Graph-cut method for determining optimal titration state configuration

This code assumes that you've run PDB2PQR as follows:

./pdb2pqr --ff=parse --ph-calc-method=pdb2pka --with-ph=7 2MKB 2MKB.pqr

and now have a subdirectory pdb2pka_output/.

Graph cut can be run by

python main.py -v <input path> <output path>

The option -v will print out pH value and the number of leftover residues to standard out.

Make sure input path contains the following files for a single protein:

• INTERACTION_MATRIX.DAT
• desolvation_energies.txt
• background_interaction_energies.txt

The directory output path will get the timing file and all titration curves.