Quick Start

CLI structure

Pharmacon follows a git-style command structure:

pharmacon <command> <subcommand> [options]

Getting help at every level

pharmacon --help                            # list all commands
pharmacon trajectory --help                 # list trajectory subcommands
pharmacon trajectory rmsd --help            # show all RMSD flags
pharmacon plot pta --help                   # show all plot flags

Supported MD engines

Pharmacon reads trajectories produced by Amber, GROMACS, CHARMM, NAMD, and OpenMM through MDAnalysis.

File type	Supported formats
Topology	`.tpr`, `.prmtop`, `.parm7`, `.psf`, `.dms`
Trajectory	`.xtc`, `.trr`, `.dcd`, `.nc`
Structure (static)	`.pdb`, `.gro`, `.crd`, `.mol2`, `.smi` (`.sdf` planned, not yet supported)

Common flags (all trajectory subcommands)

Flag	Description
`-p / --topology`	Topology file
`-x / --trajectory`	Trajectory file
`-o / --output`	Output file or directory
`--overwrite`	Overwrite existing output
`-b / --begin`	First frame (default: 0)
`-e / --end`	Last frame (default: last)
`-s / --step`	Process every Nth frame (default: 1)
`-l / --log`	Log file path
`-fl / --file-logging-level`	File log verbosity (default: DEBUG)
`-tl / --terminal-logging-level`	Terminal log verbosity (default: INFO)

Example 1 — RMSD analysis and plot

pharmacon trajectory rmsd \
    -p protein.prmtop \
    -x md.nc \
    -sel "protein and name CA" "resname LIG and not name H*" \
    -n  bb_ca ligand_heavy \
    -f  "protein and name CA" \
    -r 0 -b 0 -e 10000 -s 10 \
    -o  rmsd.pta

pharmacon plot pta -i rmsd.pta -o plots/ --overwrite

Example 2 — Protein–ligand interactions across replicates

# Analyse each replicate
for rep in rep1 rep2 rep3; do
  pharmacon trajectory pl-interactions \
      -p $rep/topol.tpr \
      -x $rep/traj.xtc \
      -prt "protein" \
      -lig "resname LIG" \
      -w  "resname WAT" \
      -o  $rep/pli.pta
done

# Merge replicates into one artifact
pharmacon merge results \
    -i rep1/pli.pta rep2/pli.pta rep3/pli.pta \
    -o pli_merged.pta

# Plot the merged artifact
pharmacon plot pta \
    -i pli_merged.pta \
    -o plots/merged/ \
    --overwrite \
    -c my_theme.ini

Example 3 — PCA

pharmacon trajectory pca \
    -p protein.prmtop \
    -x md.nc \
    -sel "protein and name CA" \
    -c 5 \
    -o pca.pta

pharmacon plot pta -i pca.pta -o pca_plots/ --overwrite
# Produces: pca_timeseries, pca_scatter, pca_variance_ratio,
#           pca_probability, pca_heatmap_fes

Example 4 — Structure properties

pharmacon structure properties -i ligands.smi  -o ligand_props.psa
pharmacon export psa -i ligand_props.psa -f csv -o ./results/

Example 5 — Inspect and export results

pharmacon dump   pta -i rmsd.pta           # pretty-print metadata
pharmacon export pta -i rmsd.pta -f csv -o ./results/

Debug mode

Set PHARMACON_DEBUG=1 to get a full traceback on unexpected errors:

PHARMACON_DEBUG=1 pharmacon trajectory rmsd ...