duartegroup / Autode

Introduction

autodE is a Python module designed for the automated calculation of reaction profiles from just SMILES strings of reactant(s) and product(s).

Dependencies

• Python > v. 3.5
• One of:
  • ORCA > v. 4.1
  • Gaussian09
  • Gaussian16
  • NWChem
• One of:
  • XTB > v. 6.1
  • MOPAC

The Python dependencies are listed in requirements.txt are best satisfied using a conda install (Miniconda or Anaconda).

Installation

To install autodE with conda:

conda install autode -c conda-forge

see the installation guide for installing from source or on Windows.

Usage

Reaction profiles in autodE are generated by initialising Reactant and Product objects, generating a Reaction from those and invoking calculate_reaction_profile(). For example, to calculate the profile for a 1,2 hydrogen shift in a propyl radical:

import autode as ade
ade.Config.n_cores = 8

r = ade.Reactant(name='reactant', smiles='CC[C]([H])[H]')
p = ade.Product(name='product', smiles='C[C]([H])C')

reaction = ade.Reaction(r, p, name='1-2_shift')
reaction.calculate_reaction_profile()

See examples/ for more examples and duartegroup.github.io/autodE/ for additional documentation.

Development

Pull requests are very welcome but must pass all the unit tests prior to being merged. Please write code and tests! Bugs and feature requests should be raised on the issue page.

Citation

If autodE is used in a publication please consider citing the paper:

@article{autodE,
  doi = {10.1002/anie.202011941},
  url = {https://doi.org/10.1002/anie.202011941},
  year = {2021},
  publisher = {Wiley},
  volume = {60},
  number = {8},
  pages = {4266--4274},
  author = {Tom A. Young and Joseph J. Silcock and Alistair J. Sterling and Fernanda Duarte},
  title = {{autodE}: Automated Calculation of Reaction Energy Profiles -- Application to Organic and Organometallic Reactions},
  journal = {Angewandte Chemie International Edition}
}