#!/usr/bin/env python3
"""Module containing the CatPDB 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.file_utils import launchlogger
from biobb_structure_utils.utils.common import check_input_path, check_output_path
[docs]
class CatPDB(BiobbObject):
"""
| biobb_structure_utils CatPDB
| Class to concat two PDB structures in a single PDB file.
| Class to concat two PDB structures in a single PDB file.
Args:
input_structure1 (str): Input structure 1 file path. File type: input. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/data/utils/cat_protein.pdb>`_. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).
input_structure2 (str): Input structure 2 file path. File type: input. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/data/utils/cat_ligand.pdb>`_. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).
output_structure_path (str): Output protein file path. File type: output. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/reference/utils/ref_cat_pdb.pdb>`_. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).
properties (dic - Python dictionary object containing the tool parameters, not input/output files):
* **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.cat_pdb import cat_pdb
prop = { }
cat_pdb(input_structure1='/path/to/myInputStr1.pdb',
input_structure2='/path/to/myInputStr2.pdb',
output_structure_path='/path/to/newStructure.pdb',
properties=prop)
Info:
* wrapped_software:
* name: In house
* license: Apache-2.0
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(
self,
input_structure1,
input_structure2,
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_structure1": input_structure1,
"input_structure2": input_structure2,
},
"out": {"output_structure_path": output_structure_path},
}
# Properties specific for BB
self.properties = properties
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs]
@launchlogger
def launch(self) -> int:
"""Execute the :class:`CatPDB <utils.cat_pdb.CatPDB>` utils.cat_pdb.CatPDB object."""
self.io_dict["in"]["input_structure1"] = check_input_path(
self.io_dict["in"]["input_structure1"],
self.out_log,
self.__class__.__name__,
)
self.io_dict["in"]["input_structure2"] = check_input_path(
self.io_dict["in"]["input_structure2"],
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()
# Business code
filenames = [
self.io_dict["in"]["input_structure1"],
self.io_dict["in"]["input_structure2"],
]
# check if self.input_structure1 and self.input_structure2 end with newline
newline = [False, False]
for idx, fname in enumerate(filenames):
with open(fname, "rb") as fh:
fh.seek(-2, 2)
last = fh.readlines()[-1].decode()
newline[idx] = "\n" in last
# concat both input files and save them into output file
with open(self.io_dict["out"]["output_structure_path"], "w") as outfile:
for idx, fname in enumerate(filenames):
with open(fname) as infile:
for line in infile:
if not line.startswith("END"):
outfile.write(line)
# if not ends in newline, add it
if not newline[idx]:
outfile.write("\n")
self.return_code = 0
# 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 cat_pdb(
input_structure1: str,
input_structure2: str,
output_structure_path: str,
properties: Optional[dict] = None,
**kwargs,
) -> int:
"""Execute the :class:`CatPDB <utils.cat_pdb.CatPDB>` class and
execute the :meth:`launch() <utils.cat_pdb.CatPDB.launch>` method."""
return CatPDB(
input_structure1=input_structure1,
input_structure2=input_structure2,
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="Concat two PDB structures in a single PDB file.",
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(
"-i1",
"--input_structure1",
required=True,
help="Input structure 1 file path. Accepted formats: pdb.",
)
required_args.add_argument(
"-i2",
"--input_structure2",
required=True,
help="Input structure 2 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
cat_pdb(
input_structure1=args.input_structure1,
input_structure2=args.input_structure2,
output_structure_path=args.output_structure_path,
properties=properties,
)
if __name__ == "__main__":
main()