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).
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
functionality of the tool:
first-principles methods:
git clone https://github.com/adrianasupady/fafoom
import fafoom
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:
Get familiar with the provided manual to learn more about the tool and the parameters.
Development goals:
Comments, feedback or development contributions are always welcome!
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