prolint.analysis.shared_contacts
================================

.. py:module:: prolint.analysis.shared_contacts

.. autoapi-nested-parse::

   Shared contacts analysis for pairwise residue correlations.



Classes
-------

.. autoapisummary::

   prolint.analysis.shared_contacts.SharedContactsAnalysis


Module Contents
---------------

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

   Bases: :py:obj:`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.

   .. seealso::

      :py:obj:`TimeSeriesAnalysis`
          Contact dynamics over time


   .. py:attribute:: name
      :value: 'shared_contacts'


      Analysis name for registry.


   .. py:attribute:: description
      :value: 'Pairwise correlations between query residues via shared database contacts'


      Human-readable description.


   .. py:method:: run(database_type: Optional[str] = None, normalize: bool = False) -> prolint.analysis.base.AnalysisResult

      Compute shared contacts correlation matrix.

      :param database_type: Filter by database residue name (e.g., "CHOL").
                            If None, includes all database molecules.
      :type database_type: str, optional
      :param normalize: Whether to normalize the matrix to 0-1 range.
      :type normalize: bool, default=False

      :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
      :rtype: AnalysisResult