PDB Traceback client

Traces back PDB files from a HADDOCK run directory.

Given an input run directory, haddock3-traceback traces back each model to the initial input molecules used, providing the rank of each intermediate model.

USAGE:

haddock3-traceback -r <run_dir>
haddock.clis.cli_traceback.cli(ap, main)[source]

Command-line interface entry point.

haddock.clis.cli_traceback.get_ori_names(n: int, pdbfile: PDBFile, max_topo_len: int) → tuple[list, int][source]

Get the original name(s) of the PDB file.

Parameters:

  • n (int) – Step number.

  • pdbfile (PDBFile) – PDBFile object.

  • max_topo_len (int) – Maximum length of the topologies found so far.

Returns:

  • ori_names (list) – List of original names.

  • max_topo_len (int) – Maximum length of the topologies found so far.

haddock.clis.cli_traceback.get_steps_without_pdbs(run_dir, all_steps)[source]

Get the modules that do not produce PDB files.

Parameters:

  • run_dir (str or pathlib.Path) – Path to the run directory.

  • all_steps (list) – List of all the steps in the run directory.

Returns:

steps_without_pdbs (list) – List of steps that did not produce PDB files.

haddock.clis.cli_traceback.load_args(ap)[source]

Load argument parser args.

haddock.clis.cli_traceback.main(run_dir: str | Path, offline: bool = False) → None[source]

Traceback CLI.

Parameters:

run_dir (str or Path) – Path to the original run directory.

haddock.clis.cli_traceback.maincli()[source]

Execute main client.

haddock.clis.cli_traceback.order_traceback_df(df_output, sel_step)[source]

Order the traceback dataframe. Each step is ordered by rank.

Parameters:

  • df_output (pandas.DataFrame) – Dataframe containing the traceback data.

  • sel_step (list) – List of selected steps.

Returns:

df_output (pandas.DataFrame) – Dataframe containing the ordered traceback data.

haddock.clis.cli_traceback.subset_traceback(traceback_df: DataFrame, cons_filename: Path) → DataFrame[source]

Generate a subset the traceback dataframe with the top 40 models.

Parameters:

  • traceback_df (pandas.DataFrame) – Dataframe containing the traceback data.

  • cons_filename (pathlib.Path) – name of the consensus file.

Returns:

rank_data_subset (pandas.DataFrame) – Dataframe containing the subset of the traceback data.

haddock.clis.cli_traceback.traceback_dataframe(data_dict: dict, rank_dict: dict, sel_step: list, max_topo_len: int) → DataFrame[source]

Create traceback dataframe by combining together ranks and data.

Parameters:

  • data_dict (dict) – Dictionary containing the data to be traced back.

  • rank_dict (dict) – Dictionary containing the ranks of the data to be traced back.

  • sel_step (list) – List of selected steps.

  • max_topo_len (int) – Maximum length of the topologies.

Returns:

df_ord (pandas.DataFrame) – Dataframe containing the traceback data.