Recipe: CG303 GA+EO Remix V7.900

created by Crashguard303

Profile

• Name: CG303 GA+EO Remix V7.900
• ID: 45959
• Shared with: Public
• Parent: None
• Children: None
• Created on: April 24, 2013 at 22:33 PM UTC
• Updated on: April 24, 2013 at 22:33 PM UTC
• Description:

  A complete rework of my old script, object-oriented parameter-/variable-structure allowing more features. Manual is included. See script code for details. Note: This script detects "important"/"cardinal" segments, if there is a change in secondary structure, but you can add more segments by selection interface (blue),too! ; This script version is also able to detect locked segments.

Code

--[[
0. general:
   GAB+EO Remix V7.900 by Crashguard303
   Copyright (C) 2013 Crashguard303 <http://fold.it/portal/user/119022>

   This program is free software: you can redistribute it and/or modify
   it under the terms of the GNU General Public License as published by
   the Free Software Foundation, either version 3 of the License, or
   (at your option) any later version.
   This program is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   GNU General Public License for more details.
   You should have received a copy of the GNU General Public License
   along with this program.  If not, see <http://www.gnu.org/licenses/>.

1. introduction:
   1.1 inspired by:
       Cartoon Villain (GA idea & first random band script of this kind)
       Rav3n_pl        (OO parameter/variable handling)
       jeff101         (EO & input-boxes idea)

   1.2 idea:
       -- This is a further development of my last GAB+EO
          which i wrote from scratch to improve table handling and modularity
          (it was a work of more than one month!)

       -- this script doesn't simply band to random segs,
          it works with a list of "cardinal" origin segs,
          which are detected and/or set by selection interface (blue) before.
          -- origin segs always stay the same (they are just turned off or on),
          -- target segs do vary
             -> this will avoid double banding

       -- new idea is to keep the number of random band parameters as small as they can be:
          the script works with 2 fixed band strengths (as the length is already random)
          -- primary bands:   do seg movement in space or relative to any other seg (depending on band mode)
          -- secondary bands: do seg movement between proximate segs.
                              they can be used to stabilize or move internal puzzle structure,
                              so their job is supporting the primary bands with their major task

       -- as i didn't want to overload the starting sequence
          with too many input boxes and selectable vals (more than 7 boxes at the moment!).
          -> you can set all vals (even the other) in the declaration section.

   1.3 features:
       -- cardinal seg auto-detection: (see 3.3.2.3)
          -- secondary-structure changes, amino-acids, etc will create a uselist
          ++ selecting segs via game interface (blue) is possible, too
       -- 3 breeding modes: (see 3.2)
                            GA
                            EO1
                            EO2
       -- 2 gene     modes: (see 3.2.2.2)
                            "dual"
                            "poly" 
       -- 6 banding  modes (see 3.3)
                           "space"
                           "center"
                           "user"
                           "furthest"
                           "random1"
                           "random2"
       ++ further settings for each

   1.4 known bugs/problems:
       1.4.1 ligand puzzles:
             -- are supported by script, but i couldn't test if it works properly!
             -> to band ligand:
                use band to "user", then slide to last segment!

2. abbreviations/terms you might find:
   2.1 structure:
   gen: gen
   clu: cluster
   seg: segment
   dst: distance
   len: length
   str: strength
   itr: iterations

   2.2 addressing:
   list: table
   idx:  index     (numerical)
   key:  key       (alphanumerical)
   val:  value

   2.3 vals:
   prm: parameter  (argument)
   cur: current    (measured)
   max: maximum
   min: minimum
   cng: change     (to add)
   res: result     (calculated)
   rnd: random     (genrated)

   2.4 other:
   gui: frontend (dialog input box)

3. features:
   3.1 terms and herd generating:
       This script (as GAB before) applies and tests combinations of random bands.
       one band combination set is named cluster (clu) here
       (GA-term: individuum).
       a testing row of different clus is a generation (gen)
       (by default, 1 generation consists of 8 clus = herd.size)
       when one generation has tested, it is evaluated.
       each clu is measured by it's score gain,
       gen will be sorted by clu's score gain, best on top.

   3.2 analyzing and breeding:
       selection of of partners
       and breeding them (mutating, too)
       is the heart of a genetic algorithm !!!

       3.2.1 analyzing:
             after  testing each gen,
             clus are sorted by the score gain they made
             -> first clu is this with best  gain,
             -> last  clu is this with worst gain,

       3.2.2 breeding:
             3.2.2.1 selection via EO:
                     EO mode decides what happens with mediocre clus:

                     -- EO_mode.cur=0: mediocre clus are breeded             (only this is GA)
                     -- EO_mode.cur=1: mediocre clus are considered as best  (soft         EO)
                     -- EO_mode.cur=2: mediocre clus are considered as worst (hard/real    EO)

                     best clus (always):
                     -- are kept (default: cluster 1 and 2 = 1...herd.breed.first)
                        and "breeded" = mixed to new ones.

                     mediocre clus (EO_mode.cur=0):
                     -- are overwritten by breeded ones
                        (default: clu 3...5 = herd.breed.first to herd.breed.last)

                     worst clus (always):
                     -- are replaced by new random ones
                       (default: clu 6...8 = herd.breed.last...herd.size)

             3.2.2.2 sex (breed mode):
                     -- imagine the clus as snails with both genders
                     -- "poly": each single gene can be from any clu by roulette!

                     -- "dual": 1 kid has only 2 parents (default):
                        -> dad is 1st breeding partner
                        -> mom is 2nd breeding partner

                        -- breeding partners can be chosen by:
                           -> their rank: 1st has best score gain
                           -> roulette:   1st appears most time, but all possible

                              -> if you breed 3 kids,
                                 roulette combinations are:

                                 -- by default:
                                    herd.breed.roulette.dad==false
                                    herd.breed.roulette.mom==true

                                    -> kid#1: dad=clu#1 & mom#1=roulette
                                    -> kid#2: dad=clu#2 & mom#2=roulette
                                    -> kid#3: dad=clu#3 & mom#3=roulette

                                 -- other setting:
                                    herd.breed.roulette.dad==false
                                    herd.breed.roulette.mom==false

                                    -> kid#1: dad=clu#1 & mom#1=dad#1+1=clu#2
                                    -> kid#2: dad=clu#2 & mom#2=dad#2+1=clu#3
                                    -> kid#3: dad=clu#3 & mom#3=dad#3+1=clu#4

                                 -- other setting:
                                    herd.breed.roulette.dad==true
                                    herd.breed.roulette.mom==false

                                    -> kid#1: dad#1=roulette & mom#1=dad#1+1
                                    -> kid#2: dad#2=roulette & mom#2=dad#2+1
                                    -> kid#3: dad#3=roulette & mom#3=dad#3+1

                                 -- other setting:
                                    herd.breed.roulette.dad==true
                                    herd.breed.roulette.mom==true

                                    -> kid#1: dad#1=roulette & mom#1=roulette
                                    -> kid#2: dad#2=roulette & mom#2=roulette
                                    -> kid#3: dad#3=roulette & mom#3=roulette

   3.3 applying bands to segments:
       3.3.1 types of connections:
             The clus which are tested will be not only from seg to seg anymore (like in old GAB)
             but also from seg to free space (if using clu.band_to.val="space"),
             allowing more freedom of direction.

       3.3.2 origin segs and target segs:
             3.3.2.1 origin segs:
                     -- are always the same
                        -- i did this to prevent double banding, simplifiy breeding
                           and keeping the clu's gene-length homogenous
                        -> you can't crossbreed a horse with a zebra because their DNAs have different lengths
                        -> in real life, dna also doesn't change length or genes get other tasks,
                           genes remain and are just active or inactive !!

                     -- segs which can be banded and their banding order
                        are stored in a uselist (selection)
                     -> but you can turn some off and change their activity by mutation
                     -> you can set them in the seg_use table declaration

             3.3.2.2 target segs:
                      -- can be different, depending on mode clu.band_to.val:
                      -- origin segs can be banded to

                      -> "space":    no   seg, but to "air" (more freedom of movement,
                                                                     but no reference to other segs anymore)
                      -> "center":   calculated  seg    (real center  seg)
                      -> "user":     selected    seg (pseudo "center" seg internally)
                      -> "furthest": calculated  seg furthest to origin seg
                      -> "random1":  another seg in seg_use list (given in table)
                      -> "random2":      rnd seg in puzzle       (all   available)

             3.3.2.3 if no list is given (in declaration section):
                     -- if you
                        -- neither change the seg_use list to your needs or
                        -- nor     select any seg by game interface:
                           -> by default, only these segs are banded,
                              where changes in secondary structures do occur
                              and which do have special residues (default: Glycine)
                              -> key idea of this new script !!!

       3.3.3 band strength:
             -- is constant for all bands now (unlike to old GAB),
                as the length is already set by random.
             -> but you can set the global band strength
                for primary and secondary bands (not always used)
--]]

function random_seed_set_val(random_seed)
 local random_seed= random_seed
 if (random_seed==nil) or (random_seed=="") then
    random_seed=os.time()+recipe.GetRandomSeed()
 else
    random_seed= tonumber(random_seed)
 end -- if random_seed

 print('Random Seed: '..random_seed)
 math.randomseed(random_seed) -- initialize random seed
 return random_seed
end -- function randomseed

function above0(x)
 if x>0 then
    return 1
 else -- if x<=0
    return -1
 end -- if x
end -- function above0

function crop_digits(x,n)
 local y=x

 y=y*10^n
 y=math.floor(y)
 y=y*10^(-n)

 return y
end -- function crop_digits

function range_wrap(x,min,max,offset)
 --[[
prevent x getting higher than max
               or lower  than min
if x gets out of range, it is set to the other boundary+it's exceeding amount

if x>max, val will be >min, if offset is 0 and float   vals are used
                   or =min, if offset is 1 and integer vals are used
if x<min, val will be <max, if offset is 0 and float   vals are used
                   or =min, if offset is 1 and integer vals are used

example:
range_wrap(1.1,0,1,0) will return 0.1 (x is by .1 >1, so it is set next to 0+.1)
range_wrap(-.1,0,1,0) will return 0.9 (x is by .1 <0, so it is set next to 1-.1)

range_wrap(11,0,10,0) will return 1 (x is by 1 >10, so it is set to  0+1)
range_wrap(-1,0,10,0) will return 9 (x is by 1 <10, so it is set to 10-1)

range_wrap(11,0,10,1) will return 0  (x is by 1 >10, so it is set to  0+1-1)
range_wrap(-1,0,10,1) will return 10 (x is by 1 < 0, so it is set to 10-1+1)
--]]

  local y=x+0
     if y>max then
        y=min+(y-max)-offset
 elseif y<min then
        y=max+(y-min)+offset
 end -- if y
 return y
end -- function range_wrap

function range_clamp(x,min,max)
 --[[
prevent x getting higher than max by setting it to max
               or lower  than min by setting it to min
--]]

  local y=x+0
     if y>max then
        y=max
 elseif y<min then
        y=min
 end -- if y
 return y
end -- range_clamp()

function random_flag1(prob)
 --[[
 return true or false randomly, depending on prob(ability)
 probability should be a float val between 0 and 1 as
 vals <0 have the same effect as =0 and
 vals >1 have the same effect as =1

 returns true, if
 prob=0:   never
 prob=0.1: sometimes
 prob=0.5: quite as often as false
 prob=0.9: most times
 prob=1:   always

 calculation example:
 -- if you want it to respond true
 -- in 1 of 10 cases
 -- use 1/10= 0.1
--]]

 return (math.random()<prob)
end -- function random_flag1

function random_flag2(prob,invert,bool)
-- return val like random_flag1(), but
-- invert=true inverts val
-- bool=false  converts boolean vals
   -- true ->  1
   -- false -> 0

 local val=random_flag1(prob)

 if invert then
    val= not(val)
 end -- if invert

 if bool==false then
    if val then
       val= 1
    else
       val= 0
    end -- if val
 end -- if bool

 return val
end -- function random_flag2

function list_show_deep(list,text)
-- full key and val as string - advanced
-- indexing: pairs
 if text==nil then
    text=tostring(list)
 end -- if text
 local k,v
 for k,v in pairs(list) do
     local ktext
     if type(k)=="number" then
        ktext= text..'['..tostring(k)..']'
     else
        ktext= text..'.'..tostring(k)
     end -- if type(k)
     if type(v)=="table" then
        list_show_deep(v,ktext)
     else
        local vtext
        if (type(v)=="number") or (type(v)=="boolean") then
           vtext= tostring(v)
        else
           vtext= '\"'..tostring(v)..'\"'
        end -- if type(v)
        print(ktext..'='..vtext)
     end -- if type(v)
 end -- for k
end -- function list_show_deep

function puzzle_ismutable()
 local ismutable= false

 for i=1,puzzle.seg_count do
     if structure.IsMutable(i) then
        ismutable= true
        break -- for i
     end -- if structure.IsMutable
 end -- for i

 return ismutable
end -- function puzzle_ismutable

function puzzle_isligand()
  local isligand
  if structure.GetSecondaryStructure(puzzle.seg_count)==not(ss=="L" or ss=="H" or ss=="E" ) then
     isligand= true
  else
     isligand= false
  end -- if structure.GetSecondaryStructure
  print('Ligand detected: '..tostring(isligand))
  return isligand
end -- function puzzle_isligand

function seg_blocks(blocks)
-- create a list of mutlitple segment sections
-- example:
   --       blocks={{1;3};{7;10}}
   -- results list={1;2;3;7;8;9;10}
 local list={}
 local i
 for i=1,#blocks do
     local j
     for j=blocks[i][1],blocks[i][2] do
         print('Appending Idx:'..(#list+1)..'=Seg:'..j)
         table.insert(list,j)
     end -- for j
 end -- for i
 return list
end -- function seg_blocks

function seg_use_list_create(seg_use)
-- table seg_use contains
   -- associative keys - their vals are information for creating the:
   -- numerical keys -   their vals are a list, which puzzle segment indices can be used
 local seg_use=seg_use

 print('Appending segs with idx given in table...')
 seg_use=seg_use_list_append(seg_use,seg_use.include.idx)

 if seg_use.include.selected.act then
    print('Appending segs depending on selection: '..tostring(seg_use.include.selected.val)..'...')
    seg_use=seg_use_list_append(seg_use,seg_list_selected_get(seg_use.include.selected.val))
 end -- seg_use.include.selected.act
 selection.DeselectAll()

 if seg_use.include.frozen.act then
    print('Appending segs depending on freeze: backbone: '..tostring(seg_use.include.frozen.backbone)..' sidechain:'..tostring(seg_use.include.frozen.sidechain))
    seg_use=seg_use_list_append(seg_use,seg_list_frozen_get(seg_use.include.frozen.backbone,seg_use.include.frozen.sidechain))
 end -- seg_use.include.frozen.act

 if seg_use.include.ss_cngs then
    print('Appending segs, where structure changes do occur...')
    seg_use=seg_use_list_append(seg_use,ss_cngs_get_seg_list())
 end -- if seg_use.include.ss_cngs

 print('Appending segs with ss given in table...')
 seg_use=seg_use_list_append(seg_use,seg_list_ss_get(seg_use.include.ss))

 print('Appending segs with aa given in table...')
 seg_use=seg_use_list_append(seg_use,seg_list_aa_get(seg_use.include.aa))

 seg_use=seg_use_filter(seg_use)
 -- sort segment list and
 -- remove duplicate entries

 print('Removing segs which are locked...')
 seg_use=seg_use_list_remove(seg_use,seg_list_locked_get())

 print('Removing segs with idx given in table...')
 seg_use=seg_use_list_remove(seg_use,seg_use.exclude.idx)

if seg_use.exclude.selected.act then
    print('Removing segs depending on selection: '..tostring(seg_use.exclude.selected.val)..'...')
    seg_use=seg_use_list_remove(seg_use,seg_list_selected_get(seg_use.exclude.selected.val))
 end -- seg_use.exclude.selected.act

 if seg_use.exclude.frozen.act then
    print('Remove segs depending on freeze: backbone: '..tostring(seg_use.exclude.frozen.backbone)..' sidechain:'..tostring(seg_use.exclude.frozen.sidechain))
    seg_use=seg_use_list_remove(seg_use,seg_list_frozen_get(seg_use.exclude.frozen.backbone,seg_use.exclude.frozen.sidechain))
 end -- seg_use.exclude.frozen

 print('Removing segs with ss given in table...')
 seg_use=seg_use_list_remove(seg_use,seg_list_ss_get(seg_use.exclude.ss))

 print('Removing segs with aa given in table...')
 seg_use=seg_use_list_remove(seg_use,seg_list_aa_get(seg_use.exclude.aa))

 print('\nScript will use these segs:')
 for i=1,#seg_use do
  print(i..': '..seg_use[i])
 end -- for i

 return seg_use
end -- function seg_use_list_create

function seg_use_list_append(use_idx,append_idx)
 local use_idx=use_idx

 if seg_use.append_all~=false then
    seg_use.append_all=true
 end -- if seg_use.append_all
 -- if seg_use.append_all is not false
 -- force it to be true
 -- as no other vals are allowed

 if seg_use.append_all then
    use_idx=seg_use_list_append_all(use_idx,append_idx)
 else -- if seg_use.append_all~=true
    use_idx=seg_use_list_append_missing(use_idx,append_idx)
 end -- if seg_use.append_all

 return use_idx
end -- function seg_use_list_append

function seg_use_list_append_all(use_idx,append_idx)
 local use_idx=use_idx
 local i
 for i=1,#append_idx do
     -- print('Appending Idx:'..(#use_idx+1)..'=Seg:'..append_idx[i])
     table.insert(use_idx,append_idx[i])
 end -- for i
 return use_idx
end -- function seg_use_list_append_all

function seg_use_list_append_missing(use_idx,append_idx)
 local use_idx=use_idx
 local i
 for i=1,#append_idx do
     if val_isintable(use_idx,append_idx[i])==false then
        print('Appending Idx:'..(#use_idx+1)..'=Seg:'..append_idx[i])
        table.insert(use_idx,append_idx[i])
     end -- if val_isintable
 end -- for i
 return use_idx
end -- function seg_use_list_append_missing

function val_isintable(list,valsearch)
-- return:
   -- true:  if list does    contain valsearch
   -- false: if list doesn't contain valsearch
 if #list==0 then
   return false
 else
   return key_getbyval(list,valsearch)~=nil
 end -- if #list
end -- function val_isintable

function key_getbyval(list,valsearch)
-- check all keys in table list
-- return first found key which has valsearch
 local keyres=nil
 local key,val

 for key,val in pairs(list) do
 -- with key loop, cycle through all keys
 -- for each key, get its val
    if val==valsearch then
    -- if val found
       keyres= key
       -- return it's key
       break -- key,val
       -- break key loop
    end -- if val
 end -- key loop

 return keyres
end -- function key_getbyval

function seg_use_list_remove(use_idx,remove_idx)
 local use_idx=use_idx

 local i=1
 for i=1,#remove_idx do
     local j=1
     while j<=#use_idx do
           if use_idx[j]==remove_idx[i] then
              print('Removing Idx:'..j..'=Seg:'..use_idx[j])
              table.remove(use_idx,j)
              j=j-1
           end -- if use_idx
           j=j+1
     end -- while j
 end -- for i

 return use_idx
end -- function seg_use_list_remove

function seg_use_filter(seg_use)
-- sort list by segment idx numbers and
-- remove duplicate entries
 local seg_use=seg_use

 -- leave seg_use.sort_ascending as it is, as it is allowed to be nil
 print('Sorting segs ascending: '..tostring(seg_use.sort_ascending))

 if seg_use.remove_double~=false then
    seg_use.remove_double=true
 end -- if seg_use.remove_double
 -- if seg_use.remove_double is not false
 -- force it to be true
 -- as no other vals are allowed
 print('Checking and removing double segs:'..tostring(seg_use.remove_double))

 local i=1
 while i<=(#seg_use-1) do
       local j=i+1
       while j<=#seg_use do
             if     seg_use[i]==seg_use[j] then
             -- if two elements in list are equal
                    if seg_use.remove_double then
                       -- print('Removing idx:'..j..' = Seg:'..seg_use[j])
                       table.remove(seg_use,j)
                       j=j-1
                       -- as element at position j was removed,
                       -- another one might have moved up to position j
                    end -- if seg_use.remove_double
             elseif ((seg_use[i]>seg_use[j])==seg_use.sort_ascending) then
             -- if they are not equal
             -- and they don't have the order as given in seg_use.sort_ascending
                    -- print('Swapping idx:'..i..'=Seg:'..seg_use[i]..' with idx:'..j..'=Seg:'..seg_use[j])
                    seg_use[i],seg_use[j]=seg_use[j],seg_use[i]
             end -- if seg_use
             j=j+1
       end -- for j
       i=i+1
 end -- while i<=(#seg_use-1)

 return seg_use
end -- function seg_use_filter

function seg_list_locked_get()
 local seg_found={}
 local i
 for i=1,puzzle.seg_count do
     if structure.IsLocked(i) then
        table.insert(seg_found,i)
     end -- if structure.IsLocked
 end -- for i
 return seg_found
end -- function seg_list_locked_get

function ss_cngs_get_seg_list()
 local seg_found={}

 local seg_count2= puzzle.seg_count-1

 local i=1
 while i<seg_count2 do
       local ss1=structure.GetSecondaryStructure(i)
       local ss2=structure.GetSecondaryStructure(i+1)
       -- check ss of seg with idx i and i+1
       if ss1~=ss2 then
       -- are ss different?
       -- primary, we want to find segs with loop-ss at the end of helix or sheet sections
       -- but sometimes helices are directly near sheets
          if     ss1=="L" then
                 -- loop found at i? (then other ss is behind i) then
                 table.insert(seg_found,i)
          elseif ss2=="L" then
                 -- loop found near i? (then other ss is at i)
                 table.insert(seg_found,(i+1))
                 i=i+1
          elseif ss1=="H" then
                 -- helix found at i? (then other ss (but no loop) is behind i)
                 table.insert(seg_found,i)
          elseif ss2=="H" then
                 -- helix found near i? (then other ss (but no loop) is at i)
                 table.insert(seg_found,(i+1))
                 i=i+1
          end -- if ssx==ss
       end -- if ss1~=ss2
       i=i+1
 end -- while i<seg_count2

 return seg_found
end -- function ss_cngs_get_seg_list

function seg_list_selected_get(selected_flag)
 local seg_found={}
 local i
 for i=1,puzzle.seg_count do
     if selection.IsSelected(i)==selected_flag then
        table.insert(seg_found,i)
     end -- if selection.IsSelected
 end -- for i
 return seg_found
end -- seg_list_selected_get

function seg_list_frozen_get(backbone_flag,sidechain_flag)
 local seg_found={}
 local i
 for i=1,puzzle.seg_count do
     local backbone,sidechain=freeze.IsFrozen(i)
     if (backbone==backbone_flag) and (sidechain==sidechain_flag) then
        table.insert(seg_found,i)
     end -- if backbone,sidechain
 end -- for i
 return seg_found
end -- function seg_list_frozen_get

function ss_cngs_show(structure_cngs_get,freeze_flag1,freeze_flag2)
 selection.DeselectAll()
 freeze.UnfreezeAll()

 print("Found changes:")
 local i
 for i=1,#seg_use do
     -- by variable i, cycle through all segs in list which have been found
     print(i..': '..seg_use[i])
     -- show seg number
     selection.Select(seg_use[i])
     -- select seg number
 end -- for i

 freeze.FreezeSelected(freeze_flag1,freeze_flag2)
 -- if flags are set, freeze selected segs, backbone and/or sidechains
 selection.DeselectAll()
end -- function ss_cngs_show

function seg_list_ss_get(use_ss)
 local seg_found={}

 local i
 for i=1,#use_ss do
     local j
     for j=1,puzzle.seg_count do
         if structure.GetSecondaryStructure(j)==use_ss[i] then
            -- print(j..': '..structure.GetSecondaryStructure(j))
            table.insert(seg_found,j)
         end -- if structure.GetSecondaryStructure
     end -- for j
 end -- for i
 return seg_found
end -- function seg_list_ss_get

function seg_list_aa_get(use_aa)
 local seg_found={}

 local i
 for i=1,#use_aa do
     local j
     for j=1,puzzle.seg_count do
         if structure.GetAminoAcid(j)==use_aa[i] then
            -- print(j..': '..structure.GetAminoAcid(j))
            table.insert(seg_found,j)
         end -- if structure.GetAminoAcid
     end -- for j
 end -- for i
 return seg_found
end -- function seg_list_aa_get

function seg_center_get()
 if (puzzle.seg_center.get_mode=="start") and (puzzle.seg_center.val~=nil) then
 -- start center seg is to get and center seg is set
       print('Stored center seg: '..puzzle.seg_center.val)
       return puzzle.seg_center.val
       -- use stored center seg
 else
 -- start center seg is not to get or center seg is not set
 -- current center seg is to get
    puzzle.seg_center.val= seg_center_get2()
    -- get current center seg
    return puzzle.seg_center.val
 end -- if puzzle.seg_center.get_mode,puzzle.seg_center.val
end -- function seg_center_get

function seg_center_get2()
--[[
find center seg of puzzle
for each seg, measure it's dst to all other segs
and sum these dsts up
center seg has lowest sum of dsts
--]]

 -- print ('Getting center segment.')
 local dist_sum={min=math.huge;min_issegidx=0}

 local i
 for i=1,puzzle.seg_count do
     dist_sum.cur=0
     local j
     for j=1,puzzle.seg_count do
         dist_sum.cur=dist_sum.cur+structure.GetDistance(i,j)
     end -- for j
     -- print('Distance sum for #'..i..' = '..dist_sum.cur)
     if dist_sum.cur<dist_sum.min then
        dist_sum.min=dist_sum.cur
        dist_sum.min_issegidx=i
        -- print('Distance sum min hit!')
        -- print('Distance sum min: #'..dist_sum.min_issegidx..' = '..dist_sum.min)
     end -- if dist_sum.cur
 end -- for i
 -- print('Distance sum min: #'..dist_sum.min_issegidx..' = '..dist_sum.min)
 -- similar to:
 print('Current center seg: '..dist_sum.min_issegidx)
 return dist_sum.min_issegidx
end -- function seg_center_get2

function seg_furthest_get(seg_target)
 -- print ('Getting furthest segment to seg#'..seg_target)
 local dist={max=0;max_issegidx=0}
 local i
 for i=1,puzzle.seg_count do
     dist.cur= structure.GetDistance(seg_target,i)
     if dist.cur>dist.max then
        dist.max= dist.cur
        dist.max_issegidx=i
        -- print('Distance max hit!')
        -- print('Distance max: #'..dist.max_issegidx..' = '..dist.max)
     end -- if dist.cur
 end -- i
 -- print('Distance max: #'..dist.max_issegidx..' = '..dist.max)

 return dist.max_issegidx
end -- seg_furthest_get

function herd_generate(clu,first,last)
 print('Generating herd from '..first..' to '..last..'...')
 local i
 for i=first,last do
     -- print('Generating clu: '..i)
     clu[i]={}
     local j
     for j=1,#seg_use do
     -- with j, cycle through all segment indices given in seg uselist
     -- print('--seg:'..j..'use:'..seg_use[j])
         clu[i][j]=band_generate(j)
         -- create clu band
     end -- for i
     clu[i].name=clu_name_get(i,"r")
 end -- for i
 return clu
end -- function herd_generate

function band_generate(seg_cur)
 local band={act=random_flag2(herd.mutate.prob.off,true,true)}
             -- depending on random flag (influenced by herd.mutate.prob.off),
             -- turn off band when indicated

 if clu.band_to.val=="space" then
    -- following vals are pure random float numbers between 0 and <1
        band.rho=    math.random()
        band.theta=  math.random()
     -- band.theta=  .5;
        band.phi=    math.random()

 else
        band.d_cng1= math.random()
        if clu.band_to.val=="random" then
        -- random segs?
           if puzzle.seg_random.get_mode=="list" then
           -- random seg in list ?
              repeat
                    band.seg_target= seg_use[math.random(1,#seg_use)]
              until band.seg_target~=seg_use[seg_cur]
              -- prevent banding seg to itself
              -- print('Random seg target of list: '..band.seg_target..' (not '..seg_use[seg_cur]..')')
           else -- puzzle.seg_random.get_mode=="all"
           -- random seg in puzzle ?
              repeat
                    band.seg_target= math.random(1,puzzle.seg_count)
              until band.seg_target~=seg_use[seg_cur]
              -- prevent banding seg to itself
              -- print('Random seg target of all: '..band.seg_target..' (not '..seg_use[seg_cur]..')')
           end -- if puzzle.seg_random.get_mode
        end -- if clu.band_to.val
 end -- if clu.band_to.val

 if clu.d_cng2.act then
 -- secondary bands are used
    band.d_cng2= math.random()
 end -- if clu.d_cng2.act

 return band
end -- function band_generate

function herd_mutate(clu,first,last)
 local clu= clu
 print('Mutating herd from '..first..' to '..last..'...')
 local i
 for i=first,last do
     if herd.mutate.genes_show.act then
        print('Mutating clu#'..i)
     end -- if if herd.mutate.genes_show.act
     local j
     for j=1,#clu[i] do
     if herd.mutate.genes_show.act then
        print('Mutating band#'..j)
     end -- if herd.mutate.genes_show.act
     clu[i][j]=band_mutate(clu[i][j])
     end -- for j
 end -- for i
 return clu
end -- function herd_mutate

function band_mutate(clu_band)
 local band={act=mutate_bool_val(clu_band.act)}

 if clu.band_to.val=="space" then
        band.rho=    mutate_float_val(clu_band.rho)
        band.theta=  mutate_float_val(clu_band.theta)
        band.phi=    mutate_float_val(clu_band.phi)

 else
        band.d_cng1= mutate_float_val(clu_band.d_cng1)
        if clu.band_to.val=="random" then
           band.seg_target= mutate_int_seg(clu_band.seg_target)
        end -- if clu.band_to.val
 end -- if clu.band_to.val

 if clu.d_cng2.act then
 -- secondary bands are used
    band.d_cng2= mutate_float_val(clu_band.d_cng2)
 end -- if clu.d_cng2.act

 return band
end -- function band_mutate

function mutate_bool_val(val)
-- depending on herd.mutate.prob.vals
-- possibly toggle band activity:
   -- band on  -> band off
   -- band off -> band on

  local val= val or false
  -- break reference
  if random_flag1(herd.mutate.prob.vals) then
  -- has random hit possibility?
     mutate_val_show('Old',val)
     val= not(val)
     -- invert boolean
     mutate_val_show('New',val)
     return val
  else
     return val
  end -- if random_flag1
end -- function mutate_bool_val

function mutate_float_val(val)
-- depending on herd.mutate.prob.vals
-- possibly change normalized val 0...1
-- by a random amount between +/-10^(min...max)

  local val= val+0
  -- break reference
  if random_flag1(herd.mutate.prob.vals) then
  -- has random hit possibility?
    mutate_val_show('Old',val)
    val= val+(math.random(0,1)*2-1)*(10^(math.random(herd.mutate.rng10e.min,herd.mutate.rng10e.max)))
    val= range_wrap(val,0,1,0)
    mutate_val_show('New',val)
    return val
  else
    return val
  end -- if random_flag1
end -- function mutate_float_val

function mutate_int_seg(val)
-- depending on herd.mutate.prob.vals
-- possibly change segment idx
-- by a random amount between +/-1

  local val= val+0
  -- break reference
  if random_flag1(herd.mutate.prob.vals) then
  -- has random hit possibility?
     mutate_val_show('Old',val)
     val= val+(random_flag2(0.6,false,false)*2-1)
     -- 0.6 (0.5 would be 50:50) means appearing:
        -- +1: more often
        -- -1: less often
     val= range_wrap(val,1,puzzle.seg_count,1)
    mutate_val_show('New',val)
    return val
  else
    return val
  end -- if random_flag1
end -- function mutate_float_val

function mutate_val_show(text,val)
 if herd.mutate.genes_show.act then
    print(text..' val: '..tostring(val))
 end -- if herd.mutate.genes_show.act
end -- function mutate_val_show

function clu_name_get(idx,kind)
-- create a table with following name elements:

return {
        gen=gen.cur;
        clu=idx;
        knd=kind;
        dat=os.date()
       }
end -- function clu_name_get

function clu_name_get_string(clu_name,dat_flag)
local OS=""
    OS= OS..'G'..clu_name.gen
    OS= OS..'C'..clu_name.clu
    OS= OS..'K'..clu_name.knd

 if dat_flag then
    OS= OS..'D'..clu_name.dat
 end -- if dat_flag
return OS
end -- function clu_name_get

function clu_apply_bands(band_use)
-- apply all fixed bands
-- and all which are stored in current clu passed by table band_use

-- for each band pair, depending on mode clu.band_to.val
-- connect origin seg (given in uselist)
-- to another seg ("center", "furthest", "random") or
-- to "space"

-- apply fixed bands given in clu.fix:
 local i
 for i=1,#clu.fix do
     -- print(clu.fix[i][1],clu.fix[i][2])
     band.AddBetweenSegments(clu.fix[i][1],clu.fix[i][2])

     local len= structure.GetDistance(clu.fix[i][1],clu.fix[i][2])+clu.fix.lencng
     len= range_clamp(len,clu.band_sys_lim.min,clu.band_sys_lim.max)
     band.SetGoalLength(band.GetCount(),len)

     band.SetStrength(band.GetCount(),clu.fix.str)
 end -- for i

 local seg_center
 if clu.band_to.val=="center" then
 -- banding to "center" is used
 -- alternative:
 -- if (clu.band_to.val=="center") or (clu.band_to.val=="space") then
 -- banding to "center" or "space" is used

    seg_center= seg_center_get()
    -- get current center segment
    -- fetch it before cycling through all clu bands,
    -- as it is the same each time
 end -- if clu.band_to.val

 -- appply random bands given in clu:
 for i=1,#band_use do
 -- with i, cycle through all clu bands and their data

  if band_use[i].act then
  -- only if current band i is act (gene is not off)

     local seg_origin= seg_use[i]
     -- get origin seg to band from seg uselist

     if clu.band_to.val=="space" then
     -- if banding to space, but not to other segs
     -- get
        -- axis reference seg indices (seg_axis_x,seg_axis_y) and
           -- calculated here
        -- spatial vals (rho, theta,phi) from normalzed vals
           -- given by clu data

        local seg_axis_x= seg_get_idx("usepuzz",seg_origin,-1)
        -- band x-angle reference is previous seg in puzzle

        local seg_axis_y= seg_get_idx("usepuzz",seg_origin,1)
        -- band y-angle reference is next seg in puzzle
        -- alternative:
        -- local seg_axis_y= seg_center
        -- band y-angle reference is center seg in puzzle

        -- rho uses band str1
        band.Add2(i,
                  seg_origin,
                  seg_axis_x,
                  seg_axis_y,
                  band_use[i].rho,
                  band_use[i].theta,
                  band_use[i].phi,
                  clu.pull.str1)

     else -- (clu.band_to.val=="center") or (clu.band_to.val=="furthest") or (clu.band_to.val=="random") then
     -- not banding to space, but to other segs
        -- having a relative dst or are random
        -- calculated here

        local seg_target1
        if     clu.band_to.val=="center" then
               seg_target1= seg_center
               -- primary target seg is center seg in puzzle
        elseif clu.band_to.val=="furthest" then
               seg_target1= seg_furthest_get(seg_origin)
               -- primary target seg is furthest to origin seg
        elseif clu.band_to.val=="random" then
               seg_target1= band_use[i].seg_target
               -- primary target seg is random
        else-- clu.band_to.val has other val
              assert(false,'function clu_apply_bands: clu.band_to.val is invalid: '..tostring(clu.band_to.val))
        end -- if clu.band_to.val
        -- primary target seg uses band str1
        band.AddBetweenSegments2(i,
                                 seg_origin,
                                 seg_target1,
                                 band_use[i].d_cng1,
                                 clu.d_cng1.min,
                                 clu.d_cng1.max,
                                 clu.pull.str1)

     end -- if clu.band_to.val

     if clu.d_cng2.act then
     -- secondary bands are used
        local seg_target2= seg_get_idx("uselist",i,1)
        -- secondary target seg is next in seg uselist
        -- secondary target seg uses band str2
        band.AddBetweenSegments2(i,
                                 seg_origin,
                                 seg_target2,
                                 band_use[i].d_cng2,
                                 clu.d_cng2.min,
                                 clu.d_cng2.max,
                                 clu.pull.str2)
     end -- if clu.d_cng2.act
  else
     -- print('B#'..i..' off')
  end -- if band_use[i].act
 end -- for i
end -- function clu_apply_bands

function seg_get_idx(seg_option,val,offset)
 if     seg_option=="uselist" then
        return seg_use[range_wrap((val+offset),1,#seg_use,1)]
        -- offset=+1 : angle reference is next seg in uselist
        -- offset=-1 : angle reference is prev seg in uselist
 elseif seg_option=="usepuzz" then
        return range_wrap((val+offset),1,puzzle.seg_count,1)
        -- offset=+1 : angle reference is next seg in puzzle
        -- offset=-1 : angle reference is prev seg in puzzle
 else
        assert(false, 'function seg_get_idx: seg_option has invalid val: '..tostring(seg_get_idx))
 end -- if seg_option
end -- function seg_get_idx

function band.Add2(i,
                   seg_origin,
                   seg_axis_x,
                   seg_axis_y,
                   rho,
                   theta,
                   phi,
                   str)
 -- print(i,seg_origin,seg_axis_x,seg_axis_y,rho,theta,phi,str)

 local seg_axis_y,cng_flag= seg_axis_y_check_idx(seg_origin,seg_axis_x,seg_axis_y)
 -- avoid seg_axis_y having the same val as seg_axis_x

 if (cng_flag and clu.band_skip_wrong)==false then

    local    R= rho^(1/3) + 0.001
    -- bend val rho 0..1 towards 1 by cubic root giving val R
    local  rho= R*(clu.rho.max-clu.rho.min)+clu.rho.min
    -- stretch R 0...1 to min...max giving rho again
           rho= range_clamp(rho,0,clu.band_sys_lim.max)
           -- rho within limits?

    local theta= math.acos(2*theta-1)+0
    -- x-angle (azimut) range: 180 degrees (here: pi)

    local   phi= 2*math.pi*phi+0
    -- y-angle (elevation) range: 360 degrees (here: 2*pi)

    local band_count1= band.GetCount()
    -- check number of bands before applying another band
    band.Add(seg_origin,
             seg_axis_x,
             seg_axis_y,
             rho,
             theta,
             phi)
    local band_count2= band.GetCount()
    -- check number of bands after applying another band

    if band_count1~=band_count2 then
    -- only if band has been created
    -- show its attributes
       print(
             'B#'..i..
             ' Seg#'..seg_origin..
             ':('..seg_axis_x..
             '&'..seg_axis_y..
             ') Rho:'..crop_digits(rho,3)..
             ' Theta:'..crop_digits(math.deg(theta),3).."o"..
             -- ..string.char(39)..
             ' Phi:'..crop_digits(math.deg(phi),3).."o"..
             ' Str:'..crop_digits(str,3)
            )

       band.SetStrength(band_count2,str)
       -- change str
    else
       print('B#'..i..' skipped')
    end -- if band_count
 else
    print('B#'..i..' skipped')
 end -- if (cng_flag and clu.band_skip_wrong) == false
end -- function band.Add2

function seg_axis_y_check_idx(seg_origin,seg_axis_x,seg_axis_y)
-- avoid seg_axis_y having the same val as seg_axis_x or seg_origin
 local seg_axis_y= seg_axis_y
 -- print('seg_axis_y: '..seg_axis_y)
 local cng_flag= false

 if (seg_axis_y==seg_axis_x) or (seg_axis_y==seg_origin) then
    seg_axis_y= range_wrap((seg_origin+1),1,puzzle.seg_count,1)
    cng_flag= true
 end -- if seg_axis_y

 --[[
 if cng_flag then
    print('Value changed')
 end -- if cng_flag
 --]]

 return seg_axis_y,cng_flag
end -- function seg_axis_y_check_idx

function band.AddBetweenSegments2(i,
                                  seg_origin,
                                  seg_target,
                                  d_cng,
                                  d_cng_min,
                                  d_cng_max,
                                  str)
 -- print(i,seg_origin,seg_target,d_cng,d_cng_min,d_cng_max,str)

 seg_target,cng_flag= seg_target_check_spat(seg_origin,seg_target)
 -- avoid seg_target beeing too close to seg_origin

 if (cng_flag and clu.band_skip_wrong)==false then
    local dst= structure.GetDistance(seg_origin,seg_target)

    local cng= (d_cng-0.5)*2
    -- as d_cng is a normalized val 0...1 internally
    -- (i don't want to mess with band lens before)
    -- stretch it to -1...1
    -- print('D_cng:'..crop_digits(d_cng,3)..' Cng:'..crop_digits(cng,3))
    local sign=   above0(cng)
          -- -1: compression
          -- +1: expansion
          cng=    sign*(math.abs(cng)*(d_cng_max-d_cng_min)+d_cng_min)
          -- as sign is stored now, truncate it from cng,
          -- resulting an absoulte val 0...1
          -- do linear transformation like cng*factor+offset
          -- (factor: delta(extremae): (max-min), offset: min)
          -- this maps 0...1 to min...max
          -- finally, multiply by sign again to get direction back
    local len= dst+cng
    -- print('Cng:'..crop_digits(cng,3)..' len:'..crop_digits(len,3))

    len= range_clamp(len,clu.band_sys_lim.min,clu.band_sys_lim.max)

    local band_count1= band.GetCount()
    -- check number of bands before applying another band
    band.AddBetweenSegments(seg_origin,seg_target)
    local band_count2= band.GetCount()
    -- check number of bands after applying another band

    if band_count1~=band_count2 then
    -- only if band has been created
    -- show its attributes
       print(
             'B#'..i..
             ' Seg#'..seg_origin..
             ':'..seg_target..
             ' Len:'..crop_digits(len,3)..
             ' (Cng:'..crop_digits(cng,3)..')'..
             ' Str:'..crop_digits(str,3)
            )
       -- print('Distance:'..crop_digits(dst,3)..' Cng:'..crop_digits(cng,3))

       band.SetGoalLength(band_count2,len)
       -- change len
       band.SetStrength(band_count2,str)
       -- change str
    else
       print('B#'..i..' skipped')
    end -- if band_count
 else
    print('B#'..i..' skipped')
 end -- if (cng_flag and clu.band_skip_wrong)==false
end -- function band.AddBetweenSegments2

function seg_target_check_spat(seg_origin,seg_target)
-- avoid seg_target beeing too close to seg_origin
-- by measuring spatial dst
 local seg_target= seg_target
 local cng_flag= false

 while structure.GetDistance(seg_origin,seg_target)<clu.seg_min_dist do
       seg_target,cng_flag= seg_target_too_close_show(seg_origin,seg_target)
 end -- structure.GetDistance

 --[[
 if cng_flag then
    print('Value changed')
 end -- if cng_flag
 --]]

 return seg_target,cng_flag
end -- seg_target_check_spat

function seg_target_too_close_show(seg_origin,seg_target)
 -- print('seg_origin='..seg_origin..':'..'seg_target='..seg_target..' too close.')
 -- print('increasing seg_target idx.')
 local seg_target= range_wrap((seg_target+1),1,puzzle.seg_count,1)
 return seg_target,true
end -- function seg_too_close_show

function pull_do()
 if pull.act then
    print('Pulling...')
    CI_apply(pull.CI_default,'Default CI for pull:')
    -- if given, apply default CI
    local i
    for i=1,#pull do
        CI_method(pull[i])
    end -- for i
 end -- if pull.act
end -- function pull_do

function release_n_fuse()
 if release.act then
    print('Releasing...')
    CI_apply(release.CI_default,'Default CI for release: ')
    -- if given, apply default CI
    CI_method_batch(release)
 end -- if release.act

 if fuse.act then
    -- print('Fusing...')
    local i
    for i=1,#fuse do
        print('Fuse#'..i..'...')
        CI_apply(fuse.CI_default,'Default CI for fuse: ')
        -- if given, apply default CI
        CI_method_batch(fuse[i])
    end -- for i
 end -- if fuse.act
end -- function release_n_fuse

function CI_method_batch(CI_method_list)
 quicksave_do("load",3)
 local i
 for i=1,#CI_method_list do
     CI_method(CI_method_list[i])
     quicksave_do("save",4)
     if quicksave_score[4]>quicksave_score[5] then
        quicksave_do("save",5)
     end -- if quicksave_score
  end -- for i
end -- function CI_method_batch

function CI_method(prm)
-- depending on passed table prm:
-- 1. if given, set CI
-- 2. for a given number of itrs and
-- 3. use a foldit tool (backbone/sidechain move or mutate)

-- i intentionally use only shake/wiggle all
-- and didn't implement local wiggle,
-- as it can make the puzzle too stiff (local maximum)

--[[
 print('CI_method prms:')
 local k,v
 for k,v in pairs(prm) do
     print(k,v)
 end
--]]

 CI_apply(prm.CI,'Current CI: ')
 -- if given, apply CI

 if type(prm.itr)=="number" then
 -- number of itrs given?
    if prm.itr>0 then
       -- depending on prm.cmd, do one of these tools:
       if     prm.cmd=="m" then
              if puzzle.ismutable then
                 if puzzle.mutate.act then
                    -- print('Mutating for '..prm.itr..' iterations...')
                    structure.MutateSidechainsAll(prm.itr)
                 end -- if puzzle.mutate.act
              end -- if puzzle.ismutable
       elseif prm.cmd=="s" then
              -- print('Shaking for '..prm.itr..' iterations...')
              structure.ShakeSidechainsAll(prm.itr)
       elseif prm.cmd=="w" then
              -- print('wiggling for '..prm.itr..' iterations...')
              structure.WiggleAll(prm.itr,prm.backbone,prm.sidechains)
       end -- if prm.cmd
    end -- if prm.itr
 end -- if prm.itr
end -- function CI_method

function CI_apply(CI,text)
 if type(CI)=="number" then
 -- CI given?
    -- print(text..CI)
    behavior.SetClashImportance(CI)
    -- set it
 end -- if type(CI)
end -- function CI_apply

function quicksave_do(mode,slot)
     if mode=="save" then
        save.Quicksave(slot)
        quicksave_score[slot]=current.GetEnergyScore()
        -- print('Quicksaved to slot:'..slot..' - Score:'..crop_digits(quicksave_score[slot],3))
 elseif mode=="load" then
        save.Quickload(slot)
        -- print('Quickloaded from slot:'..slot..' - Score:'..crop_digits(quicksave_score[slot],3))
    end -- if mode
end -- function quicksave_do

function quicksave_do_batch(mode,first,last)
 local i
 for i=first,last do
     quicksave_do(mode,i)
 end -- for i
end -- function quicksave_do

function herd_fitnessandsort(clu)
 local clu= clu
 -- print("Getting herd's scoregain minimum...")
 clu.scoregain_min= clu[1].scoregain
 -- to have a minimum gain val (gain_min) to compare
 -- get first clu's scoregain val
 local i
 for i=2,#clu do
 -- cycle through all other scoregain vals
     if clu[i].scoregain<clu.scoregain_min then
        -- new gain_min found
        clu.scoregain_min= clu[i].scoregain
        -- set it as new gain_min (worst)
     end -- if clu[i].scoregain
 end -- for i
 -- print('Old minimum clu scoregain: '..clu.scoregain_min)
 if clu.scoregain_min>0 then
 -- gain_min >0?
    clu.scoregain_min= 1
    -- we don't need to push fitness vals
    -- so resulting fitness vals will be equal to scoregain vals
 end -- if clu.scoregain_min
 -- if gain_min were <=0, we would have to push fitness vals
 -- print('New minimum clu scoregain: '..clu.scoregain_min)

 -- print("Putting clu's fitness vals...")
 -- fitness= gain-gain_min+1
 -- smallest fitness val  must be >0 (prevent fitnesses <=0)
 --   if all fitness vals were    =0, roulette would run infinitely
 -- (plus, we even want to give worst clus a small chance)
 local i
 for i=1,#clu do
     clu[i].fitness= clu[i].scoregain-clu.scoregain_min+1
     --[[
     a gain_min of 1 doesn't do a change:
        fitness= gain-gain_min+1
     is fitness= gain-1       +1
     is fitness= gain-0
     -> so we've set a good gain_min (>0) to 1 before

     -- now subtract gain_min
        (can be negative, then it will be added to push value)
        -> from clu's scoregain
           -> giving fitness==0 for worst clu
     -- then add 1, as 0 isn't allowed, too
        -> giving fitness==1 for worst clu
     --]]
 end -- for i

 clu= herd_normalize(clu)
 -- sum of all fitness vals==1

 if (herd.fitness_e~=nil) and (herd.fitness_e~=1) then
 -- bending exponent given?
    -- print("Bending clu's fitnesses...")
    local i
    for i=1,#clu do
        clu[i].fitness= clu[i].fitness^(herd.fitness_e)
        -- bend fitness val -> 1 (if 0<exponent<1)
    end -- for i

    clu= herd_normalize(clu)
    -- sum of all fitness vals==1
 end -- if herd.fitness_e

 -- print("Sorting herd by clu's fitnesses...")
 local i
 for i=1,(#clu-1) do
     local j
     for j=(i+1),#clu do
         if clu[i].fitness<clu[j].fitness then
            clu[i],clu[j]=clu[j],clu[i]
         end -- if clu[i].fitness
     end -- for j
 end -- for i
 print('\nHerd after sorting is:')
 herd_show(clu)
 -- for debugging:
 -- list_show_deep(clu,"clu")
 print()
 return clu
end -- function herd_fitnessandsort

function herd_normalize(clu)
 local clu= clu
 clu.fitness_sum= clu_fitness_sum_get(clu)

 -- print("Normalizing clu's fitnesses...")
 local i
 for i=1,#clu do
     clu[i].fitness= clu[i].fitness/clu.fitness_sum
 end -- for i
 -- print('Herd with normalized fitness is:')
 -- herd_show(clu)
 return clu
end -- function herd_normalize

function clu_fitness_sum_get(clu)
 -- print("Getting herd's fitness sum...")
 local fitness_sum= 0
 local i
 for i=1,#clu do
     fitness_sum= fitness_sum+clu[i].fitness
 end -- for i 
 -- print('Clus have fitness sum: '..fitness_sum)
 return fitness_sum
end -- function

function herd_show(clu)
 print('Gen#'..gen.cur..' had start score: '..quicksave_score[2])
 local i
 for i=1,#clu do
     print(
           'Clu#'..i..
           ' Name:'..clu_name_get_string(clu[i].name,false)..
           ' Score:'..crop_digits(clu[i].score,3)..
           ' Gain:'..crop_digits(clu[i].scoregain,3)..
           ' Fitness:'..crop_digits(clu[i].fitness,6)
          )
 end -- for i
 clu.fitness_sum= clu_fitness_sum_get(clu)
 -- print('Fitness checksum: '..clu.fitness_sum)
end -- function herd_show

function breed_n_generate(clu)
    if     herd.EO_mode.cur==2 then
           clu= herd_generate(
                              clu,
                              herd.breed.first,
                              herd.size
                             )
    elseif herd.EO_mode.cur==1 then
           clu= herd_generate(
                              clu,
                              (herd.breed.last+1),
                              herd.size
                             )
    else
           clu= herd_breed(
                           clu,
                           herd.breed.first,
                           herd.breed.last
                          )
           if herd.mutate.act then
              clu= herd_mutate(
                               clu,
                               herd.breed.first,
                               herd.breed.last
                              )
           end -- if herd.mutate.act then
           clu= herd_generate(
                              clu,
                              (herd.breed.last+1),
                              herd.size
                             )
    end -- if herd.EO_mode.cur

 return clu
end -- function breed_n_generate

function herd_breed(clu,first,last)
 local kid={}
 -- intialize kid clus breeding section 

 if     herd.breed.mode.val=="dual" then
        kid= herd_breed_dual(first,last)
        -- get kid by mom & dad breeding
 elseif herd.breed.mode.val=="poly" then
        kid= herd_breed_poly(first,last)
        -- get kid by orgy breeding
 else
        assert(false,'function herd_breed: herd.breed.mode.val is invalid: '..tostring(herd.breed.mode.val))
 end -- herd.breed.mode.val

 local i
 for i=first,last do
 -- move kids to herd
 -- overwrite old clus
    clu[i]= kid[i]
    clu[i].name= clu_name_get(i,"b")
 end -- for i

 return clu
 -- return new clu table
end -- function herd_breed

function herd_breed_dual(first,last)
 local kid={}
 -- intialize kid clus breeding section

 local i
 for i=first,last do
 -- fill breeding section
     local dad
     if herd.breed.roulette.dad then
        dad=roulette()
     else
        dad= range_wrap((i-first+1),1,herd.size,1)
     end -- if herd.breed.roulette.dad

     local mom
     if herd.breed.roulette.mom then
        mom= roulette()
        while mom==dad do
              mom=roulette()
        end -- while mom
     else
        mom= range_wrap((dad+1),1,herd.size,1)
     end -- if herd.breed.roulette.dad

     print('Breeding clu#'..i..'(kid)  from: '..
                                  'clu#'..dad..'(dad*'..crop_digits(herd.breed.dad_genes_prob,3)..')'..
                                ' + '..
                                  'clu#'..mom..'(mom*'..crop_digits((1-herd.breed.dad_genes_prob),3)..')')
     kid[i]={}
     for j=1,#clu[i] do
         if random_flag1(herd.breed.dad_genes_prob) then
            print_gene(j,dad,"dad")
            kid[i][j]=clu[dad][j]
         else
            print_gene(j,mom,"mom")
            kid[i][j]=clu[mom][j]
         end -- if random_flag1
     end -- for j
 end -- for i
 return kid
end -- function function herd_breed_dual

function herd_breed_poly(first,last)
 local kid={}
 -- intialize kid clus breeding section

 local i
 for i=first,last do
 -- fill breeding section
     print('Breeding clu#'..i..'(kid)  from: whole herd')
     kid[i]={}
     for j=1,#clu[i] do
         local parent= roulette()
         print_gene(j,parent,"roulette")
         kid[i][j]=clu[parent][j]
     end -- for j
 end -- for i
 return kid
end -- function herd_breed_poly

function print_gene(j,parent_val,parent_text)
 if herd.breed.genes_show.act then
 -- detailed gene view activated?
    print('Gene #'..j..': clu#'..tostring(parent_val)..'('..tostring(parent_text)..')')
 end -- if herd.breed.genes_show act
end -- function print_gene

function roulette()
 local fitness_target= math.random()
 -- set random fitness sum goal
 -- print('Fitness target:'..crop_digits(fitness_target,6))

 local wheel= math.random(1,herd.size)
 -- initialize random roulette wheel position
 local fitness_sum= clu[wheel].fitness
 -- get fitness val at wheel position
 -- print('Wheel current:'..wheel..' Fitness sum:'..crop_digits(fitness_sum,6))

 while fitness_sum<=fitness_target do
 -- as long as fitness sum hasn't reached fitness sum goal
       if herd.breed.roulette.israndom then
       -- if roulette is random (not default)
       -- set another random roulette wheel position
          wheel= math.random(1,herd.size)
       else
       -- if roulette is not random (default)
          wheel= range_wrap((wheel+1),1,herd.size,1)
          -- spin wheel
       end -- if herd.breed.roulette.israndom
       fitness_sum= fitness_sum+clu[wheel].fitness
       -- print('Wheel current:'..wheel..' Fitness sum:'..crop_digits(fitness_sum,6))
 end -- while fitness_sum
 -- print('Wheel end:'..wheel..' Fitness sum:'..crop_digits(fitness_sum,6))
 return wheel
end -- function roulette

function main()
 print('\nMain Programm start.')
 puzzle.random_seed= random_seed_set_val(puzzle.random_seed)

 print('Puzzle segs mutability: '..tostring(puzzle.ismutable))
 if puzzle.ismutable==false then
    puzzle.mutate.act= false
 end -- if puzzle.ismutable
 print('Puzzle segs mutation: '..tostring(puzzle.mutate.act))

 print('Herd genes off prob: '..herd.mutate.prob.off)
 print('Herd mutability prob: '..herd.mutate.prob.vals)
 if herd.mutate.prob.vals<=0 then
 -- herd mutate probability is not given
    herd.mutate.act= false
    -- deactivate hed genes mutating
    -- (not needed, but prevents calling function)
 end -- if herd.mutate.prob.vals
 print('Herd mutation: '..tostring(herd.mutate.act))
 
 if herd.breed.first>herd.breed.last then
    herd.breed.first,herd.breed.last= herd.breed.last,herd.breed.first
 end -- if herd.breed.first

 print('EO mode: '..herd.EO_mode.cur)
 print('Breed mode: '..herd.breed.mode.val)

 print('Clu band mode old: '..clu.band_to.val)
 if type(puzzle.seg_center.val)=="number" then
 -- "center" seg already given by user?
    clu.band_to.val= "user"
 end -- if type(puzzle.seg_center.val)
 
 if     clu.band_to.val=="center" then
 -- banding to center
        if puzzle.seg_center.get_mode=="start" then
        -- get center seg once?
           puzzle.seg_center.val= seg_center_get()
        end -- if puzzle.seg_center.get_mode

 elseif clu.band_to.val=="user" then
 -- banding to user-defined seg idx
    assert((puzzle.seg_center.val>0) and (puzzle.seg_center.val<(puzzle.seg_count+1)),'function main: puzzle.seg_center.val is invalid: '..tostring(puzzle.seg_center.val))
    puzzle.seg_center.get_mode="start"
    -- get center seg once!
    clu.band_to.val= "center"
    -- "user" -> "center"

 elseif string.sub(clu.band_to.val, 1, 6)=="random" then
 -- using any random bands?
        if clu.band_to.val=="random1" then
           puzzle.seg_random.get_mode= "list"
        else -- if clu.band_to.val=="random2"
           puzzle.seg_random.get_mode= "all"
        end -- if clu.band_to.val
    clu.band_to.val= "random"
 -- elseif (clu.band_to.val=="space") or (clu.band_to.val=="furthest")
 end -- if clu.band_to.val
 print('Clu band mode new: '..clu.band_to.val)

 print('Seg center get_mode: '..puzzle.seg_center.get_mode)
 print('Seg random get_mode: '..puzzle.seg_random.get_mode)
 if (clu.band_to.val=="center") and (puzzle.seg_center.get_mode== "start") then
    -- always the same "center" seg used?
    table.insert(seg_use.exclude.idx,puzzle.seg_center.val)
    -- add it's idx to exclude candidates
 end -- if clu.band_to.val,puzzle.seg_center.get_mode

 seg_use= seg_use_list_create(seg_use)
 -- create seg list based on informations given at declaration

 -- for debugging before generation testing, uncomment this:
 -- prms_show()

 gen.cur= 1
 -- initialize gen counter

 quicksave_score={}
 -- saveslot 1: script start
 -- saveslot 2: gen/clu start = before applying bands/pull
 -- saveslot 3: after pull = before release/fuse start
 -- saveslot 4: after single release/fuse step
 -- saveslot 5: after all releases/fuses per clu = best result for current clu
 -- saveslot 6: best result for current gen
 -- saveslot 7: best result so far

 -- save to all slots to initialize states & scores:
 quicksave_do_batch("save",1,7)
 recentbest.Save()
 -- print('Set Recent Best')

 clu=herd_generate(clu,1,herd.size)
 -- list_show_deep(clu,"clu") --show all clu informations

 herd.test={first=1,last=herd.size}
 -- normally, test all generated clus

 while gen.cur<=gen.max do
    print('\n\nGen: '..gen.cur)

    if herd.use.hybrid.state~=nil then
    -- hybrid loading is used, change loading state
       if gen.cur%herd.use.hybrid.gens==1 then
       -- number of gens to trigger reloading start state is reached
          herd.use.state.val= "start"
          -- load start state
       else
       -- number of gens to trigger reloading start state is not reached
          herd.use.state.val= herd.use.hybrid.state
          -- load specified state
       end -- if gen.cur
    end -- if herd.use.hybrid.state

    local loaded_text
    -- load puzzle state before pulling:
        if herd.use.state.val=="start" then
           quicksave_do("load",1)
           loaded_text= "Script Start State"
    elseif herd.use.state.val=="gen" then
           quicksave_do("load",6)
           loaded_text= "Gen's Best State"
    elseif herd.use.state.val=="script" then
           quicksave_do("load",7)
           loaded_text= "Script's Best State"
    else
           recentbest.Restore()
           loaded_text= "Recent Best State"
    end -- if herd.use.state.val
    print('Loaded: '..loaded_text..' - Score: '..crop_digits(current.GetEnergyScore(),3))

    -- save to these slots to initialize states & scores:
    quicksave_do_batch("save",2,6)

    if (herd.use.state.val=="start") and (herd.use.hybrid.state==nil) then
    -- if script start state is always loaded
       herd.test.first= 1
       -- reset test start clu (first clu of gen to test)
       while clu[herd.test.first].name.gen~=gen.cur do
       -- test start clu was not generated in this gen (it is an old one)
             herd.test.first= herd.test.first+1
             -- use next clu
             if herd.test.first>herd.size then
             -- if next clu is too high (higher than herd size)
                herd.test.first=1
                -- set it to 1 again
                break
                -- exit start clu checking
             end -- if
       end -- while clu
    end -- if if herd.use.state.val

    local clu_cur
    for clu_cur=herd.test.first,herd.test.last do
       -- print('clu: '..clu_cur)
       print('\nTesting: G'..gen.cur..
                        'C'..clu_cur..
                        '/'..herd.size..
                        '  Name: '..clu_name_get_string(clu[clu_cur].name,true))
       quicksave_do("load",2)

       band.DeleteAll()
       clu_apply_bands(clu[clu_cur])
       pull_do()

       band.DeleteAll()
       -- save to these slots to initialize states & scores:
       quicksave_do_batch("save",3,5)
       print('Score after pulling: '..crop_digits(quicksave_score[3],3))

       release_n_fuse()

       clu[clu_cur].score=quicksave_score[5]
       clu[clu_cur].scoregain=clu[clu_cur].score-quicksave_score[2]
       print("This clu's best Score: "..crop_digits(quicksave_score[5],3).." - Gain: "..crop_digits(clu[clu_cur].scoregain,3))

       if (clu_cur==herd.test.first) or (quicksave_score[5]>quicksave_score[6]) then
          quicksave_do("load",5)
          quicksave_do("save",6)
          print('New best result for this gen: '..crop_digits(quicksave_score[6],3))
       end -- if clu_cur

       if quicksave_score[6]>quicksave_score[7] then
          quicksave_do("load",6)
          quicksave_do("save",7)
          print('New best result so far! '..crop_digits(quicksave_score[7],3))
       end -- if quicksave_score
    end -- for clu_cur

    clu=herd_fitnessandsort(clu)
    -- for each clu calculate fitness given by it's score gain
    -- sort clus by fitness, best gain on top
    gen.cur=gen.cur+1
    -- increase generation counter now,
    -- so newly generated/breeded clus will 
    -- get an actual "birth date" = next gen

    if (herd.flush_gain_thr.act==false) or (clu[1].scoregain>=herd.flush_gain_thr.thr) then
    -- best gain checking is off
    -- or   gain is good enough
       clu=breed_n_generate(clu)
       -- keep good
       -- breed good over mediocre
       -- replace bad by new ones
       herd.flush_gain_reset.cur= 0
       -- reset flush counter
    else
    -- best gain checking is on
    -- and  gain is bad  enough
       print('\nTarget result for this gen: '..crop_digits(herd.flush_gain_thr.thr,3))
       print('Best result for this gen only: '..crop_digits(clu[1].scoregain,3))

       herd.flush_gain_reset.cur= herd.flush_gain_reset.cur+1
       -- increase flush counter
       print('Herd flush #'..herd.flush_gain_reset.cur)

       clu=herd_generate(clu,1,herd.size)
       -- flush entire herd
       -- replace all clus by new ones

       if herd.flush_gain_reset.act then
       -- reset after flush activated?

          if herd.flush_gain_reset.cur>herd.flush_gain_reset.thr then
             print('Number of flushs exceeded.')
             print('Restarting from script start state.')
             quicksave_do("load",1)
             -- get script start state again
             -- save to (almost) all slots to flush states & scores:
             quicksave_do_batch("save",2,7)
             recentbest.Save()
             -- print('Set Recent Best')

             herd.flush_gain_reset.cur= 0
             -- reset flush counter
          end -- if herd.flush_gain_reset.cur
       end -- if herd.flush_gain_reset.act
    end -- if herd.flush_gain_thr.act,clu[1].scoregain
 end -- while gen.cur~=gen.max
end -- function main

function prms_cng()
 local dialog_val_cng= false

 do -- dialog 0
    local ask=   dialog.CreateDialog('CG303 GAB+EO Remix - Parameters 0/7')

    ask.Input10= dialog.AddLabel("Change default values here? There are many!")
    ask.Input1a= dialog.AddCheckbox("edit",dialog_val_cng)
    ask.Input12= dialog.AddLabel("      checked: OK to change values")
    ask.Input13= dialog.AddLabel("not checked: OK to launch script")

    ask=         ask_window(ask)

    dialog_val_cng= ask.Input1a.value
 end -- do dialog 0

 if dialog_val_cng then
    if true then -- dialog 1
       local ask=   dialog.CreateDialog('CG303 GAB+EO Remix - Parameters 1/7')

       if puzzle.random_seed==nil then
          puzzle.random_seed= ""
       end -- if puzzle.random_seed

       ask.Input10= dialog.AddTextbox("Random seed ",tostring(puzzle.random_seed))
       ask.Label11= dialog.AddLabel("Blank    : use new seed"..
                                  "\nNumber: use this seed")
       ask.Label12= dialog.AddLabel(" ")

       ask.Input20= dialog.AddSlider("Herd size",herd.size,4,16,0)
       ask.Label21= dialog.AddLabel("Number of clu(ster)s for one gen(eration)")

       ask=         ask_window(ask)

       puzzle.random_seed= ask.Input10.value
       herd.size=          ask.Input20.value
    end -- if dialog 1

    if true then -- dialog 2
       local ask=   dialog.CreateDialog('CG303 GAB+EO Remix - Parameters 2/7')

       local keep=0
       if (herd.size%2)==0 then
       -- if number of clus is even
        keep=2
        -- keep 2 clus
       else
       -- ff number of clu is not even
        keep=3
        -- Keep 3 clus
       end -- if (herd.size%2)
       local breed=(herd.size-keep)/2
       -- after subtracting kept clus,
       -- divide the rest by 2
       -- first half for breeding:
       herd.breed.first=keep+1
       herd.breed.last=keep+breed
       -- other half for creating new
       -- herd.breed.last+1...herd.size will be random

       ask.Label00= dialog.AddLabel(" ")
       ask.Label01= dialog.AddLabel("Breed settings:"..
                                    "\nAfter one gen,"..
                                    "\nreplace mediocre clu# by new breeded ones")
       ask.Label02= dialog.AddLabel(" ")

       ask.Input1x= dialog.AddSlider("First",herd.breed.first,1,herd.size,0)
       ask.Label11= dialog.AddLabel("clu# to be replaced"..
                                  "\nAll < are kept as parents")
       ask.Label12= dialog.AddLabel(" ")

       ask.Input2x= dialog.AddSlider("Last",herd.breed.last,1,herd.size,0)
       ask.Label21= dialog.AddLabel("clu# to be replaced"..
                                  "\nAll > are created new")
       ask.Label22= dialog.AddLabel(" ")

       ask.Label30= dialog.AddLabel("Breed settings are also used by EO as orientation")

       ask=         ask_window(ask)

       herd.breed.first= ask.Input1x.value
       herd.breed.last=  ask.Input2x.value
    end -- if dialog 2

    if true then -- dialog 3
       local ask=   dialog.CreateDialog('CG303 GAB+EO Remix - Parameters 3/7')

       ask.Label10= dialog.AddLabel("Extremal Optimization (discard mediocre clus)")
       ask.Input1x= dialog.AddSlider("EO mode",herd.EO_mode.cur,herd.EO_mode.min,herd.EO_mode.max,0)
       ask.Label12= dialog.AddLabel(" ")
       ask.Label13= dialog.AddLabel("0: no   EO (GA!), replace m.clus by breeded ones"..
                                  "\n1: use EO, don't just leave m.clus as they are"..
                                  "\n2: use EO, don't replace m.clus by random ones")
       ask.Label14= dialog.AddLabel(" ")
       ask.Label15= dialog.AddLabel(" ")

       local state={list=herd.use.state.list}
       ask.Label20= dialog.AddLabel("Puzzle state for each gen")
       ask.Input2x= dialog.AddSlider("Load state",key_getbyval(state.list,herd.use.state.val),1,#state.list,0)
       ask.Label22= dialog.AddLabel(" ")
       ask.Label23= dialog.AddLabel(list_text(state.list))
       ask.Label24= dialog.AddLabel(" ")
       ask.Label25= dialog.AddLabel(" ")
       ask.Label26= dialog.AddLabel(" ")
       ask.Label27= dialog.AddLabel("start:    as now"..
                                  "\n            (never reach local max)"..
                                  "\ngen:     best result of last gen"..
                                  "\n            (avoid local max)"..
                                  "\nscript:  script's best"..
                                  "\n            (similar to recent)"..
                                  "\nrecent: recent best state"..
                                  "\n            (can produce local max)")
       ask.Label28= dialog.AddLabel(" ")
       ask.Label29= dialog.AddLabel(" ")
       ask.Label2A= dialog.AddLabel(" ")
       ask.Label2B= dialog.AddLabel(" ")

       local band_to={list=clu.band_to.list}
       ask.Label30= dialog.AddLabel("Band these segs to target seg:"..
                                  "\n+ in list (detected by script)"..
                                  "\n+ game interface selection (blue)")
       ask.Label31= dialog.AddLabel(" ")
       ask.Input3x= dialog.AddSlider("Band mode",key_getbyval(band_to.list,clu.band_to.val),1,#band_to.list,0)
       
       ask.Label33= dialog.AddLabel(" ")
       ask.Label34= dialog.AddLabel(" ")
       ask.Label35= dialog.AddLabel(list_text(band_to.list))
       ask.Label36= dialog.AddLabel(" ")
       ask.Label37= dialog.AddLabel(" ")
       ask.Label38= dialog.AddLabel(" ")
       ask.Label39= dialog.AddLabel("center:    'center' seg is auto-detected"..
                                   "\nuser:       'center' seg is set manually"..
                                   "\nrandom1: uselist (detected & selection) to uselist"..
                                   "\nrandom2: uselist to all of puzzle (classic)")

       ask=         ask_window(ask)

       herd.EO_mode.cur=                ask.Input1x.value
       herd.use.state.val=   state.list[ask.Input2x.value]
       clu.band_to.val=    band_to.list[ask.Input3x.value]
    end -- if dialog 3

    if clu.band_to.val=="user" then -- dialog 3.1
    -- user wants to set own "center" seg
       local ask=   dialog.CreateDialog('CG303 GAB+EO Remix - Parameters 3.1/7')
       ask.Label10= dialog.AddLabel("Set your own 'center' seg")
       ask.Input1x= dialog.AddSlider("Center seg",seg_center_get2(),1,puzzle.seg_count,0)

       ask=         ask_window(ask)

       puzzle.seg_center.val= ask.Input1x.value
    end -- if clu.band_to.val ... then dialog 3.1

    if true then -- dialog 4
       local ask=   dialog.CreateDialog('CG303 GAB+EO Remix - Parameters 4/7')
       ask.Input1a= dialog.AddCheckbox("Mutate sidechains",puzzle.mutate.act)
       ask.Label11= dialog.AddLabel("Works only if puzzle is mutable")
       ask.Label12= dialog.AddLabel(" ")


       ask.Input2a= dialog.AddCheckbox("Pull",pull.act)
       ask.Input2x= dialog.AddSlider("CI with bands",pull.CI_default,0,1,2)

       ask.Input3a= dialog.AddCheckbox("Release (1-pass)",release.act)
       ask.Input3x= dialog.AddSlider("CI without bands",release.CI_default,0,1,2)
       
       ask.Input4a= dialog.AddCheckbox("Fuse(s) (multiple-pass)",fuse.act)
       ask.Label42= dialog.AddLabel("CI is varied")

       ask=         ask_window(ask)

       puzzle.mutate.act=  ask.Input1a.value
       pull.act=           ask.Input2a.value
       pull.CI_default=    ask.Input2x.value
       release.act=        ask.Input3a.value
       release.CI_default= ask.Input3x.value
       fuse.act=           ask.Input4a.value
    end -- if dialog 4

    if true then -- dialog 5
       local ask=   dialog.CreateDialog('CG303 GAB+EO Remix - Parameters 5/7')

       local prim_min,prim_max
       if clu.band_to.val=="space" then
          -- use rho vals for sliders:
          prim_min= clu.rho.min
          prim_max= clu.rho.max
       else -- clu.band_to.val~="space"
          -- use d_cng vals for sliders:
          prim_min= clu.d_cng1.min
          prim_max= clu.d_cng1.max
       end -- if clu.band_to.val

       if string.sub(clu.band_to.val, 1, 6)=="random" then
       -- using any random bands?
          clu.d_cng2.act= false
          -- secondary bands off by default
       end -- if "random"

       ask.Input10= dialog.AddLabel("Primary bands push distance by +/-")
       ask.Input1m= dialog.AddSlider("min",prim_min,0,3.8*5,2)
       ask.Input1n= dialog.AddSlider("max",prim_max,0,3.8*5,2)
       ask.Input1s= dialog.AddSlider("strength",clu.pull.str1,0,10,2)
       ask.Input14= dialog.AddLabel(" ")

       ask.Input20= dialog.AddLabel("Secondary bands push distance by +/-")
       ask.Input2a= dialog.AddCheckbox("on",clu.d_cng2.act)
       ask.Input2m= dialog.AddSlider("min",clu.d_cng2.min,0,3.8*5,2)
       ask.Input2n= dialog.AddSlider("max",clu.d_cng2.max,0,3.8*5,2)
       ask.Input2s= dialog.AddSlider("strength",clu.pull.str2,0,10,2)
       ask.Input25= dialog.AddLabel(" ")

       ask.Input30= dialog.AddLabel("Segs with this distance are 'too close'")
       ask.Input3m= dialog.AddSlider("min",clu.seg_min_dist,0,3.8*5,2)
       ask.Input32= dialog.AddLabel("if 'too close:")
       ask.Input33= dialog.AddLabel("neither apply band"..
                                    "\nnor change (correct) target seg idx")
       ask.Input3a= dialog.AddCheckbox("skip band / don't change t.seg",clu.band_skip_wrong)
       ask.Input35= dialog.AddLabel("if banding to many segs, possibly:")
       ask.Input36= dialog.AddLabel("-    activate this or"..
                                  "\n- deactivate secondary bands")

       ask=         ask_window(ask)

       if ask.Input1m.value>ask.Input1n.value then
          ask.Input1m.value,ask.Input1n.value= ask.Input1n.value,ask.Input1m.value
       end -- if ask.Input11,ask.Input12
       if clu.band_to.val=="space" then
          clu.rho.min=      ask.Input1m.value
          clu.rho.max=      ask.Input1n.value
       else
          clu.d_cng1.min=   ask.Input1m.value
          clu.d_cng1.max=   ask.Input1n.value
       end -- if clu.band_to.val
       clu.pull.str1=       ask.Input1s.value

       clu.d_cng2.act=      ask.Input2a.value
       if ask.Input2m.value>ask.Input2n.value then
          ask.Input2m.value,ask.Input2n.value= ask.Input2n.value,ask.Input2m.value
       end -- if ask.Input22,ask.Input23
       clu.d_cng2.min=      ask.Input2m.value
       clu.d_cng2.max=      ask.Input2n.value
       clu.pull.str2=       ask.Input2s.value

       clu.seg_min_dist=    ask.Input3m.value
       clu.band_skip_wrong= ask.Input3a.value
    end -- if dialog 5

    if true then -- dialog 6
       local ask=   dialog.CreateDialog('CG303 GAB+EO Remix - Parameters 6/7')

       ask.Input10= dialog.AddLabel("Band genes and mutating ratios")
       ask.Input11= dialog.AddLabel(" ")
       ask.Input12= dialog.AddLabel("0.00= 0%   (none)"..
                                  "\n0.50= 50%  (half)"..
                                  "\n1.00= 100% (all)")
       ask.Input13= dialog.AddLabel(" ")

       ask.Input20= dialog.AddLabel("Turn this many")
       ask.Input2x= dialog.AddSlider("genes off",herd.mutate.prob.off,0,1,2)
       ask.Input22= dialog.AddLabel("(EO+GA)")
       ask.Input23= dialog.AddLabel(" ")

       ask.Input30= dialog.AddLabel("Probability of")
       ask.Input3x= dialog.AddSlider("gene mutating",herd.mutate.prob.vals,0,1,2)
       ask.Input31= dialog.AddLabel("after breeding (GA)")
       ask.Input32= dialog.AddLabel(" ")

       ask.Input40= dialog.AddLabel("Probability of")
       ask.Input4x= dialog.AddSlider("dad genes",herd.breed.dad_genes_prob,0,1,2)
       ask.Input42= dialog.AddLabel("(first breeding (GA) partner)")
       ask.Input44= dialog.AddLabel("Without mutating:")
       ask.Input45= dialog.AddLabel("1.00: kid is like dad"..
                                  "\n0.00: kid is like mom")
       ask.Input46= dialog.AddLabel(" ")
       ask.Input47= dialog.AddLabel(" ")

       local breed={mode={list=herd.breed.mode.list}}
       ask.Input50= dialog.AddLabel("Breeding behaviour (genetic roulette)")
       ask.Input5x= dialog.AddSlider("Breed mode",key_getbyval(breed.mode.list,herd.breed.mode.val),1,#breed.mode.list,0)
       -- ask.Input52= dialog.AddLabel(" ")
       ask.Label53= dialog.AddLabel(list_text(breed.mode.list))
       ask.Label54= dialog.AddLabel("Each kid from:")
       ask.Label55= dialog.AddLabel("dual: 2    clus (mom & dad) (classic)"..
                                  "\npoly: any clus (whole herd)")
       ask.Label56= dialog.AddLabel(" ")

       ask.Input60= dialog.AddLabel("Roulette is")
       ask.Input6a= dialog.AddCheckbox("random",herd.breed.roulette.israndom)
       ask.Label62= dialog.AddLabel("true:  spreaded"..
                                  "\nfalse: inertial (classic)")
       ask.Label63= dialog.AddLabel(" ")

       ask.Input70= dialog.AddLabel("Show breeding details")
       ask.Input7a= dialog.AddCheckbox("gene origin clu#(parent)",herd.breed.genes_show.act)

       ask.Input80= dialog.AddLabel("Show mutating details")
       ask.Input8a= dialog.AddCheckbox("gene value (old & new)",herd.mutate.genes_show.act)

       ask=         ask_window(ask)

       herd.mutate.prob.off=                         ask.Input2x.value
       herd.mutate.prob.vals=                        ask.Input3x.value
       herd.breed.dad_genes_prob=                    ask.Input4x.value
       herd.breed.mode.val=          breed.mode.list[ask.Input5x.value]
       herd.breed.roulette.israndom=                 ask.Input6a.value
       herd.breed.genes_show.act=                    ask.Input7a.value
       herd.mutate.genes_show.act=                   ask.Input8a.value
    end -- if dialog 6

    if true then -- dialog 7
       local ask=   dialog.CreateDialog('CG303 GAB+EO Remix - Parameters 6/7')
       ask.Input10= dialog.AddLabel("If best clu gain is less than")
       ask.Input1m= dialog.AddSlider("min",
                                     herd.flush_gain_thr.thr,
                                     herd.flush_gain_thr.min,
                                     herd.flush_gain_thr.max,
                                     1)
       ask.Input1a= dialog.AddCheckbox("flush herd completely",herd.flush_gain_thr.act)
       ask.Input13= dialog.AddLabel(" ")

       ask.Input20= dialog.AddLabel("When flushed more than this time")
       ask.Input2n= dialog.AddSlider("max",
                                     herd.flush_gain_reset.thr,
                                     herd.flush_gain_reset.min,
                                     herd.flush_gain_reset.max,
                                     0)
       ask.Input2a= dialog.AddCheckbox("reset puzzle to script start state",herd.flush_gain_reset.act)

       ask=         ask_window(ask)

       herd.flush_gain_thr.thr=    ask.Input1m.value
       herd.flush_gain_thr.act=    ask.Input1a.value
       herd.flush_gain_reset.thr=  ask.Input2n.value
       herd.flush_gain_reset.act=  ask.Input2a.value
    end -- if dialog 7
 end -- if dialog_val_cng
end -- function prms_cng

function ask_window(ask)
 ask.Labelx1=      dialog.AddLabel(" ")
 ask.Labelx2=      dialog.AddLabel(" ")
 ask.OK=           dialog.AddButton("OK", 1)
 ask.Cancel=       dialog.AddButton("Cancel", 0)
 local button_val= dialog.Show(ask)
 assert((button_val==1),'Script canceled!')
 return ask
end -- function ask_window

function list_text(list)
-- create output text with multiple lines from list
 local text= ""
 local i
 for i=1,#list do
     if text~="" then
        text= text.."\n"
     end -- if text
     text= text..tostring(i)..": "..list[i]
 end -- for i
 return text
end -- function list_text


-- declaration section:
   -- all global variables (mostly organized as table) can be set here.
   -- some of them here are used as default vals only
   -- and can be altered by gui in change section
puzzle={seg_count= structure.GetCount();
        random_seed=nil
        -- set random seed to this val
        -- if there is none,
        -- os.time()+recipe.GetrandomSeed() will be used
       }
print('Puzzle has '..puzzle.seg_count..' segments.')
puzzle.ismutable=puzzle_ismutable()
-- check if there are mutable segments
puzzle.mutate={act=(puzzle.ismutable or false)}
-- set mutating puzzle activity to the same val
-- (foldit-mutation, not equal to: mutate herd-cluster-bands)
puzzle.isligand=puzzle_isligand()
-- check if there is a ligand
puzzle.seg_center={
                   val=nil;
                   --[[
                   set which seg is considered as seg_center
                   integer number between first and last segment: use this segment index as center segment
                   puzzle.seg_count (same as last segment):       use last segment index as center segment
                   -- nil:                                        get "start" or "current"  center segment
                   --]]
                   get_mode="current"
                   --[[
                   set when seg_center is to be fetched
                   "start":                  only at script start
                                             use this when setting val to a constant number or banding to ligand
                   "current" (or any other): each time before applying bands
                   --]]
                  }
puzzle.seg_random={
                   -- get random seg from
                   get_mode="all"
                   -- "list": uselist segs
                   -- "all":  puzzle  segs
                  }

-- create list containing following segs:
seg_use={
         include={
                  idx={1;puzzle.seg_count};
                  -- with idx number: 1st and last
                  --[[
                  you can also set:
                  -- ranges instead of single indices:
                     -- idx={seg_blocks({{1;5}})};
                            includes segs 1-5
                     -- idx={seg_blocks({{1;5};{10;20}})};
                            includes segs 1-5 and 10-20
                     -- idx={seg_blocks({{1;puzzle.seg_count}})};
                            includes all segs
                  -- mix single segs and ranges:
                     -- idx=seg_use_list_append_all({1;puzzle.seg_count},seg_blocks({{10;20}});
                            includes 1st seg, last seg and 10-20
                  --]]
                  selected={act=true;val=true};
                  -- if act==true, include:
                  -- val:
                     -- true:    selected segs
                     -- false: unselected segs
                  frozen={act=false;backbone=true;sidechain=false};
                  -- if act==true:
                  -- add frozen segs
                  -- given in backbone and sidechain val
                  ss={};
                  -- with secondary structures
                     -- "L"=loop
                     -- "H"=helix
                     -- "E"=sheet
                  ss_cngs=true;
                  -- where secondary structure changes occur: yes
                  aa={"g"}
                  -- with amino acids
                  -- here:
                     -- include glycine
                  -- example:
                     -- aa={"f";"g"}
                     -- include phenylalanine; glycine
                 };
         exclude={
                  idx={};
                  -- without idx number: none
                  selected={act=false;val=false};
                  -- if act==true, exclude:
                  -- val:
                     -- true:    selected segs
                     -- false: unselected segs
                  frozen={act=false;backbone=true;sidechain=false};
                  -- if act==true:
                  -- remove frozen segs
                  -- given in backbone and sidechain val
                  -- note:
                     -- if you turn this on (act==true)
                     -- and set backbone to false and sidechain to false,
                     -- all unfrozen segs will be removed!
                  ss={};
                  -- without secondary structures
                     -- "L"=loop
                     -- "H"=helix
                     -- "E"=sheet
                  aa={}
                  -- without amino acids
                  -- example:
                     -- aa={"a";"v";"p";"w"}
                     -- exclude alanine; valine; proline; tryptophan
                 };
         append_all=false;
         -- append all segs to uselist
            -- false: append only segs which are not already in list
            --        (more to check when adding)
            -- true:  append all  segs (double segs will be removed later when sorting)
            --        (more to check when removing)
         remove_double=true;
         -- remove double segs from uselist after adding
            -- true:        remove
            -- false: don't remove (may not work, depending on how bands are applied)
         sort_ascending=true;
         -- sort segs in uselist by idx
            -- true:               lowest  idx first
            -- false:              highest idx first
            -- nil (or any other): don't sort
        }

gen={max=math.huge}
-- set number of maximum gens to test

herd={
      size=8;
      -- number of individuums
         -- won't grow anymore in this script version
      breed={first=3;
             -- first mediocre clu to be replaced by breeded one (GA)
             -- clus with lower  idx will be kept as good ones
             last=5;
             -- last mediocre clu to be replaced by breeded one (GA)
             -- clus with higher idx will be replaced by new random ones (flushed)
             mode={
             -- breed mode (if EO_mode==0)
             -- general breeding behaviour
                   val="dual";
                   -- set breed mode
                   list={
                         "dual"; -- breed kid from 2 partners only (regular)
                                 -- before breeding, select mom (& dad) once via roulette
                                 -- while breeding, select gene from mom or dad
                         "poly" --  breed kid from whole herd (each gene can be from any clu)
                                --  while breeding, select gene-donor for each gene via roulette
                                --  ignore mom & dad options
                        }
                  };
             genes_show={
             -- show detailed gene information whenn breeding
                         act=false
                         -- show which gene is from which clu
                            -- true:  show clu#(parent)
                            -- false: show possible parents only
                        };
             roulette={
             -- roulette wheel selection
                       dad=false;
                       -- use for dad (1st breeding partner)
                          -- true:        use
                          -- false: don't use (1st dad is clu#1. 2ns dad is clu#2 ...)
                       mom=true;
                       -- use for mom (2nd breeding partner)
                          -- true:        use
                          -- false: don't use (mom: next clu# after dad)
                       israndom=false
                       -- 'wheel' is complete random
                          -- true:  yes, don't spin wheel - let it jump and ignore clu order
                          --                                special, makes breeding partner selection behave different.
                          --                                -> useful for "poly" breed mode, as genes will be more scattered.
                          --                                fitness is considered, nevertheless
                          -- false:  no,       spin wheel - default, as it is usually done in GA.
                          --                                fitness is considered, but more inertially
                      };
             dad_genes_prob=0.55
             -- set the (probability) ratio of dad genes (1st breeding partner):
             -- float val between 0 and 1
                -- <=0 :   mom genes only
                -- 0.25 :  1/4 dad
                -- .5 :    1/2 dad and mom
                -- 0.75 :  3/4 dad
                -- >=1 :   dad genes only
            };
      mutate={
      -- mutate herd cluster bands after breeding
      -- (GA-mutation, not equal to: mutate puzzle-segs)
              act=true;
              -- boolean val
                 -- true:  mutate vals depending on prob.vals
                 -- false: mutate off (don't mutate breeded bands)
              genes_show={
              -- show detailed gene information whenn mutating
                          act=false
                          -- show which gene is from which clu
                             -- true:  show clu#(parent)
                             -- false: show possible parents only
                         };
              prob={off=0.25;vals=0.1};
              -- mutate probability ratios
              -- each: float val between 0 and 1
                 -- <=0 :  never
                 -- 0.5 :  1/2 of cases
                 -- >=1 :  always

                 -- off ratio: turn bands off when generated
                 -- this prevents too many act bands for 1 clu
                 -- (as a clu loads the complete uselist)
                    -- example:
                    -- if you have 10 segments in uselist,
                    -- and off==0.25,
                    -- 1/4 of clu band genes (about 2...3 will be off)

                 -- vals ratio: mutate band vals when breeded
                    -- toggles (switches) band activity (activated)
                       -- (off bands -> on and vice versa)
                    -- changes band vand vals (len, rho, theta, phi)

                 -- examples for vals:
                    -- <=0.0 :  all  band genes will be changed (then you can set herd.mutate.act= false)
                    -- ==0.1 :  1/10 of band genes
                    -- ==0.5 :  1/2  of band genes
                    -- >=1.0 :  all  band genes will be changed
              rng10e={min=-3;max=-1}
              -- mutate band float vals (len, rho, phi theta, not segs)
              -- by +/-10^(min...max)
              -- examples:
                 -- min=-1;max=-1: change by +/-0.1
                 -- min=-2;max=-1: change by +/-0.01
                 -- min=-3;max=-3: change by +/-0.001
                 -- min=-3;max=-1: change by +/-0.001, +/-0.01 +/-or 0.1
             };
      EO_mode={
      -- Extremal Optimization mode
               cur=0;
               -- integer val between 0 and 2
               -- 0 :    no EO - breed clus (regular GAB)             (default: keep 2, breed 3, generate 3)
               -- 1 :  soft EO - keep  clus instead of breeding them  (default: keep 5,          generate 3)
               -- 2 :  hard EO - flush clus instead of breeding them  (default: keep 2,          generate 6)
               min=0;
               -- for gui
               max=2
               -- for gui
              };
      flush_gain_thr={
      -- flush herd (and load start state)
      -- if best gen's clu score gain is less than threshold
                      act=true;
                      -- boolean val
                         -- true:        check best gain
                         -- false: don't check (and flush)
                      thr=0.5;
                      -- if score "gain" of best cluster is less than this thr
                      -- can be negative, too
                      min=-200;
                      -- for gui
                      max=200;
                      -- for gui
                     };
      flush_gain_reset={
      -- reset puzzle to script start state
                        act=false;
                        -- boolean val
                        -- true:        reset
                        -- false: don't reset
                        cur=0;
                        -- flush counter
                        thr=2;
                        -- reset if flush counter exceeds this thr
                        min=0;
                        -- for gui
                        max=20
                        -- for gui
                       };
      fitness_e=1;
      -- exponent for herd fitness "bending"
      -- allows worse clus to appear more often.
      -- tweaks distribution of fitness vals
      -- by passing them through this exponential function:

      -- fitness^(1/fitness_e) is a root function
      -- exponent vals <1 bend fitness vals towards 1
      -- same is done with small random vals in R= rho^(1/3) calculating section

      -- value examples: fitness_e -> fitness val
         -- 1/1 (exponent 1):  exponent won't have an effect (routine will will be skipped)
         -- 1/2 (square root): fitness 0.01  -> 0.1, then normalized
         -- 1/3 (cubic root):  fitness 0.001 -> 0.1, then normalized
         -- ... etc.
      use={
           state={
           -- load state mode
                  val="recent";
                  -- set which state will be loaded before each cluster pulling
                  -- use one of these vals (also for gui):
                  list={
                        "start"; --  initial state at script start
                                 --  use if you are really stuck or have a new puzzle
                                 --  never leads to local maximum
                        "gen"; --    best result of last gen
                               --    use to allow score dropping
                               --    and to (hopefully) escape local maximum
                        "script"; -- script's best (script-internal "recent best")
                                  -- what the script considers as best solution so far
                                  -- may not catch all states (as scores are gotten after single relax/fuse steps)
                                  -- may lead to local maximum
                        "recent" --  recent best
                                 --  what the game considers as best solution so far
                                 --  catches really best states (also inbetween relax/fuse steps)
                                 --  these states may not be stable
                                 --  may lead to local maximum
                       }
                 };  
           hybrid={
           -- hybrid state loading
           -- loads selected puzzle state given below,
           -- but "start" state each gens to reset puzzle
           -- useful if you are really stuck
           -- or just beginning
                   state=nil;
                   -- nil:      don't use hybrid state loading
                   -- "gen":    best result of last gen
                   -- "script": script's best
                   -- "recent": recent best
                   gens=10;
                   -- load "start" state each this number of gens
                   -- for all other gens, load state given above
                  }
          }
     }

clu={
     fix={
          -- here you can set some seg-pairs, which dsts should be fixed by a band
          -- example:
          -- {2;21};
          -- {31;46};
          -- fix seg2  with seg21 and
          --     seg31 with seg46
          str=2;
          -- set str of fixing bands
          lencng=0;
          -- lencng=-3.8/4;
          -- add this val to measured dst between segs
          -- giving fixing band len
          -- use vals
             -- =0 :  just keep dst of segs
             -- <0 :  do some compression
             -- >1 :  do some expansion
         };
     pull={str1=1;str2=0.1};
     -- set str of pulling bands
        -- str1:   primary bands
        -- str2: secondary bands (used if d_cng2==act)
     band_to={
     -- banding mode
              val="random2";
              -- set where segs of uselist will be banded to
              -- use one of these vals (also for gui):
              list={
                    "space"; --    band to space          (3D-Angles)
                    "center"; --   band to seg:  center   (auto-detection)
                    "user"; --     band to seg:  center   (user-defined in puzzle.seg_center.val)
                    "furthest"; -- band to seg:  furthest
                    "random1"; --  band to seg:  random      in uselist
                    "random2" --   band to seg:  random      in puzzle (classical behaviour)
                   }
             };      
     rho={min=3.8/8;max=3.8};
     -- if band_to.val=="space" (seg to "air")
     -- absolute random bandlen minimum and maximum
     d_cng1={min=3.8/8;max=3.8};
     -- if band_to.val~="space"
     -- relative primary random bandlen minimum and maximum
     -- resulting band len: current seg dist+min..max

     d_cng2={act=true;min=0;max=3.8/8};
     -- if act==true
     -- relative secondary random bandlen (uselist-seg to uselist-seg)
     -- resulting band len=current seg dist+min..max
     band_sys_lim={
     -- band len allowed (by "system")
                   min=3.8/2;
                   -- you can also put 0 here,
                   -- but then seg to seg bands can get 'too close'
                   max=10000
                   -- as said on fold.it homepage
                  };
     seg_min_dist=3.8*1.25;
     -- minimum spatial dst for seg-banding
     -- (bandable segs detection thr based on dst)
     -- segs with dst less than this val are considered as 'too close'
     -- use this to prevent:
        -- connecting one segment to its index-neighbour, but allow closing cuts
        -- creating sharp edges in puzzle
     band_skip_wrong=false;
     -- set if "wrong bands" are corrected or rejected
     -- wrong bands: segs to be banded are too close
        -- true:  reject actual band
        --        (you will have fewer bands, in worst case 0!)
        -- false: correct band target segment
        --        (will take nearest possible segment)
    }

-- set which methods are performed when pulling:
pull={act=true;
      CI_default=0.5;
      -- if no CI is given
      {CI=nil;cmd="w";itr=2;backbone=true;sidechains=false}
       -- CI=nil: don't change CI, use current (last) set value
     }

-- set which methods are performed at each end of releasing and fusing:
release_n_fuse_end={
                    -- no
                       -- act
                       -- CI_default 
                    -- because this list is appended only
                    {CI=nil;cmd="m";itr=1};
                     -- CI=nil: don't change CI, use current (last) set value
                    {CI=nil;cmd="w";itr=8;backbone=true; sidechains=true};
                    {CI=nil;cmd="m";itr=1};
                    {CI=nil;cmd="s";itr=1};
                    {CI=nil;cmd="w";itr=1;backbone=true; sidechains=true}
                   }

-- set which methods are performed when releasing:
release={act=false;
         -- fast "fuse" (quickstab) activated?
         CI_default=1;
         -- if no CI is given
         {CI=nil;cmd="m";itr=1};
          -- CI=nil: don't change CI, use current (last) set value
         {CI=nil;cmd="s";itr=1};
         {CI=nil;cmd="w";itr=4;backbone=true; sidechains=false};

         -- at the end, always the same:
         release_n_fuse_end[1];
         release_n_fuse_end[2];
         release_n_fuse_end[3];
         release_n_fuse_end[4];
         release_n_fuse_end[5]
        }

-- set which methods are performed when fusing:
-- currently there are 4 sequences of methods,
-- but you can change their number (and length for each sequence)
-- to do this,
-- copy and paste a complete sequence (each begins with --fuse#x:)
-- but take care of the braces!
fuse={act=true;
      -- complex fuse activated?
      CI_default=0.3;
      -- if no CI is given
--sequence start:
--fuse#1:
      {
       {CI=0.1;cmd="m";itr=1};
       {CI=nil;cmd="w";itr=4;backbone=true; sidechains=false};
        -- CI=nil: don't change CI, use current (last) set value

       {CI=0.7;cmd="m";itr=1};
       {CI=nil;cmd="s";itr=1};
       {CI=nil;cmd="w";itr=4;backbone=true; sidechains=false};

       {CI=1.0;cmd="s";itr=0};
       -- itr=0: just set CI back to 1

       -- at the end, always the same:
       release_n_fuse_end[1];
       release_n_fuse_end[2];
       release_n_fuse_end[3];
       release_n_fuse_end[4];
       release_n_fuse_end[5]
      };
--fuse#2:
      {
       {CI=0.3;cmd="m";itr=1};
       {CI=nil;cmd="w";itr=4;backbone=true; sidechains=false};
        -- CI=nil: don't change CI, use current (last) set value

       {CI=0.6;cmd="m";itr=1};
       {CI=nil;cmd="s";itr=1};
       {CI=nil;cmd="w";itr=4;backbone=true; sidechains=false};

       {CI=1.0;cmd="s";itr=0};
       -- itr=0: just set CI back to 1

       release_n_fuse_end[1];
       release_n_fuse_end[2];
       release_n_fuse_end[3];
       release_n_fuse_end[4];
       release_n_fuse_end[5]
      };
--fuse#3:
      {
       {CI=0.2;cmd="m";itr=1};
       {CI=nil;cmd="w";itr=4;backbone=true; sidechains=false};
        -- CI=nil: don't change CI, use current (last) set value

       {CI=0.5;cmd="m";itr=1};
       {CI=nil;cmd="s";itr=1};
       {CI=nil;cmd="w";itr=4;backbone=true; sidechains=false};

       {CI=1.0;cmd="s";itr=0};
       -- itr=0: just set CI back to 1

       release_n_fuse_end[1];
       release_n_fuse_end[2];
       release_n_fuse_end[3];
       release_n_fuse_end[4];
       release_n_fuse_end[5]
     };
--fuse#4:
      {
       {CI=0.4;cmd="m";itr=1};
       {CI=nil;cmd="w";itr=4;backbone=true; sidechains=false};
        -- CI=nil: don't change CI, use current (last) set value

       {CI=0.3;cmd="m";itr=1};
       {CI=nil;cmd="s";itr=1};
       {CI=nil;cmd="w";itr=4;backbone=true; sidechains=false};

       {CI=1.0;cmd="s";itr=0};
        -- itr=0: just set CI back to 1

       release_n_fuse_end[1];
       release_n_fuse_end[2];
       release_n_fuse_end[3];
       release_n_fuse_end[4];
       release_n_fuse_end[5]
      }
--sequence end:
     }


-- debugging section:
function prms_show()
-- a call of this function will show complete content
-- of each table which is uncommented here
-- you can also use this function to print out values,
-- then copy & paste them back into script

   list_show_deep(puzzle,"puzzle")
-- list_show_deep(seg_use,"seg_use")
-- list_show_deep(gen,"gen")
-- list_show_deep(herd,"herd")
   list_show_deep(clu,"clu")
-- list_show_deep(release_n_fuse_end,"release_n_fuse_end")
-- list_show_deep(release,"release")
-- list_show_deep(fuse,"fuse")
end -- function prms_show()

-- for debugging before prm changes, uncomment this:
-- prms_show()


-- change section:
   -- call function to change some variables/tables via gui
prms_cng()


-- show section:
   -- for debugging after prm changes, uncomment this:
-- prms_show()



-- launch section:
   -- call main program
main()

Comments

[Crashguard303]

1. introduction:
   1.1 inspired by:
   Cartoon Villain (GA idea & first random band script of this kind)
   Rav3n_pl (OO parameter/variable handling)
   jeff101 (EO & input-boxes idea)

   1.2 idea:
   – This is a further development of my last GAB+EO
   which i wrote from scratch to improve table handling and modularity
   (it was a work of more than one month!)

   -- this script doesn't simply band to random segs,
      it works with a list of "cardinal" origin segs,
      which are detected and/or set by selection interface (blue) before.
      -- origin segs always stay the same (they are just turned off or on),
      -- target segs do vary
         -> this will avoid double banding
   
   -- new idea is to keep the number of random band parameters as small as they can be:
      the script works with 2 fixed band strengths (as the length is already random)
      -- primary bands:   do seg movement in space or relative to any other seg (depending on band mode)
      -- secondary bands: do seg movement between proximate segs.
                          they can be used to stabilize or move internal puzzle structure,
                          so their job is supporting the primary bands with their major task
   
   -- as i didn't want to overload the starting sequence
      with too many input boxes and selectable vals (more than 7 boxes at the moment!).
      -> you can set all vals (even the other) in the declaration section.
   

   1.3 features:
   – cardinal seg auto-detection: (see 3.3.2.3)
   – secondary-structure changes, amino-acids, etc will create a uselist
   ++ selecting segs via game interface (blue) is possible, too
   – 3 breeding modes: (see 3.2)
   GA
   EO1
   EO2
   – 2 gene modes: (see 3.2.2.2)
   "dual"
   "poly"
   – 6 banding modes (see 3.3)
   "space"
   "center"
   "user"
   "furthest"
   "random1"
   "random2"
   ++ further settings for each

   1.4 known bugs/problems:
   1.4.1 ligand puzzles:
   – are supported by script, but i couldn't test if it works properly!
   -> to band ligand:
   use band to "user", then slide to last segment!

[Crashguard303]

. Further support:
In next time, I will have some examinations, so I won't have the time do care much about script bugs, features, spelling mistakes (or other lingual issues, as I'm not a native English speaker)
I hope, the manual is complete in this way that it answers most questions.
Maybe some other scripters can help you if there is a minor problem.

1. "Frontend":
   There are already many input-boxes for the most important values included in this script.
   I neither wanted to write a full-automatic banding-robot (so I offered "a couple" of parameters)
   nor to annoy somebody with tons of inputboxes.
   But as long as we can't store files, we only can change settings via input dialog boxes or writing them directly into the script code.
   In this script, this is a job for more advanced coders, as settings & values are stored in tables with non-flat but hierarchical structure
   (similar to elements in .CSS-Files)

So it is up to you to choose which parameters you change and in which way,
as this is our human part in this game, the rest can do ROSETTA.
The script should be stable if you don't mess up vital things.

1. (default) parameters (customizing) and uploading (advice rather for coders with few experience):
   If you find useful puzzle-adapted settings or script changes, you are free to post them
   (and your version of the script, too).
   Maybe you can recommend some settings (useful banding modes, thresholds… well, some puzzle-related things).

But -please- don't just unlock some "hidden" features
(e.g. by uncommenting print-functions used for debugging or just adding some "prints", making the script more verbose)
and upload you personal customization as "reinvention of the wheel".
A car doesn't go faster if you put some racing-stickers on it ;)
For scripts, let's concentrate on functionality, the beauty will be found in good puzzle solutions.
If everybody would change the script's appearance, we won't be able to fish out functional code anymore.

I want the script to be kept modular and relatively universal
(and genetic, for pure random bands, other scripts do exist already).
This means that removing some of the code is a bad idea, too
(apart from bug & performance fixes, of course).
So, if you do some changes and upload your script, please tell us what you did change ;)
(maybe by posting a complete function if it was changed)

If you want your own (personal) default values (or shortcuts), use the declaration section to initialize them,
then you won't have to click through all boxes anymore.