Recipe: ATGrinder 1.0

created by LociOiling

Profile

• Name: ATGrinder 1.0
• ID: 100190
• Shared with: Public
• Parent: None
• Children: None
• Created on: November 06, 2014 at 02:52 AM UTC
• Updated on: November 06, 2014 at 02:52 AM UTC
• Description:

  This recipe is intended for debugging Acid Tweeker crashes. It performs the first phase Acid Tweeker phase with a selectable starting and ending segment. A particular pose, which has been shared with scientists, causes a "AtomTree::torsion_angle_dof_id: angle range error" client crash when started on segment 45.

Code

--[[

    ATGrinder

    attempt to replicate Acid Tweeker crash

]]--

--Start Generic JET parameters and functions
recipeName = "ATGrinder"
Version = "1.0"
ReVersion  =  recipeName .. " v." .. Version

WF = 4
PROBABLEFILTER = true

bestScore = 0

startChunque = nil -- initial chuquePoint
CSVOutput = false

flagligand = false
segCnt = structure.GetCount()
segCnt2 = segCnt -- cas de ligands
while structure.GetSecondaryStructure(segCnt2) == "M" do segCnt2 = segCnt2 - 1 flagligand = true end
segStart = 1 --start from (Default option for JET)
segEnd = segCnt2 --end seg: nil=end of protein (Default option for JET) -- duplicat a verifier

ATSegStart = segStart
ATSegEnd = segEnd

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

function down ( x )
    return x - x % 1
end

function Score () 
    return current.GetEnergyScore ()
end

-- Module Random
-- Tvdl, 01-11-2012
Randomseed = os.time () % 1000000
function Seedrandom ()
    math.randomseed ( Randomseed )
    math.random ( 100 ) -- Because the first is not random
end
Seedrandom ()

--
--  begin chunquePoint Beta package
--

function beginChunque ( startChunque, prefix, scoreFunc, pose )
    local chunque = chunquePoint ( prefix, scoreFunc, pose )
    if startChunque == nil then
        chunquePrint ( chunque )
    else
        local gain = chunque [ 2 ] - startChunque [ 2 ]
        chunquePrint ( chunque, gain )
    end
    return chunque
end
function endChunque ( startChunque, prefix, scoreFunc, pose )
    local chunque = chunquePoint ( prefix, scoreFunc, pose )
    chunqueGain ( startChunque, chunque )
end

function chunquePoint ( prefix, scoreFunc, pose )
    if prefix == nil then 
        prefix = ""
    end
    local score = 0
    if pose == nil then
        score =  scoreFunc ()
    else
        if pose == nil then
            pose = current
        end
        score = scoreFunc ( pose )
    end
    local runDate, runClock, runTime         
   
    runDate = os.date ()
    runClock = os.clock()
    runTime = os.time()

    return { prefix, score, runDate, runClock, runTime }
end

function chunquePrint ( chunque, gain )
    local function round ( ii )
        return ii - ii % 0.001
    end
    if gain == nil then
        if CSVOutput then
            print ( chunque [ 1 ] ..  "," .. 
                    round ( chunque [ 2 ] ) ..  "," .. 
                    chunque [ 3 ] 
                  )
        else
            print ( chunque [ 1 ] .. ", score: " .. 
                    round ( chunque [ 2 ] ) .. ", " ..
                    chunque [ 3 ] 
                  )
        end
    else
        if CSVOutput then
            print ( chunque [ 1 ] .. "," .. 
                    round ( chunque [ 2 ] ) .. "," .. 
                    round ( gain ) .. "," ..  
                    chunque [ 3 ] 
                  )
        else
            print ( chunque [ 1 ] .. ", score: " ..
                    round ( chunque [ 2 ] ) .. ", gain: " ..
                    round ( gain ) .. ", " .. 
                    chunque [ 3 ]
                  )
        end
    end
end

function chunqueGain ( startChunk, endChunk )
    local function round ( ii )
        return ii - ii % 0.001
    end

    local Clocktime = os.difftime ( endChunk [ 5 ], startChunk [ 5 ] )
    local gain = round ( endChunk [ 2 ] - startChunk [ 2 ] ) 
    local hours = Clocktime / ( 60 * 60 ) 
    local pph = gain / hours

    if CSVOutput then
        print ( endChunk [ 1 ] .. "," ..
                round ( endChunk [ 2 ] ) .. "," ..
                round ( gain ) .. "," ..
                round ( hours ) .. "," .. 
                round ( pph ) .. "," ..
                endChunk [ 3 ]
              )
    else
        print ( endChunk [ 1 ] .. ", score: " .. 
                round ( endChunk [ 2 ] ) .. ", gain: " .. 
                round ( gain ) .. ", " ..
                endChunk [ 3 ] 
              )
        print ( endChunk [ 1 ] .. ", hours: " .. 
                round ( hours ) .. ", points per hour: " .. 
                round ( pph ) )
    end

end

--
--  end chunquePoint Beta package
--

function ds ( val )
    structure.ShakeSidechainsSelected ( val )
end

function CI ( val )
    global_ci = val
    behavior.SetClashImportance ( global_ci )
end

function WiggleSimple ( val, how )
    if PROBABLEFILTER then 
        behavior.SetSlowFiltersDisabled ( true ) 
    end
    if how == "s" then ds ( 1 )
        elseif how == "wb" then structure.WiggleSelected ( val * WF, true, false ) -- backbones
        elseif how == "ws" then structure.WiggleSelected ( val * WF, false, true ) -- sidechains
        elseif how == "wa" then structure.WiggleSelected ( val * WF, true, true ) -- all
    end
    if PROBABLEFILTER then 
        behavior.SetSlowFiltersDisabled ( OriginalFilterSetting ) 
    end 
end

function WiggleAT ( how, iters, minppi )
    local valiter = 2
    local val = 1
    if fast == true then 
        valiter = 1 
    end
    if how == nil then 
        how = "wa" 
    end
    if iters == nil then  
        iters = 3 
    end
    if ( minppi == nil ) or ( minppi < 0.01 ) then
        minppi = 0.01
    end
    if global_ci == 1.00 then 
        val = valiter 
    end
    
    local sp, ep, ig

    repeat
        iters = iters - 1
        sp = Score ()
        WiggleSimple ( val, how )
        ep = Score ()
        ig = ep - sp
    until iters <= 0 or how == "s" or ig < minppi
end

function SelectSphere ( sg, radius, nodeselect )
    if nodeselect ~= true then 
        selection.DeselectAll () 
    end
    for ii = segStart, segEnd do
        if structure.GetDistance ( sg, ii ) < radius then 
            selection.Select ( ii ) 
        end
    end
end

function SaveBest () --adapted to JET
    local sp = Score ()
    local g = sp - bestScore
    if g > 0 then
       bestScore = sp
       print ( "gained another " .. round ( g ) )
    end
end

function wiggle_out ()
    CI ( 0.6 )
    WiggleSimple ( 1, "wa" ) -- new function BK 8/4/2013
    CI ( 1.0 )
    WiggleAT ()
    WiggleAT ( "s", 1 )
    --selection.SelectAll ()
    CI ( 0.6 )
    WiggleAT ()
    CI ( 1.0 )
    WiggleAT ()
    recentbest.Restore ()
    SaveBest ()
end

function getNear ( seg )
    if Score () < g_total_score - 1000 then
        selection.Deselect ( seg )
        CI ( 0.75 )
        WiggleSimple ( 1, "s" ) -- new function BK 8/4/2013
        WiggleSimple ( 1, "ws" ) -- new function BK 8/4/2013
        selection.Select ( seg )
        CI ( 1 )
    end
    if Score () < g_total_score - 1000 then
        recentbest.Restore ()
        SaveBest ()
        return false
    end
    return true
end

function sidechain_tweak ( sphereSize, ATSegStart, ATSegEnd )
    for ATseg = ATSegStart, ATSegEnd do
        selection.DeselectAll ()
        selection.Select ( ATseg )
        structure.SetNote ( 3, "AT phase 1, segment = " .. ATseg )
        local ss=Score ()
        g_total_score = Score ()
        CI ( 0 )
        print ( "wiggling segment " .. ATseg )
        WiggleSimple ( 2, "s" )
        CI ( 1.0 )
        print ( "selecting sphere around segment " .. ATseg )
        SelectSphere ( ATseg, sphereSize )
        print ( "calling getNear ( " .. ATseg .. " )" )
        if getNear ( ATseg ) == true then
            print ( "wiggle_out for segment " .. ATseg )
            wiggle_out ()
        end
    end
end

function GetParameters ()
    local dlog = dialog.CreateDialog ( ReVersion )
    local askresult

    dlog.WF = dialog.AddSlider ( "wiggle factor", WF, 1, 5, 0 )
    dlog.ATSegStart = dialog.AddSlider ( "start segment", ATSegStart, segStart, segEnd, 0 )
    dlog.ATSegEnd = dialog.AddSlider ( "end segment", ATSegEnd, segStart, segEnd, 0 )
    dlog.PROBABLEFILTER = dialog.AddCheckbox ( "disable slow filters?", PROBABLEFILTER )

    dlog.ok = dialog.AddButton ( "OK", 1 )
    dlog.cancel = dialog.AddButton ( "Cancel",  0 )

    repeat
        askresult = dialog.Show ( dlog )
        if askresult > 0 then
            WF = dlog.WF.value
            ATSegStart = dlog.ATSegStart.value
            ATSegEnd = dlog.ATSegEnd.value
            if ATSegStart > ATSegEnd then
                ATSegStart, ATSegEnd = ATSegEnd, ATSegStart
            end
            PROBABLEFILTER = dlog.PROBABLEFILTER.value
        end
    until askresult < 2
    return askresult > 0
end


function main ()
--
--  model 010 - startup - print recipe name, puzzle name, track
--
    print (  ReVersion )
    print ( "Puzzle: " .. puzzle.GetName () )
    print ( "Track: " .. ui.GetTrackName () )

--
--  model 020 - startup - print recipe parms
--
    print ( "options:" )
    print ( "Wiggle Factor = " .. WF )
    print ( "starting AT segment = " .. ATSegStart )
    print ( "ending AT segment = " .. ATSegEnd )

    print ( "--" )
--
--  model 030 - startup - print start time, start score
--
    startChunque = beginChunque ( nil, "Start", Score )

    CI ( 1.00 )
    save.Quicksave ( 3 )--in save 3 always best solution. Load in case of crash.
    bestScore = Score ()
    sidechain_tweak ( 8, ATSegStart, ATSegEnd )
    
    cleanup ()

end

function cleanup ( error )
    print ( "---" )
--
--  model 100 - print recipe name, puzzle, track, time, score, and gain
--
    local reason
    local start, stop, line, msg
    if error == nil then
        reason = "complete"
    else
    --
    --  model 120 - civilized error reporting,
    --              thanks to Bruno K. and Jean-Bob
    --
        start, stop, line, msg = error:find ( ":(%d+):%s()" )
        if msg ~= nil then
            error = error:sub ( msg, #error )
        end
        if error:find ( "Cancelled" ) ~= nil then
            reason = "cancelled"
        else
            reason = "error"
        end
    end

    print (  ReVersion .. " " .. reason )
    print ( "Puzzle: " .. puzzle.GetName () )
    print ( "Track: " .. ui.GetTrackName () )

    if reason == "error" then
        print ( "Unexpected error detected" )
        print ( "Error line: " .. line )
        print ( "Error: \"" .. error .. "\"" )
    end

--
--  model 130 - reset clash importance, clear selections, restore structures, etc.
--
    recentbest.Restore ()
    save.Quickload ( 3 )
    selection.DeselectAll ()
    freeze.UnfreezeAll ()
    band.DeleteAll ()
    save.LoadSecondaryStructure ()
    CI ( 1 )
    behavior.SetSlowFiltersDisabled ( OriginalFilterSetting )

--
--  model 150 - report the final time, score, gain, elapsed time, and points per hour
--
    if startChunque ~= nil then
        endChunque ( startChunque, "Final", Score )
    end
end

if GetParameters () then
    xpcall ( main, cleanup )
end

Comments

[LociOiling]

See the feedback Acid Tweeker "angle range error" crashes – test case for more information.

This recipe may also be useful for debugging similar Acid Tweeker crashes. The recipe lets you select the starting and ending segments. In this case, the problem segment was found through trial and error.

One previous attempt at debugging involved creating a segment note containing the segment being tweeked. Unfortunately, the most current information was lost in the crash. For example, the segment note identified segment 19 as being worked on, but the segment 45 was actually the one that caused the crash.

This version of the recipe contains the only the first "sidechain_tweak" phase of Acid Tweeker. Many of the complications found in recent versions of Acid Tweeker have been removed.