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Recipe: HNetwork Probe 2.3
Created by LociOiling 2 1
Your rating: None Average: 4.6 (7 votes)


Name: HNetwork Probe 2.3
ID: 104052
Created on: Mon, 10/12/2020 - 14:25
Updated on: Wed, 10/14/2020 - 19:37

New options, including wiggle factor, skipping initial mutates, and shuffling the list of segments to mutate. V2.3 adds named saves.

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LociOiling's picture
User offline. Last seen 59 min 41 sec ago. Offline
Joined: 12/27/2012
New features

HNetwork Probe 2.2 has new features and some changes meant to make it easier to understand what's going on. See the comments for HNetwork Probe 2.0 for the basics of how the recipe works.

In the expanded settings dialog, there's a new "wiggle factor" setting that's similar to the ones found in EDRW/DRemixW. As before, for WF = 1, the recipe wiggles all sidechains for two cycles after a mutation. With WF = 2, it's four cycles, WF = 3 gives you six cycles, and so on.

There are also two new checkboxes. The recipe normally tries to mutate all selected mutable segments at the beginning of each run. "Skip initial mutates" causes the recipe to skip this step.

The recipe previously picked a segment at random from the list of selected mutable segments. This meant the same segment could be picked two or more times in a row. Checking "shuffle mutable list" means the recipe first shuffles the list of mutables, then processes the list in its new order. If you have ten mutable segments selected, all ten will be tried before the list is shuffled again.

On the more cosmetic side, the dialog tries to make it clearer that the default "select unfrozen" option means working on mutable segments with unfrozen sidechains. If this option is unchecked, you must specify segment ranges in the "use ranges" textbox.

The list of amino acids specified is now validated, and an error message displayed for invalid entries. An error message is also displayed if the start quick save slot is greater than the end quick save slot.

A dialog box now appears if run the recipe for a non-design puzzle or a puzzle without a hydrogen bond network condition.

The recipe now puts out a message every 100 runs just to reassure the anxious user. The new "verbose output" checkbox will produce lots more output if checked.

The recipe now includes an improved random number seed (hard to be sure on that), and an expanded cleanup routine which displays line numbers for script errors.

There are also a number of small stylistic changes to the code.

This version of the recipe includes code from Karen_CH, Timo van der Laan, rav3n_pl, Bruno Kestemont, and others.

LociOiling's picture
User offline. Last seen 59 min 41 sec ago. Offline
Joined: 12/27/2012
named saves

HNetwork Probe 2.3 adds named saves when the hydrogen bond network score improves. The saves are listed in the scriptlog when they happen, and can be seen in Open/Share Solutions (control - o).

The named saves are in addition to the original save logic, which relies on quick save slots. One advantage of named saves is that they are easier to find if the client crashes.

The named saves are identified by the overall score, followed by the hydrogen bond network score and the change in the h-bond score.

Version 2.3 includes several other changes related to saves. When the hydrogen bond network score improves, the recipe now calculates the total score, including all the conditions/filters. The details are reported in the scriptlog. If the new solution has the same total score as one already saved, it's considered a duplicate, and not saved. Otherwise, the solution is saved in a quick save slot, and in a named save.

As in previous versions, the original pose is stored in quick save slot 1. In version 2.3, the quick save sliders now protect slot 1. If there's no gain when the recipe ends, the original pose is now restored.

At the end, the recipe now turns on all filters. As before, it restores the quick save slots used, in order. The final pose is the one in the last quick save slot, showing the score with all filters on. This may or may not be the best pose.

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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, Boehringer Ingelheim, RosettaCommons