| """ |
| 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) |
|
|
|
|
| |
| def _ap() -> ArgumentParser: |
| return ap |
|
|
|
|
| def load_args(ap: ArgumentParser) -> Namespace: |
| """Load argument parser args.""" |
| return ap.parse_args() |
|
|
|
|
| def cli(ap: ArgumentParser, main: Callable[..., None]) -> None: |
| """Command-line interface entry point.""" |
| cmd = vars(load_args(ap)) |
| |
| |
| |
| main(*cmd.pop("pdb_files"), **cmd) |
|
|
|
|
| def maincli() -> None: |
| """Execute main client.""" |
| cli(ap, main) |
|
|
|
|
| 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()) |
|
|
