autofragment.rules

Fragmentation rules engine.

This module provides a flexible, extensible system for controlling which bonds can be broken during molecular fragmentation.

Core Classes:

RuleAction: Enum defining possible actions (MUST_NOT_BREAK, etc.) FragmentationRule: Abstract base class for all rules RuleEngine: Central engine for applying rules

Pre-defined Rules:

Common: AromaticRingRule, DoubleBondRule, MetalCoordinationRule Biological: PeptideBondRule, DisulfideBondRule, ProlineRingRule Materials: SiloxaneBridgeRule, MOFLinkerRule, MetalNodeRule

Modules

base	Base classes for fragmentation rules.
biological	Biological fragmentation rules for proteins and nucleic acids.
common	Common chemical fragmentation rules.
matsci	Materials science fragmentation rules.