Files and Formats

PQAnalysis separates simulation data, analysis configuration and output-table serialization. File extensions select output formats, while input content and explicit engine options determine how trajectories are read.

Four file contracts govern analysis workflows:

• Analysis Input Files defines the key-value grammar.

• Analysis Output Files defines table fields, symbols and units.

• Command-Line Reference documents table, structure and trajectory conversion.

• Package Reference identifies readers, writers and trajectory objects.

Analysis configuration

RDF, MSD, VACF and vibrational calculations use key-value input files. Lists may be written in brackets or as multiline values according to the Analysis Input Files grammar. Relative filenames inside an input file resolve against the directory that contains the file.

Trajectories and engines

Analysis commands default to PQ conventions. Use --engine when reading a supported alternative convention. Position analyses require coordinates and a consistent atom count; MSD additionally needs periodic cells for unwrapping. VACF and momentum analyses require velocity data. Molecular exclusions in RDF require topology information from a restart and moldescriptor.

The Python format definitions are documented by PQAnalysis.traj.formats.MDEngineFormat and PQAnalysis.traj.formats.TrajectoryFormat.

Selections

Analysis keys such as reference_selection use the string language documented in Atom selections.

Output and conversion

Native, CSV, TSV and PQAnalysis-generated XVG tables are mutually convertible with pqanalysis convert; see Analysis Output Files.