prolint.computers

Contact computation algorithms.

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

Submodules

• prolint.computers.base
• prolint.computers.contacts

Classes

SerialContacts	Distance-based contact detection using MDAnalysis FastNS.
ContactComputerBase	Abstract base class for contact computation algorithms.

Package Contents

class prolint.computers.SerialContacts(universe, query, database, cutoff, **kwargs)

Bases: 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.

Parameters:

• universe (Universe) – ProLint Universe instance.

• query (ExtendedAtomGroup) – Query atoms (e.g., protein).

• database (ExtendedAtomGroup) – Database atoms (e.g., lipids).

• cutoff (float) – Distance cutoff in Angstroms.

• **kwargs (dict) – Additional arguments passed to MDAnalysis AnalysisBase.

Examples

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

See also

ContactComputerBase

Abstract base class

ContactsProvider

Orchestrates contact computation

query

database

cutoff

contacts = None

contact_frames

class prolint.computers.ContactComputerBase(trajectory, verbose=False, **kwargs)

Bases: MDAnalysis.analysis.base.AnalysisBase, 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.

See also

SerialContacts

Concrete implementation using grid-based search

intersection(other)

Find contacts common to both computations.

union(other)

Combine all contacts from both computations.