API Documentation

QuantumPDB is organized into five subpackages corresponding to the pipeline stages, plus a CLI module.

qp.structure	Perform structure corrections
qp.protonate	Assign protonation states using Protoss and apply corrections.
qp.cluster	Generate QM cluster models
qp.manager	Manager for QM job submissions.
qp.analyze	Post-processing analysis with Multiwfn and job status tracking.
qp.cli	Command-line interface (CLI) entry point.