Pharmacon Documentation

Pharmacon — A Molecular Dynamics Simulation Analysis Toolkit

A unified command-line toolkit for analyzing molecular-dynamics trajectories and static structures, persisting results as signed, self-describing HDF5 artifacts, and producing publication-ready plots.

Author	Kyriakos Georgiou
Affiliation	Department of Pharmacy, University of Athens
Version	1.0.1
License	GPLv3-only (GNU General Public License v3.0 only)
Python	≥ 3.12
Manuscript	Journal of Chemical Information and Modeling (2026) — DOI: 10.1021/acs.jcim.6c00837

Note

If you use Pharmacon in your research, please cite:

Georgiou, K.; Kolocouris, A. Pharmacon: A Molecular Dynamics Simulation Analysis Toolkit. Journal of Chemical Information and Modeling (2026). DOI: 10.1021/acs.jcim.6c00837

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Getting Started

• Installation
  • Option 1 — PyPI (recommended)
  • Option 2 — Conda
  • Option 3 — Source / development
  • Optional: MPI-aware logging
  • Optional: development tools only (no editable install)
  • Verifying the installation
• Quick Start
  • CLI structure
  • Getting help at every level
  • Supported MD engines
  • Common flags (all trajectory subcommands)
  • Example 1 — RMSD analysis and plot
  • Example 2 — Protein–ligand interactions across replicates
  • Example 3 — PCA
  • Example 4 — Structure properties
  • Example 5 — Inspect and export results
  • Debug mode

Command Reference

• Command Reference
  • General syntax
  • Adding a new subcommand
• trajectory
  • rmsd
  • rmsf
  • distances
  • angles
  • h-bonds
  • pl-interactions
  • pp-interactions
  • pca
  • average-st
• structure
  • properties
  • sequence
• dump
  • dump pta
  • dump psa
• export
  • export pta
  • export psa
• plot
  • plot pta
• merge
  • merge results

Reference

• Architecture
  • Module overview
  • Adding a new subcommand
  • Dependencies
• Analyzer Module
  • RMSD
  • RMSF
  • Distances
  • Angles
  • Non-Covalent Interactions
  • Hydrogen Bonds (standalone)
  • Principal Component Analysis (PCA)
  • Average Structure
  • Sequence Extraction
  • Molecular Properties
• Periodic Boundary Conditions (PBC)
  • PBC-aware calculations
  • The -at / --add-transformations flag
  • When to enable --add-transformations
  • Recommended: pre-image the trajectory yourself
  • Subcommands that accept -at
• File Formats
  • Common root-level attributes
  • PTA — Pharmacon Trajectory Analysis
  • PSA — Pharmacon Structure Analysis
  • Inspecting artifacts
  • Exporting artifacts
• Pharmacon — Plot INI Reference
  • 1. Quick reference — what’s in this directory
  • 2. How INI files work
  • 3. Variables shared by most plots
  • 4. PTA Universal time-series — [PTA-UNIFIED]
  • 5. RMSF profile — [PTA-RMSF]
  • 6. PCA — five plot types
  • 7. Protein–Ligand Interactions (PLI) — six plot types
  • 8. Protein–Protein Interactions (PPI) — three plot types
  • 9. Hydrogen Bonds (H-bonds) — five plot types
  • 10. Common gotchas & troubleshooting
  • 11. Editing workflow tips
  • Usage recap
• Logging & Workspaces
  • Logging
  • Debug mode
  • Workspaces