Profile
- Name
- TANDEM2
- ID
- 104344
- Shared with
- Public
- Parent
- None
- Children
- None
- Created on
- January 14, 2021 at 12:02 PM UTC
- Updated on
- December 30, 2024 at 20:07 PM UTC
- Description
CONSTRUCTOR + COMPRESSOR
Best for
Code
--[[
Greetings!
It is a script that contains many other scripts and allows you to run any of them. Just choose which one to run after the start.
Alos there is an Autobot script that allows you to predefine the run sequence of basic scripts with given parameters. So you can create your
own Score gain algorythm.
How it works:
1. Each basic script have a code and some of them have a parameters. When you want to include a basic script to sequence, print code and print
all the parameters with the undescore. After the each basic script print the dot.
For example, if you want to use BlueFuze just include "BF." in the sequence. If you want to use Band Test include "BT_15_87_97.", where 15, 87
and 97 - script parameters (see description).
2. When sequence is completed, write it to text field and start the script.
3. Script will be sequentially running your predefined scripts. When All scripts completed, it checks how much score is gained. If its exceed
the limit, then the sequence runs for one more time. If not, then the Iterations ends and the new Iteration starts (from the structure when
the script was started).
The example of sequence, that I use:
"CL.FR.BT_15_87_97.BT_15_103_113.RW_2_1_10.QU_15.BF.RW_1_1_10.LW_12_2.SR."
Basic scripts.
1. Clashing.
Script code: CL
Script Parameters: none
Script Description: Making a sequence of wiggles and shakes with different clashing.
2. FastRelax.
Script code: FR
Script Parameters: none
Script Description: Well known FastRelax script :)
3. BlueFuze.
Script code: BF
Script Parameters: none
Script Description: BlueFuze.
4. WS or SW.
Script code: WS
Script Parameters: none
Script Description: Tries 4 different WS/SW tactics to improve score from destabilized status.
5. Band Test.
Script code: BT
Script Parameters:
1) Number of iterations.
2) Lowest length (in % from original).
3) Highest length (in % from original).
Script Description: Creates a random band with the length in given boundaries. Wiggle structure with band enabled, then delete band and wiggle
out. Repeat given number of Iterations.
Script example: "BT_15_87_97.".
6. Local Wiggle.
Script code: LW
Script Parameters:
1) Wiggle segment Length
2) Number of wiggle iterations.
Script Description: Makes local wiggle.
Script example: "LW_12_2.".
7. Local Rebuild.
Script code: LR
Script Parameters:
1) Rebuild segment Length
Script Description: Makes local rebuildes from the begin to the end of structure.
Script example: "LW_12_2.".
8. Quake.
Script code: QU
Script Parameters:
1) Distance between segments with bands.
Script Description: Makes bands with the given length between segments. Wiggle structure with band enabled, then delete band and wiggle out.
Script example: "QU_15.".
9. Sidechain Test.
Script code: ST
Script Parameters:
1) Segment Number
Script Description: Test every possible position of sidechain at given segment.
Script example: "ST_10.".
10. Mutate.
Script code: MU
Script Parameters: none
Script Description: Just do mutate once.
11. Mutate and Test.
Script code: MT
Script Parameters:
1) Function number.
2) Number of tries (affects only 3rd function).
Script Description:
Depending on the function number it does:
1) Test all posible changes of AA for one segment (very long).
2) Test all posible changes of AA for two segment (impossible long).
3) Test random change of 2 AAs for given number of times.
Script example: "MT_3.".
12. New Mutate
Script code: NM
Script Parameters: none
Script Description: Sequentially mutate each segment for all possible AAs.
13. Rebuilder
Script code: RE
Script Parameters:
1) Start segment.
2) End segment.
3) Number of tries.
Script Description: Rebuild the segment and check the structure by wiggles and shake.
Script example: "RE_10_13_5.".
14. Sidechain Flipper.
Script code: SF
Script Parameters: none
Script Description: Sequentially flips each sidechain.
15. Soft Relax
Script code: SR
Script Parameters: none
Script Description: The variation of FastRelax.
16. Rebuild Worst.
Script code: RW
Script Parameters:
1) Length of segment to rebuild.
2) Number of tries for each segment.
3) Number of segments to rebuild.
Script Description: Rebuilds the worst scoring segments of given length.
Script example: "RW_1_1_10.".
]]--
--v1.0: original
--v1.1: with dialog for Tandem run (check box)
--v1.2: changed dialog for Tandem run (save resolution)
--v1.2.1 Isaksson Share v1.4
--v1.2.2 Isaksson Share v1.5.1
--v1.2.3 small fix thanks to DodoBird, Isaksson Share v1.5.2
fsl={}
fsl.aminosLetterIndex=1
fsl.aminosShortIndex=2
fsl.aminosLongIndex=3
fsl.aminosPolarityIndex=4
fsl.aminosAcidityIndex=5
fsl.aminosHydropathyIndex=6
fsl.aminos = {
{'a','Ala','Alanine', 'nonpolar','neutral', 1.8},
-- {'b','Asx','Asparagine or Aspartic acid' },
{'c','Cys','Cysteine', 'nonpolar','neutral', 2.5},
{'d','Asp','Aspartic acid', 'polar','negative', -3.5},
{'e','Glu','Glutamic acid', 'polar','negative', -3.5},
{'f','Phe','Phenylalanine','nonpolar','neutral', 2.8},
{'g','Gly','Glycine', 'nonpolar','neutral', -0.4},
{'h','His','Histidine', 'polar','neutral', -3.2},
{'i','Ile','Isoleucine', 'nonpolar','neutral', 4.5},
-- {'j','Xle','Leucine or Isoleucine' },
{'k','Lys','Lysine', 'polar','positive', -3.9},
{'l','Leu','Leucine', 'nonpolar','neutral', 3.8},
{'m','Met','Methionine ', 'nonpolar','neutral', 1.9},
{'n','Asn','Asparagine', 'polar','neutral', -3.5},
-- {'o','Pyl','Pyrrolysine' },
{'p','Pro','Proline', 'nonpolar','neutral', -1.6},
{'q','Gln','Glutamine', 'polar','neutral', -3.5},
{'r','Arg','Arginine', 'polar','positive', -4.5},
{'s','Ser','Serine', 'polar','neutral', -0.8},
{'t','Thr','Threonine', 'polar','neutral', -0.7},
-- {'u','Sec','Selenocysteine' },
{'v','Val','Valine', 'nonpolar','neutral', 4.2},
{'w','Trp','Tryptophan', 'nonpolar','neutral', -0.9},
-- {'x','Xaa','Unspecified or unknown amino acid' },
{'y','Tyr','Tyrosine', 'polar','neutral', -1.3},
-- {'z','Glx','Glutamine or glutamic acid' }
}
-- Base on Local Quake 1.0 by spvinvent with helep by thom
-- Bands radiate from a structure (helix, loop or sheet) to spatially close neighbours
-- one round with the strcuture frozen one round not
-- Foregoes Fuses and generally tries to optimize for speed
use_ranked_score = 1 -- if 1, use the score being used for ranking (best normally). If 0, use the
-- old style scoring system
max_bands_per_residue = 6 -- Increase this for more bands at each segment
max_segment_length = 999 -- Don't create bands greater than this length. Set to 999 or something if you're
-- not worried about the potential for long bands creeping in,
min_exclusion = 999 -- These can be set to establish an "exclusion zone", within which no bands will
-- be created. This might be used to prevent banding to a wayward loop.
-- If min_exclusion > max_exclusion no exclusion will be set.
max_exclusion = 1
target_wiggle_reduction = 150 -- On wiggle, try and reduce the score by this amount after creating the bands.
-- If it's wildly out, reduce/increase band strength
-- for the next try (don't try to adjust for the current scramble).
max_segment_length = 10 -- Don't create bands greater than this length. Set to 999 or something if you're
-- not worried about the potential for long bands creeping in,
n_quakes = 50000 -- Go crazy
band_to_minima = true -- Band to minima or maxima in the distance. See bands_from_segment for meaning.
do_second_shake = false -- After creating the bands and pulling with them do a Shake/Wiggle/Shake
-- if do_second_shake is false (best I think) don't do the last shake.
-- Speeds things up quite a bit
scale_band_strength = true -- If true, band strength will be scaled inversely with length
monit =false
---------- A few more globals
candidate_ids_start = {}
candidate_ids_end = {}
candidate_distances = {}
n_candidates = 0
best_score = 0
function GetScore ()
if ( use_ranked_score == 1 ) then
return get_ranked_score ( true )
else
return get_score ()
end
end
function Coprime ( n )
if ( n < 31 ) then
return 1
elseif ( n >= 31*37 ) then
return 1
elseif ( n%31 ~= 0 ) then
return 31
else
return 37
end
end
function pseudorandom ( score )
-- Returns a pseudorandom number >= 0 and < 1.
-- Based on the fractional part of the score
if ( score >= 0 ) then
return score % 1
else
return (-score ) % 1
end
end
function delete_all_bands ()
band_delete ()
--band_count = get_band_count ()
-- for i = band_count , 1 , -1 do
-- band_delete ( i )
--end
end
function ShellSort ( ids , distances , n )
-- Adapted from Numerical Recipes in C
local inc = 1
repeat
inc = inc * 3 + 1
until inc > n
repeat
inc = inc / 3
inc = inc - inc % 1
for i = inc + 1 , n do
v = distances [ i ]
w = ids [ i ]
j = i
flag = false
while ( flag == false and distances [ j - inc ] > v ) do
distances [ j ] = distances [ j - inc ]
ids [ j ] = ids [ j - inc ]
j = j - inc
if ( j <= inc ) then
flag = true
end
end
distances [ j ] = v
ids [ j ] = w
end
until inc <= 1
end
function test_for_minimum ( i , seg , seg_distances )
if ( ( i ~= seg ) and
( seg_distances [ i ] <= seg_distances [ i - 1 ] ) and
( seg_distances [ i ] <= seg_distances [ i - 2 ] ) and
( seg_distances [ i ] <= seg_distances [ i + 1 ] ) and
( seg_distances [ i ] <= seg_distances [ i + 2 ] ) ) then
return true
else
return false
end
end
function test_for_maximum ( i , seg , seg_distances )
if ( ( seg_distances [ i ] >= seg_distances [ i - 1 ] ) and
( seg_distances [ i ] >= seg_distances [ i - 2 ] ) and
( seg_distances [ i ] >= seg_distances [ i + 1 ] ) and
( seg_distances [ i ] >= seg_distances [ i + 2 ] ) ) then
return true
else
return false
end
end
function get_band_segment_data ( seg )
seg_distances = {}
-- Get the function that looks like this:
-- x = residue number
-- y = distance of that segment from seg
-- ignore the degenerate minimum
n_segments = 0
segment_ids = {}
segment_distances = {}
for i = 1, n_residues do
segment_distances [ i ] = get_segment_distance ( seg , i )
end
for i = 3 , n_residues - 3 do
k = segment_distances [ i ]
if ( ( band_to_minima == true ) and
( test_for_minimum ( i , seg , segment_distances ) == true ) ) then
n_segments = n_segments + 1
segment_ids [ n_segments ] = i
segment_distances [ n_segments ] = segment_distances [ i ]
elseif ( ( band_to_minima == false ) and
( test_for_maximum ( i , seg , segment_distances ) == true ) ) then
n_segments = n_segments + 1
segment_ids [ n_segments ] = i
segment_distances [ n_segments ] = segment_distances [ i ]
end
end
ShellSort ( segment_ids , segment_distances , n_segments )
if ( n_segments >= max_bands_per_residue ) then
n_c = max_bands_per_residue
else
n_c = n_segments
end
for i = 1 , n_c do
if ( ( segment_distances [ i ] <= max_segment_length ) and
( seg < min_exclusion or seg > max_exclusion ) and
( segment_ids [ i ] < min_exclusion or segment_ids [ i ] > max_exclusion ) ) then
n_candidates = n_candidates + 1
candidate_ids_start [ n_candidates ] = seg
candidate_ids_end [ n_candidates ] = segment_ids [ i ]
candidate_distances [ n_candidates ] = segment_distances [ i ]
end
end
end
function create_bands ()
if ( scale_band_strength == true ) then
total_band_length = 0
for i = 1 , n_candidates do
total_band_length = total_band_length + candidate_distances [ i ]
end
average_band_length = total_band_length / n_candidates
end
for i = 1 , n_candidates do
band_add_segment_segment ( candidate_ids_start [ i ] , candidate_ids_end [ i ] )
if ( scale_band_strength == true ) then
band_set_strength ( i , band_strength * average_band_length / candidate_distances [ i ] )
else
band_set_strength ( i , band_strength )
end
end
end
function Quake ( seg )
select_all ()
do_unfreeze_all()
--print(GetScore())
init_score = GetScore ()
do_global_wiggle_backbone ( 5 )
--print(GetScore())
score_after_wiggle = GetScore ()
score_reduction_after_wiggle = init_score - score_after_wiggle
if ( monit ) then
print ( "seg ", seg , " score loss " , score_reduction_after_wiggle )
end
-- Adaptively change band strength based on how much the previous wiggle overshot/undershot the target. Could
-- be made much more elaborate.
if ( score_reduction_after_wiggle > target_wiggle_reduction * 1.2 ) then
band_strength = band_strength * ( 0.85 + 0.1 *pseudorandom ( score_after_wiggle ) )
elseif ( score_reduction_after_wiggle < target_wiggle_reduction * 0.8 ) then
band_strength = band_strength + ( 1 - band_strength ) * ( 0.05 + 0.1 *pseudorandom ( score_after_wiggle ) )
end
if ( monit ) then
print ( " band_strength ", band_strength )
end
delete_all_bands ()
do_unfreeze_all()
--print(GetScore())
quicksave(1)
do_shake ( 1 )
quicksave(2)
--print(GetScore())
gas = GetScore () - score_after_wiggle
if ( monit ) then
print ( " gas ", gas )
end
do_unfreeze_all()
--print(GetScore())
do_global_wiggle_all ( 10 )
--print(GetScore())
if ( do_second_shake == true ) then
score_a2w = GetScore ()
do_shake ( 1 )
score_a2s = GetScore ()
if ( score_a2s - score_a2w > 1 ) then
do_global_wiggle_all ( 6 )
--print(GetScore())
end
end
end
n_residues = get_segment_count ()
band_strength = 0.5
set_behavior_clash_importance ( 1 )
reset_recent_best ()
best_score = GetScore ()
print ( " init score ", best_score )
idx = 1
gel=1
for i = 1, n_quakes do
restore_recent_best ()
-- Need to record any improvements from the previous iteration
score = GetScore()
if ( score > best_score ) then
best_score = score
print ( "Improvement to " , score )
end
do_unfreeze_all()
delete_all_bands ()
n_candidates = 0
debut=0
if (idx==1) then debut=1
else if ( get_ss(idx)~=get_ss(idx-1) ) then debut =idx end end
if ( debut>0) then
while (idx < n_residues+1 and get_ss(idx)==get_ss(debut)) do
get_band_segment_data ( idx )
if gel ==1 then
deselect_all()
select_index(idx)
do_freeze(true,false)
end -- of gel
idx=idx+1
end
end
select_all()
if ( n_candidates > 0 ) then
create_bands ()
print ( "i: " , i , " seg ", debut," " ,idx-1 )
Quake ( idx )
end
if idx>n_residues then idx=1 if gel==1 then gel=0 else gel=1 end end
end
-- to see every line
--START Isaksson Share v1.5.2
--Copy this into your recipe and call before and after every period of time.
--Warning: all saves onto you hard disk will have to be removed manually afterwards !
--reference: supplementary material for Koepnick et al (2019) De novo protein design by citizen scientists, Nature, volume 570, pages
390-394
--https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-019-1274-4/MediaObjects/41586_2019_1274_MOESM1_ESM.pdf
--v1: script by Isaksson
--v1.2 added the dialog (BK 1/10/2019)
--v1.3 added time intervals when no gain
--v1.4 PrintVerbose, check every 60 seconds
--v1.5 option Temp name
--v1.5.2 fixed timeleft, Name to save
timeLeft=os.difftime(puzzle.GetExpirationTime(),os.time())/3600 -- in hours
print("Remaining time: "..timeLeft)
startTime=os.time() -- in seconds
userTimeInterval= 60 -- in seconds
lastchecktime = startTime -- in seconds
verbose = false -- print more or less info
save_resolution=1000
function timeLeft()
local result=os.difftime(puzzle.GetExpirationTime(),os.time())/3600 -- in hours
return result
end
function PrintVerbose(text)
if verbose then
print(text)
end
end
function ItsCheckTime()
local currentTime= os.time() -- in seconds
if currentTime-lastchecktime > userTimeInterval then
PrintVerbose(timeLeft().." hours remaining")
return true
end
return false
end
function rounding(x)--cut all afer 3-rd place
return x-x%0.001
end
function before_Solution(rnd,str_name)
if save_resolution > 999 then return end -- New BK 1/10/2019
PrintVerbose("-Before-")
hi_score = 0
hi_idx = 1
sol = save.GetSolutions()
if (sol[0] == nil) then
print("0 solutions found")
--save.SaveSolution("auto_"..rnd)
else
PrintVerbose((#sol+1) .. " solutions found")
for idx = 0, #sol do
soli = sol[idx]
if (string.find(soli.name,rnd) ~= nil) then
PrintVerbose(soli.name .. " : " .. soli.score)
if (soli.score > hi_score) then
hi_score = soli.score
hi_idx = idx
end
end
end
--print("Load the solution ...")
if(current.GetEnergyScore()+save_resolution < hi_score) then
save.LoadSolution(sol[hi_idx])
soli = sol[hi_idx]
print("Load solution: "..soli.name.." : "..rounding(soli.score,value_score_resolution))
end
end
end
function after_Solution(rnd,str_name)
if save_resolution > 999 then return end -- New BK 1/10/2019
PrintVerbose("-After-")
hi_score = 0
hi_idx = 1
sol = save.GetSolutions()
if (sol[0] == nil) then
print("0 solutions found")
str = "auto".."-"..rnd.."-"..rounding(current.GetEnergyScore(),value_score_resolution)
print("Save solution "..str)
save.SaveSolution(str)
else
PrintVerbose((#sol+1) .. " solutions found")
for idx = 0, #sol do
soli = sol[idx]
if (string.find(soli.name,rnd) ~= nil) then
PrintVerbose(soli.name .. " : " .. soli.score)
if (soli.score > hi_score) then
hi_score = soli.score
hi_idx = idx
end
end
end
PrintVerbose("Save the solution ...")
band.DeleteAll()
if(current.GetEnergyScore()-save_resolution > hi_score) then
str = str_name.."-"..rnd.."-"..rounding(current.GetEnergyScore(),value_score_resolution)
print("Save solution: "..str)
save.SaveSolution(str)
end
end
end
str_name= ui.GetTrackName() -- copy-paste anywhere on top of the recipe
rnd= "Temp" -- Warning: edit before in order to cach the right loop name
--How to use:
--Uncomment and insert the following 2 lines on the right places, before or after each loop:
--if ItsCheckTime() then before_Solution(rnd,str_name) end -- as often as possible after score evaluations, e.g. in savebest(), or before any
action
--after_Solution(rnd,str_name) -- after any gain (will not save any loaded solution)
--Uncommend and copy-paste the following 2x2 lines within the dialog on the right places:
--ask.LabelRowBeforeSave = dialog.AddLabel("Keep save resolution to 1000 to avoid local saves") --(optional) copy-paste and adapt in the
dialog
--ask.save_resolution = dialog.AddSlider("Save resolution:", 1000, 0.3, 1000, 1) --copy-paste and adapt in the dialog (parameters)-- 1000
means no sharing
--ask.save_Name = dialog.AddTextbox("Name to save: ", rnd)
--rnd=ask.save_Name.value
--save_resolution=ask.save_resolution.value -- copy-paste and adapt after the dialog.show
--if save_resolution < 1000 then print("Checking for solutioun every "..userTimeInterval.." seconds") end
--End of Isaksson Share
function BlueFuze()
if ItsCheckTime() then before_Solution(rnd,str_name) end -- as often as possible after score evaluations, e.g. in savebest(), or before any
action
behavior.SetClashImportance(.05)
structure.ShakeSidechainsAll(1)
behavior.SetClashImportance(1)
structure.WiggleAll(8)
behavior.SetClashImportance(.07)
structure.ShakeSidechainsAll(1)
behavior.SetClashImportance(1)
structure.WiggleAll(8)
recentbest.Restore()
behavior.SetClashImportance(.3)
structure.WiggleAll(1)
behavior.SetClashImportance(1)
structure.WiggleAll(8)
recentbest.Restore()
after_Solution(rnd,str_name)
end
function SoftRelaxFull()
if ItsCheckTime() then before_Solution(rnd,str_name) end --
local function SoftRelax()
local function StepC(Clashing,Shakes,Wiggles)
behavior.SetClashImportance(Clashing)
structure.ShakeSidechainsAll(Shakes)
structure.WiggleAll(Wiggles)
end
local shakes=2 --number of shakes
local wiggles=3 --number of wiggles
StepC(0.55,shakes,wiggles)
StepC(0.25,shakes,wiggles)
StepC(0.05,shakes,wiggles)
StepC(0.25,shakes,wiggles)
StepC(0.55,shakes,wiggles)
StepC(1,shakes,wiggles)
end
local ss
local minPpi=1
local Step=1
repeat
ss=current.GetEnergyScore()
SoftRelax()
print(Step..". Score: "..math.max(current.GetEnergyScore(),ss).." gain: "..math.max(current.GetEnergyScore()-ss,0))
Step = Step+1
recentbest.Restore()
until current.GetEnergyScore()-ss<minPpi
after_Solution(rnd,str_name)
end
function FastRelaxFull()
if ItsCheckTime() then before_Solution(rnd,str_name) end --
local function FastRelax()
local function StepC(Clashing,Shakes,Wiggles)
behavior.SetClashImportance(Clashing)
structure.ShakeSidechainsAll(Shakes)
structure.WiggleAll(Wiggles)
end
local shakes=2 --number of shakes
local wiggles=5 --number of wiggles
StepC(0.02,shakes,wiggles)
StepC(0.25,shakes,wiggles)
StepC(0.55,shakes,wiggles)
StepC(1,shakes,wiggles)
end
local ss
local minPpi=2
local Step=1
repeat
ss=current.GetEnergyScore()
FastRelax()
print(Step..". Score: "..math.max(current.GetEnergyScore(),ss).." gain: "..math.max(current.GetEnergyScore()-ss,0))
Step = Step+1
recentbest.Restore()
until current.GetEnergyScore()-ss<minPpi
after_Solution(rnd,str_name)
end
function clashing(Repeat)
if ItsCheckTime() then before_Solution(rnd,str_name) end --
local i = 1
local sc
while i<10 do
sc = current.GetEnergyScore()
behavior.SetClashImportance(i/10)
structure.WiggleAll(i)
behavior.SetClashImportance(1)
structure.MutateSidechainsAll(1)
structure.WiggleAll(20)
structure.MutateSidechainsAll(1)
structure.WiggleAll(4)
print("Clashing: " .. i/10 .. ", score: " .. current.GetEnergyScore()-sc)
if sc<current.GetEnergyScore() and Repeat==1 and i < 8
then i = 1
else i = i+1
end
recentbest.Restore()
end
after_Solution(rnd,str_name)
end
function ws_or_sw(params)
if ItsCheckTime() then before_Solution(rnd,str_name) end --
local function ws_or_sw_1()
structure.WiggleAll(15)
structure.MutateSidechainsAll(1)
structure.WiggleAll(10)
structure.MutateSidechainsAll(1)
structure.WiggleAll(5)
print("WS score: "..current.GetEnergyScore())
end
local function ws_or_sw_2()
structure.MutateSidechainsAll(1)
structure.WiggleAll(15)
structure.MutateSidechainsAll(1)
structure.WiggleAll(10)
structure.ShakeSidechainsAll(1)
structure.WiggleAll(5)
print("SW score: "..current.GetEnergyScore())
end
local function ws_or_sw_3()
behavior.SetClashImportance(0.5)
structure.WiggleAll(4)
behavior.SetClashImportance(1)
structure.MutateSidechainsAll(1)
structure.WiggleAll(15)
structure.MutateSidechainsAll(1)
structure.WiggleAll(10)
structure.ShakeSidechainsAll(1)
structure.WiggleAll(5)
print("SW 0.5 score: "..current.GetEnergyScore())
end
local function ws_or_sw_4()
for i=3, 10 do
behavior.SetClashImportance(i/10)
structure.WiggleAll(1)
if i==3 or i==6 then structure.ShakeSidechainsAll(1) end
end
structure.ShakeSidechainsAll(1)
structure.WiggleAll(15)
structure.ShakeSidechainsAll(1)
structure.WiggleAll(5)
print("Step clash: "..current.GetEnergyScore())
end
selection.SelectAll()
save.Quicksave(100)
if params[1]==1 then save.Quickload(100) ws_or_sw_1() end
if params[2]==1 then save.Quickload(100) ws_or_sw_2() end
if params[3]==1 then save.Quickload(100) ws_or_sw_3() end
if params[4]==1 then save.Quickload(100) ws_or_sw_4() end
recentbest.Restore()
after_Solution(rnd,str_name)
end
function Band_tests(Start_LengthP,End_LengthP,Clashing,Iteration,TotalIteration)
if ItsCheckTime() then before_Solution(rnd,str_name) end --
local function PullPart(Segment1,Segment2,LengthP,Strength)
band.DeleteAll()
band.AddBetweenSegments(Segment1,Segment2)
band.SetStrength(1,Strength)
band.SetGoalLength(1,structure.GetDistance(Segment1,Segment2)*LengthP)
structure.WiggleAll(1)
band.DeleteAll()
end
local startSeg=math.random(1,structure.GetCount()-9)
while structure.IsLocked(startSeg) do startSeg=math.random(1,structure.GetCount()-9) end
local endSeg=math.random(startSeg+8,structure.GetCount())
local LengthP=math.random(Start_LengthP,End_LengthP)
local startScore = current.GetEnergyScore()
if TotalIteration == 0 then TotalIterationStr = "inf" else TotalIterationStr = TotalIteration end
if LengthP>97 and LengthP<=100 then LengthP=Start_LengthP end
if LengthP>100 and LengthP<103 then LengthP=End_LengthP end
PullPart(startSeg,endSeg,LengthP/100,10)
structure.MutateSidechainsAll(1)
structure.WiggleAll(15)
structure.MutateSidechainsAll(1)
structure.WiggleAll(5)
behavior.SetClashImportance(Clashing)
structure.WiggleAll(5)
behavior.SetClashImportance(1)
structure.WiggleAll(15)
recentbest.Restore()
print(Iteration .."/".. TotalIterationStr .. "; " .. startSeg .. "-" .. endSeg .. ", score: "
..math.max(startScore,current.GetEnergyScore()) .. ", gain: " .. math.max(0,current.GetEnergyScore()-startScore))
after_Solution(rnd,str_name)
end
function local_wiggle(Len,Num)
if ItsCheckTime() then before_Solution(rnd,str_name) end --
local NumSegm = structure.GetCount()
local sc1
for i = 1, NumSegm-Len+1, 1 do
Score = current.GetEnergyScore()
selection.DeselectAll()
selection.SelectRange(i, i+Len-1)
structure.LocalWiggleSelected(Num)
sc1=current.GetEnergyScore()-Score
if sc1 <0.0001 then sc1=0 end
print(i .. "-" .. i+Len-1 .. "/" .. NumSegm .. ", score: " .. current.GetEnergyScore() .. ", gain: " .. sc1)
recentbest.Restore()
end
after_Solution(rnd,str_name)
end
function local_rebuild_all(Length,Clashing)
if ItsCheckTime() then before_Solution(rnd,str_name) end --
local function local_rebuild(Start,Len,Clsh)
local sc=current.GetEnergyScore()
local newScore
selection.DeselectAll()
selection.SelectRange(Start,Start+Len-1)
for i=1,3 do
if current.GetEnergyScore()-sc<0.05 and sc-current.GetEnergyScore()<0.05 then structure.RebuildSelected(i) end
end
if current.GetEnergyScore()-sc>0.05 or sc-current.GetEnergyScore()>0.05 then
selection.SelectAll()
structure.MutateSidechainsSelected(1)
structure.WiggleAll(20)
structure.ShakeSidechainsAll(1)
selection.DeselectAll()
selection.SelectRange(Start,Start+Len-1)
structure.LocalWiggleSelected(15)
selection.SelectAll()
structure.WiggleAll(15)
newScore=current.GetEnergyScore()
if Clsh<1 then
behavior.SetClashImportance(Clsh)
structure.WiggleAll(4)
behavior.SetClashImportance(1)
structure.MutateSidechainsSelected(1)
structure.WiggleAll(15)
structure.ShakeSidechainsAll(1)
structure.WiggleAll(10)
if current.GetEnergyScore()>newScore then newScore=current.GetEnergyScore() end
end
if newScore-sc<0.0001 then sc=0 else sc=newScore-sc end
print(Start .. "-" .. Start+Len-1 .. "/" .. structure.GetCount() .. ", score: " .. current.GetEnergyScore() .. ", gain: " .. sc)
end
end
for z=1,structure.GetCount()-Length do
recentbest.Save()
local_rebuild(z,Length,Clashing)
recentbest.Restore()
end
after_Solution(rnd,str_name)
end
function RebuildWorst(Length,RebuildsTries,Clashing,NumSegsForRebuild)
if ItsCheckTime() then before_Solution(rnd,str_name) end --
local function Worst_Segments(Length)
local function Sort(tab)
for x=1,#tab-1 do
for y=x+1,#tab do
if tab[x][3]>tab[y][3] then
tab[x],tab[y]=tab[y],tab[x]
end
end
end
return tab
end
local NumSegs=structure.GetCount()
local segsInfo={}
for i=1, NumSegs-Length+1 do
segsInfo[i]={i,i+Length-1,current.GetSegmentEnergyScore(i)}
for j=2, Length do
segsInfo[i]={segsInfo[i][1],segsInfo[i][2],segsInfo[i][3] + current.GetSegmentEnergyScore(i+j-1)}
end
end
segsInfo=Sort(segsInfo)
return segsInfo
end
local NumSegs=structure.GetCount()
local WorstSegs=Worst_Segments(Length)
local segsForRebuild={}
local Step=1
local str=""
local sc=current.GetEnergyScore()
for i=1,math.min(#WorstSegs,NumSegsForRebuild) do
segsForRebuild={}
selection.DeselectAll()
for j=math.max(WorstSegs[i][1]-1,1), math.min(WorstSegs[i][2]+1,NumSegs) do segsForRebuild[#segsForRebuild + 1] = j end
Step=1
str=""
RebuildsTriesNum=RebuildsTries+1
RebuildsTriesNum=RebuildsTriesNum-1
while Step<=RebuildsTriesNum do
sc=current.GetEnergyScore()
for l=1, #segsForRebuild do selection.Select(segsForRebuild[l]) end
for l=1,10 do
if current.GetEnergyScore()-sc<0.05 and sc-current.GetEnergyScore()<0.05 then structure.RebuildSelected(i) end
end
if current.GetEnergyScore()-sc>0.05 or sc-current.GetEnergyScore()>0.05 then
structure.MutateSidechainsAll(1)
structure.WiggleAll(15)
structure.ShakeSidechainsAll(1)
structure.WiggleSelected(10)
structure.WiggleAll(10)
if Clashing<1 then
behavior.SetClashImportance(Clashing)
structure.WiggleAll(4)
behavior.SetClashImportance(1)
structure.MutateSidechainsAll(1)
structure.WiggleAll(10)
structure.ShakeSidechainsAll(1)
structure.WiggleAll(5)
end
end
str=Step .." Try " .. ", " .. segsForRebuild[1] .. "-" .. segsForRebuild[#segsForRebuild] .. ", score: " .. current.GetEnergyScore()
if current.GetEnergyScore()-sc > 0.0001 then
str = str .. ", +" .. current.GetEnergyScore()-sc
Step=0
end
print(str)
Step = Step + 1
recentbest.Restore()
sc=current.GetEnergyScore()
end
end
after_Solution(rnd,str_name)
end
function quake(Length,ScoreDelta,Shake,Clashing)
if ItsCheckTime() then before_Solution(rnd,str_name) end --
function quake_one(Start,Diff,Delta,Shk,Clsh)
local function set_bands(Str)
for z=1, band.GetCount() do
band.SetStrength(z,Str)
end
end
local numSegments=structure.GetCount()
local sc=current.GetEnergyScore()
local sc1
band.DeleteAll()
selection.DeselectAll()
for i=0, numSegments/Diff do
for j=i+1, numSegments/Diff do
if Start+i*Diff<=numSegments and Start+j*Diff<=numSegments then
band.AddBetweenSegments(Start+i*Diff,Start+j*Diff)
end
end
end
Band_str=0.08
selection.SelectAll()
while math.abs(current.GetEnergyScore()-sc)<=Delta do
set_bands(Band_str)
structure.WiggleAll(1)
Band_str=Band_str+0.03
end
band.DeleteAll()
if Shk==2 then structure.MutateSidechainsAll(1) end
if Shk==1 then structure.ShakeSidechainsAll(1) end
structure.WiggleAll(15)
structure.ShakeSidechainsAll(1)
structure.WiggleAll(10)
structure.ShakeSidechainsAll(1)
structure.WiggleAll(5)
sc1=current.GetEnergyScore()
if Clsh<1 then
behavior.SetClashImportance(Clsh)
structure.WiggleAll(1)
behavior.SetClashImportance(1)
structure.ShakeSidechainsAll(1)
structure.WiggleAll(10)
structure.ShakeSidechainsAll(1)
structure.WiggleAll(5)
end
if current.GetEnergyScore()>sc1 then sc2=current.GetEnergyScore() else sc2=sc1 end
print(Start .. ":" .. Diff .. ", score: " .. sc2 .. ", gain: " .. sc2-sc)
end
for i=1, Length-1 do
quake_one(i,Length,ScoreDelta,Shake,Clashing)
recentbest.Restore()
band.DeleteAll()
recentbest.Save()
end
after_Solution(rnd,str_name)
end
function sidechain_shock(Seg)
if ItsCheckTime() then before_Solution(rnd,str_name) end --
local SnapCnt=rotamer.GetCount(Seg)
local sc=current.GetEnergyScore()
print("Segment: " .. Seg .. ", snaps: " .. SnapCnt .. ", start: " .. current.GetEnergyScore())
save.Quicksave(100)
for i=1, SnapCnt do
save.Quickload(100)
rotamer.SetRotamer(Seg,i)
if SnapCnt>2 and current.GetEnergyScore~=sc then
selection.DeselectAll()
selection.Select(Seg)
structure.LocalWiggleSelected(20)
selection.SelectAll()
structure.WiggleAll(10)
structure.ShakeSidechainsAll(1)
selection.DeselectAll()
selection.Select(Seg)
structure.LocalWiggleSelected(20)
selection.SelectAll()
structure.ShakeSidechainsAll(1)
structure.WiggleAll(10)
structure.WiggleAll(10,false,true)
end
print(Seg .. "/" .. structure.GetCount() .. ", " .. i .. "/" .. SnapCnt .. ", score: " .. current.GetEnergyScore() .. ", gain: " ..
current.GetEnergyScore()-sc)
end
after_Solution(rnd,str_name)
end
function sidechain_test_all()
if ItsCheckTime() then before_Solution(rnd,str_name) end --
for j=1, structure.GetCount() do
recentbest.Save()
if rotamer.GetCount(j)>2 then sidechain_shock(j) end
recentbest.Restore()
end
after_Solution(rnd,str_name)
end
function mutate(Shk, Num)
if ItsCheckTime() then before_Solution(rnd,str_name) end --
selection.SelectAll()
if Shk==1 then structure.ShakeSidechainsAll(Num) end
if Shk==2 then structure.MutateSidechainsAll(Num) end
after_Solution(rnd,str_name)
end
function Mutate_And_Test(RunFunction,NumTries)
if ItsCheckTime() then before_Solution(rnd,str_name) end --
local function mutate_and_test_1(n,Clsh,IsAll,Num)
local score1
structure.SetAminoAcid(n,fsl.aminos[Num][fsl.aminosLetterIndex])
score1 = current.GetEnergyScore()
structure.ShakeSidechainsAll(1)
behavior.SetClashImportance(Clsh)
structure.WiggleAll(10)
behavior.SetClashImportance(1)
if current.GetEnergyScore()-score1>0.003 or score1-current.GetEnergyScore()>0.003
then
if IsAll==0
then
selection.DeselectAll()
selection.Select(n)
structure.MutateSidechainsSelected(1)
else
structure.MutateSidechainsAll(1)
end
structure.WiggleAll(10)
end
end
local function full_1_step(Clsh)
local str_dop = ""
local score0
for i = 1, #mutable do
for j = 1, 20 do
score0 = current.GetEnergyScore()
str_dop = ""
mutate_and_test_1(mutable[i],Clsh,0,j)
str_dop = mutable[i] .. "_" .. fsl.aminos[j][fsl.aminosLetterIndex] .. ": " .. current.GetEnergyScore()
recentbest.Restore()
if current.GetEnergyScore() > score0 + 0.0001 then
str_dop = str_dop .. ", +" .. current.GetEnergyScore() - score0
end
print(str_dop)
end
end
end
local function full_2_step(Clsh)
local str = ""
local str_dop = ""
local score0
for i1 = 1, #mutable-1 do
for j1 = 1, 20 do
str = mutable[i1] .. "_" .. fsl.aminos[j1][fsl.aminosLetterIndex] .. " + "
for i2 = i1+1, #mutable do
for j2 = 1, 20 do
score0 = current.GetEnergyScore()
structure.SetAminoAcid(i1,fsl.aminos[j1][fsl.aminosLetterIndex])
mutate_and_test_1(mutable[i2],Clsh,0,j2)
str_dop = mutable[i2] .. "_" .. fsl.aminos[j2][fsl.aminosLetterIndex] .. ": " .. current.GetEnergyScore()
recentbest.Restore()
if current.GetEnergyScore() > score0 + 0.0001
then
str_dop = str_dop .. ", +" .. current.GetEnergyScore() - score0
end
print(str .. str_dop)
end
end
end
end
end
function random_2_step(Clsh,NumTries)
local str = ""
local str_dop = ""
local score0
local step = 1
NumTries=NumTries+1
NumTries=NumTries-1
while step <= NumTries do
score0 = current.GetEnergyScore()
i1 = math.random(#mutable)
j1 = math.random(20)
str = mutable[i1] .. "_" .. fsl.aminos[j1][fsl.aminosLetterIndex] .. " + "
i2 = math.random(#mutable)
j2 = math.random(20)
structure.SetAminoAcid(i1,fsl.aminos[j1][fsl.aminosLetterIndex])
mutate_and_test_1(mutable[i2],Clsh,step%2,j2)
str_dop = mutable[i2] .. "_" .. fsl.aminos[j2][fsl.aminosLetterIndex] .. ": " .. current.GetEnergyScore()
recentbest.Restore()
if current.GetEnergyScore() > score0 + 0.0001
then
str_dop = str_dop .. ", +" .. current.GetEnergyScore() - score0
end
step = step + 1
print(str .. str_dop)
end
end
mutable={}
Clsh = 0.9
for i=1, structure.GetCount() do
if structure.IsMutable(i) then mutable[#mutable+1]=i end
end
if RunFunction == 1 then full_1_step(Clsh) end
if RunFunction == 2 then full_2_step(Clsh) end
if RunFunction == 3 then random_2_step(Clsh,NumTries) end
after_Solution(rnd,str_name)
end
function new_mutate(Num)
if ItsCheckTime() then before_Solution(rnd,str_name) end --
structure.SetAminoAcid(Num,fsl.aminos[1][1])
maxScore=current.GetEnergyScore()
bestAcid=fsl.aminos[1][1]
for i=2, #fsl.aminos do
structure.SetAminoAcid(Num,fsl.aminos[i][1])
if current.GetEnergyScore()>maxScore then
maxScore=current.GetEnergyScore()
bestAcid=fsl.aminos[i][1]
end
end
structure.SetAminoAcid(Num,bestAcid)
after_Solution(rnd,str_name)
end
function new_mutate_all()
if ItsCheckTime() then before_Solution(rnd,str_name) end --
mutable={}
for i=1, structure.GetCount() do
if structure.IsMutable(i) then mutable[#mutable+1]=i end
end
for j=1, #mutable do
new_mutate(mutable[j])
recentbest.Restore()
print(mutable[j].."_"..structure.GetAminoAcid(mutable[j])..", score: "..current.GetEnergyScore())
end
after_Solution(rnd,str_name)
end
function rebuilder(startSegm,endSegm,Clashing,Num)
if ItsCheckTime() then before_Solution(rnd,str_name) end --
local Cnt=1
local str=""
local segsForRebuild={}
local NumSegs=structure.GetCount()
local sc=current.GetEnergyScore()
for i=math.max(startSegm,1), math.min(endSegm,NumSegs) do segsForRebuild[#segsForRebuild + 1] = i end
RebuildTries=Num+1
RebuildTries=RebuildTries-1
while Cnt<=RebuildTries do
selection.DeselectAll()
for i=1, #segsForRebuild do selection.Select(segsForRebuild[i]) end
for i=1,10 do
if current.GetEnergyScore()-sc<0.05 and sc-current.GetEnergyScore()<0.05 then structure.RebuildSelected(i) end
end
if current.GetEnergyScore()-sc>0.05 or sc-current.GetEnergyScore()>0.05 then
structure.MutateSidechainsAll(1)
structure.WiggleAll(20)
structure.ShakeSidechainsAll(1)
structure.WiggleSelected(15)
structure.WiggleAll(15)
if Clashing<1 then
behavior.SetClashImportance(Clashing)
structure.WiggleAll(4)
behavior.SetClashImportance(1)
structure.MutateSidechainsAll(1)
structure.WiggleAll(15)
structure.ShakeSidechainsAll(1)
structure.WiggleAll(10)
end
end
str=Cnt .." Try " .. ", " .. segsForRebuild[1] .. "-" .. segsForRebuild[#segsForRebuild] .. ", score: " .. current.GetEnergyScore()
if current.GetEnergyScore()-sc > 0.0001 then str = str .. ", +" .. current.GetEnergyScore()-sc end
print(str)
Cnt = Cnt + 1
recentbest.Restore()
sc=current.GetEnergyScore()
end
after_Solution(rnd,str_name)
end
function sidechain_flip_all()
if ItsCheckTime() then before_Solution(rnd,str_name) end --
local function sidechain_flip(Seg)
local SnapCnt=rotamer.GetCount(Seg)
for i=1, SnapCnt do
rotamer.SetRotamer(Seg,i)
end
end
local sc=current.GetEnergyScore()
for j=1, structure.GetCount() do
recentbest.Save()
sc=current.GetEnergyScore()
if rotamer.GetCount(j)>2 then sidechain_flip(j) end
recentbest.Restore()
print(j .. "/" .. structure.GetCount() .. " (" .. rotamer.GetCount(j) .. "), score: " .. current.GetEnergyScore() .. ", gain: " ..
current.GetEnergyScore()-sc)
end
after_Solution(rnd,str_name)
end
function p_Time(startTime,ScoreGain)
local ss=(os.time()-startTime)*60
local mm=(((os.time()-startTime-ss)*3600)/60)
local hh=(os.time()-startTime-mm*60-ss)/3600
print("Time: "..hh..":"..mm..":"..ss..". ".."Score: "..current.GetEnergyScore()..", Total: +"..ScoreGain)
end
---------------------------------------------------------------
--------------------- MAIN PROGRAM -------------------
---------------------------------------------------------------
recentbest.Save()
startScore=current.GetEnergyScore()
startTime=os.time()
math.randomseed(startTime)
local ask = dialog.CreateDialog("All in One.")
ask.LabelRow000 = dialog.AddLabel("Please choose the script to run:")
ask.LabelRow001 = dialog.AddLabel("1. BlueFuze.")
ask.LabelRow002 = dialog.AddLabel("2. Clashing.")
ask.LabelRow003 = dialog.AddLabel("3. FastRelax.")
ask.LabelRow004 = dialog.AddLabel("4. WS or SW.")
ask.LabelRow005 = dialog.AddLabel("5. Band Test.")
ask.LabelRow006 = dialog.AddLabel("6. Local Wiggle.")
ask.LabelRow007 = dialog.AddLabel("7. Local Rebuild.")
ask.LabelRow008 = dialog.AddLabel("8. Rebuild Worst.")
ask.LabelRow009 = dialog.AddLabel("9. Quake.")
ask.LabelRow010 = dialog.AddLabel("10. Sidechain Test.")
ask.LabelRow011 = dialog.AddLabel("11. Mutate.")
ask.LabelRow012 = dialog.AddLabel("12. Mutate and Test.")
ask.LabelRow013 = dialog.AddLabel("13. New Mutate.")
ask.LabelRow014 = dialog.AddLabel("14. Rebuilder.")
ask.LabelRow015 = dialog.AddLabel("15. Sidechain Flipper.")
ask.LabelRow016 = dialog.AddLabel("16. SoftRelax.")
ask.LabelRow017 = dialog.AddLabel("17. Autobot.")
ask.Script = dialog.AddSlider("Function to run:", 17, 1, 17, 0)
ask.save_resolution = dialog.AddSlider("Save after gain > ", 1000, 0.3, 1000, 1) -- from isaksson share
ask.save_Name = dialog.AddTextbox("Name2share", rnd)
ask.OK = dialog.AddButton("OK", 1)
ask.Cancel = dialog.AddButton("Cancel", 0)
ask.About = dialog.AddButton("About", 2)
DialogResult = dialog.Show(ask)
ScriptNumber = ask.Script.value
save_resolution=ask.save_resolution.value -- from isaksson share
if save_resolution < 1000 then print("Checking for solution every "..userTimeInterval.." seconds") end
rnd=ask.save_Name.value
if (DialogResult == 1) then
if (ScriptNumber == 1) then
print("Start score: "..startScore)
recipe.SectionStart("BlueFuze")
BlueFuze()
p_Time(startTime,recipe.SectionEnd()-startScore)
elseif (ScriptNumber == 2) then
ScriptAsk = dialog.CreateDialog("Script Dialog. Clashing.")
ScriptAsk.Repeat = dialog.AddCheckbox("Repeat when gain score", false)
ScriptAsk.OK = dialog.AddButton("OK", 1)
ScriptAsk.Cancel = dialog.AddButton("Cancel", 0)
ScriptDialogResult = dialog.Show(ScriptAsk)
if ScriptAsk.Repeat.value==true then Repeat=1 else Repeat=0 end
print("Start score: "..startScore)
recipe.SectionStart("Clashing")
clashing(Repeat)
p_Time(startTime,recipe.SectionEnd()-startScore)
elseif (ScriptNumber == 3) then
print("Start score: "..startScore)
recipe.SectionStart("FastRelax")
FastRelaxFull()
p_Time(startTime,recipe.SectionEnd()-startScore)
elseif (ScriptNumber == 4) then
params = {
1, -- WS
1, -- SW
1, -- WS_0.5
1 -- WS Step
}
print("Start score: "..startScore)
recipe.SectionStart("WS or SW")
ws_or_sw(params)
p_Time(startTime,recipe.SectionEnd()-startScore)
elseif (ScriptNumber == 5) then
ScriptAsk = dialog.CreateDialog("Script Dialog. Band Test.")
ScriptAsk.Start_LengthP = dialog.AddSlider("Start Length (percents):", 90, 10, 300, 0)
ScriptAsk.End_LengthP = dialog.AddSlider("Start Length (percents):", 110, 10, 300, 0)
ScriptAsk.Clashing = dialog.AddSlider("Clashing", 0.5, 0, 1, 1)
ScriptAsk.OK = dialog.AddButton("OK", 1)
ScriptAsk.Cancel = dialog.AddButton("Cancel", 0)
ScriptDialogResult = dialog.Show(ScriptAsk)
Start_LengthP=ScriptAsk.Start_LengthP.value
End_LengthP=ScriptAsk.End_LengthP.value
Clashing=ScriptAsk.Clashing.value
print("Start score: "..startScore)
Iteration = 1
while Iteration>0 do
Band_tests(Start_LengthP,End_LengthP,Clashing,Iteration,0)
Iteration = Iteration + 1
end
elseif (ScriptNumber == 6) then
ScriptAsk = dialog.CreateDialog("Script Dialog. Local Wiggle.")
ScriptAsk.Length = dialog.AddSlider("Segment Length", 7, 1, structure.GetCount()/2, 0)
ScriptAsk.Wig_Num = dialog.AddSlider("Number of Wiggles", 2, 1, 30, 0)
ScriptAsk.TotalWiggle = dialog.AddCheckbox("Total wiggle", false)
ScriptAsk.OK = dialog.AddButton("OK", 1)
ScriptAsk.Cancel = dialog.AddButton("Cancel", 0)
ScriptDialogResult = dialog.Show(ScriptAsk)
Length=ScriptAsk.Length.value
Wig_Num=ScriptAsk.Wig_Num.value
TotalWiggle=ScriptAsk.TotalWiggle.value
print("Start score: "..startScore)
recipe.SectionStart("Local Wiggle")
if TotalWiggle then
Length=15
for i=Length,1,-1 do local_wiggle(i,Wig_Num) end
else local_wiggle(Length,Wig_Num)
end
p_Time(startTime,recipe.SectionEnd()-startScore)
elseif (ScriptNumber == 7) then
ScriptAsk = dialog.CreateDialog("Script Dialog. Local Rebuild.")
ScriptAsk.Length = dialog.AddSlider("Segment Length", 3, 1, structure.GetCount()/2, 0)
ScriptAsk.Clashing = dialog.AddSlider("Clashing", 0.6, 0, 1, 1)
ScriptAsk.OK = dialog.AddButton("OK", 1)
ScriptAsk.Cancel = dialog.AddButton("Cancel", 0)
ScriptDialogResult = dialog.Show(ScriptAsk)
Length=ScriptAsk.Length.value
Clashing=ScriptAsk.Clashing.value
print("Start score: "..startScore)
recipe.SectionStart("Local Rebuild")
local_rebuild_all(Length,Clashing)
p_Time(startTime,recipe.SectionEnd()-startScore)
elseif (ScriptNumber == 8) then
ScriptAsk = dialog.CreateDialog("Script Dialog. Rebuild Worst.")
ScriptAsk.Length = dialog.AddSlider("Segment Length", 1, 1, structure.GetCount()/2, 0)
ScriptAsk.Clashing = dialog.AddSlider("Clashing", 0.6, 0, 1, 1)
ScriptAsk.Rebuilds = dialog.AddSlider("Rebuild tries", 3, 1, 100, 0)
ScriptAsk.OK = dialog.AddButton("OK", 1)
ScriptAsk.Cancel = dialog.AddButton("Cancel", 0)
ScriptDialogResult = dialog.Show(ScriptAsk)
Length=ScriptAsk.Length.value
Clashing=ScriptAsk.Clashing.value
RebuildsTries=ScriptAsk.Rebuilds.value
print("Start score: "..startScore)
recipe.SectionStart("Rebuild Worst")
RebuildWorst(Length,RebuildsTries,Clashing,100)
p_Time(startTime,recipe.SectionEnd()-startScore)
elseif (ScriptNumber == 9) then
ScriptAsk = dialog.CreateDialog("Script Dialog. Quake.")
ScriptAsk.Length = dialog.AddSlider("Segment Length", 15, 1, structure.GetCount()/2, 0)
ScriptAsk.Clashing = dialog.AddSlider("Clashing", 0.6, 0, 1, 1)
ScriptAsk.Shake = dialog.AddSlider("Shake", 1, 0, 2, 0)
ScriptAsk.ScoreDelta = dialog.AddSlider("ScoreDelta", 15, 0, 200, 1)
ScriptAsk.OK = dialog.AddButton("OK", 1)
ScriptAsk.Cancel = dialog.AddButton("Cancel", 0)
ScriptDialogResult = dialog.Show(ScriptAsk)
Length=ScriptAsk.Length.value
Clashing=ScriptAsk.Clashing.value
Shake=ScriptAsk.Shake.value
ScoreDelta=ScriptAsk.ScoreDelta.value
print("Start score: "..startScore)
recipe.SectionStart("Quake")
quake(Length,ScoreDelta,Shake,Clashing)
p_Time(startTime,recipe.SectionEnd()-startScore)
elseif (ScriptNumber == 10) then
print("Start score: "..startScore)
recipe.SectionStart("Sidechain Test")
sidechain_test_all()
p_Time(startTime,recipe.SectionEnd()-startScore)
elseif (ScriptNumber == 11) then
Shake_Type = 2 -- 1: Shake, 2: Mutate
Shake_times = 1 -- Number of shake times
print("Start score: "..startScore)
recipe.SectionStart("Mutate")
mutate(Shake_Type,Shake_times)
p_Time(startTime,recipe.SectionEnd()-startScore)
elseif (ScriptNumber == 12) then
ScriptAsk = dialog.CreateDialog("Script Dialog. Mutate and Test.")
ScriptAsk.RunFunction = dialog.AddSlider("Function to run:", 3, 1, 3, 0)
ScriptAsk.OK = dialog.AddButton("OK", 1)
ScriptAsk.Cancel = dialog.AddButton("Cancel", 0)
ScriptDialogResult = dialog.Show(ScriptAsk)
RunFunction=ScriptAsk.RunFunction.value
print("Start score: "..startScore)
recipe.SectionStart("Mutate and Test")
Mutate_And_Test(RunFunction,10000)
p_Time(startTime,recipe.SectionEnd()-startScore)
elseif (ScriptNumber == 13) then
print("Start score: "..startScore)
recipe.SectionStart("New Mutate")
new_mutate_all()
p_Time(startTime,recipe.SectionEnd()-startScore)
elseif (ScriptNumber == 14) then
ScriptAsk = dialog.CreateDialog("Script Dialog. Rebuilder.")
ScriptAsk.startSegm = dialog.AddSlider("Start segment", 1, 1, structure.GetCount()-1, 0)
ScriptAsk.endSegm = dialog.AddSlider("End segment", 2, 2, structure.GetCount(), 0)
ScriptAsk.Clashing = dialog.AddSlider("Clashing", 0.6, 0, 1, 1)
ScriptAsk.OK = dialog.AddButton("OK", 1)
ScriptAsk.Cancel = dialog.AddButton("Cancel", 0)
ScriptDialogResult = dialog.Show(ScriptAsk)
startSegm=ScriptAsk.startSegm.value
endSegm=ScriptAsk.endSegm.value
Clashing=ScriptAsk.Clashing.value
if startSegm>endSegm
then
print("Start segment should be no more than End segment")
else
print("Start score: "..startScore)
rebuilder(startSegm,endSegm,Clashing,10000)
p_Time(startTime,recipe.SectionEnd()-startScore)
end
elseif (ScriptNumber == 15) then
print("Start score: "..startScore)
recipe.SectionStart("Sidechain Flipper")
sidechain_flip_all()
p_Time(startTime,recipe.SectionEnd()-startScore)
elseif (ScriptNumber == 16) then
print("Start score: "..startScore)
recipe.SectionStart("SoftRelax")
SoftRelaxFull()
p_Time(startTime,recipe.SectionEnd()-startScore)
elseif (ScriptNumber == 17) then
ScriptAsk = dialog.CreateDialog("Script Dialog. Autobot.")
ScriptAsk.RestartGain = dialog.AddSlider("Score threshold:", 0, 0, 100, 1)
ScriptAsk.Sequence = dialog.AddTextbox("Sequence:", "CL.FR.BT_15_87_97.BT_15_103_113.RW_2_1_10.QU_15.BF.RW_1_1_10.LW_12_2.SR.")
ScriptAsk.OK = dialog.AddButton("OK", 1)
ScriptAsk.Cancel = dialog.AddButton("Cancel", 0)
ScriptDialogResult = dialog.Show(ScriptAsk)
RestartGain=ScriptAsk.RestartGain.value
SequenceStr = ScriptAsk.Sequence.value
local Sequence = {}
local i=0
for Script in string.gmatch(SequenceStr, "[%w_]+%.") do
i=i+1
Sequence[i] = {}
Sequence[i][1] = string.sub(Script,1,2)
local j=1
for ScriptParam in string.gmatch(string.sub(Script,4), "%w+[_%.]") do
j=j+1
Sequence[i][j] = string.sub(ScriptParam,1,string.len(ScriptParam)-1)
end
end
print("The Sequence.")
for i=1,#Sequence do
if Sequence[i][1] == "CL" then print(i..": Clashing")
elseif Sequence[i][1] == "FR" then print(i..": FastRelax")
elseif Sequence[i][1] == "BF" then print(i..": BlueFuze")
elseif Sequence[i][1] == "WS" then print(i..": WS or SW")
elseif Sequence[i][1] == "BT" then print(i..": Band Test,"..Sequence[i][2]..","..Sequence[i][3]..","..Sequence[i][4])
elseif Sequence[i][1] == "LW" then print(i..": Local Wiggle,"..Sequence[i][2]..","..Sequence[i][3])
elseif Sequence[i][1] == "LR" then print(i..": Local Rebuild,"..Sequence[i][2]..","..Sequence[i][3])
elseif Sequence[i][1] == "QU" then print(i..": Quake,"..Sequence[i][2])
elseif Sequence[i][1] == "ST" then print(i..": Sidechain Test,"..Sequence[i][2])
elseif Sequence[i][1] == "MU" then print(i..": Mutate")
elseif Sequence[i][1] == "MT" then print(i..": Mutate and Test,"..Sequence[i][2]..","..Sequence[i][3])
elseif Sequence[i][1] == "NM" then print(i..": New Mutate")
elseif Sequence[i][1] == "RE" then print(i..": Rebuilder,"..Sequence[i][2]..","..Sequence[i][3]..","..Sequence[i][4])
elseif Sequence[i][1] == "SF" then print(i..": Sidechain Flipper")
elseif Sequence[i][1] == "SR" then print(i..": Soft Relax")
elseif Sequence[i][1] == "RW" then print(i..": Rebuild Worst,"..Sequence[i][2]..","..Sequence[i][3]..","..Sequence[i][4])
else print(i..": UNKNOWN")
end
end
print("Start score: "..startScore)
p_Time(startTime,0)
save.Quicksave(1)
Iteration=1
while Iteration<100 do
print("Start of Iteration: "..Iteration)
save.Quickload(1)
recentbest.Save()
ScoreGain=RestartGain + 1
step=1
while ScoreGain>=RestartGain do
startScoreStep=current.GetEnergyScore()
startTimeStep=os.time()
for i=1,#Sequence do
if Sequence[i][1] == "CL"
then
recipe.SectionStart("Clashing")
clashing(0)
elseif Sequence[i][1] == "FR"
then
recipe.SectionStart("FastRelax")
FastRelaxFull()
elseif Sequence[i][1] == "BF"
then
recipe.SectionStart("BlueFuze")
BlueFuze()
elseif Sequence[i][1] == "WS"
then
recipe.SectionStart("WS or SW")
params = {1,1,1,1}
ws_or_sw(params)
elseif Sequence[i][1] == "BT"
then
recipe.SectionStart("Band Test")
for l=1,Sequence[i][2] do
Band_tests(Sequence[i][3],Sequence[i][4],0.5,l,Sequence[i][2])
end
elseif Sequence[i][1] == "LW"
then
recipe.SectionStart("Local Wiggle")
local_wiggle(Sequence[i][2],Sequence[i][3])
elseif Sequence[i][1] == "LR"
then
recipe.SectionStart("Local Rebuild")
local_rebuild_all(Sequence[i][2],0.6)
elseif Sequence[i][1] == "QU"
then
recipe.SectionStart("Quake")
quake(Sequence[i][2],15,1,0.6)
elseif Sequence[i][1] == "ST"
then
recipe.SectionStart("Sidechain Test")
sidechain_shock(Sequence[i][2])
elseif Sequence[i][1] == "MU"
then
recipe.SectionStart("Mutate")
mutate(2,1)
elseif Sequence[i][1] == "MT"
then
recipe.SectionStart("Mutate and Test")
Mutate_And_Test(Sequence[i][2],Sequence[i][3])
elseif Sequence[i][1] == "NM"
then
recipe.SectionStart("New Mutate")
new_mutate_all()
elseif Sequence[i][1] == "RE"
then
recipe.SectionStart("Rebuilder")
rebuilder(Sequence[i][2],Sequence[i][3],0.6,Sequence[i][4])
elseif Sequence[i][1] == "SF"
then
recipe.SectionStart("Sidechain Flipper")
sidechain_flip_all()
elseif Sequence[i][1] == "SR"
then
recipe.SectionStart("Soft Relax")
SoftRelaxFull()
elseif Sequence[i][1] == "RW"
then
recipe.SectionStart("Rebuild Worst")
RebuildWorst(Sequence[i][2],Sequence[i][3],0.6,Sequence[i][4])
else
recipe.SectionStart("UNKNOWN")
print(i..": UNKNOWN")
end
print("Score: "..current.GetEnergyScore()..", +"..recipe.SectionEnd())
p_Time(startTime,current.GetEnergyScore()-startScore)
end
print("Iteration: "..Iteration..". Step: "..step)
p_Time(startTime,current.GetEnergyScore()-startScore)
step=step+1
ScoreGain=current.GetEnergyScore()-startScoreStep
end
print("End of Iteration: "..Iteration)
Iteration=Iteration+1
end
end
elseif (DialogResult == 2) then
ScriptAsk = dialog.CreateDialog("About.")
ScriptAsk.NewLabel = dialog.AddLabel("Made by Grom.")
ScriptAsk.OK = dialog.AddButton("OK", 1)
ScriptDialogResult = dialog.Show(ScriptAsk)
end
--START Isaksson Share v1.5.2
--Copy this into your recipe and call before and after every period of time.
--Warning: all saves onto you hard disk will have to be removed manually afterwards !
--reference: supplementary material for Koepnick et al (2019) De novo protein design by citizen scientists, Nature, volume 570, pages
390-394
--https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-019-1274-4/MediaObjects/41586_2019_1274_MOESM1_ESM.pdf
--v1: script by Isaksson
--v1.2 added the dialog (BK 1/10/2019)
--v1.3 added time intervals when no gain
--v1.4 PrintVerbose, check every 60 seconds
--v1.5 option Temp name
--v1.5.2 fixed timeleft, Name to save
timeLeft=os.difftime(puzzle.GetExpirationTime(),os.time())/3600 -- in hours
print("Remaining time: "..timeLeft)
startTime=os.time() -- in seconds
userTimeInterval= 60 -- in seconds
lastchecktime = startTime -- in seconds
verbose = false -- print more or less info
save_resolution=1000
function timeLeft()
local result=os.difftime(puzzle.GetExpirationTime(),os.time())/3600 -- in hours
return result
end
function PrintVerbose(text)
if verbose then
print(text)
end
end
function ItsCheckTime()
local currentTime= os.time() -- in seconds
if currentTime-lastchecktime > userTimeInterval then
PrintVerbose(timeLeft().." hours remaining")
return true
end
return false
end
function rounding(x)--cut all afer 3-rd place
return x-x%0.001
end
function before_Solution(rnd,str_name)
if save_resolution > 999 then return end -- New BK 1/10/2019
PrintVerbose("-Before-")
hi_score = 0
hi_idx = 1
sol = save.GetSolutions()
if (sol[0] == nil) then
print("0 solutions found")
--save.SaveSolution("auto_"..rnd)
else
PrintVerbose((#sol+1) .. " solutions found")
for idx = 0, #sol do
soli = sol[idx]
if (string.find(soli.name,rnd) ~= nil) then
PrintVerbose(soli.name .. " : " .. soli.score)
if (soli.score > hi_score) then
hi_score = soli.score
hi_idx = idx
end
end
end
--print("Load the solution ...")
if(current.GetEnergyScore()+save_resolution < hi_score) then
save.LoadSolution(sol[hi_idx])
soli = sol[hi_idx]
print("Load solution: "..soli.name.." : "..rounding(soli.score,value_score_resolution))
end
end
end
function after_Solution(rnd,str_name)
if save_resolution > 999 then return end -- New BK 1/10/2019
PrintVerbose("-After-")
hi_score = 0
hi_idx = 1
sol = save.GetSolutions()
if (sol[0] == nil) then
print("0 solutions found")
str = "auto".."-"..rnd.."-"..rounding(current.GetEnergyScore(),value_score_resolution)
print("Save solution "..str)
save.SaveSolution(str)
else
PrintVerbose((#sol+1) .. " solutions found")
for idx = 0, #sol do
soli = sol[idx]
if (string.find(soli.name,rnd) ~= nil) then
PrintVerbose(soli.name .. " : " .. soli.score)
if (soli.score > hi_score) then
hi_score = soli.score
hi_idx = idx
end
end
end
PrintVerbose("Save the solution ...")
band.DeleteAll()
if(current.GetEnergyScore()-save_resolution > hi_score) then
str = str_name.."-"..rnd.."-"..rounding(current.GetEnergyScore(),value_score_resolution)
print("Save solution: "..str)
save.SaveSolution(str)
end
end
end
str_name= ui.GetTrackName() -- copy-paste anywhere on top of the recipe
rnd= "Temp" -- Warning: edit before in order to cach the right loop name
--How to use:
--Uncomment and insert the following 2 lines on the right places, before or after each loop:
--if ItsCheckTime() then before_Solution(rnd,str_name) end -- as often as possible after score evaluations, e.g. in savebest(), or before any
action
--after_Solution(rnd,str_name) -- after any gain (will not save any loaded solution)
--Uncommend and copy-paste the following 3x2 lines within the dialog on the right places:
--ask.LabelRowBeforeSave = dialog.AddLabel("Keep save resolution to 1000 to avoid local saves") --(optional) copy-paste and adapt in the
dialog
--ask.save_resolution = dialog.AddSlider("Save resolution:", 1000, 0.3, 1000, 1) --copy-paste and adapt in the dialog (parameters)-- 1000
means no sharing
--ask.save_Name = dialog.AddTextbox("Name to save: ", rnd)
--rnd=ask.save_Name.value
--save_resolution=ask.save_resolution.value -- copy-paste and adapt after the dialog.show
--if save_resolution < 1000 then print("Checking for solution every "..userTimeInterval.." seconds") end
--End of Isaksson Share