Recipe: Helix Mutator 0.1 -- brow42

created by brow42

Profile

• Name: Helix Mutator 0.1 -- brow42
• ID: 48794
• Shared with: Public
• Parent: None
• Children: None
• Created on: April 05, 2014 at 20:53 PM UTC
• Updated on: April 05, 2014 at 20:53 PM UTC
• Description:

  Mutates helices so that they are part polar and half hydrophobic. Choose a helix by freezing it or selecting it. orange = 30% ala 70% leu. blue = 50/50 lys/glutamate

Code

--[[
 * Helix Mutator 0.1
  * Original Author: Brow42

  * Version 0.1 April 5 2014

  * Mutate hidden residues to alanine or leucine,
  * mutate exposed residues to lysine or glutamate
  *
  * Also various functions for researching helices
--]]

title = "Helix Mutator 0.1"
-- acidic
D = 'd' -- aspartate
E = 'e' -- glutamate
-- basic
K = 'k' -- lycine
R = 'r' -- arginine
-- hydrophobic
A = 'a' -- alanine
L = 'l' -- leucine

HydroThreshold = 40 -- negative hiding score for leu
sequence = "DDAAEEA" -- default heptad
IgnoreSS = true

function IsHelix(i) return structure.GetSecondaryStructure(i) == 'H' or IgnoreSS end
_lastloop = 0
function ResetSeq(i) _lastloop = i and i or 0 end
function Seq(i,thesequence)
    thesequence = thesequence or sequence
    if not IsHelix(i) then _lastloop = i end
    i = i - _lastloop
    if i == 0 then return nil end
    i = 1 + (i - 1) % thesequence:len()
    return thesequence:sub(i,i)
end

NSeg = structure.GetCount()

DeselectAll = selection.DeselectAll
GetAA = structure.GetAminoAcid
GetHiding = function(i) return current.GetSegmentEnergySubscore(i,'hiding') end

function True(j) return true end

function SelectIf(predicate,range)
    if range == nil then range = {1,NSeg} end
    ResetSeq(range[1]-1)
    for i = range[1],range[2] do
        if predicate(i) then selection.Select(i) end
    end
end

function Unique(tab)
    local tmp1, tmp2 = {}, {}
    for i = 1,tab:len() do tmp1[tab:sub(i,i)] = true end
    for u,v in pairs(tmp1) do tmp2[#tmp2 + 1] = u end
    return tmp2
end

function Apply(thesequence,range,predicate)
    predicate = predicate or True
    thesequence = thesequence or sequence
    local types = Unique(thesequence)
    DeselectAll()
    for i = 1,#types do
        SelectIf(function(j) return IsHelix(j) and Seq(j,thesequence) == types[i] and predicate(j) end,range)
        structure.SetAminoAcidSelected(types[i])
        DeselectAll()
    end
end

ERROR_BOTH = -1
function FindSelected()
    local appending = false
    local f,s,h
    local range
    local list = {}
    for i = 1, NSeg do
        f,s = freeze.IsFrozen(i), selection.IsSelected(i)
        h = IsHelix(i)
        if s and f then return ERROR_BOTH end
        if (f or s) and h then
            if appending then range[2] = i
            else
                range = {i,i}
                list[#list+1] = range
                appending = true
            end
        else
            if appending then appending = false end
        end
    end
    return list
end

-- ================================== Begin New Dialog Library Functions
-- Add a wall of text from a table
function dialog.AddLabels(d,msg,nlabels) -- pass in # of existing autolabels
    local nlabels = nlabels or #(d._Order or {}) -- default, valid if never delete dialog elements
    if type(msg) == 'string' then
        msg = { msg }
    end
    for i = 1,#msg do
        d['autolabel'..tostring(i+nlabels)] = dialog.AddLabel(msg[i])
    end
end
-- Create but don't display a wall of text and 1 or 2 buttons
function dialog.CreateMessageBox(msg,title,buttontext1,buttontext0)
    title = title or ''
    local d = dialog.CreateDialog(title)
    dialog.AddLabels(d,msg)
    buttontext1 = buttontext1 or 'Ok'
    d.button = dialog.AddButton(buttontext1,1)
    if buttontext0 ~= nil then d.button0 = dialog.AddButton(buttontext0,0) end
    return d
end
-- Display a dialog box
function dialog.ShowMessageBox(msg,title,buttontext1,buttontext0)
    return dialog.Show(dialog.CreateMessageBox(msg,title,buttontext1,buttontext0))
end
-- Display a box AND print to the output
function ErrorMessage(msg,buttontext1,buttontext0)
    if type(msg) == 'string' then
        msg = { msg }
    end
    for i = 1,#msg do
        print(msg[i])
    end
    return dialog.ShowMessageBox(msg,title,buttontext1,buttontext0)
end

-- ================ Begin Main ================
list = FindSelected()

if list == ERROR_BOTH then
    rc = ErrorMessage("Used both selection and freezing. Clear both?","Yes","No")
    if rc == 1 then
        selection.DeselectAll()
        freeze.UnfreezeAll()
    end
    return
end

if #list == 0 then
    ErrorMessage({"Nothing selected. Choose 1 helix","by freezing or selecting."})
    return
end

if #list ~= 1 then
    ErrorMessage("Need exactly 1 helix selected.")
    return
end

print(title)
print(puzzle.GetName())
print(os.date())
seed = (os.time() * 5779) % 10000
math.randomseed(seed)
print("random seed =",seed)
math.random()

Apply(L,list[1])
--Apply(K,list[1],function(j) return GetHiding(j) <= -HydroThreshold end)
new_seq = {}
for i = list[1][1],list[1][2] do
    r = math.random()
    if GetHiding(i) <= - HydroThreshold then
        aa = r < 0.5 and K or E
    else
        aa = r < 0.3 and A or L
    end
    new_seq[#new_seq+1] = aa
end
Apply(table.concat(new_seq,''),list[1])