Steps to run the protein rotamer optimization workflow.
Author: Dennis Shasha

1. Start with onebody energies (i.e. energies of each rotamer
position taken by itself) and twobody energies (energies of rotamer
pairs of positions that are near each other).

2. The format is tab separated, so run a sed script to put those files
in comma-separated csv format.

2.5 Replace the headers so the onebody file has the header of:
position,rotamer,energy
and the two body file as the header of:
firstposition,firstrotamer,secondposition,secondrotamer,energy

2.7 There might be some last lines to eliminate too 

3. Run python3 vikram_setup.py
which replaces the database tables for one and twobody energies.

4. Run python3 vikram_protein.py

Or in nohup form runvik whose contents are:
python3 vikram_protein.py > vikram.out 2> vikram.err
So the call would be 
nohup runvik &
exit

NB: The "exit" is very important

5. Wait

Other notes:
# command line with sqlite:
# sqlite3 aquarium.db
# To unlock an sqlite database type on the command line
# mv aquarium.db tmp.db
# cp tmp.db aquarium.db

# To run with nohup, put
# python3 vikram_protein.py > vikram.out 2> vikram.err
# in file runvik
# chmod +x runvik
# nohup runvik &