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Recipe: Random Squeezes v1.7.1
Created by jeff101 65 135
Your rating: None Average: 4.4 (33 votes)


Name: Random Squeezes v1.7.1
ID: 45002
Created on: Mon, 12/17/2012 - 17:21
Updated on: Tue, 12/18/2012 - 19:34

Wiggling with random clashing importance. To squeeze improvements from any somewhat stable solution. If there is much to gain, tends to reap more than simple wiggling (with ci=1), and then keeps trying. If there is little movement, often there is a sweet spot ci that gets you out of a local minimum, and it is found after many fruitless iterations. Supports exploration puzzles and mutable sidechains. Preserves secondary structure, bands and orignal CI. Single-step undo.

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jeff101's picture
User offline. Last seen 9 hours 13 min ago. Offline
Joined: 04/20/2012
Groups: Go Science
New features in Random Squeezes v1.7.1:

Random Squeezes v1.7.1 with default options should behave like v1.7.0 did, but v1.7.1 has a new option to vary ci less randomly using bins.

If the initial number of bins is set to 2, one bin is for ci=0-0.5, and the other is for ci=0.5-1. v1.7.1 does one ci from each bin. Once it has done this, it doubles the number of bins to 4, with bins for ci=0-0.25, 0.25-0.5, 0.5-0.75, and 0.75-1. It sees which of these bins have already been used and then picks the next few ci from the remaining bins. When those 4 bins have all been tried once, it doubles the number of bins again to 8, then later to 16, etc., always giving a power of 2. When the score improves, the number of bins gets reset to its initial value.

Other initial numbers of bins can be used. If the initial number of bins is 3, the 3 bins stand for ci=0-0.33, 0.33-0.66, and 0.66-1. Later these become 9 bins, then 27 bins, then 81 bins, etc., tripling the number of bins each time to always give a power of 3.

v1.7.1 also has a verbose mode which lists more things in Recipe Output as it runs.

Joined: 05/14/2013
Groups: None

Works well. Got me unstuck a treat.

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, RosettaCommons