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Recipe: CG303 GA+EO Remix V7.870
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Name: CG303 GA+EO Remix V7.870
ID: 45953
Created on: Tue, 04/23/2013 - 15:19
Updated on: Tue, 04/23/2013 - 22:19
Description:

A complete rework of my old script, object-oriented parameter-/variable-structure allowing more features. Manual is included. See script code for details. Note: 1.: This script detects "important"/"cardinal" segments, if there is a change in secondary structure, but you can add more segments by selection interface (blue). 2.: As we can't get locked (grey) segments by script a.t.m., you will have to exclude them via script parameters.



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Joined: 09/18/2009
Groups: SETI.Germany
Manual excerpt

1. introduction:
1.1 inspired by:
Cartoon Villain (GA idea & first random band script of this kind)
Rav3n_pl (OO parameter/variable handling)
jeff101 (EO & input-boxes idea)

1.2 idea:
-- This is a further development of my last GAB+EO
which i wrote from scratch to improve table handling and modularity
(it was a work of more than one month!)

-- this script doesn't simply band to random segs,
it works with a list of "cardinal" segs.
-- origin segs always stay the same (they are just turned off or on),
-- target segs change
-> this will avoid double banding
-- new idea is to keep the number of random band parameters as small as they can be
so it works with 2 fixed band strengths (as the length is already random)

-- as i didn't want to overload the starting sequence
with too many input boxes and selectable vals (more than 7 boxes at the moment!).
-> you can set all vals (even the other) in the declaration section.

1.3 features:
-- cardinal seg auto-detection: (see 3.3.2.3)
-- secondary-structure changes, amino-acids, etc will create a uselist
++ selecting segs via game interface (blue) is possible, too
-- 3 breeding modes: (see 3.2)
GA
EO1
EO2
-- 2 gene modes: (see 3.2.2.2)
"dual"
"poly"
-- 6 banding modes (see 3.3)
"space"
"center"
"user"
"furthest"
"random1"
"random2"
++ further settings for each

1.4 known bugs/problems:
1.4.1 ligand puzzles:
-- are supported by script, but i couldn't test if it works properly!
-> to band ligand:
use band to "user", then slide to last segment!

1.4.2 locked segs (grey in game):
-- can't be detected at the moment :(
-> work with a proper seg_use list.
you can:
-> pass seg indices as table in declaration section or
-> make a selection via game's selection interface (blue)
(although this wouldn't remove locked ones)

Joined: 09/18/2009
Groups: SETI.Germany
3 more things:

1.: In next time, I will have some examinations, so I won't have the time do care much about script bugs, features, spelling mistakes (or other lingual issues, as I'm not a native English speaker)
I hope, the manual is complete in this way that it answers most questions.
Maybe some other scripter can help you if there is a minor problem.

2.: There are already many input-boxes for the most important values in this script.
I neither wanted to write a full-automatic banding-robot
(so I offered "a couple" of parameters changeable by a "frontend")
nor annoy somebody with tons of inputboxes,
but as long as we can't store files, we only can change settings via input dialog boxes or writing them directly into the script code (something for advanced coders).
We definitely use file access to store and load settings!

So it is up to you to choose which parameters you change and in which way,
as this is our human part in this game, the rest can do ROSETTA.
If you don't know how to change parameters, please leave them as they are!
I wrote the script this way that it should be stable if you don't mess up vital things.

3.: (no personal thing):
If you find useful puzzle-adapted settings or script changes, you are free to post them, but please don't just unlock some "hidden" features (e.g. by uncommenting print-functions used for debugging -> more text in output) and do as if you've reinvented the wheel.
A car doesn't go faster if you put some racing-stickers on it.
For scripts, let's concentrate on functionality, the beauty will be found in good puzzle solutions.

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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