Recipe: Band cysteines

created by latin krepin

Profile

• Name: Band cysteines
• ID: 108574
• Shared with: Public
• Parent: None
• Children:
  • Band cysteines (COPY)
• Created on: March 11, 2024 at 08:58 AM UTC
• Updated on: March 11, 2024 at 09:48 AM UTC
• Description:

  band cysteine sulfurs close enough to make a disulfide bond. should work on most puzzles without input

Code

MIN_CYS_DISTANCE=6
DISULFIDE_BOND_LENGTH=2.05
BAND_STRENGTH=10

function MakePairsSet(segment_list)
    -- make sure each pair appears only once
    pairs_set={}
    for _, segment1 in pairs(segment_list) do
        for _, segment2 in pairs(segment_list) do
            if segment1 ~= segment2 then
                if segment1 > segment2 then
                    subset={segment2,segment1}
                else
                    subset={segment1,segment2}
                end
                -- use string as key because same tables can have different hashes
                key=table.concat(subset, '_')
                if pairs_set[key] == nil then
                    pairs_set[key] = subset
                end
            end
        end
    end
    return pairs_set
end

function GetCysteines()
    cysteines={}
    cys_index=1
    for i=1, structure.GetCount() do
        aa=structure.GetAminoAcid(i)
        if aa=='c' then
            cysteines[cys_index]=i
            cys_index=cys_index+1
        end
    end
    return cysteines
end


cysteines = GetCysteines()
cysteine_pairs = MakePairsSet(cysteines)

for _, cysteine_pair in pairs(cysteine_pairs) do
    cysteine1, cysteine2 = unpack(cysteine_pair)
    band55 = band.AddBetweenSegments(cysteine1,cysteine2,5,5)
    band_length = band.GetLength(band55)
    band.Delete(band55)

    if band_length < MIN_CYS_DISTANCE then
        band66 = band.AddBetweenSegments(cysteine1,cysteine2,6,6)
        band.SetGoalLength(band66, DISULFIDE_BOND_LENGTH)
        band.SetStrength(band66, BAND_STRENGTH)
    end

end