prolint.analysis.shared_contacts

Shared contacts analysis for pairwise residue correlations.

Classes

SharedContactsAnalysis

Analyze pairwise correlations between query residues.

Module Contents

class prolint.analysis.shared_contacts.SharedContactsAnalysis(universe, contacts: prolint.core.contact_provider.ComputedContacts)

Bases: prolint.analysis.base.BaseAnalysis

Analyze pairwise correlations between query residues.

Identifies query residue pairs that interact with the same database molecule simultaneously, revealing potential cooperative binding sites.

See also

TimeSeriesAnalysis

Contact dynamics over time

name = 'shared_contacts'

Analysis name for registry.

description = 'Pairwise correlations between query residues via shared database contacts'

Human-readable description.

run(database_type: str | None = None, normalize: bool = False) → prolint.analysis.base.AnalysisResult

Compute shared contacts correlation matrix.

Parameters:

• database_type (str, optional) – Filter by database residue name (e.g., “CHOL”). If None, includes all database molecules.

• normalize (bool, default=False) – Whether to normalize the matrix to 0-1 range.

Returns:

Result with data containing:

• labels : list of int query residue IDs

• matrix : 2D list of int/float shared contact counts

• residue_to_index : dict mapping residue ID to matrix index

Return type:

AnalysisResult