API Reference

This section provides auto-generated documentation for all OptiMHC modules and classes.

Modules

Module	Description
Core	Configuration, pipeline orchestration, PSM container, and logging
I/O	Input parsers for PepXML, PIN, and mzML formats
Feature Generators	Base class and all feature implementations
Rescoring	Mokapot integration and machine learning models
Visualization	Plotting functions for results and diagnostics
CLI	Command-line interface