prolint.analysis.kinetics

Kinetics analysis for binding/unbinding dynamics.

Attributes

logger

Classes

KineticsAnalysis

Kinetics analysis for binding/unbinding dynamics.

Module Contents

prolint.analysis.kinetics.logger

class prolint.analysis.kinetics.KineticsAnalysis(universe, contacts: prolint.core.contact_provider.ComputedContacts)

Bases: prolint.analysis.base.BaseAnalysis

Kinetics analysis for binding/unbinding dynamics.

Computes binding kinetics metrics including on/off rates, residence times, and survival curves with optional exponential fits.

MIN_EVENTS_MONO

Minimum events required for monoexponential fit (default: 5).

Type:

int

MIN_EVENTS_BI

Minimum events required for biexponential fit (default: 25).

Type:

int

See also

TimeSeriesAnalysis

Contact counts over time

name = 'kinetics'

Analysis name for registry.

description = 'Binding kinetics, residence times, and survival curves'

Human-readable description.

MIN_EVENTS_MONO = 5

MIN_EVENTS_BI = 25

run(query_residue: int, database_residue: int | None = None, database_type: str | None = None, mode: Literal['individual', 'accumulated'] = 'individual', fit_survival: bool = True, max_lag: int = 100) → prolint.analysis.base.AnalysisResult

Compute kinetics analysis for a query residue.

Parameters:

• query_residue (int) – Query residue ID to analyze.

• database_residue (int, optional) – Specific database residue ID. Required for “individual” mode.

• database_type (str, optional) – Database residue name (e.g., “CHOL”). Required for “accumulated” mode.

• mode ({"individual", "accumulated"}, default="individual") –

  Analysis mode:

  • ”individual”: Single residue-residue pair kinetics

  • ”accumulated”: Aggregated kinetics across all molecules of a type

• fit_survival (bool, default=True) – Whether to fit exponential models to survival curves.

• max_lag (int, default=100) – Maximum lag time for survival curve computation.

Returns:

Result with data containing:

• mode : str analysis mode

• kinetics : dict with koff, kon, kd, residence_times, occupancy, n_events, n_frames

• survival_curve : dict with lag_times, survival_probability, mono_fit, bi_fit, selected_model

• residence_distribution : dict with bins and counts

• contact_frames : list of frame indices with contacts

Return type:

AnalysisResult

Raises:

ValueError – If database_residue not provided for “individual” mode, or database_type not provided for “accumulated” mode.