Recipe: Contacts (actual) to RR file v0.1

created by Susume

Profile

• Name: Contacts (actual) to RR file v0.1
• ID: 101869
• Shared with: Public
• Parent: Contacts to RR file
• Children: None
• Created on: February 15, 2016 at 04:32 AM UTC
• Updated on: February 15, 2016 at 04:32 AM UTC
• Description:

  Prints all actual contacts in CASP RR file format for use in external viewing program such as CMView. Before using output, replace spaces in data rows (not header rows) with tabs.

Code

-- Contacts to RR file
--   Prints actual contacts in CASP RR format for viewing in external program such as CMView.
--   CMView reads an RR file and displays a contact map, which can then be saved as a PNG file.
--     It can also compare two contact maps in one image.
--   Before using output, replace spaces in data rows (NOT header rows) with tabs.

SPACE = " "
MINDIST = 0
MAXDIST = 12  --pairs of residues closer than this many angstroms will appear in the RR file
SeqLineLen = 50  --max characters per line in primary sequence

SegCount = structure.GetCount()
PuzzleName = puzzle.GetName()
PuzzleNum = string.match(PuzzleName, "%d%d%d%d")

function Header()
    print("PFRMAT RR")
    print("TARGET T"..PuzzleNum)  --CMView contact viewer expects a T on front of target number
    print("MODEL 1")
end

function PrimarySequence()
    Seg = 0 -- segment counter
    repeat
        SeqLine = ""
        Char = 0 -- count of characters in Line
        repeat
            Seg = Seg+1
            SeqLine = SeqLine..structure.GetAminoAcid(Seg)
            Char = Char+1
        until Char==SeqLineLen or Seg==SegCount
        print(string.upper(SeqLine))
    until Seg==SegCount
end

function Footer()
    print("END")
end

function DataRows()
    for i = 1, SegCount-2 do
        for j = i+2, SegCount do
            --Weight = contactmap.GetHeat(i, j)
            Weight = 1 --because these are actual contacts
            if structure.GetDistance(i,j) <= MAXDIST then
                print(i..SPACE..j..SPACE..MINDIST..SPACE..MAXDIST..SPACE..Weight)
            end
        end
    end
end

function Main()
    Header()
    PrimarySequence()
    DataRows()
    Footer()
end

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Main()