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ChemPy (Rust)

License: MIT

Note

Project Evolution This project has been converted from its original Python implementation to a Pure Rust crate. While the Python version has been integrated into the RMG-Py ecosystem, this repository now serves as a high-performance Rust port of the foundational ChemPy toolkit.

ChemPy (Rust) is a high-performance toolkit for chemistry, chemical engineering, and materials science applications, with a focus on molecular structures, thermodynamics, and chemical kinetics.

Features

  • Fast Graph Isomorphism: Efficient VF2-based molecular graph comparison.
  • Thermodynamic Models: Support for NASA polynomials and Wilhoit models.
  • Kinetics: Arrhenius models and rate coefficient calculations.
  • States: Partition function and density of states calculations.

Getting Started

Add this to your Cargo.toml:

[dependencies]
chempy = { git = "https://github.com/elkins/ChemPy.git", branch = "rust-conversion" }

Development

Run tests with:

cargo test

Python Comparison (Legacy)

The original Python implementation is preserved in the python/ directory for behavioral and performance comparison.

To run the original Python tests:

cd python
pip install -e .
pytest unittest/

To run original Python benchmarks:

cd python
pytest unittest/benchmarksTest.py --benchmark-only

Glossary & Acronyms

  • SMILES: Simplified Molecular Input Line Entry System. A notation for representing chemical structures as strings.
  • InChI: International Chemical Identifier. A standardized string representation for chemical substances.
  • NASA Polynomials: A standard format (initially developed by NASA) for representing thermodynamic data ($C_p, H, S$) as a function of temperature.
  • Wilhoit Model: A robust thermodynamic model for heat capacity that ensures physical behavior at extremely low ($T \to 0$) and high ($T \to \infty$) temperatures.
  • VF2 Algorithm: A high-performance algorithm for graph and subgraph isomorphism matching, used here for molecular pattern recognition.
  • GA (Group Additivity): A method for estimating thermodynamic properties of molecules based on their constituent functional groups.
  • SCF Energy: Self-Consistent Field energy; the electronic energy of a molecule calculated via quantum chemical methods (e.g., Gaussian).
  • Partition Function: A function that describes the statistical properties of a system in thermodynamic equilibrium.

References

  • Pitzer, K. S. (1946). "The Energy Levels of Restricted Rotors." J. Chem. Phys. 14, p. 239-243. (Used for hindered rotor calculations).
  • East, A. L. L. and Radom, L. (1997). "Ab initio statistical thermodynamical models for the computation of high-temperature thermodynamic functions." J. Chem. Phys. 106, p. 6655-6674. (Foundational for StatesModel).
  • Cordella, L. P., Foggia, P., Sansone, C., and Vento, M. (2004). "A (Sub)Graph Isomorphism Algorithm for Matching Large Graphs." IEEE Trans. Pattern Anal. Mach. Intell. 26, p. 1367-1372. (The VF2 algorithm used in graph.rs).
  • Wilhoit, R. C. (1975). "Thermodynamic properties of normal and branched alkanes." J. Phys. Chem. Ref. Data 2, p. 427-437. (The Wilhoit heat capacity model).
  • Burcat, A. and Ruscic, B. (2005). "Third Millennium Ideal Gas Thermodynamic Data for Combustion and Air-Pollution Use." TAE 960 Report. (Source for NASA polynomial standards).

License

ChemPy is licensed under the MIT License - see LICENSE for details.

Acknowledgments

ChemPy was originally developed by Joshua W. Allen in Python and has been ported to Rust to ensure its long-term performance and maintainability.