prolint.computers
=================

.. py:module:: prolint.computers

.. autoapi-nested-parse::

   Contact computation algorithms.

   This module provides classes for computing distance-based contacts
   between atom groups in molecular dynamics trajectories.



Submodules
----------

.. toctree::
   :maxdepth: 1

   /autoapi/prolint/computers/base/index
   /autoapi/prolint/computers/contacts/index


Classes
-------

.. autoapisummary::

   prolint.computers.SerialContacts
   prolint.computers.ContactComputerBase


Package Contents
----------------

.. py:class:: SerialContacts(universe, query, database, cutoff, **kwargs)

   Bases: :py:obj:`prolint.computers.base.ContactComputerBase`


   Distance-based contact detection using MDAnalysis FastNS.

   Computes contacts between query and database atom groups using
   a grid-based neighbor search algorithm for efficiency.

   :param universe: ProLint Universe instance.
   :type universe: Universe
   :param query: Query atoms (e.g., protein).
   :type query: ExtendedAtomGroup
   :param database: Database atoms (e.g., lipids).
   :type database: ExtendedAtomGroup
   :param cutoff: Distance cutoff in Angstroms.
   :type cutoff: float
   :param \*\*kwargs: Additional arguments passed to MDAnalysis AnalysisBase.
   :type \*\*kwargs: dict

   .. rubric:: Examples

   >>> from prolint import Universe
   >>> u = Universe("topology.gro", "trajectory.xtc")
   >>> contacts = u.compute_contacts(cutoff=7.0)

   .. seealso::

      :py:obj:`ContactComputerBase`
          Abstract base class
      
      :py:obj:`ContactsProvider`
          Orchestrates contact computation


   .. py:attribute:: query


   .. py:attribute:: database


   .. py:attribute:: cutoff


   .. py:attribute:: contacts
      :value: None



   .. py:attribute:: contact_frames


.. py:class:: ContactComputerBase(trajectory, verbose=False, **kwargs)

   Bases: :py:obj:`MDAnalysis.analysis.base.AnalysisBase`, :py:obj:`abc.ABC`


   Abstract base class for contact computation algorithms.

   Extends MDAnalysis AnalysisBase with contact-specific operations.
   Subclasses implement specific algorithms for detecting contacts
   between atom groups.

   .. seealso::

      :py:obj:`SerialContacts`
          Concrete implementation using grid-based search


   .. py:method:: intersection(other)

      Find contacts common to both computations.



   .. py:method:: union(other)

      Combine all contacts from both computations.