_model_pdbqt.ExtractModelPDBQT.launch>` method."""
return ExtractModelPDBQT(input_pdbqt_path=input_pdbqt_path,
output_pdbqt_path=output_pdbqt_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="Extracts a model from a PDBQT file with several models.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
parser.add_argument('--config', required=False, help='Configuration file')
# Specific args of each building block
required_args = parser.add_argument_group('required arguments')
required_args.add_argument('--input_pdbqt_path', required=True, help='Input PDBQT file. Accepted formats: pdbqt.')
required_args.add_argument('--output_pdbqt_path', required=True, help='Output PDBQT file. Accepted formats: pdbqt.')
args = parser.parse_args()
args.config = args.config or "{}"
properties = settings.ConfReader(config=args.config).get_prop_dic()
# Specific call of each building block
extract_model_pdbqt(input_pdbqt_path=args.input_pdbqt_path,
output_pdbqt_path=args.output_pdbqt_path,
properties=properties)
if __name__ == '__main__':
main()