Pharmacon — Molecular Dynamics Suite
Copyright (C) 2026 Kyriakos Georgiou
Department of Pharmacy, National and Kapodistrian University of Athens

This program is free software: you can redistribute it and/or modify it
under the terms of the GNU General Public License, version 3 only, as
published by the Free Software Foundation.

This program is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
for more details.

A copy of the GNU General Public License v3 is distributed with this
software as LICENSE.txt and is also available at:

    https://www.gnu.org/licenses/gpl-3.0.txt

SPDX-License-Identifier: GPL-3.0-only

================================================================================
ACADEMIC CITATION
================================================================================

If you use Pharmacon — in whole or in part — in any
work that results in a publication (including but not limited to peer-reviewed
articles, preprints, conference papers, posters, theses, technical reports,
books, and public datasets), please cite the following reference:

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

BibTeX:

    @article{georgiou_pharmacon,
      author  = {Georgiou, Kyriakos and Kolocouris, Antonios},
      title   = {Pharmacon: A Molecular Dynamics Simulation Analysis Toolkit},
      journal = {Journal of Chemical Information and Modeling},
      year    = {2026},
      doi     = {10.1021/acs.jcim.6c00837},
      url     = {https://doi.org/10.1021/acs.jcim.6c00837}
    }

Citing Pharmacon supports its continued development and allows the author to
track academic impact. Thank you.

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THIRD-PARTY COMPONENTS
================================================================================

Pharmacon depends on the following third-party open-source libraries. Each is
distributed under its own license; the SPDX identifiers below are best-effort
summaries — consult each project for the authoritative terms.

Required runtime dependencies (declared in pyproject.toml):

  - MDAnalysis        (GPL-2.0-or-later) https://www.mdanalysis.org/
  - configobj         (BSD-3-Clause)     https://github.com/DiffSK/configobj
  - h5py              (BSD-3-Clause)     https://www.h5py.org/
  - matplotlib        (Matplotlib;       https://matplotlib.org/
                       PSF-based)
  - networkx          (BSD-3-Clause)     https://networkx.org/
  - numpy             (BSD-3-Clause)     https://numpy.org/
  - periodictable     (Public Domain)    https://github.com/pkienzle/periodictable
  - psutil            (BSD-3-Clause)     https://github.com/giampaolo/psutil
  - pyarrow           (Apache-2.0)       https://arrow.apache.org/
  - pyfiglet          (MIT)              https://github.com/pwaller/pyfiglet
  - pyjokes           (BSD-3-Clause)     https://pyjok.es/
  - rdkit             (BSD-3-Clause)     https://www.rdkit.org/
  - rich              (MIT)              https://github.com/Textualize/rich
  - rich-argparse     (MIT)              https://github.com/hamdanal/rich-argparse
  - scipy             (BSD-3-Clause)     https://scipy.org/
  - typing_extensions (PSF-2.0)          https://github.com/python/typing_extensions

Optional dependencies — MPI extra ([mpi]):

  - mpi4py            (BSD-3-Clause)     https://mpi4py.readthedocs.io/

Optional dependencies — development extra ([dev]):

  - pytest            (MIT)              https://pytest.org/
  - MDAnalysisTests   (GPL-2.0-or-later) https://www.mdanalysis.org/

Note on copyleft: MDAnalysis and MDAnalysisTests are distributed under
GPL-2.0-or-later. Pharmacon imports MDAnalysis at runtime; redistribution of
combined works is subject to the terms of the GPL.

Users are responsible for complying with the licenses of all third-party
dependencies they install and use alongside Pharmacon.
