Recipe: global design

created by Deleted player

Profile

• Name: global design
• ID: 108242
• Shared with: Public
• Parent: None
• Children:
  • global design (COPY)
• Created on: March 29, 2023 at 09:32 AM UTC
• Updated on: April 01, 2023 at 12:14 PM UTC
• Description:

  trying to automate the proteins for all kind of puzzles, this is a test recipe, please feel free to educate me with your thoughts/experience/tips and so on, thank you

Code

function round ( ii )
    return ii - ii % 0.001
end

function behavior()
    if behavior.GetBackboneHBondImportance() < 3 then
        imp=behavior.GetBackboneHBondImportance()+1
    	behavior.SetBackboneHBondImportance(imp)
    end
    if behavior.GetClashImportance() < 1 then
    	imp= behavior.GetClashImportance()+1
    	behavior.SetClashImportance(imp)
    end
    if behavior.GetDensityImportance() < 3 then
    	imp=behavior.GetDensityImportance()+1
    	behavior.SetDensityImportance(imp)
    end
    if behavior.GetHidingImportance() < 3 then
        imp=behavior.GetHidingImportance()+1
    	behavior.SetHidingImportance(imp)
    end
    if behavior.GetPackingImportance() < 3 then
        imp=behavior.GetPackingImportance()+1
    	behavior.SetPackingImportance(imp)
    end
    if behavior.GetPairwiseImportance() < 3 then
    	imp=behavior.GetPairwiseImportance()+1
    	behavior.SetPairwiseImportance(imp)
    end
    if behavior.GetSidechainHBondImportance() < 3 then
    	imp=behavior.GetSidechainHBondImportance()+1
    	behavior.SetSidechainHBondImportance(imp)
    end
    if behavior.GetWigglePower() == "l" or behavior.GetWigglePower() == "h" then
    	behavior.SetWigglePower("a")
    end
end

function rotamers(rr, scr)
    rotamer.GetCount(rr)
    save.Quicksave ( 4 )
    for rot = 1, rotamer.GetCount ( rr ) do
        rotamer.SetRotamer ( rr, rot )
        if current.GetSegmentEnergySubscore ( rr, "sidechain" ) > scr then
            save.Quicksave ( 4 )
        end
    end
    save.Quickload ( 4 )
end


function normalSeg ( seg2, segcnt, symnum )
    if seg2 <= segcnt or symnum == 0 then
        return seg2, 0 
    end
    local endz = {}
    for sym = 1, symnum do
        endz [ #endz + 1 ] = segcnt * sym + sym + 1
    end
    local adjseg = 0
    local adjsym = 0
    for rng = #endz, 1, -1 do 
        if seg2 >= endz [ rng ] then
            adjseg = seg2 - endz [ rng ] + 1
            adjsym = rng
            break
        end
    end
    return adjseg, adjsym
end

function bonds(cc,ss )
    segcnt = structure.GetCount ()
    symcnt = structure.GetSymCount () 
    bond = structure.GetHBonds ()
    for ii = 1, #bond do
        local res2, chn = normalSeg (  bond [ ii ] [ "res2" ], segcnt, symcnt )
        bx = band.AddBetweenSegments ( bond [ ii ] [ "res1" ], res2, bond [ ii ] [ "atom1" ], bond [ ii ] [ "atom2" ], chn )
        if bx ~= nil and bx ~= 0 then
            blen = band.GetLength ( bx )
            band.SetGoalLength(bx, blen)
        end
    end
end

function abego(aa, st)
    ab = structure.GetABEGO ( aa )
    if structure.GetABEGO(aa) == "A" then
        bonds(bb, st)
    elseif structure.GetABEGO(aa) == "B" then
        bonds(bb, st)
    elseif structure.GetABEGO(aa) == "E" then
        bonds(bb, st)
    elseif structure.GetABEGO(aa) == "G" then
        bonds(bb, st)
    elseif structure.GetABEGO(aa) == "O" then
        bonds(bb, st)
    end
end
    
segCnt = structure.GetCount()
bestscorepart =  creditbest.GetScore()
currentscorepart = 0
while currentscorepart <  bestscorepart do
    for ii = 1, segCnt do
        absolutebest.Restore()
    	bestengscorepart =  creditbest.GetEnergyScore()
    	currentengscorepart = 0
    	while currentengscorepart < bestengscorepart do
    	    local scoreparts = {}
    	    scoreparts = puzzle.GetPuzzleSubscoreNames()
        	for jj = 1, #scoreparts do
        	    local sub = round ( current.GetSegmentEnergySubscore ( ii, scoreparts [ jj ] ) )
        	    print( scoreparts [ jj ] .. ": " .. sub )
    			if sub ~= 0 then
    				if structure.IsHydrophobic(ii) == "false" then
    					rotamers(jj, sub)
    					abego(ii, struc)
    				else
    					struc = structure.GetSecondaryStructure(ii)
    					amino = structure.GetAminoAcid(ii)
    					if struc == "H" then
    					    structure.SetAminoAcid(ii, "c")
    						rotamers(jj, sub)
    						abego(ii, struc)
    					else
    						rotamers(jj, sub)
    						abego(ii, struc)
    					end
    				end
    			else
    				chains={"g";"a";"v";"c";"p";"t";"s";"i";"l";"n";"d";"m";"h";"q";"e";"f";"k";"y";"r";"w"}
                    if structure.CanMutate(ii, chains[ jj ])  == "true" then
                        if struc == "H" then
                            structure.SetAminoAcid(ii, "c")
                            rotamers(jj, sub)
                            abego(ii, struc)
                        end
                    else
                        rotamers(jj, sub)
                        abego(ii, struc)
                    end
    			end
    			selection.Select(ii)
                structure.IdealizeSelected()
                structure.RebuildSelected(1)
                structure.WiggleSelected(1, true, true)
                selection.Deselect(ii)
    		end
    		selection.Select(ii)
        	freeze.FreezeSelected(true, true)
            selection.Deselect(ii)
            selection.DeselectAll()
            structure.ShakeSidechainsAll(1)
            structure.WiggleAll(1, false , true)
            structure.WiggleAll(1, true , true)
    		currentengscorepart = bestengscorepart
        	bestengscorepart =  creditbest.GetEnergyScore()
        	recentbest.Save()
        end
        selection.Select(ii)
    	freeze.FreezeSelected(true, true)
        selection.Deselect(ii)
        selection.DeselectAll()
        structure.ShakeSidechainsAll(1)
        structure.WiggleAll(1, false , true)
        structure.WiggleAll(1, true , true)
    end
    currentscorepart = bestscorepart
    bestscorepart =  creditbest.GetScore()
    recentbest.Save()
end