For all pairs that bond the same way in both on and off modes, subtract one point for each pair that when flipped causes the secondary structure to change in either mode and two points if it causes the secondary structure to change in both modes. (This is a switch variant on an old idea; pardon me if I forget the proper attribution.)
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This is a great idea!
I think I can help with the attribution. It sounds like a switch variation of John’s idea for single state puzzles.
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That’s the one!
Dear jandersonlee,
Your strategy has been added to our implementation queue and we should have it completed within the next two to three weeks. You can check the status of the implementation here.
We will also be uploading the code used to write your strategy on this page if you are interested in reading it later.
After implementing your idea, we will post the direct link to the code here. Then, we will then optimize the parameters, and test it. At that point, we will tell you the correlation of how good your strategy was and what the new optimized parameters are.
Thanks for sharing your idea!
Vineet Kosaraju
The EteRNA Team
Dear jandersonlee,
I am pleased to announce that a preliminary version of your strategy has been implemented with 14 lines of code. The code might slightly change in the future to remove bugs, but you can check the current version here. We will soon work on optimizing your parameters and testing the strategy.
Thank you again for sharing your switch strategy!
Vineet Kosaraju
The EteRNA Team