added EnzymeTree-Generator via QuickCheck

sketch.md.lhs

@@ -154,9 +154,10 @@ plant.
 >               | Photosynthesis
 >      deriving (Show, Enum, Bounded, Eq)
 >
-> data Component = PP
+> data Component = GenericComponent Int
+>                | PP
 >                | FPP
->      deriving (Show, Enum, Bounded, Eq)
+>      deriving (Show, Eq)
 
 Compounds are either direct nutrients or already processed components
 
@@ -173,15 +174,14 @@ Enzymes
 
 Enzymes are the main reaction-driver behind synthesis of intricate compounds.
 
+> data Synthesis = Synthesis [(Compound, Amount)] (Compound,Amount)
 > data Enzyme = Enzyme
 >        { enzymeName            :: String
 >          -- ^ Name of the Enzyme. Enzymes with the same name are supposed
 >          --   to be identical.
 >        , substrateRequirements :: [(Nutrient,Amount)]
 >          -- ^ needed for reaction to take place
->        , substrateIntolerance  :: [(Nutrient,Amount)]
->          -- ^ inhibits reaction if given nutrients are above the given concentration
->        , synthesis             :: [(Compound,Amount)] -> [(Compound,Amount)]
+>        , synthesis             :: [Synthesis]
 >          -- ^ given x in amount a, this will produce y in amount b
 >        , dominance             :: Maybe Amount
 >          -- ^ in case of competition for nutrients this denotes the priority
@@ -199,18 +199,14 @@ Enzymes are the main reaction-driver behind synthesis of intricate compounds.
 Example "enzymes" could be:
 
 > pps :: Enzyme -- uses Phosphor from Substrate to produce PP
-> pps = Enzyme "PPS" [(Phosphor,1)] [] syn Nothing
+> pps = Enzyme "PPS" [(Phosphor,1)] syn Nothing
 >  where
->    syn compAvailable = [(Substrate Phosphor,i*(-1)),(Produced PP,i)]
->      where
->        i = getAmountOf (Substrate Phosphor) compAvailable
+>    syn = [Synthesis [(Substrate Phosphor, 1)] (PP, 1)]
 >
-> fpps :: Enzyme -- PP -> FPP
-> fpps = Enzyme "FPPS" [] [] syn Nothing
+> fpps :: Enzyme
+> fpps = Enzyme "FPPS" [] syn Nothing
 >  where
->    syn compAvailable = [(Produced PP,i*(-1)),(Produced FPP,i*0.5)]
->      where
->        i = getAmountOf (Produced PP) compAvailable
+>    syn = [Synthesis [(PP, 1)] (FPP, 1)]
 
 
 ---
@@ -272,7 +268,7 @@ internal state how many nutrients and compounds are currently inside the plant.
 > data Plant = Plant
 >      { genome            :: Genome
 >        -- ^ the genetic characteristic of the plant
->      , absorbNutrients   :: Environment -> [(Nutrient,Amount)]
+>      , absorbNutrients   :: Environment -> [(Component,Amount)]
 >        -- ^ the capability to absorb nutrients given an environment
 >      }
 > instance Show Plant where
@@ -303,7 +299,8 @@ The following example yields in the example-environment this population:
 >      a <- activation
 >      return $ (,,) <$> e' <*> [q] <*> [a]
 >
->    defaultAbsorption (Environment s _) = limit Phosphor 2
+>    defaultAbsorption (Environment s _) = (\(a,b) -> (Substrate a,b))
+>                                        . limit Phosphor 2
 >                                        . limit Nitrate 1
 >                                        . limit Sulfur 0
 >                                        <$> s
@@ -334,10 +331,10 @@ an environment.
 
 ---
 
-> produceCompounds :: Plant -> [(Nutrient, Amount)] -> [Compound]
+> produceCompounds :: Plant -> [(Compound, Amount)] -> [Compound]
 > produceCompounds (Plant genes _) = undefined
 >   -- this will take some constrained linear algebra-solving
-
+>
 > deterPredators :: [(Predator, Probability)] -> [Compound] -> Probability
 > deterPredators ps cs = sum $ do
 >       c <- cs -- for every compound