libprodigy: classes and functions related to the use of prodigy

Set of functionalities to run prodigy.

class haddock.libs.libprodigy.CheckInstall

Bases: object

Verify that installation of prodigy is ok.

static import_prodigy_libs() → None

Import prodigy prot and lig libraries.

class haddock.libs.libprodigy.ModelScore(model_index: int)

Bases: object

Simple class for holding score for a model.

class haddock.libs.libprodigy.ProdigyBaseJob(model: PDBFile, params: dict[str, Any], index: int = 1)

Bases: ABC

Managing the computation of prodigy scores within haddock3.

abstract static get_worker() → object

Return the appropriate worker.

run() → ModelScore

Execute the _run method.

class haddock.libs.libprodigy.ProdigyWorker(model: str | Path, params: dict[str, Any])

Bases: ABC

Prodigy Worker class.

static deltaG_to_pKd(deltaG: float, kelvins: float = 298.3) → float

Convert a deltaG (in Kcal/mol) to pKd.

Parameters:

• deltaG (float) – DeltaG value (in Kcal/mol)

• kelvins (float, optional) – Temperature at which to perform the conversion. By default 298.3 (25 degrees Celcius)

Returns:

pKd (float) – The corresponding pKd value at given temperature.

abstract evaluate_complex() → float

Logic to evaluate a complex using prodigy.

pkd_converter(deltaG: float) → float

Decide if deltaG must be converted to pKd.

Parameters:

deltaG (float) – Input DeltaG value

Returns:

score (float) – The converted DeltaG to pKd if self.topKd is true, else the input DeltaG.

run() → None

Execute the _run method.