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Recipe: Quaking Rebuild V2 1.0

created by spvincent
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Name
Quaking Rebuild V2 1.0
ID
35801
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Created on
November 27, 2011 at 02:40 AM UTC
Updated on
November 27, 2011 at 02:40 AM UTC
Description

Loop Rebuild modified so that after Rebuild/Shake/Wiggle etc: it performs some Local Quakes rather than Fuses in an attempt to improve the score.

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Code

max_rebuild_length = 5 -- Maximum rebuild length. min_rebuild_length = 5 -- - Must be less than or equal to max_rebuild_length. Suggest not going below 4. number_of_rebuilds = 8 -- It'll look for the best score from this number of rebuilds. Change to taste. start_idx = 0 -- if this is a residue id, use it as the start point. If not -- use a semi-random number computed from the score ss_control = 3 -- ss_control == 1 Only rebuilds loops -- ss_control == 2 Rebuilds everything. Helices and sheets will be temporarily converted to loops -- ss_control == 3 Rebuild loops but allows a single non-loop residue in the rebuild segment. -- they'll be temporarily converted to loops loop_forever = true -- just keep going. Good for overnight running. min_residue = 1 -- Change these if you want to rebuild part of a protein only. For example, to -- rebuild 53-64, set min_residue to 53 and max_residue to 64. To restore, set to -- 1 and 9999 (or any large number) respectively max_residue = 999 kClashImportanceDuringRebuild = 1 -- Might try reducing this to get more a different rebuild than the highest scoring -- one, which might overstate -- the importance of clashing which can be remedied by a quick shake. -- If, after rebuild, shake, wiggle, etc. , the score is close enough to the starting score, attempt some quakes. -- close enough is defined by the entry in kQuakingThresholds indexed by the size of segment being rebuilt kQuakingThresholds = { 8 , 8 , 8 , 15 , 25 , 30 , 35 } nQuakingThresholds = 7 -- Use of quicksave slots kOriginalStructureOrNewBest = 1 kBestPostRebuild = 2 -- Stores the best non-improved structure in Quicksave slot 10 (but can change this below) . The structure that's saved -- is the best before WS etc, so if this script fails to produce (or even if it does) you can load the structure in -- slot 10 and try WS in different ways. kBestNonImprovedStructure = 10 original_secondary_structure = {} n_residues = 0 curr_score = 0 multiplier = 1 ----- -- The Local Quake bit. Copied from LQ1.2 for expediency -- Bands radiate from a segment to spatially close neighbours -- 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 start_idx = 0 -- Set to a valid residue to start with that residue: otherwise -- start with a semi-random one, second_offset = 3 -- Set to 0 for a single centre. This is the most likely one to change. opposite_centre = false -- overrides second_offset if true target_wiggle_reduction = 120 -- 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 = 20 -- 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 n_quakes = 10 -- A reasonable number 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 current.GetScore () else return current.GetEnergyScore () 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 roundto3 ( i ) -- printing convenience return i - i % 0.001 end function delete_all_bands () band.DeleteAll () 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 ] = structure.GetDistance ( 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 most_distant_minimum = segment_ids [ n_segments ] 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.AddBetweenSegments ( candidate_ids_start [ i ] , candidate_ids_end [ i ] ) if ( scale_band_strength == true ) then band.SetStrength ( i , band_strength * average_band_length / candidate_distances [ i ] ) else band.SetStrength ( i , band_strength ) end end end function Quake ( seg ) selection.SelectAll () init_score = GetScore () structure.WiggleSelected ( 1 ) score_after_wiggle = GetScore () score_reduction_after_wiggle = init_score - score_after_wiggle -- 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 delete_all_bands () structure.ShakeSidechainsSelected ( 1 ) gas = GetScore () - score_after_wiggle if ( monit ) then print ( "law " .. roundto3 ( init_score - score_after_wiggle ) .. " gas " .. roundto3 ( gas ) .. " band_strength " .. roundto3 ( band_strength ) ) end structure.WiggleSelected ( 8 ) if ( do_second_shake == true ) then score_a2w = GetScore () structure.ShakeSidechainsSelected ( 1 ) score_a2s = GetScore () if ( score_a2s - score_a2w > 1 ) then structure.WiggleSelected ( 4 ) end end end function local_quake ( start_idx ) band_strength = 0.5 behavior.SetClashImportance ( 1 ) recentbest.Save () best_score_lq = GetScore () inc = Coprime ( n_residues ) idx_lq = start_idx for i = 1, n_quakes do recentbest.Restore () -- Need to record any improvements from the previous iteration,. score_lq = GetScore() if ( score_lq > best_score_lq ) then best_score_lq = score_lq print ( " Gain to " .. roundto3 ( score_lq - score_lq % 0.01 ) ) end delete_all_bands () n_candidates = 0 get_band_segment_data ( idx_lq ) if ( opposite_centre == true ) then second_idx = most_distant_minimum get_band_segment_data ( most_distant_minimum ) elseif ( second_offset ~= 0 ) then second_idx = idx_lq + second_offset while ( second_idx > n_residues ) do second_idx = second_idx - n_residues end get_band_segment_data ( second_idx ) end if ( n_candidates > 0 ) then create_bands () if ( second_offset ~= 0 ) then print ( " i: " .. i .. " seg ".. idx_lq .. "," .. second_idx ) else print ( " i: " .. i .. " seg ".. idx_lq ) end Quake ( idx_lq ) end idx_lq = idx_lq + inc if ( idx_lq > n_residues ) then idx_lq = idx_lq - n_residues end end -- for recentbest.Restore () delete_all_bands () end ------ function IsSegmentALoop ( first , last ) -- Returns number of non-loop residues (helices or sheets) n_non_loops = 0 for i = first , last do if ( structure.GetSecondaryStructure ( i ) ~= "L" ) then n_non_loops = n_non_loops + 1 end end return n_non_loops end function ConvertToLoop ( first , last ) for k = first , last do if ( original_secondary_structure [ k ] ~= "L" ) then selection.DeselectAll ( ) selection.Select ( k ) structure.SetSecondaryStructureSelected ( "L" ) end end end function RestoreStructure ( first , last ) for k = first, last do selection.DeselectAll () selection.Select ( k ) structure.SetSecondaryStructureSelected ( original_secondary_structure [ k ] ) 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 nudge ( score ) selection.SelectAll () --recentbest.Save () behavior.SetClashImportance ( 0.2 + 0.2 * pseudorandom ( score ) ) structure.WiggleSelected ( 1 ) behavior.SetClashImportance ( 1 ) structure.WiggleSelected ( 8 ) recentbest.Restore () end function WiggleShakeWiggle ( start_idx , end_idx ) -- returns the score after doing a WSW: shortcircuiting if things don't look promising score_a = GetScore () structure.WiggleSelected ( 15 ) recentbest.Restore () score_after_wiggle = GetScore () if ( score_after_wiggle - score_a < 10*multiplier and best_score - score_after_wiggle > 30*multiplier ) then -- The wiggle got stuck and didn't achieve anything nudge ( score_after_wiggle ) score_after_wiggle = GetScore () end if ( monit ) then --print ( "After first wiggle (bb) : ".. roundto3 ( best_score - score_after_wiggle ) ) end if ( best_score - score_after_wiggle > 100*multiplier ) then -- Not worth continuing return score_after_wiggle end structure.ShakeSidechainsSelected ( 1 ) score_after_second_shake = GetScore () if ( true ) then --score_after_second_shake - score_after_wiggle > 0.5 ) then structure.WiggleSelected ( 10 ) recentbest.Restore () score_after_second_wiggle = GetScore () if ( true ) then -- score_after_second_wiggle - score_after_second_shake < 1 and best_score - score_after_second_wiggle < 50*multiplier ) then -- The second shake did something but the subsequent wiggle didn't nudge ( score_after_second_wiggle ) score = GetScore () return score else return score_after_second_wiggle end else return score_after_second_shake end end function post_rebuild ( score_after_rebuild , start_idx , end_idx ) -- Tries to recover after a rebuild. if ( best_score - score_after_rebuild > 3000*multiplier ) then structure.ShakeSidechainsSelected ( 2 ) elseif ( best_score - score_after_rebuild > 1500*multiplier ) then structure.ShakeSidechainsSelected ( 1 ) end -- First try WSW curr_score = WiggleShakeWiggle ( start_idx , end_idx ) end function rebuild_seg ( start_idx , end_idx ) -- return codes -- -- 0 rebuild had no effect: seg probably locked -- 1 no improvement -- 2 improvement selection.DeselectAll () selection.SelectRange ( start_idx , end_idx ) -- for some reason, do_local_rebuild ( 1) often leaves the protein unchanged k = 0 repeat k = k + 1 behavior.SetClashImportance ( kClashImportanceDuringRebuild ) structure.RebuildSelected ( k ) behavior.SetClashImportance ( 1 ) score_after_rebuild = GetScore () until score_after_rebuild ~= best_score or k > 2 if ( score_after_rebuild == best_score ) then -- If the scores are still equal we probably have a locked segment return 0 end recentbest.Save () if ( number_of_rebuilds > 1 ) then behavior.SetClashImportance ( kClashImportanceDuringRebuild ) structure.RebuildSelected ( number_of_rebuilds - 1 ) behavior.SetClashImportance ( 1 ) recentbest.Restore () end -- Now do the post rebuild wiggle and shakes score_after_rebuild = GetScore () selection.SelectAll () -- Compute a value delta which will be used later to determine if we are -- "sufficiently" close to our original best score. If it turns out later that -- we are, then nudge it around rebuild_length = end_idx - start_idx + 1 if ( rebuild_length > nQuakingThresholds ) then delta = kQuakingThresholds [ nQuakingThresholds ] * multiplier -- sanity check for lengthy rebuild segs else delta = kQuakingThresholds [ rebuild_length ] * multiplier end save.Quicksave ( kBestPostRebuild ) post_rebuild ( score_after_rebuild , start_idx , end_idx ) if ( best_score - curr_score < delta ) then print ( " cur score " .. roundto3 ( curr_score ) ) local_quake ( start_idx ) end if ( ss_control > 1 ) then save.LoadSecondaryStructure () end curr_score = GetScore () if ( curr_score > best_score ) then best_score = curr_score improvement_made = true save.Quicksave ( kOriginalStructureOrNewBest ) print ( "Improvement to ".. roundto3 ( best_score ) ) end if ( curr_score > qs10_best_score and improvement_made == false ) then recentbest.Save () qs10_best_score = curr_score save.Quickload ( kBestPostRebuild ) -- Bracket the area with frozen segments for easy recognition selection.DeselectAll () if ( start_idx > 1 ) then selection.Select ( start_idx - 1 ) end if ( end_idx < n_residues ) then selection.Select ( end_idx + 1 ) end freeze.FreezeSelected ( true , false ) save.Quicksave ( kBestNonImprovedStructure ) recentbest.Restore () end if ( improvement_made == true ) then return 2 else return 1 end end function rebuild ( rebuild_length ) n_possible_segs = n_residues - rebuild_length + 1 inc = Coprime ( n_possible_segs ) -- The point of this Coprime, start_idx business is so we go through the protein in a -- nonuniform way. Rather than rebuilding 1-4, 2-5 , 3-6 for example, we might do 21 4, 53-57, 3-6 -- or something like that for i = 1 , n_possible_segs do improvement_made = false end_idx = start_idx + rebuild_length - 1 if ( start_idx >= min_residue and end_idx <= max_residue and ( ss_control == 2 or ( ss_control == 1 and IsSegmentALoop ( start_idx , end_idx ) == 0 ) or ( ss_control == 3 and IsSegmentALoop ( start_idx , end_idx ) < 2 ) ) ) then rb = rb + 1 print ( "rb ".. rb .. " " .. start_idx .."-" .. end_idx .. " (" ..i .. "/" .. n_possible_segs .. ")" ) save.Quickload ( kOriginalStructureOrNewBest ) if ( ss_control > 1 ) then ConvertToLoop ( start_idx , end_idx ) end best_score = GetScore () k = rebuild_seg ( start_idx, end_idx ) if ( ss_control > 1 ) then save.LoadSecondaryStructure () end end start_idx = start_idx + inc if ( start_idx > n_possible_segs ) then start_idx = start_idx - n_possible_segs end end -- for i end -- Tidy up if necessary band.DeleteAll () n_residues = structure.GetCount () if ( ss_control > 1 ) then for i = 1, n_residues do original_secondary_structure [ i ] = structure.GetSecondaryStructure ( i ) end end save.SaveSecondaryStructure () rb = 0 save.Quicksave ( kOriginalStructureOrNewBest ) behavior.SetClashImportance ( 1 ) best_score = GetScore () print ( "Start score : " .. roundto3 ( best_score ) ) if ( start_score == 0 ) then print ( "Suggest quitting as starting score < = 0" ) end if ( ss_control == 1 ) then print ( "Loops only" ) elseif ( ss_control == 2 ) then print ( "Loops, sheets, and helices" ) else print ( "Loops with one non-loop allowed" ) end if ( max_residue > n_residues ) then max_residue = n_residues end if ( min_residue < 1 ) then min_residue = 1 end if ( max_residue <= min_residue ) then print ( "Rebuild range error" ) loop_forever = false end multiplier = current.GetExplorationMultiplier () if ( multiplier <1 ) then multiplier = 1 end if ( true ) then -- min_residue > 1 or max_residue < n_residues ) then print ( "Rebuild range " .. min_residue .. " to " .. max_residue ) else print ( "Rebuild all" ) end qs10_best_score = 0 if ( start_idx < 1 or start_idx > n_residues ) then r = pseudorandom ( best_score ) start_idx = 1 + n_residues * r start_idx = start_idx - start_idx % 1 end repeat for rebuild_length = max_rebuild_length , min_rebuild_length , -1 do rebuild ( rebuild_length ) end until loop_forever == false save.Quickload ( kOriginalStructureOrNewBest )

Comments

harp Lv 1

I get an error message saying "unknown script version." Perhaps I am doing something wrong?

BootsMcGraw Lv 1

You have to be running FoldIt in "beta" mode to be able to run V2 scripts.

Find the folder that has FoldIt game data. In that folder is a file called "options.txt". Open that file, and find the line that reads "update_group" : "main". Change "main" to "beta" and save the file.

Beware that some folks have experienced big problems when trying to run the game in beta mode. Some have advised making a backup of your entire FoldIt directories before you go beta.

harp Lv 1

Thanks Boots. I did that and I think I know what you mean by big problems. For example, now that I have switched, I can't turn off the music! I just thought it was my old computer playing games:0 When I do get my new one, I will make copies. Thanks again.