duartegroup / autode

automated reaction profile generation

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Introduction

autodE is a Python module initially designed for the automated calculation of reaction profiles from SMILES strings of reactant(s) and product(s). Current features include: transition state location, conformer searching, atom mapping, Python wrappers for a range of electronic structure theory codes, SMILES parsing, association complex generation, and reaction profile generation.

Dependencies

• Python > v. 3.7
• One of:
  • ORCA > v. 4.0
  • Gaussian09
  • Gaussian16
  • NWChem > 6.5
  • QChem > 5.4
• 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.

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()  # creates 1-2_shift/ and saves profile

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

Development

There is a slack workspace for development and discussion - please email to be added. Pull requests are very welcome but must pass all the unit tests prior to being merged. Please write code and tests! See the todo list for features on the horizon. Bugs and feature requests should be raised on the issue page.

NOTE: We'd love more contributors to this project!

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}
}

Contributors

• Tom Young (@t-young31)
• Joseph Silcock (@josephsilcock)
• Kjell Jorner (@kjelljorner)
• Thibault Lestang (@tlestang)
• Domen Pregeljc (@dpregeljc)
• Jonathon Vandezande (@jevandezande)
• Shoubhik Maiti (@shoubhikraj)
• Daniel Hollas (@danielhollas)