FragIt
FragIt is a python based tool that allows you to quickly fragment "any" molecule and use the produced output file(s) as an a starting point for input files in quantum chemistry programs that supports such fragment based methods.
FragIt was made out of the need to quickly benchmark many different molecules while developing new fragment based methods and is now being released in the hope that it is useful for others in their research. You can read about FragIt in the published paper.
Currently, FragIt supports the fragment molecular orbital method in GAMESS. FragIt also comes with a standard purpose XYZ writer that dumps each fragment in a separate .xyz file. Finally, there is a new XYZ-MFCC writer to support molecular fragmentation with conjugate caps that will yield capped fragments and caps for MFCC. New output writers can be added easily to support other methods and programs.
Obtaining FragIt
Since you found this file, it is obvious that you also found the source code. You can obtain the latest version from github where tagged releases are also available.
Installing FragIt
FragIt is a python library and installation is quite straight forward
python setup.py install
to install it in the default locations. To install it in a custom location, you can run the following
python setup.py install --prefix=/path/to/custom/installation
Remember to add the installation paths to your environment variables:
export PATH=/path/to/custom/installation/bin:$PATH
export PYTHONPATH=/path/to/custom/installation/lib/python2.7/site-packages:$PYTHONPATH
shown here for a python 2.7 installation example.
Running FragIt
in a terminal, you can type
fragit
to see its help message.
See the wiki for more examples of how to use FragIt.
Requirements
In order to run FragIt, you need the following installed on your system:
- The FragIt source code, look above for information on how to obtain it
- Open Babel 2.3 or newer with python language bindings enabled. Github user andersx wrote a guide to how that is accomplished.
- Numpy 1.5 or newer.
- Python version 2.7 or 3.5 (or later).