Altering the band system
|Opened on:||Saturday, May 28, 2011 - 08:47|
|Last modified:||Saturday, May 28, 2011 - 08:47|
When I am solving a puzzle, I view the protein as one long chain of segments, each segment having a pushing and pulling force to it. The pushing force comes from the need for the atoms to have their space and the pulling force comes from the need to keep as much energy in the protein as possible (i.e so the hydrophobes don't lose their charges to conducting water). Therefore, I currently use bands as springs to account for the energy piece. Then I tighten the springs all the way up to maximize the energy in the protein (like a fusion reaction, or so I like to think of it) and use fold.its current functions to release the energy in different ways until the "clashes" go away, or the atom spaces are sufficiently large. This way, the highest score I get comes from being able to "wiggle" and "shake" my way from the max energy in the lowest time.
Essentially, my proposal is this: incorporate the "compactness forces" (i.e. from shake and wiggle) into the band system and just have every segment connected to every other segment by a band. Since the bands represent the sum of the pushing and pulling forces, they can be limited and defined by the user.
-- This would enable optimizing functions for score types and/or locations
-- Editing the bands according to density functions/user input would yield increased trajectory production
-- "Disabling all bands" would instead ensure atoms would have at least as much room as necessary and the protein is entirely stable (although not necessarily ideal)
-- After disabling bands, individual bands activated thereafter are the same as traditional bands
-- Implementation is difficult due to the math which must be handled every cycle (however, if handled in a similar manner to a physics engine like Nvidia's PhysX the calculations can be sufficiently simplified)