Source code for utils.extract_model
#!/usr/bin/env python3
"""Module containing the ExtractModel class and the command line interface."""
import argparse
import shutil
from typing import Optional
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 ExtractModel(BiobbObject):
"""
| biobb_structure_utils ExtractModel
| This class is a wrapper of the Structure Checking tool to extract a model from a 3D structure.
| Wrapper for the `Structure Checking <https://github.com/bioexcel/biobb_structure_checking>`_ tool to extract a model 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_model.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_model.pdb>`_. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).
properties (dic - Python dictionary object containing the tool parameters, not input/output files):
* **models** (*list*) - (None) List of models to be extracted from the input_structure_path file. If empty, all the models of the structure will be returned.
* **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.
* **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
Examples:
This is a use example of how to use the building block from Python::
from biobb_structure_utils.utils.extract_model import extract_model
prop = {
'models': [ 1, 2, 3 ]
}
extract_model(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.models = properties.get("models", [])
self.properties = properties
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs]
@launchlogger
def launch(self) -> int:
"""Execute the :class:`ExtractModel <utils.extract_model.ExtractModel>` utils.extract_model.ExtractModel 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 models properly
models = check_format_models(self.models, self.out_log)
if models == "All":
shutil.copyfile(
self.io_dict["in"]["input_structure_path"],
self.io_dict["out"]["output_structure_path"],
)
return 0
else:
# create temporary folder
tmp_folder = fu.create_unique_dir()
fu.log("Creating %s temporary folder" % tmp_folder, self.out_log)
filenames = []
for model in models:
tmp_file = tmp_folder + "/model" + str(model) + ".pdb"
self.cmd = [
self.binary_path,
"-i",
self.stage_io_dict["in"]["input_structure_path"],
"-o",
tmp_file,
"--force_save",
"models",
"--select",
str(model),
]
# Run Biobb block
self.run_biobb()
filenames.append(tmp_file)
# concat tmp_file and save them into output file
with open(self.io_dict["out"]["output_structure_path"], "w") as outfile:
for i, fname in enumerate(filenames):
with open(fname) as infile:
outfile.write("MODEL " + "{:>4}".format(str(i + 1)) + "\n")
for line in infile:
if not line.startswith("END"):
outfile.write(line)
else:
outfile.write("ENDMDL\n")
# Copy files to host
self.copy_to_host()
# Remove temporal files
self.tmp_files.extend(
[self.stage_io_dict.get("unique_dir", ""), tmp_folder]
)
self.remove_tmp_files()
self.check_arguments(output_files_created=True, raise_exception=False)
return self.return_code
[docs]
def check_format_models(models, out_log):
"""Check format of models list"""
if not models:
fu.log("Empty models parameter, all models will be returned.", out_log)
return "All"
if not isinstance(models, list):
fu.log(
"Incorrect format of models parameter, all models will be returned.",
out_log,
)
return "All"
return models
[docs]
def extract_model(
input_structure_path: str,
output_structure_path: str,
properties: Optional[dict] = None,
**kwargs,
) -> int:
"""Execute the :class:`ExtractModel <utils.extract_model.ExtractModel>` class and
execute the :meth:`launch() <utils.extract_model.ExtractModel.launch>` method."""
return ExtractModel(
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 model 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_model(
input_structure_path=args.input_structure_path,
output_structure_path=args.output_structure_path,
properties=properties,
)
if __name__ == "__main__":
main()