Recipe: PutAllContactMapBands

created by KarenCH

Profile

• Name: PutAllContactMapBands
• ID: 49545
• Shared with: Public
• Parent: None
• Children: None
• Created on: July 26, 2014 at 13:08 PM UTC
• Updated on: July 26, 2014 at 13:08 PM UTC
• Description:

  Puts bands between all the contact map points.

Code

----------------------------- Constants to change as desired ------------------------------
defaultStrength = 1.0
doTip1 = false
doTip2 = false
UseSetLengthForAlreadyContactedSegs = false
UseCompressionAndStrengthGame = true

--------------------------- Boring constants ------------------------------
heatThreshold = 0.96
segCt = structure.GetCount()

----------------------------------------------------- 
-- THE BANDER
----------------------------------------------------- 
function PutAllContactMapBands( heatThreshold, strength, doTip1, doTip2 )
    print( "AllCMBands" )
    changeSucceeded = false
    for i = 1, segCt-2 do
        for j = i+2, segCt do
            if contactmap.GetHeat(i, j) >= heatThreshold then
                local goalLength = nil
                if UseCompressionAndStrengthGame then
                    if contactmap.IsContact( i, j ) then
                        goalLength = 0.9 * structure.GetDistance( i , j )
                        strength = 0.5 * defaultStrength
                    else 
                        goalLength = 0.7 * structure.GetDistance( i , j )
                        strength = 1.5 * defaultStrength
                    end
                elseif UseSetLengthForAlreadyContactedSegs and contactmap.IsContact( i, j ) then 
                    goalLength = structure.GetDistance( i, j )
                    strength = defaultStrength
                end
                changeSucceeded = BandBetweenSegsWithParameters( 
                                        i, j, strength, goalLength,
                                        doTip1, doTip2 ) 
                                  or changeSucceeded
            end
        end
    end
    if not changeSucceeded then print "ContactMap Failed" end
    return changeSucceeded
end

----------------------------------------------------- 
-- BOILERPLATE STUFF
----------------------------------------------------- 
function BandBetweenSegsWithParameters( seg1, seg2, strength, goalLength, fromTip1, fromTip2 )
    -- caller can set goalLength without setting strength by providing strength = 0.0
    if not ( IsMovableSeg( seg1) or IsMovableSeg( seg2) ) then return false end
    if fromTip1 == nil then fromTip1 = false end
    if fromTip2 == nil then fromTip2 = false end
    if fromTip1 then tip1 = GetTipAtomOfSeg(seg1) else tip1 = 0 end
    if fromTip2 then tip2 = GetTipAtomOfSeg(seg2) else tip2 = 0 end

    local bIdx = band.AddBetweenSegments( seg1, seg2, tip1, tip2 )
    if bIdx ~= band.GetCount( ) then 
        DebugPrint( "failed to add band from "..seg1.." to "..seg2)
        return false 
    end

    if goalLength ~= nil then 
        band.SetGoalLength( bIdx, goalLength ) 
    end
    if strength ~= nil and strength > 0.0 then 
        band.SetStrength( bIdx, strength )
    end
    return true
end

function IsMovableSeg( seg1 )
   if seg1 == nil or seg1 < 1 or seg1 > segCt then return false end

   local BB, SC = freeze.IsFrozen( seg1 )
   local sl = structure.IsLocked( seg1 )
   return not (BB or SC or sl)
end

-- for branched aas, simply picks one (longer, one with donor/acceptor tip, or if no difference then either)
function GetAtomOfTip( aa )
    if aa == "a" then return 10
    elseif aa == "c" then return 11
    elseif aa == "d" then return 8
    elseif aa == "e" then return 9
    elseif aa == "f" then return 20
    elseif aa == "g" then return 0 -- glycine has no tip. just use a backbone atom
    elseif aa == "h" then return 17
    elseif aa == "i" then return 18
    elseif aa == "k" then return 9
    elseif aa == "l" then return 16
    elseif aa == "m" then return 17
    elseif aa == "n" then return 14
    elseif aa == "p" then return 13
    elseif aa == "q" then return 9
    elseif aa == "r" then return 22
    elseif aa == "s" then return 11
    elseif aa == "t" then return 6
    elseif aa == "v" then return 13
    elseif aa == "w" then return 24
    elseif aa == "y" then return 12
    else return 0
    end
end

function GetTipAtomOfSeg( idx )
    return GetAtomOfTip( structure.GetAminoAcid( idx ))
end


----------------------------------------------------- 
-- THE CALL
----------------------------------------------------- 
PutAllContactMapBands( heatThreshold, defaultStrength, doTip1, doTip2 )