Recipe: Band Hbonds

created by Bruno Kestemont

Profile

• Name: Band Hbonds
• ID: 109257
• Shared with: Public
• Parent: None
• Children: None
• Created on: November 22, 2025 at 12:24 PM UTC
• Updated on: January 01, 2026 at 08:11 AM UTC
• Description:

  from wiki

Code

--  example 3 - add a band between the indicated atoms
--              get the current length of the band, 
--              report in a compact format
--  
function round ( ii )
    return ii - ii % 0.001
end    
--
--  normalSeg - convert possible symmetric segment number
--              to segment number and chain
--
--  arguments:
--
--  seg2   - segment number to convert
--  segcnt - length of chain
--  symnum - number of symmetric chains (0 to n)
--
--  returns:
--
--  seg    - segment number, in the range 1 to segcnt
--  symchn - symmetric chain number (0 to n)
--
function normalSeg ( seg2, segcnt, symnum )
    if seg2 <= segcnt or symnum == 0 then
        return seg2, 0 
    end
    local endz = {}
    for sym = 1, symnum do
        endz [ #endz + 1 ] = segcnt * sym + sym + 1
    end
    local adjseg = 0
    local adjsym = 0
    for rng = #endz, 1, -1 do 
        if seg2 >= endz [ rng ] then
            adjseg = seg2 - endz [ rng ] + 1
            adjsym = rng
            break
        end
    end
    return adjseg, adjsym
end
 
bonds = structure.GetHBonds ()
print ( #bonds .. " hydrogen bonds found" )
segcnt = structure.GetCount ()
symcnt = structure.GetSymCount ()      
for ii = 1, #bonds do
    local res2, chn = normalSeg (  bonds [ ii ] [ "res2" ], segcnt, symcnt )
    bx = band.AddBetweenSegments ( bonds [ ii ] [ "res1" ], res2,
            bonds [ ii ] [ "atom1" ], bonds [ ii ] [ "atom2" ], chn )
    if bx ~= nil and bx ~= 0 then
        blen = band.GetLength ( bx )
        print ( "bond " .. ii .. 
            ", " .. bonds [ ii ] [ "res1" ] .. 
            " ( " .. bonds [ ii ] [ "atom1" ] .. 
            " ) - " .. res2 ..
            " ( " .. bonds [ ii ] [ "atom2" ] ..
            " ), chain = " .. chn ..
            ", width = " .. round ( bonds [ ii ] [ "width" ] ) .. 
            ", current length = " .. round ( blen ) )
        end
end