Recipe: Reverser 1.0.1 -- Brow42

created by brow42

Profile

• Name: Reverser 1.0.1 -- Brow42
• ID: 46756
• Shared with: Public
• Parent: None
• Children: None
• Created on: August 10, 2013 at 17:19 PM UTC
• Updated on: August 10, 2013 at 17:19 PM UTC
• Description:

  Uses bands to pull segments to their opposite segment. If protein knots, make (disabled) cutpoints first! Good for ED puzzles.

Code

--[[ 
====================================
  * Reverser

  * Original Author: Brow42
  
  * Version 1.0  Aug 10, 2013
  * Bands segments to segment opposite position
  * Mainly for ED Puzzles
--]]

-- ===================================  Begin Options

options = {skip = 0, strength = 10, sidechains = false, disabled = true}

-- Globals

version = '1.0.1'
title='Sequence Reverser '..version
max_skip = 5 -- for the skip sliders
nseg = structure.GetCount()

-- ================================== End Defaults


-- ================================== Begin New Dialog Library Functions
--[[
  Throws up a dialog containing just text, provided as a string or table
  of strings in the first argument. Title and buttons are optional. Return
  value is 1 if the first button is clicked and 0 if the second button is clicked
  or the window is closed.
--]]
function dialog.MessageBox(msg,title,buttontext1, buttontext0)
    title = title or ''
    local d = dialog.CreateDialog(title)
    if type(msg) == 'string' then d['1'] = dialog.AddLabel(msg)
    else for i = 1,#msg do
            d[tostring(i)] = dialog.AddLabel(msg[i])
        end
    end
    buttontext1 = buttontext1 or 'Ok'
    d.button = dialog.AddButton(buttontext1,1)
    if buttontext0 then d.button0 = dialog.AddButton(buttontext0,0) end
    return d
end

function dialog.ShowMessageBox(msg,title,buttontext1,buttontext0)
    return dialog.Show(dialog.MessageBox(msg,title,buttontext1,buttontext0))
end

-- ================================== End New Dialog Library Functions

-- ================================== Begin Zero Length Bands

-- ==================== Begin Dialog Code

-- This function defines our dialog and calls the functions to set and read values
-- First arg is the current option state and optional second arg is a remembered 
-- default.
function ShowMenu()
    local d = dialog.CreateDialog(title)

    d.l1 = dialog.AddLabel("Make protein reverse on Wiggle")
    d.l2 = dialog.AddLabel("If protein turns into not, try cut points")
    d.l3 = dialog.AddLabel("(at u-turns and helices) Disable Them!")
    d.skip = dialog.AddSlider("Skip Segments:",options.skip,0,max_skip,0)
    d.str = dialog.AddSlider("Strength:",options.strength,1,10,0)
    d.sc = dialog.AddCheckbox("Band Sidechains Too",options.sidechains)
    d.dis = dialog.AddCheckbox("Sidechain bands initially Disabled",options.disabled)
    d.ok = dialog.AddButton("Band",1)
    d.cancel = dialog.AddButton("Cancel", 0)

    local rc = dialog.Show(d)
    options.sidechains = d.sc.value
    options.skip = d.skip.value
    options.strength = d.str.value
    options.disabled = d.dis.value
    return rc
end

-- Recursive table printer
function PrintTable(tab,indent)
    indent = indent or ''
    for i,v in pairs(tab) do
         if type(v) == 'table' then do print(indent,i) PrintTable(v,indent..'   ') end 
        else print(indent,i,v) end
    end
end


--[[
-- True if nothing is specified
function AllSegments()
    return AllStructures() and allFrozen()
    and not (option.do_selected or option.uturn) and #_seglist == 0
end

-- True if no structures or all structures specified
function AllStructures()
    return not (option.do_loop or option.do_sheet or option.do_helix) or 
        (option.do_loop and option.do_sheet and option.do_helix)
end

-- True of neither or both are checked
function AllFrozen()
    return (option.do_frozen and option.do_notfrozen) or not (option.do_frozen or option.do_notfrozen)
end

-- Returns true if a segment satisfies all conditions (except range)
function DoSegment(i)
    local s = structure.GetSecondaryStructure(i)
    local f = freeze.IsFrozen(i) or structure.IsLocked(i)
    local retval = true
    retval = retval and s ~= 'M'
    retval = retval and (_allstructures or ( option.do_loop and s == 'L') or (option.do_sheet and s == 'E') or (option.do_helix and s == 'H'))
    retval = retval and (_allfrozen or (option.do_frozen and f) or (option.do_notfrozen and not f))
    retval = retval and (not option.do_selected or selection.IsSelected(i))
    retval = retval and (not option.uturn or IsUTurn(i))
    retval = retval and ( (i - option.skip_offset -1) % (1+option.skip) == 0)
    return retval
end
--]]

fsl = fsl or {}
fsl.atom = fsl.atom or {}
fsl.atom.atomcount = { -- shorter table just for identifying terminals
    a=10, c=11, d=12, e=15, f=20, g=7, h=17, i=19, k=22, l=19,
    m=17, n=14, p=15, q=17, r=24, s=11, t=14, v=16, w=24, y=21
}

function fsl.atom._IsDisulfideBonded(iSeg)
    local s = current.GetSegmentEnergySubscore(iSeg,'disulfides')
    return tostring(s) ~= '-0'
end
function fsl.atom._IsTerminalTest(aa,count,disulfide)
    local diff = count - fsl.atom.atomcount[aa]
    if disulfide then diff = diff + 1 end -- because count is one less because a H was removed
    if diff == 0 then return false, false, disulfide
    elseif diff == 1 then return false, true, disulfide
    elseif diff == 2 then return true, false, disulfide
    elseif diff == 3 then return true, true, disulfide
    end
    error('Strange atom count, report this!')
end

function ZLB(iSeg,atom,weight)
    local nSeg = structure.GetCount()
    local seg2, seg3
    local minlen = 0.001
    atom = atom or 0
    weight = weight or 1.0
    if (iSeg == 1) then seg2,seg3 = 2,3
   elseif iSeg == nSeg then seg2,seg3 = nSeg-1,nSeg-2
   else seg2,seg3 = iSeg-1, iSeg+1 end
    local iBand = band.Add(iSeg,seg2,seg3,minlen,0,0,atom)
    if iBand > 0 then
        band.SetGoalLength(iBand,minlen)
        band.SetStrength(iBand,weight)
    end
    return iBand
end

function GetSidechainAtom(iSeg)
            local first,last,disulfide = fsl.atom._IsTerminalTest(
                structure.GetAminoAcid(iSeg), structure.GetAtomCount(iSeg), fsl.atom._IsDisulfideBonded(iSeg))
            local offset = last and 5 or 4 -- number slider is added to (min 1) to get C-Beta atom
    return offset+1
end

function MakeSwapBand(src,dest)
    local aa1,aa2 = structure.GetAminoAcid(src),structure.GetAminoAcid(dest)
    local iband
    if  structure.GetSecondaryStructure(src) == 'M' or  structure.GetSecondaryStructure(dest) == 'M' then return end

    iband = ZLB(dest,2,options.strength)
    if iband == 0 then return
    else
        local iband2 = band.AddToBandEndpoint(src,iband)
        if iband2 > 0 then
            band.SetGoalLength(iband2,0.001)
        end
        band.Delete(iband)
    end

    if options.sidechains and structure.GetAminoAcid(src) ~= 'g' and structure.GetAminoAcid(dest) ~= 'g' then
        local atom1 = GetSidechainAtom(src)
        local atom2 = GetSidechainAtom(dest)
        iband = ZLB(dest,atom2,options.strength)
        if iband == 0 then return
        else
            local iband2 = band.AddToBandEndpoint(src,iband,atom1)
            if iband2 ~= 0 then
                band.SetGoalLength(iband2,0.001)
                if options.disabled then band.Disable(iband2) end
            end
            band.Delete(iband)
        end
   end
end
 
function round(x,n)
    return math.floor(0.5 + x * 10^n) / 10^n
end

_NOrigBands = band.GetCount()
function DeleteBands()
    print("Deleting bands")
    if _NOrigBands == 0 then band.DeleteAll() end
    while band.GetCount() > _NOrigBands do
        band.Delete(band.GetCount())
    end
end

function OnError(err)
    if err:find("Cancel") then
        print("Cancelled")
        DeleteBands()
    end
    return err
end

-- ==================== Begin Main
rc = ShowMenu()
if rc == 0 then return end

rc,err = xpcall(function()
    for i = 1,nseg,1+options.skip do
        MakeSwapBand(i,nseg-i+1)
    end
end, OnError)


print("Done.")