Recipe: Ligand Atom Number

created by Bruno Kestemont

Profile

• Name: Ligand Atom Number
• ID: 109303
• Shared with: Public
• Parent: None
• Children: None
• Created on: January 01, 2026 at 08:42 AM UTC
• Updated on: January 01, 2026 at 08:57 AM UTC
• Description:

  Displays the atom numbers in notes linked with bands

Code

--Ligand atom numbers
--one band to each atom of the ligand and a segment with a note displaying atom number
--if you want to see better, first erase all notes using appropriate recipe.


SStartTime=os.time()
InitialClashImportance = behavior.GetClashImportance()
NonLockedSegList = {}
segCt = structure.GetCount()
MinUnlockedSeg = 1
MaxUnlockedSeg = segCt

segCnt2=segCt
while structure.GetSecondaryStructure(segCnt2)=="M" do segCnt2=segCnt2-1 end
FirstLigand= segCnt2 + 1 -- not used if no ligand, segCt if only 1 ligand
LastLigand= segCt -- not used if no ligand
tetraed={1,7,13,19}-- the segnumbers choosen as ref tetraed


if segCnt2 == segCt then
	AtomsInLigand = 0
	return
else 
	AtomsInLigand = structure.GetAtomCount(segCt)--problem is that hydrogen are also banded, which is not very usefull I think
end

Atoms2count=AtomsInLigand
helptext0="Total number of atoms in ligand (including H):"
helptext="If you want to limit bands to heavy atoms,"
helptext2="indicate number of heavy atoms above"
helptext3="You have to count them on screen"

--Options to edit in recipe (TO DO: in dialog)
HeavyAtoms=24 --to input manually for each ligand

function askInputOutput()
	repeat
    local dlog=dialog.CreateDialog("Limit atoms")
		dlog.L0=dialog.AddLabel(helptext0)
		dlog.InputText=dialog.AddTextbox("Input:", Atoms2count)
		dlog.L1=dialog.AddLabel(helptext)
		dlog.L2=dialog.AddLabel(helptext2)
		dlog.L3=dialog.AddLabel(helptext3)
		dlog.copy = dialog.AddButton ( "Go" , 1 )
		dlog.cancel = dialog.AddButton ( "Quit" , 0 )
    local result=dialog.Show(dlog)
    if result==1 then 
		InputText=dlog.InputText.value
			Atoms2count=tonumber(InputText)
	end
	until result<2
end

askInputOutput()

--band to ligand
print("adding a band to each ligand atom")

-- Search for first empty note
function noteSegment()
  for i=structure.GetCount(),1,-1 do
    if structure.GetNote(i) ~= "" then
      if i == structure.GetCount() then return(-1) else return(i+1) end
    end -- if
  end -- for
  return(1)
end -- function

note_segment = noteSegment()
dr_string = ""

function saveNote(i)
    structure.SetNote(note_segment,i)
end -- function


	for i = 1, Atoms2count do
		bn=band.AddBetweenSegments(note_segment,segCt,0,i)
		band.SetStrength(bn,0.1)
		band.SetGoalLength(bn,band.GetLength(bn))
		band.Disable(bn)
		saveNote(i)
		note_segment=note_segment+1
	end

Comments

[Bruno Kestemont]

Because the atom number varies for the same compound.
This is because the atom numbers of a ligand is detremined by the way the compound was build in foldit.
The first rank is determined by the heavy atoms. For example if you start with a single carbon, this will be number 1, and the 4 hydrogens will be numbered 2 to 5.
If now you add a nitrogen with a normal singel link, it will be numbered 2 and the hydrogens will be renumbered 3 to 8.

But if you stard with the nitrogen, this will be numbered 1 and the carbon 2 (then the hydrogens).

If you download a library compound, the all numbering of the heavy atoms starts with the one of the library compound.

In conclusion: if you submit your compound to the library and it matches a library compound, if you download the related library compound, it will be with a different numbering.