Pseudocode version    

1.  Get Input:

    1. PDB codes or any other coordinates files.
    2. Chain ID's of each pdb file.
    3. Experimental association rate (k_on).
    4. Experimental ionic strength.
    5. Target ionic strength.
    6. Charge rules.
    7. Mode of work(calcualte energy only or find hotspots too).

2.  For each pdb file {

        1. Separate pdb file into chains.
        2. Combine desired chains (pairwise).
        3. Assign charges to atoms.
        4. Find missing atoms. if found, print to log file.
        5. Find interface residues (less/equal than 4 Angstroms).
        6. Reduce calcuation set to charged atoms only.
        7. Calculate Coulombic energy of 1st chain.
        8. Calculate Coulombic energy of 2nd chain.
        9. Calculate Coulombic energy of the complex.
        10. Calcuate energy difference.
        11. Calculate association rate at 0.022M.
        12. Extract basal rate
        13. calculate k_on at target salt
        14.  If mode of work is hotspots {
                  For each residue position {
                       For each charge type (Positive and Negative) {
                            1. Assign charge to selected atoms.
                            2. Calculate Coulombic energy of 1st chain.
                            3. Calculate Coulombic energy of 2nd chain.
                            4. Calculate Coulombic energy of the complex.
                            5. Calcuate energy difference.
                            6. Calculate k_on at target salt.
                            7. Print rate increase (the new rate/experimental rate).
                        }
                  }
              Else do next pdb
     }