Recipe: Tvdl BridgeFuze 1.0.0

created by Timo van der Laan

Profile

• Name: Tvdl BridgeFuze 1.0.0
• ID: 43845
• Shared with: Public
• Parent: None
• Children: None
• Created on: August 10, 2012 at 11:46 AM UTC
• Updated on: August 10, 2012 at 11:46 AM UTC
• Description:

  Just the standard Fuze, but keeping cys-bridges intact.

Code

-- BridgeFuze 1.0.0 Tvdl
-- A standard fuze but will keep sulfide bridges intact.

-- Handy shorts module
CI=behavior.SetClashImportance
segCnt=structure.GetCount()
while structure.GetSecondaryStructure(segCnt)=="M" do segCnt=segCnt-1 end

-- Score functions
function Score()
    if normal==nil or normal==true then
        -- FIX for big negatives
        local total= current.GetEnergyScore()

        return total
    else
        return current.GetScore()
    end
end

function SegScore()
    local total=8000
    for i=1,segCnt do
        total=total+current.GetSegmentEnergyScore(i)
    end
    return total
end

function RBScore()
    if normal==nil or normal==true then
        return recentbest.GetEnergyScore()
    else
        return recentbest.GetScore()
    end
end

function round3(x)--cut all afer 3-rd place
    return x-x%0.001
end

bestScore=Score()
function SaveBest()
    local g=Score()-bestScore
    if g>0 then
        if g>0.01 then print("Gained another "..round3(g).." pts.") end
        bestScore=Score()
        save.Quicksave(3)
    end
end

-- Wiggle function
-- Note the extra parameter to be used if only selected parts must be done
function Wiggle(how, iters, minppi,onlyselected)
    --score conditioned recursive wiggle/shake
    --fixed a bug, absolute difference is the threshold now
    if how==nil then how="wa" end
    if iters==nil then iters=6 end
    if minppi==nil then minppi=0.1 end
    if onlyselected==nil then onlyselected=false end

    if iters>0 then
        iters=iters-1
        local sp=Score()
        if onlyselected then
            if how == "s" then
                -- Shake is so slow on big ones, so first try one round
                structure.ShakeSidechainsSelected(1)
                if math.abs(Score()-sp) > minppi then structure.ShakeSidechainsSelected(1) end
            elseif how == "wb" then structure.WiggleSelected(2,true,false)
            elseif how == "ws" then structure.WiggleSelected(2,false,true)
            elseif how == "wa" then structure.WiggleSelected(2,true,true)
            end
        else
            if how == "s" then
                -- Shake is so slow on big ones, so first try one round
                structure.ShakeSidechainsAll(1)
                if math.abs(Score()-sp) > minppi then structure.ShakeSidechainsAll(1) end
            elseif how == "wb" then structure.WiggleAll(2,true,false)
            elseif how == "ws" then structure.WiggleAll(2,false,true)
            elseif how == "wa" then structure.WiggleAll(2,true,true)
            end
        end
        if math.abs(Score()-sp) > minppi then return Wiggle(how, iters, minppi,onlyselected) end
    end
end

-- end of handy shorts module

-- Position stack module 1.0
-- uses slot 50 and higher
Stackmin=50
StackMarks={}
StackPos=50
function PushPosition()
    if StackPos==100 then
        print("Position stack overflow, exiting")
        exit()
    end
    save.Quicksave(StackPos)
    StackPos=StackPos+1
end

function PopPosition()
    if StackPos==50 then
        print("Position stack underflow, exiting")
        exit()
    end
    StackPos=StackPos-1
    save.Quickload(StackPos)
end
function PushMarkPosition()
    StackMarks[#StackMarks+1]=StackPos
    PushPosition()
end
function PopMarkPosition()
    if #StackMarks == 0 then
        print("No marked position found, just popping")
    else
        StackPos=StackMarks[#StackMarks]+1
        StackMarks[#StackMarks]= nil
    end
    PopPosition()
end
function ClrTopPosition()
    if StackPos > 50 then StackPos=StackPos-1 end
end

-- Segment set and list module
-- Notice that most functions assume that the sets are well formed
-- (=ordered and no overlaps)
-- 02-05-2012 TvdL Free to use for non commercial purposes

function SegmentListToSet(list)
    local result={}
    local f=0
    local l=-1
    table.sort(list)
    for i=1,#list do
        if list[i] ~= l+1 and list[i] ~= l then
            -- note: duplicates are removed
            if l>0 then result[#result+1]={f,l} end
            f=list[i]
        end
        l=list[i]
    end
    if l>0 then result[#result+1]={f,l} end
    --print("list to set")
    --SegmentPrintSet(result)
    return result
end

function SegmentSetToList(set)
    local result={}
    for i=1,#set do
        --print(set[i][1],set[i][2])
        for k=set[i][1],set[i][2] do
            result[#result+1]=k
        end
    end
    return result
end

function SegmentCleanSet(set)
-- Makes it well formed
    return SegmentListToSet(SegmentSetToList(set))
end

function SegmentInvertSet(set,maxseg)
-- Gives back all segments not in the set
-- maxseg is added for ligand
    local result={}
    if maxseg==nil then maxseg=structure.GetCount() end
    if #set==0 then return {{1,maxseg}} end
    if set[1][1] ~= 1 then result[1]={1,set[1][1]-1} end
    for i=2,#set do
        result[#result+1]={set[i-1][2]+1,set[i][1]-1}
    end
    if set[#set][2] ~= maxseg then result[#result+1]={set[#set][2]+1,maxseg} end
    return result
end

function SegmentInList(s,list)
    table.sort(list)
    for i=1,#list do
        if list[i]==s then return true
        elseif list[i]>s then return false
        end
    end
    return false
end

function SegmentInSet(set,s)
    for i=1,#set do
        if s>=set[i][1] and s<=set[i][2] then return true
        elseif s<set[i][1] then return false
        end
    end
    return false
end

function SegmentJoinList(list1,list2)
    local result=list1
    if result == nil then return list2 end
    for i=1,#list2 do result[#result+1]=list2[i] end
    table.sort(result)
    return result
end

function SegmentJoinSet(set1,set2)
    return SegmentListToSet(SegmentJoinList(SegmentSetToList(set1),SegmentSetToList(set2)))
end

function SegmentCommList(list1,list2)
    local result={}
    table.sort(list1)
    table.sort(list2)
    if #list2==0 then return result end
    local j=1
    for i=1,#list1 do
        while list2[j]<list1[i] do
            j=j+1
            if j>#list2 then return result end
        end
        if list1[i]==list2[j] then result[#result+1]=list1[i] end
    end
    return result
end

function SegmentCommSet(set1,set2)
    return SegmentListToSet(SegmentCommList(SegmentSetToList(set1),SegmentSetToList(set2)))
end

function SegmentSetMinus(set1,set2)
    return SegmentCommSet(set1,SegmentInvertSet(set2))
end

function SegmentPrintSet(set)
    print(SegmentSetToString(set))
end

function SegmentSetToString(set)
    local line = ""
    for i=1,#set do
        if i~=1 then line=line..", " end
        line=line..set[i][1].."-"..set[i][2]
    end
    return line
end

function SegmentSetInSet(set,sub)
    if sub==nil then return true end
    -- Checks if sub is a proper subset of set
    for i=1,#sub do
        if not SegmentRangeInSet(set,sub[i]) then return false end
    end
    return true
end

function SegmentRangeInSet(set,range)
    if range==nil or #range==0 then return true end
    local b=range[1]
    local e=range[2]
    for i=1,#set do
        if b>=set[i][1] and b<=set[i][2] then
            return (e<=set[i][2])
        elseif e<=set[i][1] then return false end
    end
    return false
end
--- End of Segment Set module

-- Module Find Segment Types
function FindMutables()
    local result={}
    for i=1,structure.GetCount() do if structure.IsMutable(i) then result[#result+1]=i end end
    return SegmentListToSet(result)
end
function FindFrozen()
    local result={}
    for i=1,structure.GetCount() do if freeze.IsFrozen(i) then result[#result+1]=i end end
    return SegmentListToSet(result)
end
function FindLocked()
    local result={}
    for i=1,structure.GetCount() do if structure.IsLocked(i) then result[#result+1]=i end end
    return SegmentListToSet(result)
end
function FindSelected()
    local result={}
    for i=1,structure.GetCount() do if selection.IsSelected(i) then result[#result+1]=i end end
    return SegmentListToSet(result)
end
function FindAAtype(aa)
    local result={}
    for i=1,structure.GetCount() do
        if structure.GetSecondaryStructure(i)== aa then result[#result+1]=i end
    end
    return SegmentListToSet(result)
end
function FindAminotype(at)
    -- This one returns a list not a set
    local result={}
    for i=1,structure.GetCount() do
        if structure.GetAminoAcid(i) == at then result[#result+1]=i end
    end
    return result
end

-- end Module Find Segment Types
-- Start of module for bridgechecking
Cyslist={}
savebridges=false --default no bridgechecking
nrofbridges=0

function setCyslist()
    Cyslist=FindAminotype("c")
    nrofbridges=CountBridges()
end

function IsBridge(i)
    return ''..current.GetSegmentEnergySubscore(i,'disulfides') ~= '-0'
end

function CountBridges()
    local count = 0
    for i = 1,#Cyslist do
        if IsBridge(Cyslist[i]) then count = count + 1 end
    end
    return count
end

function BridgesBroken()
    return savebridges == true and CountBridges() < nrofbridges
end
-- End module bridgechecking
-- Bridgekeeping Fuze module
-- Picks up all gains by using recentbest
-- But makes sure no bridges are broken

function BridgeFuzeEnd()
    PushPosition()
    CI(1)
    Wiggle("wa",1)
    Wiggle("s",1)
    Wiggle()
    if RBScore()> Score() then BridgerestoreRB() end
    if not BridgesBroken() then
        SaveBest()
        ClrTopPosition()
    else
        PopPosition()
    end
end
function BridgeFuze1(ci1,ci2)
    PushPosition()
    CI(ci1)
    Wiggle("s",1)
    CI(ci2)
    Wiggle("wa",1)
    if not BridgesBroken() then
        ClrTopPosition()
    else
        PopPosition()
    end
end
function BridgeFuze2(ci1,ci2)
    PushPosition()
    CI(ci1)
    Wiggle("wa",1)
    CI(1)
    Wiggle("wa",1)
    CI(ci2)
    Wiggle("wa",1)
    if not BridgesBroken() then
        ClrTopPosition()
    else
        PopPosition()
    end
end
function reBridgeFuze(scr,slot)
    local s=Score()
    if s<scr then
        save.Quickload(slot)
    else
        scr=s
        save.Quicksave(slot)
    end
    return scr
end
function BridgerestoreRB()
    PushPosition()
    recentbest.Restore()
    if BridgesBroken() then
        PopPosition()
    else ClrTopPosition() end
end
function BridgeFuze(slot)
    local scr=Score()

    PushPosition()
    recentbest.Save()
    BridgeFuze1(0.3,0.6) BridgeFuzeEnd()
    scr=reBridgeFuze(scr,slot)
    BridgeFuze2(0.3,1)
    if RBScore()>Score() then BridgerestoreRB() end
    SaveBest()
    scr=reBridgeFuze(scr,slot)
    BridgeFuze1(0.05,1)
    if RBScore()>Score() then BridgerestoreRB() end
    SaveBest()
    scr=reBridgeFuze(scr,slot)
    BridgeFuze2(0.7,0.5) BridgeFuzeEnd()
    scr=reBridgeFuze(scr,slot)
    BridgeFuze1(0.07,1)
    if RBScore()>Score() then BridgerestoreRB() end
    SaveBest()
    reBridgeFuze(scr,slot)
    if RBScore()>Score() then BridgerestoreRB() end
    SaveBest()
end
-- end bridgekeeping Fuze module

version="1.0.0"
function main()
    local ss=Score()
    print("Tvdl BridgeFuze "..version)
    print("Starting score: "..round3(ss))
    savebridges=true
    setCyslist() --Finds the Cys and counts the bridges
    print("Nr of Cys: "..#Cyslist.." Bridges: "..nrofbridges/2)
    save.Quicksave(3) --Not sure if this is needed
    save.Quicksave(4) --Not sure if this is needed
    recentbest.Save() --Not sure if this is needed
    BridgeFuze(4)
    print("End of BridgeFuze.")
    print("Endscore: "..round3(Score()).." Total gain: "..round3(Score()-ss))
end

function Cleanup(err)
    print("Restoring best position and Class Importance")
    print(err)
    CI(1)
    save.Quickload(3)
end

xpcall(main,Cleanup)

Comments

[Timo van der Laan]

It keeps all the good gains, but gains that have broken a bridge are discarded.
If cancelled it will reset CI and the best good score.

Beware:
If a gain was discarded the credit best might contain a broken bridge.