Source code for utils.extract_molecule
#!/usr/bin/env python3
"""Module containing the ExtractMolecule class and the command line interface."""
import argparse
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 (
_from_string_to_list,
check_input_path,
check_output_path,
)
[docs]
class ExtractMolecule(BiobbObject):
"""
| biobb_structure_utils ExtractMolecule
| This class is a wrapper of the Structure Checking tool to extract a molecule from a 3D structure.
| Wrapper for the `Structure Checking <https://github.com/bioexcel/biobb_structure_checking>`_ tool to extract a molecule 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_molecule.pdb>`_. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).
output_molecule_path (str): Output molecule file path. File type: output. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/reference/utils/ref_extract_molecule.pdb>`_. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).
properties (dic - Python dictionary object containing the tool parameters, not input/output files):
* **molecule_type** (*string*) - ("all") type of molecule to be extracted. If all, only waters and ligands will be removed from the original structure. Values: all, protein, na, dna, rna, chains.
* **chains** (*list*) - (None) if chains selected in **molecule_type**, specify them here, e.g: ["A", "C", "N"].
* **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_molecule import extract_molecule
prop = {
'molecule_type': 'chains',
'chains': ['A', 'N', 'F']
}
extract_molecule(input_structure_path='/path/to/myStructure.pdb',
output_molecule_path='/path/to/newMolecule.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_molecule_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_molecule_path": output_molecule_path},
}
# Properties specific for BB
self.molecule_type = properties.get("molecule_type", "all")
self.chains = _from_string_to_list(properties.get("chains", []))
self.binary_path = properties.get("binary_path", "check_structure")
self.properties = properties
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs]
def create_command_list(self, command_list_path):
"""Creates a command list file as a input for structure checking"""
instructions_list = ["ligands --remove All", "water --remove Yes"]
if self.molecule_type != "all":
if self.molecule_type == "chains":
instructions_list.append("chains --select " + ",".join(self.chains))
else:
instructions_list.append("chains --select " + self.molecule_type)
with open(command_list_path, "w") as clp:
for line in instructions_list:
clp.write(line.strip() + "\n")
return command_list_path
[docs]
@launchlogger
def launch(self) -> int:
"""Execute the :class:`ExtractMolecule <utils.extract_molecule.ExtractMolecule>` utils.extract_molecule.ExtractMolecule 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_molecule_path"] = check_output_path(
self.io_dict["out"]["output_molecule_path"],
self.out_log,
self.__class__.__name__,
)
# Setup Biobb
if self.check_restart():
return 0
self.stage_files()
# create temporary folder
tmp_folder = fu.create_unique_dir()
fu.log("Creating %s temporary folder" % tmp_folder, self.out_log)
# create command list file
command_list_file = self.create_command_list(tmp_folder + "/extract_prot.lst")
# run command line
self.cmd = [
self.binary_path,
"-i",
self.io_dict["in"]["input_structure_path"],
"-o",
self.io_dict["out"]["output_molecule_path"],
"--force_save",
"--non_interactive",
"command_list",
"--list",
command_list_file,
]
# Run Biobb block
self.run_biobb()
# 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 extract_molecule(
input_structure_path: str,
output_molecule_path: str,
properties: Optional[dict] = None,
**kwargs,
) -> int:
"""Execute the :class:`ExtractMolecule <utils.extract_molecule.ExtractMolecule>` class and
execute the :meth:`launch() <utils.extract_molecule.ExtractMolecule.launch>` method."""
return ExtractMolecule(
input_structure_path=input_structure_path,
output_molecule_path=output_molecule_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 molecule 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_molecule_path",
required=True,
help="Output heteroatom 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_molecule(
input_structure_path=args.input_structure_path,
output_molecule_path=args.output_molecule_path,
properties=properties,
)
if __name__ == "__main__":
main()