Code
--[[
MicroIdealize 4.0
Test version - LociOiling - 2017/12/18
For use on puzzle 1440 and perhaps other aflatoxin puzzles, attempt to
determine whether idealizing locked segments has any effect.
Lots of TimoTech inserted to make it happen. Also some Loci code
Maybe some other code got hurt.
It happens.
]]--
Recipe = "Microidealize"
Version = "4.0 test"
ReVersion = Recipe .. " " .. Version
kOriginalStructureOrNewBest = 1 -- the starting structure, or any subsequent improvement, will be stored in this quicksave slot
best_score = 0
idealize_length = 3
min_residue = 1
max_residue = 999
worst_first = true
score_type = 1
original_slow_filters_setting = 0
kDefaultWiggle = 12
kSphereRadius = 10
segCnt = 0
segCnt2 = 0
dolocked = false -- if locked sections present, work on locked sections only
locksphr = false -- if locked sections present, include locked sections in wiggle sphere
ulcksphr = true -- if locked sections present, include unlocked sections in wiggle sphere
lockedL = {} -- list of locked segments
lockedS = {} -- set of locked segments
unlockedS = {} -- set of unlocked segments
idealz = {} -- table of ideality by segment
--
-- worklist offsets
--
WLSEG1 = 1
WLSEG2 = 2
WLIDEAL = 3
WLAFTER = 4
--
-- ideal list offsets
--
IDSEG = 1
IDLCK = 2
IDIDEAL = 3
IDAFTER = 4
function r3 ( i )
return i - i % 0.001
end
--
-- Segment set and list module v0.3
--
-- Find lists and sets of segments with various properties, such as selected or frozen.
--
-- A "list" is one-dimensional table containing segment numbers.
--
-- A "set" is a two-dimensional table containing segment number ranges.
--
-- For example, given a list of segments:
--
-- list = { 1, 2, 3, 7, 8, 11, 13, 14, 15 }
--
-- the corresponding set is:
--
-- set = { { 1, 3 }, { 7, 8 }, { 11, 11 }, {13, 15 } }
--
-- Most functions assume that the sets are well-formed,
-- meaning they are ordered and have no overlaps
--
-- 02-05-2012 TvdL Free to use for non commercial purposes
--
-- v0.2 - LociOiling - 2017/11/03
-- + add primary FindUnlocked function
-- v0.3 - LociOiling
-- + add FindRotamers function
--
function SegmentListToSet ( list ) -- retirer doublons
local result = {}
local f = 0
local l = -1
table.sort ( list )
for ii = 1, #list do
if list [ ii ] ~= l + 1 and list [ ii ] ~= l then
-- note: duplicates are removed
if l > 0 then result [ #result + 1 ] = { f, l } end
f = list [ ii ]
end
l = list [ ii ]
end
if l > 0 then result [ #result + 1 ] = { f, l } end
return result
end
function SegmentSetToList ( set ) -- faire une liste a partir d'une zone
local result = {}
for ii = 1, #set do
for k = set [ ii ] [ 1 ], set [ ii ] [ 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 SegmentInvertList(list)
table.sort(list)
local result={}
for i=1,#list-1 do
for j=list[i]+1,list[i+1]-1 do result[#result+1]=j end
end
for j=list[#list]+1,segCnt2 do result[#result+1]=j end
return result
end
function SegmentInList ( s, list ) -- verifier si segment est dans la liste
table.sort ( list )
for ii = 1, #list do
if list [ ii ] == s then
return true
elseif list [ ii ] > s then
return false
end
end
return false
end
function SegmentInSet ( set, s ) --verifie si segment est dans la zone
for ii = 1, #set do
if s >= set [ ii ] [ 1 ] and s <= set [ ii ] [ 2 ] then
return true
elseif s < set [ ii ] [ 1 ] then
return false
end
end
return false
end
function SegmentJoinList ( list1, list2 ) -- fusionner 2 listes de segments
local result = list1
if result == nil then
return list2
end
for ii = 1, #list2 do
result [ #result + 1 ] = list2 [ ii ]
end
table.sort ( result )
return result
end
function SegmentJoinSet ( set1, set2 ) --fusionner (ajouter) 2 zones
return SegmentListToSet ( SegmentJoinList ( SegmentSetToList ( set1 ), SegmentSetToList ( set2 ) ) )
end
function SegmentCommList ( list1, list2 ) -- chercher intersection de 2 listes
local result = {}
table.sort ( list1 )
table.sort ( list2 )
if #list2 == 0 then return result end
local j = 1
for ii = 1, #list1 do
while list2 [ j ] < list1 [ ii ] do
j = j + 1
if j > #list2 then return result end
end
if list1 [ ii ] == list2 [ j ] then result [ #result + 1 ] = list1 [ ii ] end
end
return result
end
function SegmentCommSet ( set1, set2 ) -- intersection de 2 zones
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 ) -- pour pouvoir imprimer
local line = ""
for ii = 1, #set do
if ii ~= 1 then line = line .. ", " end
line = line .. set [ ii ] [ 1 ] .. "-" .. set [ ii ] [ 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 ii = 1, #sub do
if not SegmentRangeInSet ( set, sub [ ii ] ) then return false end
end
return true
end
function SegmentRangeInSet ( set, range ) --verifier si zone est dans suite
if range == nil or #range == 0 then return true end
local bb = range [ 1 ]
local ee = range [ 2 ]
for ii = 1, #set do
if bb >= set [ ii ] [ 1 ] and bb <= set [ ii ] [ 2 ] then
return ( ee <= set [ ii ] [ 2 ] )
elseif ee <= set [ ii ] [ 1 ] then
return false
end
end
return false
end
function SegmentSetToBool ( set ) --vrai ou faux pour chaque segment utilisable ou non
local result = {}
for ii = 1, structure.GetCount () do
result [ ii ] = SegmentInSet ( set, ii )
end
return result
end
--- End of Segment Set module
-- Module Find Segment Types
function FindMutablesList ()
local result = {}
for ii = 1, segCnt2 do
if structure.IsMutable ( ii ) then
result [ #result + 1 ] = ii
end
end
return result
end
function FindMutables()
return SegmentListToSet ( FindMutablesList () )
end
function FindFrozenList ()
local result = {}
for ii = 1, segCnt2 do
if freeze.IsFrozen ( ii ) then
result [ #result + 1 ] = ii
end
end
return result
end
function FindFrozen ()
return SegmentListToSet ( FindFrozenList () )
end
function FindLockedList ()
local result = {}
for ii = 1, segCnt2 do
if structure.IsLocked ( ii ) then
result [ #result + 1 ] = ii
end
end
return result
end
function FindLocked ()
return SegmentListToSet ( FindLockedList () )
end
function FindUnlockedList ()
local result = {}
for ii = 1, segCnt2 do
if not structure.IsLocked ( ii ) then
result [ #result + 1 ] = ii
end
end
return result
end
function FindUnlocked ()
return SegmentListToSet ( FindUnlockedList () )
end
function FindZeroScoreList ()
local result = {}
for ii = 1, segCnt do
local sub = 0
for jj = 1, #SubScores do
sub = sub + current.GetSegmentEnergySubscore ( ii, SubScores [ jj ] [ 1 ] )
end
if sub == 0 then
result [ #result + 1 ] = ii
end
end
return result
end
function FindZeroScore ()
return SegmentListToSet ( FindZeroScoreList () )
end
function FindRotamersList ()
local result = {}
for ii = 1, segCnt do
local rots = rotamer.GetCount ( ii )
if rots > 1 then
result [ #result + 1 ] = ii
end
end
return result
end
function FindRotamers ()
return SegmentListToSet ( FindRotamersList () )
end
function FindSelectedList ()
local result = {}
for ii = 1, segCnt do
if selection.IsSelected ( ii ) then
result [ #result + 1 ] = ii
end
end
return result
end
function FindSelected()
return SegmentListToSet ( FindSelectedList () )
end
function FindAAtypeList ( aa )
local result = {}
for ii = 1, segCnt2 do
if structure.GetSecondaryStructure ( ii ) == aa then
result [ #result + 1 ] = ii
end
end
return result
end
function FindAAtype ( aa )
return SegmentListToSet ( FindAAtypeList ( aa ) )
end
function FindAminotype ( at ) --NOTE: only this one gives a list not a set
local result={}
for ii = 1, segCnt2 do
if structure.GetAminoAcid ( ii ) == at then
result [ #result + 1 ] = ii
end
end
return result
end
--
-- end Segment set and list module v0.3
--
-- Thanks too Rav4pl
function ShuffleTable(tab) --randomize order of elements
local cnt=#tab
for i=1,cnt do
local r=math.random(cnt)
tab[i],tab[r]=tab[r],tab[i]
end
return tab
end
function GetScore ()
if ( score_type == 1 ) then
score = current.GetEnergyScore ()
elseif ( score_type == 2 ) then
behavior.SetFiltersDisabled ( false )
score = current.GetScore ()
behavior.SetFiltersDisabled ( true )
end
return score
end
function DoesPuzzleHaveFilters ()
local init_setting = behavior.GetFiltersDisabled ()
if ( init_setting == false ) then
score_without_sf = current.GetScore ()
behavior.SetFiltersDisabled ( true )
score_with_sf = current.GetScore ()
else
score_with_sf = current.GetScore ()
behavior.SetFiltersDisabled ( false )
score_without_sf = current.GetScore ()
end
behavior.SetFiltersDisabled ( init_setting )
if ( math.abs ( score_without_sf - score_with_sf ) > 1e-3 ) then
return true
else
return false
end
end
function SphereSelect ( start_idx, end_idx )
selection.DeselectAll ()
for ii = 1, segCnt2 do
for jj = start_idx, end_idx do
if lockedL [ ii ] then
if locksphr then
if structure.GetDistance ( ii , jj ) < kSphereRadius then
selection.Select ( ii )
end
end
else
if ulcksphr then
if structure.GetDistance ( ii , jj ) < kSphereRadius then
selection.Select ( ii )
end
end
end
end
end
end
--
-- GetWorklist
--
-- return set of segments to work on
--
-- sSet - segment set
-- lenX - length
-- gMinR - minimum residue
-- gMaxR - maximum residue
--
function GetWorklist ( sSet, lenX, gMinR, gMaxR )
local lsx = {}
for uu = 1, #sSet do
local minR = sSet [ uu ] [ 1 ]
local maxR = sSet [ uu ] [ 2 ]
if ( #sSet == 1 and minR >= gMinR and maxR <= gMaxR )
or ( #sSet > 1 and minR > gMinR and maxR <= gMaxR )
then
for ii = minR, maxR - lenX + 1 do
lsx [ #lsx + 1 ] = { ii, ii + lenX - 1, nil, nil, nil }
end
end
end
return lsx
end
function GoSegment ( start_idx, end_idx )
save.Quickload ( kOriginalStructureOrNewBest )
if ( start_idx > 1 ) then
structure.InsertCut ( start_idx )
end
if ( end_idx < segCnt2 ) then
structure.InsertCut ( end_idx )
end
selection.DeselectAll ()
selection.SelectRange ( start_idx , end_idx )
structure.IdealizeSelected ()
if ( start_idx > 1 ) then
structure.DeleteCut ( start_idx )
end
if ( end_idx < segCnt2 ) then
structure.DeleteCut ( end_idx )
end
SphereSelect ( start_idx, end_idx )
structure.WiggleSelected ( kDefaultWiggle )
local score = GetScore ()
if ( score > best_score ) then
best_score = score
print ( "Improvement to ".. r3 ( best_score ) )
save.Quicksave ( kOriginalStructureOrNewBest )
end
end
function ScoreIdealitySection ( seg1, seg2 )
local ideal = 0
for ii = seg1, seg2 do
ideal = ideal + current.GetSegmentEnergySubscore ( ii, "ideality" )
end
return ideal
end
function ScoreIdeality ( wlist )
for ii = 1, #wlist do
wlist [ ii ] [ WLIDEAL ] = ScoreIdealitySection ( wlist [ ii ] [ WLSEG1 ], wlist [ ii ] [ WLSEG2 ] )
end
return wlist
end
function SortIdealAsc ( xyzzy )
table.sort ( xyzzy, function ( a, b ) return a [ WLIDEAL ] < b [ WLIDEAL ] end)
return xyzzy
end
function Idealize ()
local inc
local worklist = {}
if dolocked then
worklist = GetWorklist ( lockedS, idealize_length, min_residue, max_residue )
else
worklist = GetWorklist ( unlockedS, idealize_length, min_residue, max_residue )
end
worklist = ScoreIdeality ( worklist )
if worst_first then
worklist = SortIdealAsc ( worklist )
else
worklist = ShuffleTable ( worklist )
end
for ii = 1, #worklist do
print ( "Idealizing "
.. worklist [ ii ] [ WLSEG1 ] ..
"-"
.. worklist [ ii ] [ WLSEG2 ] ..
", ideality = "
.. r3 ( worklist [ ii ] [ WLIDEAL ] ) ..
" ("
.. ii ..
"/"
.. #worklist ..
")"
)
GoSegment ( worklist [ ii ] [ WLSEG1 ], worklist [ ii ] [ WLSEG2 ] )
worklist [ ii ] [ WLAFTER ] = ScoreIdealitySection ( worklist [ ii ] [ WLSEG1 ], worklist [ ii ] [ WLSEG2 ] )
local ggain = worklist [ ii ] [ WLAFTER ] - worklist [ ii ] [ WLIDEAL ]
if ggain >= 0.001 then
print ( "ideality gained " .. r3 ( ggain ) )
end
end
end
function GetParameters ()
local dlog = dialog.CreateDialog ( ReVersion )
dlog.idealize_length = dialog.AddSlider ( "Idealize length" , idealize_length , 1 , 20 , 0 )
dlog.min_residue = dialog.AddSlider ( "Min residue" , 1 , 1 , segCnt2 , 0 )
dlog.max_residue = dialog.AddSlider ( "Max residue" , segCnt2 , 1 , segCnt2 , 0 )
dlog.worst_first = dialog.AddCheckbox ( "Worst first?" , worst_first )
if #lockedS > 0 then
dlog.dolocked = dialog.AddCheckbox ( "Do locked segments only?" , dolocked )
dlog.locksphr = dialog.AddCheckbox ( "Include locked in wiggle?" , locksphr )
dlog.ulcksphr = dialog.AddCheckbox ( "Include unlocked in wiggle?" , ulcksphr )
end
if DoesPuzzleHaveFilters () == true then
score_type = 2
end
dlog.score_type = dialog.AddSlider ( "Score type" , score_type , 1 , 2 , 0 )
dlog.ok = dialog.AddButton ( "OK" , 1 )
dlog.cancel = dialog.AddButton ( "Cancel" , 0 )
if ( dialog.Show ( dlog ) > 0 ) then
idealize_length = dlog.idealize_length.value
min_residue = dlog.min_residue.value
max_residue = dlog.max_residue.value
worst_first = dlog.worst_first.value
score_type = dlog.score_type.value
if #lockedS > 0 then
dolocked = dlog.dolocked.value
locksphr = dlog.locksphr.value
ulcksphr = dlog.ulcksphr.value
end
return true
else
return false
end
end
--
-- Ident - print identifying information at beginning and end of recipe
--
-- slugline - first line to print - normally recipe name and version
--
function Ident ( slugline )
local function round ( ii )
return ii - ii % 0.001
end
print ( slugline )
print ( "Puzzle: " .. puzzle.GetName () .. " (" .. puzzle.GetPuzzleID () .. ")" )
print ( "Track: " .. ui.GetTrackName () )
gname = user.GetGroupName ()
if gname ~= nil then
gname = " (" .. gname .. ")"
else
gname = ""
end
print ( "User: " .. user.GetPlayerName () .. gname )
local scoretype = scoreboard.GetScoreType ()
local scort = ""
if scoretype == 0 then
scort = "soloist"
elseif scoretype == 1 then
scort = "evolver"
elseif scoretype == 2 then
scort = "all hands"
elseif scoretype == 3 then
scort = "no score"
else
scort = "unknown/error"
end
print ( "Rank: " .. scoreboard.GetRank ( scoretype ) .. " (" .. scort .. ")" )
local sGroup = scoreboard.GetGroupScore ()
if sGroup ~= nil then
print ( "Group rank / score: " .. scoreboard.GetGroupRank () .. " / " .. round ( 10 * ( 800 - sGroup ) ) )
end
end
function Initialize ()
segCnt = structure.GetCount()
segCnt2 = segCnt
while structure.GetSecondaryStructure ( segCnt2 ) == "M" do
segCnt2 = segCnt2 - 1
end
print ( "initial segment count: " .. segCnt )
if segCnt ~= segCnt2 then
print ( "ligand found, adjusted segment count: " .. segCnt2 )
end
for ii = 1, segCnt2 do
lockedL [ #lockedL + 1 ] = structure.IsLocked ( ii )
end
lockedS = FindLocked ()
print ( #lockedS .. " locked sections found" )
unlockedS = FindUnlocked ()
print ( #unlockedS .. " unlocked sections found" )
--
-- record locked status and ideality of each segment
--
for ii = 1, segCnt2 do
local ideal = current.GetSegmentEnergySubscore ( ii, "ideality" )
idealz [ #idealz + 1 ] = { ii, lockedL [ ii ], ideal, 0, }
end
end
function main ()
Ident ( ReVersion )
save.Quicksave ( kOriginalStructureOrNewBest )
best_score = GetScore ()
print ( "Start score " .. r3 ( best_score ) )
Initialize ()
original_slow_filters_setting = behavior.GetFiltersDisabled ()
if ( GetParameters () == false ) then
return -- graceful exit
end
if ( score_type == 2 ) then
behavior.SetFiltersDisabled ( true )
end
print ( "Idealize length: " .. idealize_length )
if #lockedS > 0 then
print ( "Idealize locked: " .. tostring ( dolocked ) )
print ( "Include locked in sphere: " .. tostring ( locksphr ) )
print ( "Include unlocked in sphere: " .. tostring ( ulcksphr ) )
end
print ( "Worst first: " .. tostring ( worst_first ) )
print ( "--" )
Idealize ()
for ii = 1, segCnt2 do
idealz [ ii ] [ IDAFTER ] = current.GetSegmentEnergySubscore ( ii, "ideality" )
end
print ( "--spreadsheet output--" )
print ( "segment\tlocked\tbefore\tafter\tdiff" )
for ii = 1, #idealz do
local locked
if lockedL [ idealz [ ii ] [ IDSEG ] ] then
locked = "L"
else
locked = "U"
end
local before = r3 ( idealz [ ii ] [ IDIDEAL ] )
local after = r3 ( idealz [ ii ] [ IDAFTER ] )
local diff = r3 ( after - before )
print ( idealz [ ii ] [ IDSEG ] .. "\t" .. locked .. "\t" .. before .. "\t" .. after .. "\t" .. diff )
end
cleanup ()
end
function cleanup ( errmsg )
if CLEANUPENTRY ~= nil then
return
end
CLEANUPENTRY = true
print ( "---" )
local reason
local start, stop, line, msg
if errmsg == nil then
reason = "complete"
else
--
-- model 120 - civilized error reporting,
-- thanks to Bruno K. and Jean-Bob
--
start, stop, line, msg = errmsg:find ( ":(%d+):%s()" )
if msg ~= nil then
errmsg = errmsg:sub ( msg, #errmsg )
end
if errmsg:find ( "Cancelled" ) ~= nil then
reason = "cancelled"
else
reason = "error"
end
end
--
-- model 100 - print recipe name, puzzle, track, time, score, and gain
--
Ident ( ReVersion .. " " .. reason )
if reason == "error" then
print ( "Unexpected error detected" )
print ( "Error line: " .. line )
print ( "Error: \"" .. errmsg .. "\"" )
end
--
-- model 130 - reset clash importance, clear selections, restore structures, etc.
--
behavior.SetClashImportance ( 1.0 )
behavior.SetFiltersDisabled ( original_slow_filters_setting )
save.Quickload ( kOriginalStructureOrNewBest )
if errmsg == nil then
end
end
--main ()
xpcall ( main, cleanup )
