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Recipe: Ebola Rebuild 1.12.2
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Name: Ebola Rebuild 1.12.2
ID: 45692
Created on: Sat, 03/16/2013 - 07:02
Updated on: Mon, 06/24/2013 - 14:28
Description:

By Jan-Bob ------------ DRW+GAB, =Ebola Rebuild 1.12.1 translated to english



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Joined: 09/24/2012
Groups: Go Science
DRW+GAB Find worst segments,

DRW+GAB

Find worst segments, tries several Deep Rebuilds, Fuzes the best solution then GAB (bands) the best fuzed solution,
Go to next worst segments etc.

A lot of options are available (after automatic check of pertinent options like mutable or not etc): segment min en max lengths, filters to start or not Fuze and GAB, all to loop or not, etc.

On cancel, restores the best structures and keeps track of the latest options in a note in segment 1. This allows to restart from previous activity.

Joined: 09/24/2012
Groups: Go Science
The original author is

The original author is Jean-Bob

He agreed to share this recipe once translated to English. Now he takes some long holliday.

All other versions are in Fench.

NEW to ver 1.11.6 = English version

L'Aliance Francophone hopes you will enjoy.

Please report bugs by copy-paste of what is written in Note of segment 1 and send it to this page.

Bruno

Joined: 09/24/2012
Groups: Go Science
The original author is

The original author is Jean-Bob

He agreed to share this recipe once translated to English. Now he takes some long holliday.

All other versions are in French.

NEW to ver 1.11.6 = English version

L'Aliance Francophone hopes you will enjoy.

Please report bugs by copy-paste of what is written in Note of segment 1 and send it to this page.

Bruno

Roukess's picture
User offline. Last seen 4 years 17 weeks ago. Offline
Joined: 10/26/2010
This recipe combines the

This recipe combines the power of the rebuilds from DRW with the ability of GAB to increase the score by banding some segments.
Moreover, we made some improvements :
Whole prot : The possibility to rebuild and GAB one by one each segments of the protein, from segment 1 to segment max.
ScoreFilter : Select the minimum score required to launch GAB. Tick "Do not launch GAB" if you only want to rebuild and fuse.
Allow loss : Ebola will not restore the highscore if the score is included in this Loss threshold
FastFuse : Use 1 fuse instead of 5
Saving module : If you tick the "Start again since the last stop" box, Ebola will restart at the same segment as before stopping the last Ebola run. The data from the last run is stored in a note on segment 1
Language : The structure of the script permits to translate very easily the dialogs in many languages.

"More" options :
Rebuild Filter : Skip wiggle after the rebuild if the score is not included between these 2 values compared to the highscore (highscore-Minfilter Subscore management : Consider only one of these subscores to define the worse segments
ForceZone : Rebuild only a selected part of the protein. It is possible to enter many zones. Tick "Walk in the Forcezone" to rebuild from the first to the last segment each zones.
Launch automatically GAB : Launch automatically GAB if the threshold is exceeded
Precise band : Bands from GAB always start from next to the rebuild segments.
Display more information : Display more information in the output of the recipe

"GAB" options :
Number of critters, generations and allowed loss

Nevertheless, it takes a lot of time for each cycle. Excellent recipe for an overnight folding!

Joined: 09/24/2012
Groups: Go Science
10 apr 2013

Now bilingual: L'Alliance Francophone and marie_s get it in French. Please contact me if you want other linguistic versions, or if you want to see it in French.

Joined: 04/01/2013
Groups: None
Error message

maxContSegs:10 forceZone, allowLoss:true scoringMode:Backbone curSeg:1 herd,renew:4,firstGen:10,breedBest:3,breedBastards:2,keepBest:5,newRandom:4,maxBadGen:6,shuffle:true,maxGen:2 mutateAlways:false contSegsMax:12 solsPerScore:2 qstabThresh:1 onlyMutable:false rebuildCI:0.8 contSegsMin:7 useLigand:false passGAB:false mutateOnceCI:0.21 scoreFilter:20 fastMode:false fastFuse:false rebuildLoops:true curArray,1|1:11|2:-51.082419025879|3:* backbone:-51.082419025879
,2|1:10|2:-49.729362534766|3:* backbone:-49.729362534766
,3|1:12|2:-44.991079450522|3:* backbone:-44.991079450522
,4|1:9|2:-44.057049192758|3:* backbone:-44.057049192758
,5|1:28|2:-43.071154704375|3:* clashing:-43.071154704375
,6|1:30|2:-42.216364566698|3:* clashing:-42.216364566698
,7|1:29|2:-41.344078640533|3:* clashing:-41.344078640533
,8|1:31|2:-40.272502654169|3:* clashing:-40.272502654169
,9|1:32|2:-39.373918562726|3:* clashing:-39.373918562726
,10|1:45|2:-38.797102945374|3:* backbone:-38.797102945374
,11|1:48|2:-38.456597845988|3:* backbone:-38.456597845988
,12|1:65|2:-37.656429921894|3:* clashing:-37.656429921894
,13|1:27|2:-37.302348497267|3:* clashing:-37.302348497267
,14|1:63|2:-37.195951382538|3:* clashing:-37.195951382538
rebuildBest:false mutateOnce:false minRebuild:5000 bands,maxUp:6.1,minChng:3,minDist:4,minStr:0.3,minLen:2,minSkip:5,maxStr:1.1,maxDn:6.9 critter,breedScore:-20,maxBands:5,keepConditions:true,minBands:2,totalLoss:90,keepScore:-50,maxLoss:0,giveUp:200 fuzeThresh:10 preciseBands:false fastQstab:true maxCI:1 resumeScript:false pullCI:0.55 subscores,1|1:clashing|2:packing|3:hiding|4:bonding|5:backbone|6:sidechain|7:disulfides|8:other,2|1:clashing|2:packing|3:backbone,3|1:hiding|2:bonding|3:sidechain,4|1:other,mode|1:All|2:Backbone|3:Sidechain|4:Other energy:false maxVal:-5 forceZoneStr: recipeName:EbolaRebuild stIndex:2 verbose:false wholeProt:false rebuildNum:30 autoGab:true segs:7 maxRebuild:0.001 lossThresh:200 gabThresh:30 zoneWalk:false numSegs:14

Joined: 09/24/2012
Groups: Go Science
Not on, sepsis puzzles (e.g 702)

Ebola does'nt support puzzles with cuts (like Sepsis puzzles).

Joined: 09/24/2012
Groups: Go Science
Bug 'nil value' fixed

Thanks JDScienceTeacher !

Joined: 09/24/2012
Groups: Go Science
bug detectlog

does not recognise all lockpuzzles (not working on 713-.
See line 676

Joined: 09/24/2012
Groups: Go Science
to verify

if rebuild does not gain, abandonning all solutions? (to be verified)

Joined: 09/24/2012
Groups: Go Science
Limitations for 722

For puzzles like 722, the only option that work is "whole protein" (or second panel "forcezone" and "walk the forcezone")

Joined: 09/24/2012
Groups: Go Science
Update 24 Jun 2013

Se recent best at the start so that you can reset the puzzle and start again where you want.

Joined: 02/08/2012
Groups: None
help with the menu options

What are rebuild filters? What are forced zones?

Also, it would be amazing if this script could work on selected segments.

Joined: 02/08/2012
Groups: None
ignore those questions

ignore those questions. sorry. i should of read all the comments before commenting.

Joined: 09/24/2012
Groups: Go Science
help for translating to Dutch, German etc

Please post here your translation and give me your group name or your name. Then on next versions, you'll get the log in your language:
Copy-paste the following text and just translate (or even correct my english in) what is between " ", NOT changing the bizarre codes beginning with %, neither my comments after --
For non ascii letters, i'll have to change them to a special code later on, I'll find a solution)

i18n={
ask={
ok="OK",
cancel="Cancel",
options={
mainTitle="Ebola Rebuild options",
l1="Segments",
contSegsMin="Segments min",
contSegsMax="Segments max",
numSegs="Segments/zone",
wholeProt="Whole protein",
l2="Rebuild",
rebuildNum="Rebuild/zone",
solsPerScore="Solutions/zone",
l3="Threshold for GAB",
scoreFilter="GAB Filter",
passGAB ="Do not launch GAB",
l4="Score",
allowLoss="Allow loss",
lossThresh="loss threshold",
l5="Others",
rebuildLoops ="Transform protein to loop",
fastMode ="Only do rebuild+shake",
fastFuse="Fast Fuse (Faster, less points)",
mutateOnce="Mutate once",
resumeScript="Start again since the last stop",
advanced="More",
GABOptions="GAB"
},
gab={
mainTitle="GAB Options",
l1="Generations",
totalLoss="GAB max loss",
maxGen="Max generations",
l2="Max generations without gain for :",
renew="Start again",
maxBadGen="Stop",
l3="Critters",
firstGen="Crits 1r gén.",
maxLoss="Loss max/crit",
giveUp="Give up threshold",
keepConditions="Keep conditions",
fuzeThresh="Launch fuse threshold",
l4="Other",
l5="Use Ligand options : 0-Never, 1-Random, 2-Allways",
useLigand="Use Ligand"
},
advanced={
mainTitle="Advanced options",
l1="Rebuild filter",
minRebuild="Min filter",
maxRebuild="Max filter",
l2="Subscore management",
l3="Scores : 1-all, 2-backbone 3-sidechain, 4-other",
stIndex="Score type",
l4="Force zone",
l5="Format: Start1,End1-Start2,End2...",
forceZoneStr="Forced zone :",
zoneWalk ="Walk in the forced zone",
l6="Launch automatically GAB",
autoGab="Allow GAB to be automatically launched",
gabThresh ="Launch threshold",
l7="Others",
rebuildCI="Clash rebuild",
preciseBands="Precise bands",
rebuildBest="Rebuild best segments",
verbose="Display more informations"
}
},
recipe={
sb=">>> Still %.3f points to gain. Score : %.3f.",
gb1="Impossible to save bands. Disabling.",
gb2="Bands saved. Deleting.",
tsc=">> Gain : %.3f points. Score : %.3f.",
tso1="Solution %i. Score : %.3f.",
tso2a="Launching GAB.",
tso2b="Gain GAB auto : %.3f. Score : %.3f.",
tso3="Fail of the solution.",
tso4="Best solution. Score : %.3f.",
tso5="Fail of the rebuild, next zone.",
dlr="* Rebuild #%i.",
dlr2=">>> Microgain saved.",
is1="No segment fit to the requested critter.",
is2="Whole protein rebuild.",
is3="Script state loaded.",
e1=" %i contiguous segments zone.",
e2="Rebuild of segments %i-%i.",
e3="* Zone score : %.3f.",
e4="* Data :",
e5="WARNING: Loss allowed. Score : %.3f. Total : -%.3f.", -- BK 19/3/2013
e6="Total Ebola gain: %.3f. Score : %.3f.", --- ajoute Ebola BK 19/3/13
e7="Frozen segment detected. Next zone.",
m1="Script recovered.",
m2="Start of Ebola Rebuild. Mode : %q. Score : %.3f.",
m3a="Initial parameters treatment completed.",
m3b="Whole protein walking.",
fh="Creating %i random critters...",
critter="%s : %i bands.",
ab="* Impossible to create bands. GAB stopped.",
sh1="Launching %i critters...",
sh2a="Critter %s : %.3f.",
sh2b="Unrespected critter. Give up.",
bh="Breeding...",
g1="Launching GAB.",
g2="* Generation : %i. Score : %.3f. Gain : %.3f",
g3="Create a completely random generation…",
g4="* GAB final score : %.3f. Total Gain: %.3f.", -- idem BK
lw1="Loading Highscore....",
lw2="Loading secondary structure...",
lw3="Loading bands...",
lw4="Saving script state", -- added BK 21/3/13
de1="User stop.",
de2="unexpected error detected.",
de3="Error line: %i.",
de4="Error : %s."
}
}

spmm's picture
User offline. Last seen 44 weeks 6 days ago. Offline
Joined: 08/05/2010
Groups: Void Crushers
log file appearing on lower part of screen after cancel

Hi, I cancelled this in the selection interface after getting some points, thankyou. It seemed as if a log file was being displayed right across
the bottom section of the screen. I was able to hot key back to the standard interface and it disappeared.
Closed the puzzle and reopened - the strip was still there!
Ran another script and cancelled that and it disappeared.

Cheers
spmm

spmm's picture
User offline. Last seen 44 weeks 6 days ago. Offline
Joined: 08/05/2010
Groups: Void Crushers
you should really remove this script

until it is working properly

Joined: 09/24/2012
Groups: Go Science
Working on new version

I'm testing a new version with my team, in 2 languages and at least 2 OSs.

This version (latest maintenance = June) is not maintained anymore. It will be replaced when the new version will be strong enough.

Joined: 09/24/2012
Groups: Go Science
tip for puzzles with locks

Only option "Whole" does work on puzzles with locked segments

Joined: 09/24/2012
Groups: Go Science
Concerning log script that may appear on screen (spmm)

This is normal, it's the note of segment 1, used to restore the best structures and keep track of the latest options. This allows to restart from previous activity.
If you don't want to see this, don't display the notes on screen when running.

Joined: 09/24/2012
Groups: Go Science
Debugged version here:
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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