plot

Render publication-ready plots directly from Pharmacon artifacts. The plotter auto-discovers which analysis groups are present in the file and dispatches to the appropriate rendering functions. Plot appearance is fully customisable via INI configuration files — see Pharmacon — Plot INI Reference for the full reference.

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plot pta

Generate all compatible plots for every group found in a .pta file. The type of figure produced depends on the analysis stored in the file:

Analysis in file	Plots produced
rmsd, distances, angles	Time-series line plot (PTA-UNIFIED)
rmsf	Per-atom RMSF profile
pl_interactions	Stacked column (×2), heatmap (×2), pie charts, ligand monitor heatmap
pp_interactions	Timeline heatmap, residue heatmap, stacked column
hbonds	Residue×residue heatmap, occupancy ranking, H-bond network graph, timeline, count-per-frame
pca	Time series, scatter, variance-ratio scree, FES heatmap, probability heatmap

Plots that require per-frame data are automatically skipped on merged files (is_merged=True).

Arguments

Flag	Required	Description
-i / --input	Yes	Input .pta file
-o / --output	Yes	Output directory where plot files will be written
-c / --config	No	Pharmacon INI file with plot-settings overrides (see Pharmacon — Plot INI Reference)
--overwrite	No	Overwrite existing output directory contents
-mw / --maxwarnings	No	Maximum coercion warnings per plot before the plot is skipped (default: 0)
-l / --log	No	Log file (default: plot_pta.log)
-fl / --file-logging-level	No	File log verbosity (default: DEBUG)
-tl / --terminal-logging-level	No	Terminal log verbosity (default: INFO)

Examples

Plot RMSD results:

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

Plot protein–ligand interactions:

pharmacon plot pta \
    -i pl_interactions.pta \
    -o ./plots/

Plot a merged artifact with a custom INI theme:

pharmacon plot pta \
    -i pli_merged.pta \
    -o ./plots/ \
    -c my_theme.ini \
    --overwrite

Use the master INI that covers every plot type:

pharmacon plot pta \
    -i run.pta \
    -o ./plots/ \
    -c examples/plot_ini/all_plots.ini

Generate all PCA plots:

pharmacon trajectory pca -p topol.tpr -x traj.xtc -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