Safe Haskell	None
Language	Haskell2010

Biobase.Types.Energy

Description

Different types of energies and conversion between.

TODO enthalpy TODO entropy

Synopsis

newtype DG = DG {
- dG :: Double
}
newtype DDG = DDG {
- dDG :: Discretized (1 :% 100)
}

Documentation

newtype DG Source #

Gibbs free energy change.

For RNA structure, the change in energy from the unfolded structure to the given structure.

In units of kcal / mol.

TODO shall we phantom-type the actual units?

Constructors

DG
Fields dG :: Double

Instances

Eq DG Source #
Instance details Defined in Biobase.Types.Energy Methods (==) :: DG -> DG -> Bool # (/=) :: DG -> DG -> Bool #
Fractional DG Source #
Instance details Defined in Biobase.Types.Energy Methods (/) :: DG -> DG -> DG # recip :: DG -> DG # fromRational :: Rational -> DG #
Data DG Source #
Instance details Defined in Biobase.Types.Energy Methods gfoldl :: (forall d b. Data d => c (d -> b) -> d -> c b) -> (forall g. g -> c g) -> DG -> c DG # gunfold :: (forall b r. Data b => c (b -> r) -> c r) -> (forall r. r -> c r) -> Constr -> c DG # toConstr :: DG -> Constr # dataTypeOf :: DG -> DataType # dataCast1 :: Typeable t => (forall d. Data d => c (t d)) -> Maybe (c DG) # dataCast2 :: Typeable t => (forall d e. (Data d, Data e) => c (t d e)) -> Maybe (c DG) # gmapT :: (forall b. Data b => b -> b) -> DG -> DG # gmapQl :: (r -> r' -> r) -> r -> (forall d. Data d => d -> r') -> DG -> r # gmapQr :: (r' -> r -> r) -> r -> (forall d. Data d => d -> r') -> DG -> r # gmapQ :: (forall d. Data d => d -> u) -> DG -> [u] # gmapQi :: Int -> (forall d. Data d => d -> u) -> DG -> u # gmapM :: Monad m => (forall d. Data d => d -> m d) -> DG -> m DG # gmapMp :: MonadPlus m => (forall d. Data d => d -> m d) -> DG -> m DG # gmapMo :: MonadPlus m => (forall d. Data d => d -> m d) -> DG -> m DG #
Num DG Source #
Instance details Defined in Biobase.Types.Energy Methods (+) :: DG -> DG -> DG # (-) :: DG -> DG -> DG # (*) :: DG -> DG -> DG # negate :: DG -> DG # abs :: DG -> DG # signum :: DG -> DG # fromInteger :: Integer -> DG #
Ord DG Source #
Instance details Defined in Biobase.Types.Energy Methods compare :: DG -> DG -> Ordering # (<) :: DG -> DG -> Bool # (<=) :: DG -> DG -> Bool # (>) :: DG -> DG -> Bool # (>=) :: DG -> DG -> Bool # max :: DG -> DG -> DG # min :: DG -> DG -> DG #
Read DG Source #
Instance details Defined in Biobase.Types.Energy Methods readsPrec :: Int -> ReadS DG # readList :: ReadS [DG] # readPrec :: ReadPrec DG # readListPrec :: ReadPrec [DG] #
Show DG Source #
Instance details Defined in Biobase.Types.Energy Methods showsPrec :: Int -> DG -> ShowS # show :: DG -> String # showList :: [DG] -> ShowS #
Generic DG Source #
Instance details Defined in Biobase.Types.Energy Associated Types type Rep DG :: Type -> Type # Methods from :: DG -> Rep DG x # to :: Rep DG x -> DG #
NumericLimits DG Source #
Instance details Defined in Biobase.Types.Energy Methods minFinite :: DG # maxFinite :: DG #
NumericEpsilon DG Source #
Instance details Defined in Biobase.Types.Energy Methods epsilon :: DG #
NFData DG Source #
Instance details Defined in Biobase.Types.Energy Methods rnf :: DG -> () #
Hashable DG Source #
Instance details Defined in Biobase.Types.Energy Methods hashWithSalt :: Int -> DG -> Int # hash :: DG -> Int #
ToJSON DG Source #
Instance details Defined in Biobase.Types.Energy Methods toJSON :: DG -> Value # toEncoding :: DG -> Encoding # toJSONList :: [DG] -> Value # toEncodingList :: [DG] -> Encoding #
FromJSON DG Source #
Instance details Defined in Biobase.Types.Energy Methods parseJSON :: Value -> Parser DG # parseJSONList :: Value -> Parser [DG] #
Binary DG Source #
Instance details Defined in Biobase.Types.Energy Methods put :: DG -> Put # get :: Get DG # putList :: [DG] -> Put #
Serialize DG Source #
Instance details Defined in Biobase.Types.Energy Methods put :: Putter DG # get :: Get DG #
Default DG Source #
Instance details Defined in Biobase.Types.Energy Methods def :: DG #
Unbox DG Source #
Instance details Defined in Biobase.Types.Energy
Vector Vector DG Source #
Instance details Defined in Biobase.Types.Energy Methods basicUnsafeFreeze :: PrimMonad m => Mutable Vector (PrimState m) DG -> m (Vector DG) # basicUnsafeThaw :: PrimMonad m => Vector DG -> m (Mutable Vector (PrimState m) DG) # basicLength :: Vector DG -> Int # basicUnsafeSlice :: Int -> Int -> Vector DG -> Vector DG # basicUnsafeIndexM :: Monad m => Vector DG -> Int -> m DG # basicUnsafeCopy :: PrimMonad m => Mutable Vector (PrimState m) DG -> Vector DG -> m () # elemseq :: Vector DG -> DG -> b -> b #
MVector MVector DG Source #
Instance details Defined in Biobase.Types.Energy Methods basicLength :: MVector s DG -> Int # basicUnsafeSlice :: Int -> Int -> MVector s DG -> MVector s DG # basicOverlaps :: MVector s DG -> MVector s DG -> Bool # basicUnsafeNew :: PrimMonad m => Int -> m (MVector (PrimState m) DG) # basicInitialize :: PrimMonad m => MVector (PrimState m) DG -> m () # basicUnsafeReplicate :: PrimMonad m => Int -> DG -> m (MVector (PrimState m) DG) # basicUnsafeRead :: PrimMonad m => MVector (PrimState m) DG -> Int -> m DG # basicUnsafeWrite :: PrimMonad m => MVector (PrimState m) DG -> Int -> DG -> m () # basicClear :: PrimMonad m => MVector (PrimState m) DG -> m () # basicSet :: PrimMonad m => MVector (PrimState m) DG -> DG -> m () # basicUnsafeCopy :: PrimMonad m => MVector (PrimState m) DG -> MVector (PrimState m) DG -> m () # basicUnsafeMove :: PrimMonad m => MVector (PrimState m) DG -> MVector (PrimState m) DG -> m () # basicUnsafeGrow :: PrimMonad m => MVector (PrimState m) DG -> Int -> m (MVector (PrimState m) DG) #
type Rep DG Source #
Instance details Defined in Biobase.Types.Energy type Rep DG = D1 (MetaData "DG" "Biobase.Types.Energy" "BiobaseTypes-0.2.0.1-B9coIbijR6NEFcCxvqIOZp" True) (C1 (MetaCons "DG" PrefixI True) (S1 (MetaSel (Just "dG") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Double)))
newtype Vector DG Source #
Instance details Defined in Biobase.Types.Energy newtype Vector DG = V_DG (Vector Double)
newtype MVector s DG Source #
Instance details Defined in Biobase.Types.Energy newtype MVector s DG = MV_DG (MVector s Double)

newtype DDG Source #

Discretized DG.

Constructors

DDG
Fields dDG :: Discretized (1 :% 100)

Instances

Enum DDG Source #
Instance details Defined in Biobase.Types.Energy Methods succ :: DDG -> DDG # pred :: DDG -> DDG # toEnum :: Int -> DDG # fromEnum :: DDG -> Int # enumFrom :: DDG -> [DDG] # enumFromThen :: DDG -> DDG -> [DDG] # enumFromTo :: DDG -> DDG -> [DDG] # enumFromThenTo :: DDG -> DDG -> DDG -> [DDG] #
Eq DDG Source #
Instance details Defined in Biobase.Types.Energy Methods (==) :: DDG -> DDG -> Bool # (/=) :: DDG -> DDG -> Bool #
Num DDG Source #
Instance details Defined in Biobase.Types.Energy Methods (+) :: DDG -> DDG -> DDG # (-) :: DDG -> DDG -> DDG # (*) :: DDG -> DDG -> DDG # negate :: DDG -> DDG # abs :: DDG -> DDG # signum :: DDG -> DDG # fromInteger :: Integer -> DDG #
Ord DDG Source #
Instance details Defined in Biobase.Types.Energy Methods compare :: DDG -> DDG -> Ordering # (<) :: DDG -> DDG -> Bool # (<=) :: DDG -> DDG -> Bool # (>) :: DDG -> DDG -> Bool # (>=) :: DDG -> DDG -> Bool # max :: DDG -> DDG -> DDG # min :: DDG -> DDG -> DDG #
Read DDG Source #
Instance details Defined in Biobase.Types.Energy Methods readsPrec :: Int -> ReadS DDG # readList :: ReadS [DDG] # readPrec :: ReadPrec DDG # readListPrec :: ReadPrec [DDG] #
Real DDG Source #
Instance details Defined in Biobase.Types.Energy Methods toRational :: DDG -> Rational #
Show DDG Source #
Instance details Defined in Biobase.Types.Energy Methods showsPrec :: Int -> DDG -> ShowS # show :: DDG -> String # showList :: [DDG] -> ShowS #
Generic DDG Source #
Instance details Defined in Biobase.Types.Energy Associated Types type Rep DDG :: Type -> Type # Methods from :: DDG -> Rep DDG x # to :: Rep DDG x -> DDG #
Unbox DDG Source #
Instance details Defined in Biobase.Types.Energy
Vector Vector DDG Source #
Instance details Defined in Biobase.Types.Energy Methods basicUnsafeFreeze :: PrimMonad m => Mutable Vector (PrimState m) DDG -> m (Vector DDG) # basicUnsafeThaw :: PrimMonad m => Vector DDG -> m (Mutable Vector (PrimState m) DDG) # basicLength :: Vector DDG -> Int # basicUnsafeSlice :: Int -> Int -> Vector DDG -> Vector DDG # basicUnsafeIndexM :: Monad m => Vector DDG -> Int -> m DDG # basicUnsafeCopy :: PrimMonad m => Mutable Vector (PrimState m) DDG -> Vector DDG -> m () # elemseq :: Vector DDG -> DDG -> b -> b #
MVector MVector DDG Source #
Instance details Defined in Biobase.Types.Energy Methods basicLength :: MVector s DDG -> Int # basicUnsafeSlice :: Int -> Int -> MVector s DDG -> MVector s DDG # basicOverlaps :: MVector s DDG -> MVector s DDG -> Bool # basicUnsafeNew :: PrimMonad m => Int -> m (MVector (PrimState m) DDG) # basicInitialize :: PrimMonad m => MVector (PrimState m) DDG -> m () # basicUnsafeReplicate :: PrimMonad m => Int -> DDG -> m (MVector (PrimState m) DDG) # basicUnsafeRead :: PrimMonad m => MVector (PrimState m) DDG -> Int -> m DDG # basicUnsafeWrite :: PrimMonad m => MVector (PrimState m) DDG -> Int -> DDG -> m () # basicClear :: PrimMonad m => MVector (PrimState m) DDG -> m () # basicSet :: PrimMonad m => MVector (PrimState m) DDG -> DDG -> m () # basicUnsafeCopy :: PrimMonad m => MVector (PrimState m) DDG -> MVector (PrimState m) DDG -> m () # basicUnsafeMove :: PrimMonad m => MVector (PrimState m) DDG -> MVector (PrimState m) DDG -> m () # basicUnsafeGrow :: PrimMonad m => MVector (PrimState m) DDG -> Int -> m (MVector (PrimState m) DDG) #
type Rep DDG Source #
Instance details Defined in Biobase.Types.Energy type Rep DDG = D1 (MetaData "DDG" "Biobase.Types.Energy" "BiobaseTypes-0.2.0.1-B9coIbijR6NEFcCxvqIOZp" True) (C1 (MetaCons "DDG" PrefixI True) (S1 (MetaSel (Just "dDG") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 (Discretized (1 :% 100)))))
newtype Vector DDG Source #
Instance details Defined in Biobase.Types.Energy newtype Vector DDG = V_DDG (Vector Int)
newtype MVector s DDG Source #
Instance details Defined in Biobase.Types.Energy newtype MVector s DDG = MV_DDG (MVector s Int)