fafoom-dev

Continuing development of genetic algorithm for biomolecules in different environments.

# Fafoom - Flexible algorithm for optimization of molecules

Fafoom is a tool for sampling the conformational space of organic molecules. Fafoom is intended to work with FHI-aims (Fritz Haber Institute ab initio molecular simulations package).

News

• the paper "First-principles molecular structure search with a genetic algorithm" is now published in Journal of Chemical Information and Modeling; DOI: 10.1021/acs.jcim.5b00243

• a new branch targeting the implementation of a further degree of freedom ('orientation') has been created

Requirements

• functionality of the tool:

  • Python (used for testing: 2.7.6)
  • Numpy (used for testing: 1.8.2)
  • RDKit (used for testing: Release_2015_03_1)

• first-principles methods:

  • (recommended) FHI-aims (Fritz Haber Institute ab initio molecular simulations package)
  • (alternative) NWChem (NWChem: Open Source High-Performance Computational Chemistry)
  • (alternative) ORCA (- An ab initio, DFT and semiempirical SCF-MO package -)

How to use

1) Clone the fafoom repository

git clone https://github.com/adrianasupady/fafoom

2) Export the fafoom directory to you PYTHONPATH

3) In python:

import fafoom

Example of usage

An implementation of a genetic algorithm is provided in the examples folder. Depending on the used parameter file following genetic algorithm based searches can be run:

• parameters_aims.txt for first-principles (FHI-aims required)
• parameters_ff.txt for force fields (force fields accessed from RDKit)
• parameters_nwchem.txt for first-principles via NWChem (NWChem required)
• parameters_orca.txt for first-principles via ORCA (ORCA required)

Get familiar with the provided manual to learn more about the tool and the parameters.

Outlook

Development goals:

• flexible formulation of the scoring function, e.g. allowing for optimizing a user-defined property
• adding more kinds of degrees of freedom, e.g. orientation of a molecule
• adding wrappers for different molecular simulations packages

Comments, feedback or development contributions are always welcome!

License

Fafoom is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

Fafoom is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.

You should have received a copy of the GNU Lesser General Public License along with fafoom. If not, see http://www.gnu.org/licenses/.

Copyright 2015 Adriana Supady