PDB preprocessing client

HADDOCK3 PDB preprocessing client.

Process PDB files for agreement with HADDOCK3 requirements. Follows the logic implemented in the 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

haddock.clis.cli_pp.cli(ap: ArgumentParser, main: Callable[[...], None]) → None

Command-line interface entry point.

haddock.clis.cli_pp.load_args(ap: ArgumentParser) → Namespace

Load argument parser args.

haddock.clis.cli_pp.main(*pdb_files: str | Path, dry: bool = False, output_directory: str | Path | None = None, suffix: str = '_processed', topfile: str | Path | None = 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.

haddock.clis.cli_pp.maincli() → None

Execute main client.