Package Reference

The Function Index page documents callable analysis, numerical and I/O interfaces. The tables below map principal data types to the generated module reference.

Core types

Type	Role
PQAnalysis.atomic_system.AtomicSystem	One structure with coordinates, cell and topology
PQAnalysis.traj.Trajectory	Ordered atomic-system frames
PQAnalysis.topology.Topology	Atoms, residues, molecular identity and bonded topology
PQAnalysis.topology.Selection	Atom selection parser and index resolution
PQAnalysis.analysis.output.AnalysisTable	Numerical analysis data coupled to scientific column metadata
PQAnalysis.analysis.output.AnalysisSchema	Stable fields, symbols, units and plot defaults

Package areas

Package	Scope
Analysis	Calculations, input readers, result models and output writers
Input and output	Trajectory, restart, topology and simulation-file readers and writers
Trajectories	Engine formats, trajectory containers and high-level operations
Atomic systems	Coordinates, cells and topology-bearing systems
Topology and selection	Selections, residues, bonded topology and SHAKE definitions
Package index	Generated module hierarchy

Use the analysis guides for physical conventions, the function index for callable workflows and the generated reference for implementation details.