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Recipe: Scaffolding sheets V1.1
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Name: Scaffolding sheets V1.1
ID: 9448
Created on: Fri, 08/27/2010 - 07:52
Updated on: Fri, 08/27/2010 - 14:52
Description:

Now with distance scaling. See script for details.



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Joined: 09/18/2009
Groups: SETI.Germany
That's how the code does look like

-- Scaffolding by Crashguard303
-- Script request by Mat747
-- Included faster band removing, submitted by rav3n_pl

-- Applies bands between segments,
-- if their SPATIAL and INDEX distance is inbetween an user-specified range,
-- resulting a relative position lock of these segments (scaffolding).

-- NOTE:
-- At the moment, FoldIt doesn't allow us to set band lengths greater than 20.
-- We can't apply bands between adjacent segments, so these are skipped

function YesNo(Bool)
local Bool=Bool
local OS
if Bool==true then
OS="yes"
else
OS="no"
end -- if
return OS
end -- function

function ss_check(SegA,SegB)

local SegAss=get_ss(SegA)
local SegBss=get_ss(SegB)
local ss_flag=false

if SegAss~=SegBss then -- if secondary structure is unequal
if BandMixed==true then -- And connecting mixed ss is okay
ss_flag=true
end -- if BandMixeed
else -- so if ss is equal
if SegAss=="L" then -- loops found
if BandLoops==true then
ss_flag=true
end -- if BandLoops
elseif SegAss=="H" then -- helices found
if BandHelices==true then
ss_flag=true
end -- if BandHelices
else -- No loops and helices, so it must be sheets
if BandSheets==true then
ss_flag=true
end -- if BandSheets
end -- if SegAss is letter
end -- if SegAss unequal
return ss_flag
end -- function

function DistanceCheck(k,l)
local k=k
local l=l
local Distance
local DistanceFlag=false
Distance=get_segment_distance(k,l) -- get distance
if Distance*DistFactor<=20 then
-- The game doesn't allow bands longer than 20, so check resulting band length=distance*factor
if Distance>=MinSdist then -- above or equal minimum?
if Distance<=MaxSdist then -- below or equal maximum?
DistanceFlag=true
end -- if Distance
end -- if Distance
if InvertFlag==true then DistanceFlag=not(DistanceFlag) end -- Invert result, if desired
end -- if Distance<=20
return Distance,DistanceFlag
end -- function

function Scaffolding()

if MinIdist>MaxIdist then MinIdist,MaxIdist=MaxIdist,MinIdist end
-- If Min>Max, swap them because it wouldn't make sense
if MinIdist<1 then MinIdist=1 end -- if value is smaller than 1, set it to 1

if MinSdist>MaxSdist then MinSdist,MaxSdist=MaxSdist,MinSdist end
-- If Min>Max, swap them because it wouldn't make sense
if MinSdist<1 then MinSdist=1 end -- if value is smaller than 1, set it to 1

if DeleteAllBands then
local BandsToDelete=get_band_count()
if BandsToDelete>0 then
print("Removing ",BandsToDelete," bands...")
for k=1,BandsToDelete do
print(k)
band_delete(1)
end -- k loop
end -- if BandsToDelete>0
print()
end -- if DeleteAllBands

print("Connecting segments with strength: ",Strength)
print()
local OS
if InvertFlag==false then
OS=""
else
OS="out of "
end -- if
print("Distance range spatial: ",OS,MinSdist," to ",MaxSdist)
print("Distance factor: ",DistFactor)
print("Distance range index: ",MinIdist," to ",MaxIdist)
print()
print("Connect:")
print("Mixed: ",YesNo(BandMixed))
print("Loops: ",YesNo(BandLoops))
print("Helices: ",YesNo(BandHelices))
print("Sheets: ",YesNo(BandSheets))
print()

local kFinish=NumSegs-MinIdist
local k

for k=1,kFinish do -- k=first segment index to check
local lStart=k+MinIdist
local lFinish=k+MaxIdist
if lFinish>NumSegs then lFinish=NumSegs end
local l

for l=lStart, lFinish do -- l=second segment index to check
Distance,DistanceFlag=DistanceCheck(k,l) -- Get distance and distance flag
if DistanceFlag then -- Does distance match?
if ss_check(k,l) then -- Do secondary structures match?
print("Connected ",k,":",l," distance:",Distance) -- Show
band_add_segment_segment(k,l) -- Connect
local TempBandCount=get_band_count() -- Get new band amount
Distance=Distance*DistFactor -- Change distance value by applying Factor
band_set_length(TempBandCount,Distance) -- Change length of last band
band_set_strength(TempBandCount,Strength) -- Change strength of last band
end -- if ss_check
end -- if DistanceFlag
end -- l loop
end -- k loop
end -- function

-- CHANGE PARAMETERS HERE:
NumSegs=get_segment_count() -- Get amount of segments

DeleteAllBands=true -- delete all bands before script start, boolean value
-- If true, all existing bands are deleted before script is executed.
-- If false, previous bands are kept, however.

MinIdist=5 -- Minimum INDEX segment distance to band, INTEGER value
-- Minimum value:2,
-- because the game doesn't connect bands if the segments are too close
MaxIdist=NumSegs-1 -- Maximum INDEX segment distance to band, INTEGER value
MinSdist=4 -- Minimum SPATIAL segment distance to band, FLOAT value
MaxSdist=6 -- Maximum SPATIAL segment distance to band, FLOAT value
DistFactor=1 -- Factor, which changes the band length according to its spatial distance, float value, >=0
-- values<1 pull segments together,
-- values keep them in postion,
-- values>1 push them apart
-- Examples:
-- If a segment distance is 4, and factor is 2, the band length will be 8.
-- If a segment distance is 4, and factor is .5, the band length will be 2.
InvertFlag=false -- Distance inverting, boolean value
-- Set this to true if you want to invert spatial distance banding
-- Be careful with this option, it can create many bands if MinSdist and MaxSdist are close!

Strength=1 -- Band strength of the scaffold, float value

BandMixed=false -- Boolean value. If true, banding mixed secondary structures is allowed
BandLoops=false -- Boolean value. If true, banding loop to loop is allowed
BandHelices=false -- Boolean value. If true, banding helix to helix is allowed
BandSheets=true -- Boolean value. If true, banding sheet to sheet is allowed
-- Note: If you change BandMixed,BandLoops,BandHelices AND BandSheets to false
-- NO band will be applied. You will just waste some of your precious time.

Scaffolding() -- Call script with these parameters

Joined: 09/18/2009
Groups: SETI.Germany
More...

This script is most useful after alignment, to keep the puzzle from "exploding", which means parts flying apart when wiggle is performed.

Using it, I recommend "Strength" values equal or below 1, to allow the segments some movement.

Do your alignment, apply scaffolding, then do wiggle, and when wiggling, slowly remove some bands.

Joined: 08/24/2010
Very powerful

Very useful when using sidechain, or rebuild recipes. They prevent the protein from ripping apart.

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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