Recipe: CG303 Scaffolding Helices V2.50

created by Crashguard303

Profile

• Name: CG303 Scaffolding Helices V2.50
• ID: 41821
• Shared with: Public
• Parent: None
• Children:
  • Scaffolding Helices V2.50
  • CG303 Scaffolding Helices V2.50.1
• Created on: May 21, 2012 at 10:37 AM UTC
• Updated on: May 21, 2012 at 10:37 AM UTC
• Description:

  Lua V2 translation, now with input window. ; When playing with clash importance, this script can help you preventing atom bonds from breaking apart. ; This example tries to maintain atom bonds between helix segments. ; It can also be used for sheets, but then you will have to check sheet manipulating and use other distance values (higher index distance). ; Feel free to offer some useful parameters (for sheets). ; By default, the script does only keep the distances between segments by generating bands having the same length as each distance. Changing the length factor, you can even compress or decompress sections. ; Another strategy when playing with clash importance is to choose only bands with big lengths (maintaning only large distances), allowing minor changes in connections. ; Have fun!

Code

-- 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 OS

 if Bool then
   OS="yes"
  else
   OS="no"
 end -- if BOOL

 return OS
end -- function

function ss_check(SegA,SegB)

 local SegAss=structure.GetSecondaryStructure(SegA)
 local SegBss=structure.GetSecondaryStructure(SegB)
 local ss_flag=false

 if SegAss~=SegBss then -- if secondary structure is unequal
   if Band_ss_mixed then -- And connecting mixed ss is okay
    ss_flag=true
   end -- if BandMixeed
  else -- so if ss is equal
   if Band_ss_equal[SegAss]then
     ss_flag=true
   end -- if Band_ss_equal
 end -- if SegAss unequal

 return ss_flag
end -- function

function DistanceCheck(k,l)
 local k=k
 local l=l
 local Distance=structure.GetDistance(k,l) -- get distance
 local DistanceFlag=false

 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 Band_Invert_Result then DistanceFlag=not(DistanceFlag) end -- Invert result, if desired

return Distance,DistanceFlag
end -- function

function Scaffolding()
 print("Executing...")

 if Band_DeleteAll_Before then
  print("Deleting old bands.")
  band.DeleteAll()
 end

 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?
   local OS="Connecting "..k..":"..l.." distance:"..Distance
   print(OS) -- Show
   band.AddBetweenSegments(k,l) -- Connect
   local TempBandCount=band.GetCount() -- Get new band amount
   Distance=Distance*Band_DistFactor -- Change distance value by applying Factor
   band.SetGoalLength(TempBandCount,Distance) -- Change length of last band
   band.SetStrength(TempBandCount,Band_Strength) -- Change strength of last band
   end -- if ss_check
   end -- if DistanceFlag
  end -- l loop
 end -- k loop

 print("Finished.")
end -- function

function InputDialog ()
 local ask = dialog.CreateDialog("Set parameters")

 ask.Band = dialog.AddLabel("Band which secondary structure:")
 ask.Helixes = dialog.AddCheckbox("Helix-Helix", Band_ss_equal["H"])
 ask.Sheets = dialog.AddCheckbox("Sheet-Sheet", Band_ss_equal["E"])
 ask.Loops = dialog.AddCheckbox("Loop-Loop", Band_ss_equal["L"])
 ask.Mixed = dialog.AddCheckbox("Mixed", Band_ss_mixed)

 ask.Distance = dialog.AddLabel("Band which distance:")
 ask.MinIdist = dialog.AddSlider("Min INDEX:", MinIdist, 2, (NumSegs-1), 0)
 ask.MaxIdist = dialog.AddSlider("Max INDEX:", MaxIdist, 2, (NumSegs-1), 0)
 ask.MinSdist = dialog.AddSlider("Min SPATIAL:", MinSdist, 0, ((NumSegs-1)*4), 1)
 ask.MaxSdist = dialog.AddSlider("Max SPATIAL:", MaxSdist, 0, ((NumSegs-1)*4), 1)

 ask.Properties = dialog.AddLabel("Band properties:")
 ask.Band_DistFactor = dialog.AddSlider("Band Factor", Band_DistFactor, 0.0, 10.0, 1)
 ask.Band_Strength = dialog.AddSlider("Band Strength", Band_Strength, 0.1, 10.0, 1)
 ask.Band_DeleteAll_Before = dialog.AddCheckbox("Delete all other bands before", Band_DeleteAll_Before)
 ask.Band_Invert_Result = dialog.AddCheckbox("Invert banding result (careful with this option!)", Band_Invert_Result)

 ask.OK = dialog.AddButton("OK", 1)
 ask.Cancel = dialog.AddButton("Cancel", 0)
 
 if dialog.Show(ask)>0 then -- If OK was pressed
   Band_ss_equal["H"]=ask.Helixes.value
   Band_ss_equal["E"]=ask.Sheets.value
   Band_ss_equal["L"]=ask.Loops.value
   Band_ss_mixed=ask.Mixed.value

   MinIdist=ask.MinIdist.value
   MaxIdist=ask.MaxIdist.value
   MinSdist=ask.MinSdist.value
   MaxSdist=ask.MaxSdist.value

   if MinIdist>MaxIdist then MinIdist,MaxIdist=MaxIdist,MinIdist end
   -- If Min>Max, swap them because it wouldn't make sense

   if MinSdist>MaxSdist then MinSdist,MaxSdist=MaxSdist,MinSdist end
   -- If Min>Max, swap them because it wouldn't make sense

   Band_DistFactor=ask.Band_DistFactor.value
   Band_Strength=ask.Band_Strength.value
   Band_DeleteAll_Before=ask.Band_DeleteAll_Before.value
   Band_Invert_Result=ask.Band_Invert_Result.value

   return true
  else  -- If OK was not pressed
   print("Canceled.")
   return false
 end -- if dialog.Show(ask)
end -- function

-- Default parameters:
NumSegs=structure.GetCount()
                                                       -- Get amount of segments
Band_ss_equal={}
                                                       -- Initialize table containing information which equal secondary structures are allowed to be banded
Band_ss_equal["L"]=false
                                                       -- Boolean value. If true, banding loop to loop is allowed
Band_ss_equal["H"]=true
                                                       -- Boolean value. If true, banding helix to helix is allowed
Band_ss_equal["E"]=false
                                                       -- Boolean value. If true, banding sheet to sheet is allowed
Band_ss_mixed=false
                                                       -- Boolean value. If true, banding mixed secondary structures is allowed

                                                       -- Note: If you change Band_ss_mixed,BandLoops,BandHelices AND BandSheets to false,
                                                       -- NO band will be applied. You will just waste some of your precious time.

MinIdist=3
                                                       -- 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=4
-- MaxIdist=NumSegs-1
                                                       -- Maximum INDEX segment distance to band, INTEGER value
MinSdist=4
                                                       -- Minimum SPATIAL segment distance to band, FLOAT value
MaxSdist=8
                                                       -- Maximum SPATIAL segment distance to band, FLOAT value
Band_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

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

                                                       -- 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.
Band_DeleteAll_Before=false
                                                       -- 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.

Band_Invert_Result=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!

if InputDialog() then
                                                       -- Show/change values with input dialog
                                                       -- If OK was pressed
  Scaffolding()
                                                       -- call script with set parameters
end

Comments

[Crashguard303]

…is here:

pastebin.com

http://pastebin.com/DkvihJkn