"""
HADDOCK3 PDB preprocessing client.
Process PDB files for agreement with HADDOCK3 requirements. Follows the
logic implemented in the :py:mod:`haddock.gear.preprocessing`. See
documentation pages for more details.
You can use the `--dry` option to report on the performed changes
without actually performing the changes.
Corrected PDBs are saved to new files named after the `--suffix` option.
Original PDBs are never overwritten, unless `--suffix` is given an empty
string.
You can pass multiple PDB files to the command-line.
Usage::
haddock-pp file1.pdb file2.pdb
haddock-pp file1.pdb file2.pdb --suffix _new
haddock-pp file1.pdb file2.pdb --dry
"""
import argparse
import sys
from pathlib import Path
from haddock import log
from haddock.core.typing import (
ArgumentParser,
Callable,
FilePath,
Namespace,
Optional,
)
from haddock.gear.preprocessing import process_pdbs, read_additional_residues
from haddock.libs.libcli import add_output_dir_arg
from haddock.libs.libio import add_suffix_to_files, save_lines_to_files
SUFFIX_DEFAULT = "_processed"
ap = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.RawDescriptionHelpFormatter,
)
ap.add_argument(
"pdb_files",
help="Input PDB files.",
nargs="+",
)
ap.add_argument(
"-d",
"--dry",
help="Perform a dry run. Informs changes without modifying files.",
action="store_true",
)
ap.add_argument(
"-t",
"--topfile",
help="Additional .top files.",
nargs="*",
)
ap.add_argument(
"-s",
"--suffix",
help=f"Suffix to output files. Defaults to {SUFFIX_DEFAULT!r}",
default=SUFFIX_DEFAULT,
)
add_output_dir_arg(ap)
# client helper functions
def _ap() -> ArgumentParser:
return ap
[docs]def load_args(ap: ArgumentParser) -> Namespace:
"""Load argument parser args."""
return ap.parse_args()
[docs]def cli(ap: ArgumentParser, main: Callable[..., None]) -> None:
"""Command-line interface entry point."""
cmd = vars(load_args(ap))
# I use this `pop` structure to maintain the unpacking argument in
# the `main` function because I foresee the `main` to be used from
# other parts of the software(s)
main(*cmd.pop("pdb_files"), **cmd)
[docs]def maincli() -> None:
"""Execute main client."""
cli(ap, main)
[docs]def main(
*pdb_files: FilePath,
dry: bool = False,
output_directory: Optional[FilePath] = None,
suffix: str = SUFFIX_DEFAULT,
topfile: Optional[FilePath] = None,
) -> None:
"""
Process PDB files.
Parameters
----------
dry : bool
Whether to perform a dry test only.
output_directory : str or ``pathlib.Path``
The directory where to save the output. Defaults to the current
working directory.
suffix : str
The suffix to append to the new files. Will be added before the
file extension. Original extension will be kept.
topfile : str or ``pathlib.Path``
The path to an additional HADDOCK3 topology file.
"""
log.info("Starting processing PDB files.")
log.info(f"Total number of PDB files: {len(pdb_files)}")
if dry:
log.info(
"You selected the `--dry` option. No new files will be created. "
"A report of the changes that would be performed in the PDB files "
"will be printed."
)
new_residues = read_additional_residues(topfile) if topfile else None
log.info("Processing the PDB files... " "This may take a bit if there are many.")
processed_pdbs = process_pdbs(
*pdb_files,
dry=dry,
user_supported_residues=new_residues,
)
if dry:
log.info("Everything done. Exiting...")
sys.exit(0)
log.info("Finished processing PDBs. Saving to disk...")
if output_directory is None:
output_directory = Path.cwd()
else:
output_directory = Path(output_directory)
log.info("Output dir: {!r}".format(str(output_directory)))
output_directory.mkdir(parents=True, exist_ok=True)
pdb_names = (Path(output_directory, Path(pdb).name) for pdb in pdb_files)
out_files = add_suffix_to_files(pdb_names, suffix)
save_lines_to_files(out_files, processed_pdbs)
log.info("Everything done. Exiting...")
return
if __name__ == "__main__":
sys.exit(maincli()) # type: ignore