diff --git a/Biobase/Secondary/Constraint.hs b/Biobase/Secondary/Constraint.hs
--- a/Biobase/Secondary/Constraint.hs
+++ b/Biobase/Secondary/Constraint.hs
@@ -6,11 +6,15 @@
 
 module Biobase.Secondary.Constraint where
 
+import Data.Char (toLower)
 import Data.Primitive.Types
 import qualified Data.Vector.Generic as VG
 import qualified Data.Vector.Generic.Mutable as VGM
 import qualified Data.Vector.Unboxed as VU
 
+import Data.PrimitiveArray
+import Data.PrimitiveArray.Ix
+
 import Biobase.Secondary.Diagrams
 
 
@@ -32,12 +36,77 @@
 nobonusCC = VU.fromList ".x"
 {-# NOINLINE nobonusCC #-}
 
+-- | Given a 'Constraint', create an NxN matrix with bonus energies. These
+-- energies can be included in all pair-creating functions and will disallow or
+-- strongly favor certain pairings, while others will receive neither bonus nor
+-- malus.
+--
+-- In case, a pair (i,j) is annotated as both, bonus- and malus-receiving, it
+-- will be set to receive a malus. This can happen, if something like "<" would
+-- give a bonus, but "x" gives a malus (and other cases).
+--
+-- TODO and again, we should parametrize over "Energy", "Score", etc (that is,
+-- Prim a)
 
+bonusTable :: Double -> Double -> Constraint -> PrimArray (Int,Int) Double
+bonusTable bonus malus (Constraint constraint) = arr where
+  arr = fromAssocs (0,0) (n,n) 0 $ bonusBr ++ bonusAn ++ bonusBa ++ malusBr ++ malusAn ++ malusX
+  n = VU.length constraint -1
+  infixl 1 `xor`
+  xor a b = a && not b || not a && b
+  -- "()" bonus energies
+  bonusBr = [ ((i,j),bonus)
+            | (i,('(',j)) <- zip [0..] $ VU.toList constraint
+            ]
+  malusBr = [ ((i,j),malus)
+            | i <- [0..n]
+            , j <- [i..n]
+            , let bi = constraint VU.! i
+            , let bj = constraint VU.! j
+            , fst bi == '(' && snd bi /= j || fst bj == ')' && snd bj /= i
+            ]
+  bonusAn = [ ((i,j),bonus)
+            | i<-[0..n]
+            , fst (constraint VU.! i) == '<'
+            , j<-[i+1..n]
+            ] ++
+            [ ((i,j),bonus)
+            | j<-[0..n]
+            , fst (constraint VU.! j) == '>'
+            , i<-[0..j-1]
+            ]
+  malusAn = [ ((i,j),malus)
+            | i<-[0..n]
+            , j<-[i+1..n]
+            , fst (constraint VU.! j) == '<'
+            ] ++
+            [ ((i,j),malus)
+            | i<-[0..n]
+            , j<-[i+1..n]
+            , fst (constraint VU.! i) == '>'
+            ]
+  bonusBa = [ ((i,j),bonus)
+            | i<-[0..n]
+            , j<-[i+1..n]
+            , fst (constraint VU.! i) == '|' || fst (constraint VU.! j) == '|'
+            ]
+  malusX  = [ ((i,j),malus)
+            | i<-[0..n]
+            , j<-[i+1..n]
+            , fst (constraint VU.! i) == 'x' || fst (constraint VU.! j) == 'x'
+            ]
 
+{-
+testC = putStrLn $ f as where
+  f [] = ""
+  f xs = show (take 9 xs) ++ "\n" ++ f (drop 9 xs)
+  as = toList $ bonusTable (1) 2 (mkConstraint "(<<..x|>)")
+-}
+
 -- * Instances
 
 instance MkConstraint String where
-  mkConstraint xs = mkConstraint . VU.fromList $ xs
+  mkConstraint xs = mkConstraint . VU.fromList . map toLower $ xs
 
 instance MkConstraint (VU.Vector Char) where
   mkConstraint cs = Constraint $ VU.zip cs ks where
diff --git a/BiobaseXNA.cabal b/BiobaseXNA.cabal
--- a/BiobaseXNA.cabal
+++ b/BiobaseXNA.cabal
@@ -1,5 +1,5 @@
 name:           BiobaseXNA
-version:        0.5.1.0
+version:        0.5.2.0
 author:         Christian Hoener zu Siederdissen
 maintainer:     choener@tbi.univie.ac.at
 homepage:       http://www.tbi.univie.ac.at/~choener/
@@ -17,6 +17,10 @@
                 efficient encodings for short sequences, as required by RNA
                 folding tools. Extended RNA secondary structures can be
                 represented as well.
+                .
+                Changes since 0.5.1.0
+                .
+                * bonusTable for constrained folding
 
 extra-source-files:
 
@@ -28,7 +32,8 @@
     text,
     tuple,
     vector >=0.7 && <0.8,
-    vector-read-instances
+    vector-read-instances,
+    PrimitiveArray
 
   exposed-modules:
     Biobase.Primary