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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. 4.2
  • 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

git clone https://github.com/duartegroup/autodE.git
cd autodE
conda install --file requirements.txt --channel conda-forge
python setup.py install

see the installation guide for more detailed instructions.

Usage

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

from autode import *
Config.n_cores = 8

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

reaction = 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.