--[[ link NH spin systems with matching connections ]]
--[[ using HncocaNH and hNcocaNH data ]]
--[[ pick spin systems and H+1, N+1 correlations before running this script]]
t = {}
t.project=cara:getProject()
t.Systems=t.project:getSystems()
--t.Hdelta = 0.02
--t.Ndelta = 0.2
t.Hdelta = dlg.getDecimal("LinkNH","HN tolerance (ppm) = ",0.02)
t.Ndelta = dlg.getDecimal("LinkNH","N tolerance (ppm) = ",0.2)
t.newSystems = 0
t.connection = 0
t.unresolved = 0
-- --------------------------------------------------------------

for id1,system in pairs(t.Systems) do
	t.Spins = system:getSpins()
	t.succHshift=nil
	t.succNshift=nil
	if system:getSucc() == nil then
		for id2,spin in pairs(t.Spins) do
		  t.Spin = spin:getLabel()
		  if t.Spin=="H+1" then
			t.succHshift=spin:getShift()
		  end
		  if t.Spin=="N+1" then
			t.succNshift=spin:getShift()
		  end
		end
	-- --------------------------------------------------------------
		if t.succHshift~=nil and t.succNshift~=nil then
			-- find the succeeding system
			t.matchfound = 0
			for id3,system2 in pairs(t.Systems) do
				t.Spins2 = system2:getSpins()
				t.matchHshift=nil
				t.matchNshift=nil
				for id2,spin2 in pairs(t.Spins2) do
					t.Spin2 = spin2:getLabel()
					if t.Spin2=="H" then
						t.matchHshift=spin2:getShift()
					end
					if t.Spin2=="N" then
						t.matchNshift=spin2:getShift()
					end
				end
				if t.matchHshift~=nil and t.matchNshift~=nil then
					t.Hdiff = ((t.succHshift-t.matchHshift)/t.Hdelta)^2
					t.Ndiff = ((t.succNshift-t.matchNshift)/t.Ndelta)^2
					if math.sqrt(t.Hdiff + t.Ndiff) < 1.0 then
						-- print(id1, "Hurray!", id3, t.succHshift, t.succNshift)
						t.succSystem = system2
						t.matchfound = t.matchfound + 1
					end
				end
			end
			if t.matchfound >= 2 then
				t.unresolved = t.unresolved + 1
				print("Ambiguous connections found for system: "..system:getId())
			else
				if t.matchfound == 0 then
				-- create new spin system
					t.newSystems = t.newSystems + 1
					t.succSystem = t.project:createSystem()
					--t.succ = table.getn(t.project:getSystems())
					t.succHspin = t.project:createSpin("H", t.succHshift)
					t.project:assignSpin(t.succHspin, t.succSystem)
					t.project:setLabel(t.succHspin, "H")
					t.succNspin = t.project:createSpin("N", t.succNshift)
					t.project:assignSpin(t.succNspin, t.succSystem)
					t.project:setLabel(t.succNspin, "N")
				end
				t.succ = t.succSystem:getId()
				if t.succSystem:getPred() == nil then
					t.project:linkSystems(system, t.succSystem)
					t.connection = t.connection + 1
					print("Spin systems "..id1.." and "..t.succ.." linked.")
				else
					print("Spin system "..id1.." attempted target "..t.succ.." already linked.")
				end
			end
		end
	else
		print("Spin system "..id1.." already linked.")
	end
end
dlg.showInfo("Done", t.connection.." spin systems linked.\n"..t.newSystems.." new systems created.\n"..t.unresolved.." ambiguous connections.")
t = nil