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About#

ChemNetworks is a program designed for high-throughput graph theoretical analyses of molecular dynamics simulations utilizing Z-matrix-like structure definitions to search for arbitrary sets of atomic interactions. It is designed to be easily extensible, allowing developers to add new N-Body Z-matrix interactions, and arbitrary graph analyses using the igraph C library.

Documentation Overview#

This documentation covers the following aspects of ChemNetworks:

  1. Compilation and Usage
  2. The Input File
    1. The SETTINGS Block
    2. The TRAJECTORY Block
    3. The ZMATRIX Block
    4. The GRAPH Block
    5. Z-matrix Commands
    6. Analysis Commands
  3. Developer Guide
    1. Execution Workflow
    2. I/O Namespace
    3. Creating Custom Z-matrix Commands
    4. Creating Custom Analyses
  4. Examples
    1. Overview
    2. Input File Tutorial
    3. Z-matrix Examples

Source Code#

The source code for ChemNetworks is hosted on GitLab:

https://gitlab.com/ChemNetworks/ChemNetworks

If you find bugs, have feature requests, or would like to contribute, please open an issue there.

How to Cite#

If you use this code in your work, please cite the following:

Pope, D. J.; Elowitt, J.; Zhang, B.; Parashar, M.; Clark, A. ChemNetworks: New Capabilities for High-Throughput, Real-Time Chemical Graph Construction and Analysis. ChemRxiv 2026 , 2026. https://doi.org/10.26434/chemrxiv.15001158/v1

Ozkanlar, A., & Clark, A. E. (2014). ChemNetworks: A complex network analysis tool for chemical systems. Journal of Computational Chemistry, 35(6), 495–505. https://doi.org/10.1002/jcc.23506

Csardi, G., & Nepusz, T. (2006). The igraph software package for complex network research. InterJournal, Complex Systems, 1695.

If using the DSPACESTRJ trajectory file type:#

Docan, C., Parashar, M., & Klasky, S. (2010). DataSpaces: An interaction and coordination framework for coupled simulation workflows. HPDC 2010 - Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing, 15(2), 25–36. https://doi.org/10.1145/1851476.1851481

If using XTC or GROXTC trajectory file type:#

R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. MDAnalysis: A Python package for the rapid analysis of molecular dynamics simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. doi: 10.25080/majora-629e541a-00e

N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. J. Comput. Chem. 32 (2011), 2319-2327, doi:10.1002/jcc.21787

Acknowledgements#

The support and resources from the Center for High Performance Computing at the University of Utah are gratefully acknowledged.