For calculating the transfer integral between two molecules using the counterpoise method. There are two scripts:

1) generateCOMS-CP.py

This script creates three Gaussian input files (.com) of: molecule A with ghost atoms of molecule B, molecule B with ghost atoms of molecule A, and the pair of molecules with no ghost atoms (moleculeAB). The script can also perform translation and rotation from the initial geometry files (.xyz)

2) calc-CP.py

After running the .com files produced in the first script through Gaussian, this program performs the counterpoise calculation on the Gaussian output files (.log).

Code based on: https://github.com/Jenny-Nelson-Group/counterpoise-J