Reaction Mechanism Generator - Python Reaction Stencil (pReSt)

The python Reaction Stencil (pReSt) generates the reaction rules using a set of elementary steps for a reaction system.

Documentation

See our documentation page for examples.

Developer

Udit Gupta ([email protected])

Dependencies

• Python3
• ASE : Used for reading in 3-D molecular structures
• Numpy : Used for vector and matrix operations
• rdkit : Used for performing bond transformations
• NetworkX : Used for performing graph manipulation

Getting Started

1. Install using pip::

pip install pReSt

Currently being resolved

Files for using the Visualization tool

1. species.xyz - Species files containing 3-D coordinates for each molecule
2. reaction.txt - A list of elementary steps containing species provided along with species.xyz file

Features in the Reaction Mechanism Generator:

• Reaction rule generation
• Reaction network generation using reaction rules from a database
• Checking if a reaction exists in the database
• Generating 3-D molecular structures using SMILES strings (In Progress)

License

This project is licensed under the GNU LGPL License - see the LICENSE.md file for details

Contributing

If you have a suggestion or find a bug, please post to our Issues page with the enhancement or bug tag respectively.

Finally, if you would like to add to the body of code, please:

• fork the development branch
• make the desired changes
• write the appropriate unit tests
• submit a pull request.

Questions

If you are having issues, please post to our Issues page with the help wanted or question tag. We will do our best to assist.

Funding

This material is based upon work supported by the Department of Energy's Office of Energy Efficient and Renewable Energy's Advanced Manufacturing Office under Award Number DE-EE0007888-9.5.

Special Thanks

• Guen Ho Gu (Discussion)
• Qiang Li (Discussion)