Clean HADDOCK3 runs

Clean the output of an HADDOCK3 run directory.

The clean process performs file archiving and file compressing operations.

All .inp and .out files are deleted except for the first one, which is compressed to .gz. On the other hand, all .seed and .con files are compressed and archived to .tgz files. Finally, .pdb and .psf files are compressed to .gz.

The <run_directory> can either be a whole HADDOCK3 run folder or a specific folder of the workflow step. <ncores> defines the number of threads to use; by default uses a single core.

Usage:

haddock3-clean -h
haddock3-clean <run_directory>
haddock3-clean run1
haddock3-clean run1/1_rigidbody
haddock3-clean run1 -n  # uses all cores
haddock3-clean run1 -n 2  # uses 2 cores

haddock.clis.cli_clean.cli(ap: ArgumentParser, main: Callable[[...], None]) → None[source]: Command-line interface entry point.

haddock.clis.cli_clean.load_args(ap: ArgumentParser) → Namespace[source]: Load argument parser args.

haddock.clis.cli_clean.main(run_dir: str | Path, ncores: int | None = 1) → None[source]

Clean a HADDOCK3 directory.

Usually, this concerns compressing and archiving files (see below).

Parameters:

run_dir (str or pathlib.Path.) – The path to the run directory or to a folder of a specific step of the workflow.
ncores (int, or None) – The number of cores to use. If None, use all possible threads. Defaults to 1.