prolint.analysis.timeseries

Time series analysis for contact dynamics over trajectory.

Attributes

logger

Classes

DatabaseContactsAnalysis

Compute per-database-molecule contact timeline for a query residue.

TimeSeriesAnalysis

Analyze contact dynamics over trajectory time.

Module Contents

prolint.analysis.timeseries.logger[source]
class prolint.analysis.timeseries.DatabaseContactsAnalysis(universe, contacts: prolint.core.contact_provider.ComputedContacts)[source]

Bases: prolint.analysis.base.BaseAnalysis

Compute per-database-molecule contact timeline for a query residue.

Creates a binary contact matrix showing which database molecules are in contact with a specific query residue at each frame.

See also

TimeSeriesAnalysis

Aggregated contact counts over time

name = 'database_contacts'[source]

Analysis name for registry.

description = 'Per-database-molecule contact timeline'[source]

Human-readable description.

run(query_residue: int, database_type: str | None = None, frame_start: int = 0, frame_end: int | None = None, frame_step: int = 1, top_n: int | None = None) → prolint.analysis.base.AnalysisResult[source]

Compute binary contact matrix for a query residue.

Parameters:

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

  • database_type (str, optional) – Filter by database residue name (e.g., “CHOL”).

  • frame_start (int, default=0) – First frame to process.

  • frame_end (int, optional) – Last frame (exclusive). Defaults to total frames.

  • frame_step (int, default=1) – Step between frames.

  • top_n (int, optional) – If specified, return only the top N database IDs with the most contacts. Useful for reducing response size when many database molecules have minimal contacts.

Returns:

Result with data containing:

  • database_ids : list of int sorted database molecule IDs

  • frames : list of int frame indices

  • contact_matrix : dict mapping database_id to list of int (0 or 1)

Return type:

AnalysisResult

class prolint.analysis.timeseries.TimeSeriesAnalysis(universe, contacts: prolint.core.contact_provider.ComputedContacts)[source]

Bases: prolint.analysis.base.BaseAnalysis

Analyze contact dynamics over trajectory time.

Computes per-frame contact counts for query residues, useful for understanding how contact behavior varies throughout the simulation.

See also

DatabaseContactsAnalysis

Per-molecule binary contact timeline

KineticsAnalysis

Binding kinetics and residence times

name = 'timeseries'[source]

Analysis name for registry.

description = 'Contact counts over trajectory time'[source]

Human-readable description.

run(database_type: str | None = None, query_residues: List[int] | None = None, frame_start: int = 0, frame_end: int | None = None, frame_step: int = 1) → prolint.analysis.base.AnalysisResult[source]

Compute contact count time series.

Parameters:

  • database_type (str, optional) – Filter by database residue name (e.g., “CHOL”).

  • query_residues (list of int, optional) – Specific query residues to include. If None, includes all residues with contacts.

  • frame_start (int, default=0) – First frame to process.

  • frame_end (int, optional) – Last frame (exclusive). Defaults to total frames.

  • frame_step (int, default=1) – Step between frames.

Returns:

Result with data containing:

  • query_residues : list of int query residue IDs

  • frames : list of int frame indices

  • contact_counts : dict mapping residue_id to list of counts

Return type:

AnalysisResult