Recipe: Set SS

created by LociOiling

Profile

• Name: Set SS
• ID: 49161
• Shared with: Public
• Parent: None
• Children:
  • Set SS 1400
  • Set SS 1784
  • Set SS 60
  • Set SS 1952 BAM
• Created on: May 19, 2014 at 22:58 PM UTC
• Updated on: May 19, 2014 at 22:58 PM UTC
• Description:

  Sets secondary structure. For use with Get SS or similar. Replace the ssList variable with the output from Get SS or similar recipes.

Code

--
--  set secondary structure
--
--  example of setting secondary structure
--
--  replace ssList with your secondary structure
--

--                 1         2         3         4         5         6         7         8         9
--        12345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345
ssList = "LLLLLLEEEEELLLLLLLLLEEEEEEELLLLLLLLLLLEEELLEELLLLLEELLLLLEEEELLLLLLLLLLEEELLLLLLLLEELLLLLLLLLLL"
--        12345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345
--                 1         2         3         4         5         6         7         8         9

--                 
-- function
--
function setSS ( tab )
    for ii = 1, math.min ( #tab, structure.GetCount () ) do
        print ( "position " .. ii .. " = \'" .. string.sub ( tab, ii, ii ) .. "\'" ) 
        structure.SetSecondaryStructure ( ii, string.sub ( tab, ii, ii ) )
    end
    if #tab > structure.GetCount () then 
        print ( "specified structure list is longer than protein, ignored last " 
                    .. #tab - structure.GetCount () ..
                "entries" )
    end
    if #tab < structure.GetCount () then 
        print ( "specified structure list is shorter than protein, last " 
                    .. structure.GetCount () - #tab ..
                "segments unchanged" )
    end

end

--call
setSS ( ssList )

Comments

[LociOiling]

After releasing this quick and dirty recipe, it turned out Brow42 had created something better a long time back. Brow's version of the recipe displays the primary and secondary structures, and lets you change them right in the recipe dialog. This is a lot better than my initial approach, which requires running one recipe to write out the structures, editing the scriptlog file to save the results, and running another recipe to restore the structures.

See "AA Copy Paste Compare v 1.1.1 – Brow42" for a full-function recipe that works with both primary and secondary structure. https://fold.it/portal/recipe/38147

I created "SS Edit" as simpler version of Brow's recipe, that works only with secondary structures in a single dialog box. https://fold.it/portal/recipe/49164