update AS changes

README.md

@@ -1,17 +1,26 @@
 # Fafoom - Flexible algorithm for optimization of molecules 
+:warning: **Fafoom is no longer maintained and will not be updated to Python 3** :warning:
+
 
 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 2.7
-  * Numpy
-  * RDKit (used version: Release_2014_09_2)
+  * Python (used for testing: 2.7.6) - Python3 is not supported!
+  * 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
 
@@ -24,16 +33,30 @@ Fafoom is a tool for sampling the conformational space of organic molecules. Faf
 
     import fafoom
 
-## Examples of usage
+## Example of usage
 
-Three examples are provided with the source code in the examples folder:
+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:
 
-* genetic algorithm based search utilizing first-principles (FHI-aims required)
-* genetic algorithm based search utilizing force fields (force fields accessed from RDKit)
-* genetic algorithm based search utilizing first-principles via NWChem (NWChem required)
+* 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.