Recipe: Contact Cement 1.01

created by LociOiling

Profile

• Name: Contact Cement 1.01
• ID: 49061
• Shared with: Public
• Parent: None
• Children:
  • Contact Cement Weight 1.0
  • Contact Cement 2.0
  • Contact Cement 4.00
  • Contact Cement 4.00
• Created on: July 17, 2014 at 19:23 PM UTC
• Updated on: July 17, 2014 at 19:23 PM UTC
• Description:

  Checks for contacts with non-zero heat. Displays fun facts about any such contacts found. Bands any contacts above a user-specifed heat cutoff. Version 1.01 includes fixes Bruno Kestemont made in version 2.02

Code

--[[

    Contact Cement

    Original Author: LociOiling
    Version 1.0 May 5, 2014

    This recipe checks the contact heat for each pair of segments.

    The recipe reports the number of contacts with non-zero heat, and displays
    the minimum, maximum, mean, and median contact heat.

    The recipe can band contacts with a heat value at or above a specified minimum.
    The minimum is initially set to the mean heat.
    The bands are created with default strength and length.

    Version 1.01 July 13, 2014
    *   fix issues found by Bruno Kestemont in version 2

]]--
--
--  globals section
--
Recipe = "Contact Cement"
Version = "1.01"
ReVersion = Recipe .. " v" .. Version

bndcut = 1
heatmap = {}
tHeat = 0 
minHeat = 0
maxHeat = 0
meanHeat = 0
mediHeat = 0

segCnt = structure.GetCount()
segCnt2 = segCnt
while structure.GetSecondaryStructure ( segCnt2 ) == "M" do segCnt2 = segCnt2 - 1 end
max_residue = segCnt2

--
--  end of globals section
--

function r4 ( i )
    return i - i % 0.0001
end

function SortByHeat ( tab ) 
    local ii
    local jj
    for ii = 1, #tab - 1 do
        for jj = ii + 1, #tab do
            local h1 = tab [ ii ] [ 3 ]
            local h2 = tab [ jj ] [ 3 ]

            if h2 > h1 then
                tab [ ii ], tab [ jj ] = tab [ jj ], tab [ ii ]
            end
        end
    end
    return tab
end

function GetContacts( )

    local ii 
    local jj

    for ii = 1, segCnt2 - 1 do
        for jj = ii + 1, segCnt2 do
            if ( ii ~= jj ) then
                local heat = contactmap.GetHeat ( ii, jj )
                if ( heat > 0 ) then
                    local heatpnt = { ii, jj, heat }
                    heatmap [ #heatmap + 1 ] = heatpnt
                    tHeat = tHeat + heat
                end
            end
        end
    end

    print ( #heatmap .. " contacts with non-zero heat found" )
    if ( #heatmap > 0 ) then
        SortByHeat ( heatmap )
        print ( "seg1,seg2,heat" )
        minHeat = 9999999
        maxHeat = 0
        for ii = 1, #heatmap do
            print ( heatmap [ ii ] [ 1 ] 
                        .. "," .. 
                    heatmap [ ii ] [ 2 ] 
                        .. "," .. 
                    heatmap [ ii ] [ 3 ] )
            if heatmap [ ii ] [ 3 ] > maxHeat then maxHeat = heatmap [ ii ] [ 3 ] end
            if heatmap [ ii ] [ 3 ] < minHeat then minHeat = heatmap [ ii ] [ 3 ] end
        end
        print ( "minimum contact heat = " .. r4 ( minHeat ) )
        print ( "maximum contact heat = " .. r4 ( maxHeat ) )
        meanHeat = tHeat / #heatmap 
        print ( "mean contact heat = " .. r4 ( meanHeat ) )
        ii = math.floor ( #heatmap / 2 )
        mediHeat = heatmap [ ii ] [ 3 ] 
        if #heatmap % 2 == 0 then           -- even number of entries
            ii = ii + 1
            mediHeat = ( mediHeat + heatmap [ ii ] [ 3 ] ) / 2
        end
        print ( "median contact heat = " .. r4 ( mediHeat ) )
    end
end

function BandContacts ()
    local ii
    local bndCnt = 0
    for ii = 1, #heatmap do
        if heatmap [ ii ] [ 3 ] >= bndcut then
            band.AddBetweenSegments ( heatmap [ ii ] [ 1 ],  heatmap [ ii ] [ 2 ] )
            bndCnt = bndCnt + 1
        else
            break
        end
    end
    print ( "contact heat cutoff = " .. bndcut )
    print ( bndCnt .. " contacts banded" )
end

function GetParams()
    local dlg = dialog.CreateDialog( ReVersion )

    if #heatmap == 0 then
        dlg.l0 = dialog.AddLabel ( "No contacts found." )
        dlg.l1 = dialog.AddLabel ( "This recipe is for puzzles with a contact map." )
        dlg.cancel = dialog.AddButton ( "Cancel", 0 )
        dialog.Show ( dlg ) 
        return false
    else
        dlg.l0 = dialog.AddLabel ( #heatmap .. " contacts with non-zero heat found" )
        dlg.l1 = dialog.AddLabel ( "minimum contact heat = " .. r4 ( minHeat ) )
        dlg.l2 = dialog.AddLabel ( "maximum contact heat = " .. r4 ( maxHeat ) )
        dlg.l3 = dialog.AddLabel ( "mean contact heat = "   .. r4 ( meanHeat ) )
        dlg.l4 = dialog.AddLabel ( "median contact heat = " .. r4 ( mediHeat ) )
        if meanHeat ~= maxHeat then 
            dlg.l5 = dialog.AddLabel ( "Select minimum heat to band" )
            dlg.bndpct = dialog.AddSlider ( "Heat cutoff" ,  meanHeat, minHeat, maxHeat, 3 )
        end

        dlg.ok = dialog.AddButton ( "OK", 1 )
        dlg.cancel = dialog.AddButton ( "Cancel", 0 )

        if dialog.Show ( dlg ) > 0 then
            if meanHeat ~= maxHeat then 
                bndcut = dlg.bndpct.value
            else
                bndcut = meanHeat
            end
            return true
        else
            print( "dialog cancelled" )
        end
    end
    return false
end

function cleanup ( error )
    local reason
    local start, stop, line, msg
    if error == nil then
        reason = "complete"
    else

        start, stop, line, msg = error:find ( ":(%d+):%s()" )
        error = error:sub ( msg, #error )
        if error:find ( "Cancelled" ) ~= nil then
            reason = "cancelled"
        else
            reason = "error"
        end
    end
    print (  ReVersion .. " " .. reason )
    print ( "Puzzle: " .. puzzle.GetName () )
    print ( "Track: " .. ui.GetTrackName () )

    if reason == "error" then
        print ( "Unexpected error detected" )
        print ( "Error line: " .. line )
        print ( "Error: \"" .. error .. "\"" )
    end
end

function main()
    print ( ReVersion )
    GetContacts ()
    if GetParams() then
        BandContacts ()
    end
end

xpcall ( main, cleanup )

Comments

[LociOiling]

The recipe displays the minimum, maximum, mean, and median heat of the non-zero contacts it finds.

The heat cutoff slider allows you to band any contacts at or above the specified heat. The initial cutoff value is the mean contact heat, which seems to be 1 in the limited testing conducted so far.

The bands created have default length and strength.

If you don't wish to band the contacts, simply click cancel.

The contacts are also listed in the scriptlog in comma-separated value (CSV) format, suitable for import into spreadsheets and such.

[Bruno Kestemont]

This saves a lot of hand folding time !

[Deleted user]

Thank you for sharing and making this neat and clear recipe.

To further it, it would be nice to see an :
1- Upper threshold for Contacts.
2- Make the bond strength linked to the heat map
3- Only work on certain protein segments at a time

These are my 2 cents.

[LociOiling]

This version of Contact Cement includes some fixes Bruno Kestemont made in Contact Cement 2.02.

The original version of Contact Cement crashed if all contacts had the same strength. The original version also misreported the median contact heat.

As a banding tool, this version has been made obsolete by recent enhancements to the contact map tool. The contact map tool now allows you to band either all contacts or only empty contacts.

This version of the recipe is still useful, since it prints out a complete list of contacts in comma-delimited (CSV) format. The list can be easily imported into a spreadsheet or another tool for further analysis.

This version is also useful as a simple starting point for more ambitious contact tools.