autofragment.rules.biological

Biological fragmentation rules for proteins and nucleic acids.

This module provides rules specifically designed for protein and DNA/RNA systems, with configurable actions per user requirements.

Key design principle: Biological rules are CONFIGURABLE, not absolute, allowing users to choose appropriate fragmentation strategies for their specific use case (FMO, residue-based, domain-based, etc.).

Classes

AlphaBetaCarbonRule([rule_action, priority])	Mark alpha-beta carbon bonds as preferred break points.
DisulfideBondRule([rule_action, priority])	Configurable disulfide bridge handling.
HydrogenBondRule([rule_action, ...])	Configurable hydrogen bond handling.
PeptideBondRule([rule_action, priority])	Configurable peptide bond handling.
ProlineRingRule([priority])	Never break bonds within proline's pyrrolidine ring.