Add a new behavior slider named "Bonding Force":
1 = normal behavior (maybe you could add a snap action to this point)
0 = donators and acceptors are neutral
-1 = donators and acceptors push each other away
10 = donators and acceptors try to bond no matter the cost, causing the backbone to bend
So, you want to change the charge of the atoms?
Nice idea.
I forgot something:
Add a check box "affect selection only".
When it's checked it affects only the parts of the protein you selected (in selection interface), when not it affects the whole protein.
Makes sense, as the proteine is sorrunded by other chemicals, which can affect the charge of some proteine atoms.
Only one thing:
If you get a good result, it would not be a physical correct solution as it is.
So, at the end, you will always have to turn the atoms' properties to normal again, and do a shake/wiggle to look if they stay where they are.
This must be guaranteed in some way, if a solution is uploaded.
A physical incorrect solution shouldn't get a good score in the first place. I think that would work pretty similar to a reduced clashing importance.
Behavior slider went obsolete in… 2011? Closing.