https://github.com/berquist/autode

automated reaction profile generation

https://github.com/berquist/autode

Repository

automated reaction profile generation

https://github.com/berquist/autodE/blob/master/

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![alt text](autode/common/llogo.png)
***
## 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](https://www.python.org/) > v. 3.5
* One of:
   * [ORCA](https://sites.google.com/site/orcainputlibrary/home/) > v. 4.1
   * [Gaussian09](https://gaussian.com/glossary/g09/)
   * [Gaussian16](https://gaussian.com/gaussian16/)
   * [NWChem](http://www.nwchem-sw.org/index.php/Main_Page)
* One of:
   * [XTB](https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/xtb/xtb/) > v. 6.1
   * [MOPAC](http://openmopac.net/)

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

## Installation

To install **autodE** with [conda](https://anaconda.org/conda-forge/autode):
```
conda install autode -c conda-forge
```
see the [installation guide](https://duartegroup.github.io/autodE/install.html) 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:

```python
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/](https://github.com/duartegroup/autodE/tree/master/examples) for
more examples and [duartegroup.github.io/autodE/](https://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!
See the [todo list](https://github.com/duartegroup/autodE/projects/1) for features on the horizon. 
Bugs and feature requests should be raised on the [issue page](https://github.com/duartegroup/autodE/issues). 

> **_NOTE:_**  We'd love more contributors to this project! 


## Citation

If **autodE** is used in a publication please consider citing the [paper](https://doi.org/10.1002/anie.202011941):
 
```
@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}
}
```

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