Recipe: Bravo Hydro PulleR v3.0

created by bravosk8erboy

Profile

• Name: Bravo Hydro PulleR v3.0
• ID: 108953
• Shared with: Public
• Parent: Rav3n_pl Hydro PulleR v2.1
• Children:
  • Bravo Hydro PulleR v4.0
• Created on: December 30, 2024 at 15:11 PM UTC
• Updated on: July 20, 2025 at 18:10 PM UTC
• Description:

  Pull all hydrophobic to all other hydrophobics in loop

Code

--[[
Bravo Random Hydro Puller v3.0 based on Rav3n_pl Hydro PulleR v2.1
Pulling all hydrophobes to all hydrophope segments
v2.1 - Using 1st sidechain atom to pull.

v3.0 - Using tip atom of the sidechain instead of beta carbon to pull.
     - Removed Random segment selection and loop count. changed to try every hydrophobic segment instead.
     - added repeat main if score improvement was found. no try forever or arbitrary number.
]] --

--- OPTIONS

minBS = 0.3 --starning minimum bands strenght
maxBS = 1.0 --maximum bads str
maxLoss = 10 --minimum percentage loss when pulling. ie 5% of 10000 is 500pts
pullingCI = 0.6 --clash importance while pulling
fastQstab = true -- for 1s1w as stabilize (faster)
doFuze = 100 --run fuze when score after qstabilize is close to best. If negative  run fuze only if  gain after qstab
energy = false --set true for exploration puzzles if want seek stability
pullDist = 4 --make bands shorter by that many units
minDist = 2 --minimum distance between segments

-- end of options
-- Initialize variables
local starting_score = current.GetScore()
local best_score = starting_score
local segment_count = structure.GetCount()

math.randomseed(recipe.GetRandomSeed())

p = print
CI = behavior.SetClashImportance
segCnt = structure.GetCount()
while structure.GetSecondaryStructure(segCnt) == 'M' do
    segCnt = segCnt - 1
end

function Score()
    local s
    if energy == true then
        s = current.GetEnergyScore()
    else
        s = current.GetScore()
    end
    return s
end

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

function abs(x)
    if x < 0 then
        x = -x
    end
    return x
end

function Wiggle(how, iters, minppi) --score conditioned recursive wiggle/shake
    if how == nil then
        how = 'wa'
    end
    if iters == nil then
        iters = 6
    end
    if minppi == nil then
        minppi = 0.1
    end

    if iters > 0 then
        iters = iters - 1
        local sp = Score()
        if how == 's' then
            structure.ShakeSidechainsSelected(1)
        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)
        end
        if Score() - sp > minppi then
            return Wiggle(how, iters, minppi)
        end
    end
end

function AllLoop() --turning entire structure to loops
    local ok = false
    for i = 1, segCnt do
        local s = structure.GetSecondaryStructure(i)
        if s ~= 'L' then
            save.SaveSecondaryStructure()
            ok = true
            break
        end
    end
    if ok then
        selection.SelectAll()
        structure.SetSecondaryStructureSelected('L')
    end
end

function RandomInt(high)
    return math.random(high)
end

function SaveBest()
    local s = Score()
    local g = s - best_score
    if g > 0 then
        if g > 0.01 then
            p('Gained another ' .. round(g) .. ' pts.')
        end
        best_score = s
        save.Quicksave(1)
    end
end

function bandstr(str) --set all band strengt
    for i = 1, band.GetCount() do
        band.SetStrength(i, str)
    end
end

function down(x) --cut all after comma
    return x - x % 1
end
function round(x) --cut all afer 3-rd place
    return x - x % 0.001
end

function SaveRB()
    save.Quicksave(4)
    recentbest.Restore()
    SaveBest()
    save.Quickload(4)
end

function qStab()
    selection.SelectAll()
    CI(0.1)
    Wiggle('s', 1)
    if fastQstab == false then
        CI(0.4)
        Wiggle('wa', 1)
        CI(1)
        Wiggle('s', 1)
    end
    CI(1)
    Wiggle()
end

function FuzeEnd()
    CI(1)
    Wiggle('wa', 1)
    Wiggle('s', 1)
    Wiggle()
    srb()
end
function Fuze1(ci1, ci2)
    CI(ci1)
    Wiggle('s', 1)
    CI(ci2)
    Wiggle('wa', 1)
end
function Fuze2(ci1, ci2)
    CI(ci1)
    Wiggle('wa', 1)
    CI(1)
    Wiggle('wa', 1)
    CI(ci2)
    Wiggle('wa', 1)
end
function srb()
    recentbest.Restore()
    SaveBest()
end
function Fuze()
    p('Fuzing...')
    selection.SelectAll()
    recentbest.Save()
    Fuze1(0.3, 0.6)
    FuzeEnd()
    Fuze2(0.3, 1)
    srb()
    Fuze1(0.05, 1)
    srb()
    Fuze2(0.7, 0.5)
    FuzeEnd()
    Fuze1(0.07, 1)
    srb()
end

function MakeBands(pullSg)
    band.DeleteAll()
    for i = 1, segCnt do
        if structure.IsHydrophobic(i) then
            local bn1 = band.GetCount()
            local setDist = structure.GetDistance(i, pullSg) - pullDist - minDist
            if setDist > 1 then
                band.AddBetweenSegments(i, pullSg, atomIndex(i), atomIndex(pullSg)) --pull using tip of sidechain segment
                bn1 = band.GetCount() - bn1
                if bn1 > 0 then
                    band.SetGoalLength(band.GetCount(), setDist)
                end
            end
        end
    end
end

-- Custom atom indices for each amino acid type with inline comments
-- Indices atom values for the tip of the side chains.
    -- There might be a better index to pull to hide the side chain better. play around with these.
    -- 20 common amino acids. doesn't handle unkown or ligands
atom_indices = {
    a={5},   --a-ALA-Alanine
    c={6},   --c-CYS-Cystein
    d={6},   --d-ASP-Aspartate
    e={7},   --e-GLU-Glutamate
    f={11},  --f-PHE-Phenylalanine
    g={2},   --g-GLY-Glycine
    h={10},  --h-HIS-Histidine
    i={8},   --i-ILE-IsoLeucine
    k={9},   --k-LYS-Lysine
    l={6},   --l-LEU-Leucine
    m={8},   --m-MET-Methionine
    n={6},   --n-ASN-Asparagine
    p={6},   --p-PRO-Proline
    q={7},   --q-GLN-Glutamine
    r={9},   --r-ARG-Argenine
    s={6},   --s-SER-Serine
    t={6},   --t-THR-Threonine
    v={7},   --v-VAL-Valine
    w={14},  --w-TRP-Tryptophan
    y={12}   --y-TYR-Tyrosine
}


function atomIndex(segment_index)
    local aminoAcid = structure.GetAminoAcid(segment_index)
    
    -- Check if aminoAcid exists in atom_indices
    if atom_indices[aminoAcid] == nil then
        return 5 -- Use beta carbon instead (first atom of the sidechain)
    end
    
    local AtomIndexOfTipOfSideChain = atom_indices[aminoAcid][1] --returns the number value from a aminoacid letter code.
    
    return AtomIndexOfTipOfSideChain 
end


function main()
    local initialScore = current.GetScore()
    local lastBS = minBS
    local qsc = Score()
    save.Quicksave(1)
    p('Starting Hydro Puller,  Start score: ' .. round(qsc))

    
    x = 0
    while x < segCnt do
    x=x+1
        while true do --random hydro segment
            if structure.IsHydrophobic(x) then
                break
            end
            x=x+1
            if x>segCnt then
                break
            end
        end
        
        if x>segCnt then
            break
        end

        local ls = Score()
        local loss = round(ls * (maxLoss / 100))
        p(' pulling seg: ' .. x)
        MakeBands(x)
        p('Made ' .. band.GetCount() .. ' bands, pulling until loss of ' .. loss .. ' pts.')
        -- selection.SelectAll()
        CI(pullingCI)
        recentbest.Save()
        for str = lastBS, maxBS, 0.07 do --search enough band strenght to move
            recentbest.Restore() --because sometimes it makes points during pull :D
            local ss = Score()
            bandstr(str)
            structure.WiggleAll(1, true, false)
            if ss - Score() > loss then
                lastBS = str - 0.1
                if lastBS < minBS then
                    lastBS = minBS
                end
                break
            end
        end
        band.DeleteAll()
        SaveRB() --because sometimes it missing fractions
        p('Stabilizing...')
        CI(1)
        recentbest.Save() --after pulling
        qStab()
        if Score() > ls + doFuze then
            SaveBest()
            Fuze(4)
        end
        SaveBest()
        save.Quickload(1) --load best state
        p('Current score: ' .. round(Score()) .. ' Total gain: ' .. Total_gain())
    end
    p('Total gain: ' .. Total_gain())
    
        -- repeat main if score inproved
    if current.GetScore() > initialScore then
        main()
    end
    
    if ending_print_once then
        ending_print()
    end
end


-- end of script


-- start of standard Bravo Template



function Total_gain()
    return (best_score-starting_score)
end

-- Function to check and update the best score
function check_and_update_score(segment)
    local new_score = current.GetScore()
    if new_score > best_score then
        gain = new_score - best_score
        best_score = new_score
        save.Quicksave(1)
        
        if gain > 0.001 then-- was printing pointless gains with to much clutter. still want to keep score improvement though
           print(" Seg: " .. segment .. " Score: " .. best_score .. "   Gain: " .. gain)
        end

        return  -- Score improved
    else
        save.Quickload(1)
        return  -- Score did not improve
    end
end

ending_print_once = true
function ending_print()
    if ending_print_once then
        -- Print the best score and total gain
        local total_gain = best_score - starting_score
        print("Best score: " .. best_score)
        print("Total gain: " .. total_gain)
        ending_print_once = false
    end
end

-- Error handler function
function error_handler(err)
    print("Error: " .. err)
    check_and_update_score(0)  --error can't pass segment info so i use "0"
    ending_print()
    return
end

xpcall(main, error_handler)