Recipe: Label Cysteines

created by marsfan

Profile

• Name: Label Cysteines
• ID: 103594
• Shared with: Public
• Parent: None
• Children: None
• Created on: June 15, 2020 at 01:00 AM UTC
• Updated on: June 15, 2020 at 01:00 AM UTC
• Description:

  Add/remove a note to each segment that has a cysteine sidechain. useful to help find them in puzzles that have Disulfide bonds.

Code

cysteineFlag = "<C>  " -- String to add to note to indicate presence of cystine



-- Add flags cysteine segments
function addFlags()
    local note = ""
    -- loop through all segments, looking for cysteines
    for segment=1, structure.GetCount() do
        if structure.GetAminoAcid(segment) == 'c' then
            -- Get current note, in case we need to append to it. (We don't want to delete existing notes)
            note = structure.GetNote(segment)
            -- If the string already has a cystine flag, do not add another
            if (not string.find(note, cysteineFlag) == 1) then
                note = note
            -- If string is not empty, then add the flag to the start of the string.
            elseif not (string == nil or string == "") then
                note = cysteineFlag..note
            -- Otherwise, just add the cysteine flag
            else
                note = cysteineFlag
            end
            -- Set the note
            structure.SetNote(segment, note)
        end
    end
end

-- Remove flags from sidechain
function removeFlags()
    local note = ""
    --loop through all segments, removing cysteine flags
    for segment = 1, structure.GetCount() do
        note = structure.GetNote(segment)
        note = string.gsub(note, cysteineFlag, "")
        structure.SetNote(segment, note)
    end
end


-- Main Function
function main()
    -- Set up menu to choose to add/delete the flags
    menu = dialog.CreateDialog("Cysteine Labeler")
    menu.add = dialog.AddButton("Add", 1)
    menu.remove = dialog.AddButton("Remove", 2)
    menu.cancel = dialog.AddButton("Cancel", 0)
    
    -- Show menu, get user choice
    local choice = dialog.Show(menu)
    -- Run operation depending on use choice
    if choice == 1 then
        addFlags()
    elseif choice == 2 then
        removeFlags()
    end
end


-- Run the main function
main()

Comments

[Bruno Kestemont]

I see that you are investing in the custom use of notes.

It's an interesting exploration path for many different uses.

Suggestion: (in selection interface you can see all notes together, not in default interface):

-add an visible element like a freeze or a band in space in order to show the cysteins (or the notes to be read)

A band in space can immediately be used in hand fold next step and it can be deleted easilly with deletebands.