prolint.contacts.base
=====================

.. py:module:: prolint.contacts.base

.. autoapi-nested-parse::

   Base contact storage module.

   This module provides the abstract base class for contact storage strategies.



Classes
-------

.. autoapisummary::

   prolint.contacts.base.BaseContactStore


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

.. py:class:: BaseContactStore(ts, contact_frames, norm_factor: float = 1.0)

   Abstract base class for contact storage strategies.

   Defines the interface for storing and computing metrics on contact data.
   Subclasses implement specific storage and aggregation strategies.

   :param ts: MDAnalysis Universe instance.
   :type ts: Universe
   :param contact_frames: Nested dict mapping residue_id -> database_id -> list of frame indices.
   :type contact_frames: dict
   :param norm_factor: Normalization factor for duration calculations.
   :type norm_factor: float, default=1.0

   .. seealso::

      :py:obj:`ExactContacts`
          Concrete implementation for exact contact aggregation


   .. py:attribute:: norm_factor


   .. py:attribute:: contact_frames


   .. py:method:: run(database_resnames: Union[str, List] = None)
      :abstractmethod:


      Process contact frames into aggregated contact data.

      :param database_resnames: Residue names to process. If None, processes all.
      :type database_resnames: str or list of str, optional

      :raises NotImplementedError: Subclasses must implement this method.



   .. py:method:: compute(metric: str, target_resname=None)

      Compute a standard metric on contacts.

      :param metric: Metric to compute.
      :type metric: {"max", "sum", "mean", "occupancy"}
      :param target_resname: Filter by residue name.
      :type target_resname: str, optional

      :returns: Computed metric values.
      :rtype: dict

      :raises ValueError: If metric is not recognized.



   .. py:method:: compute_metric(metric: str, target_resname=None)
      :abstractmethod:


      Compute a specific metric. Implemented by subclasses.

      :param metric: Metric to compute.
      :type metric: str
      :param target_resname: Filter by residue name.
      :type target_resname: str, optional

      :raises NotImplementedError: Subclasses must implement this method.



   .. py:method:: apply_function(func: Callable, target_resname=None)
      :abstractmethod:


      Apply a custom function to contact data.

      :param func: Function to apply to contact durations.
      :type func: callable
      :param target_resname: Filter by residue name.
      :type target_resname: str, optional

      :raises NotImplementedError: Subclasses must implement this method.



   .. py:property:: contacts

      Processed contact data.

      :returns: Contact data organized by residue and database molecule.
      :rtype: dict

      :raises ValueError: If run() has not been called yet.