haddock.modules.analysis.caprieval.capri module

CAPRI module.

class haddock.modules.analysis.caprieval.capri.CAPRI(identificator: str, model: PDBFile | Path, path: Path, reference: PDBFile | Path, params: MutableMapping[str, Any])

Bases: object

CAPRI class.

static add_chain_from_segid(pdb_path: PDBFile | Path) → Path

Replace the chainID with the segID.

Parameters:

pdb_path (PosixPath or haddock.libs.libontology.PDBFile) – PDB file to be replaced

calc_dockq() → None

Calculate the DockQ metric.

calc_fnat(cutoff: float = 5.0) → None

Calculate the frequency of native contacts.

Parameters:

cutoff (float) – The cutoff distance for the intermolecular contacts.

calc_ilrmsd(cutoff: float = 10.0) → None

Calculate the Interface Ligand RMSD.

Parameters:

cutoff (float) – The cutoff distance for the intermolecular contacts.

calc_irmsd(cutoff: float = 5.0) → None

Calculate the I-RMSD.

Parameters:

cutoff (float) – The cutoff distance for the intermolecular contacts.

calc_lrmsd() → None

Calculate the L-RMSD.

check_chains(obs_chains)

Check observed chains against the expected ones.

Logic: if chain B is among the observed chains and is not selected as

the receptor chain, then ligand_chains = [“B”] (default behaviour).

Otherwise, ligand_chains becomes equal to all the other chains (once

receptor chain is removed).

Parameters:

obs_chains (list) – List of observed chains.

has_cluster_info() → bool

Check wether this object contains cluster information.

Returns:

bool – True if this object contains cluster information.

static identify_interface(pdb_f: PDBFile | Path, cutoff: float = 5.0) → dict[str, list[int]]

Identify the interface.

Parameters:

• pdb_f (PosixPath or haddock.libs.libontology.PDBFile) – PDB file of the model to have its atoms identified

• cutoff (float, optional) – Cutoff distance for the interface identification.

Returns:

interface_resdic (dict[str, list[int]]) – Dictionary holding list of interface residues ids for each chains.

make_output() → None

Output the CAPRI results to a .tsv file.

run() → None

Get the CAPRI metrics.

exception haddock.modules.analysis.caprieval.capri.CAPRIError(msg: str = '')

Bases: Exception

Raised when something goes wrong with the CAPRI class.

haddock.modules.analysis.caprieval.capri.calc_stats(data: list) → tuple[float, float]

Calculate the mean and stdev.

Parameters:

data (list) – List of values.

Returns:

• mean (float) – Mean of the values.

• stdev (float) – Standard deviation of the values.

haddock.modules.analysis.caprieval.capri.capri_cluster_analysis(capri_list: Iterable[CAPRI], model_list: Iterable[PDBFile], output_fname: str | Path, clt_threshold: int, sort_key: str, sort_ascending: bool, path: str | Path) → None

Consider the cluster results for the CAPRI evaluation.

haddock.modules.analysis.caprieval.capri.get_previous_cns_step(sel_steps: list) → str | None

Get the previous CNS step.

Parameters:

run_path (Path) – Path to the run folder.

Returns:

cns_step (str) – Name of the CNS step.

haddock.modules.analysis.caprieval.capri.load_contacts(pdb_f: Path | PDBFile, cutoff: float = 5.0, numbering_dic: dict[str, dict[int, int]] | None = None, model2ref_chain_dict: dict[str, str] | None = None) → set[tuple]

Load residue-based contacts.

Parameters:

• pdb_f (PosixPath or haddock.libs.libontology.PDBFile) – PDB file of the model to have its atoms identified

• cutoff (float, optional) – Cutoff distance for the interface identification.

Returns:

set(con_list) (set) – set of unique contacts

haddock.modules.analysis.caprieval.capri.merge_data(capri_jobs: list[haddock.modules.analysis.caprieval.capri.CAPRI]) → list[haddock.modules.analysis.caprieval.capri.CAPRI]

Merge CAPRI data.

haddock.modules.analysis.caprieval.capri.rearrange_ss_capri_output(output_name: str, output_count: int, sort_key: str, sort_ascending: bool, path: str | Path) → None

Combine different capri outputs in a single file.

Parameters:

• output_name (str) – Name of the output file.

• output_count (int) – Number of output files to combine.

• sort_key (str) – Key to sort the output files.

• path (Path) – Path to the output directory.

haddock.modules.analysis.caprieval.capri.save_scoring_weights(cns_step: str) → Path

Save the scoring weights in a json file.

Parameters:

cns_step (str) – Name of the CNS step.

Returns:

scoring_params_fname (Path) – Path to the json file.