Command Reference

Pharmacon exposes six top-level commands, each grouping related subcommands.

Command	Description
trajectory	Analyze MD trajectories: RMSD, RMSF, distances, angles, hydrogen bonds, protein–ligand and protein–protein interactions, PCA, average structure
structure	Analyze static structures: molecular properties and amino-acid sequence extraction
dump	Print metadata and group tree of `.pta` / `.psa` files to stdout
export	Export `.pta` / `.psa` data to CSV, TSV, or FASTA
plot	Render publication-ready plots from `.pta` files using optional INI configuration
merge	Merge multiple `.pta` replicates from the same topology into one aggregated artifact

General syntax

pharmacon <command> <subcommand> [options]

pharmacon --help                          # top-level help
pharmacon trajectory --help               # trajectory subcommands
pharmacon trajectory rmsd --help          # RMSD flags

Adding a new subcommand

Pharmacon uses auto-discovery. Drop a .py file into the appropriate src/pharmacon/command_line/<command>/ directory. The module must export:

SUBCOMMAND_NAME: str          # e.g. "my-analysis"
SUMMARY: str                  # one-line description

def build_parser(subparsers, parents): ...
def validate(args): ...
def run(args): ...

No registration step is required — the registry discovers it at import time. See Architecture for the full development pattern.