prolint.computers.contacts

Serial contact computation module.

This module provides the SerialContacts class for efficient distance-based contact detection using grid search.

Attributes

logger

Classes

SerialContacts

Distance-based contact detection using MDAnalysis FastNS.

Module Contents

prolint.computers.contacts.logger

class prolint.computers.contacts.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