-- Hoogle documentation, generated by Haddock
-- See Hoogle, http://www.haskell.org/hoogle/


-- | Protein Databank file format library
--   
--   Protein Data Bank file format is a most popular format for holding
--   biological macromolecular data.
--   
--   This is a very fast sequential parser:
--   
--   <ul>
--   <li>below 7s for the largest entry in PDB - 1HTQ which is over 70MB -
--   as compared with</li>
--   <li>11s of RASMOL 2.7.5,</li>
--   <li>or 2m15s of BioPython with Python 2.6 interpreter.</li>
--   </ul>
--   
--   In its parallel incarnation it is most probably the fastest parser for
--   PDB format.
--   
--   It is aimed to not only deliver event-based interface, but also a
--   high-level data structure for manipulating data in spirit of
--   BioPython's PDB parser.
--   
--   <a>hPDB - Haskell library for processing atomic biomolecular
--   structures in Protein Data Bank format - Michal Jan Gajda. BMC
--   Research Notes 2013, 6:483.</a>
@package hPDB
@version 1.2.0


-- | Opening and reading a either normal or gzipped file in an efficient
--   way - either using strict <tt>ByteString</tt> or mmap
module Bio.PDB.IO.OpenAnyFile

-- | Read file contents as strict <tt>ByteString</tt>. Uses mmap if
--   possible. May decompress file contents, if needed.
readFile :: FilePath -> IO ByteString

-- | Write file contents as strict <tt>ByteString</tt>.
writeFile :: FilePath -> (Handle -> IO a) -> IO ()


-- | This module wraps 3D vector operations, and adds missing ones.
module Bio.PDB.Structure.Vector
data Vector3 :: *
Vector3 :: !Scalar -> !Scalar -> !Scalar -> Vector3
v3x :: Vector3 -> !Scalar
v3y :: Vector3 -> !Scalar
v3z :: Vector3 -> !Scalar

-- | Unpacks an abstract 3D vector into a triple of <a>Double</a>s.
unpackVector3 :: Vector3 -> (Double, Double, Double)

-- | Normalises to a unit vector in the same direction as input.
vnormalise :: Vector3 -> Vector3

-- | Computes a dot product of two 3D vectors.
vdot :: Vector3 -> Vector3 -> Double

-- | Scalar product. (asterisk - <a>*</a> - indicates side on which one can
--   put a scalar.)
(*|) :: Double -> Vector3 -> Vector3

-- | Scalar product. (asterisk - <a>*</a> - indicates side on which one can
--   put a scalar.)
(|*) :: Vector3 -> Double -> Vector3

-- | Maps an operation on a pair of <a>Double</a>s onto a pair of 3D
--   vectors coordinatewise.
vzip :: (Double -> Double -> Double) -> Vector3 -> Vector3 -> Vector3

-- | Maps an operation that modifies a <a>Double</a> onto a 3D vector.
vmap :: (Double -> Double) -> Vector3 -> Vector3

-- | 2-norm of a vector (also called a magnitude or length.)
vnorm :: Vector3 -> Double

-- | Finds a vector component of the first vector that is a projection onto
--   direction of second vector.
vproj :: Vector3 -> Vector3 -> Vector3

-- | Returns a component of the vector v that is perpendicular to w.
vperpend :: Vector3 -> Vector3 -> Vector3

-- | Finds a component of the vector v that is perpendicular to all vectors
--   in a list.
vperpends :: Vector3 -> [Vector3] -> Vector3

-- | Compute dihedral between three bond vectors using spherical angle
--   formula.
vdihedral :: Vector3 -> Vector3 -> Vector3 -> Double
instance Arbitrary Vector3


-- | Collections used within the Structure, currently aliases for the
--   <tt>Vector</tt> and <tt>MVector</tt> types.
module Bio.PDB.Structure.List

-- | Type alias for a immutable sequence of elements.
type List a = Vector a

-- | Type alias for a mutable sequence of elements.
data TempList m a

-- | Allocate initial space for a new mutable vector.
initialNew :: Int -> ST m (TempList m a)

-- | Create a new mutable vector.
new :: MonadTrans t => Int -> t (ST m) (TempList m a)

-- | Appends an element to a mutable vector.
add :: MonadTrans t => TempList s a -> a -> t (ST s) ()

-- | Finalizes a mutable vector, and returns immutable vector. [Does it
--   shrink allocated space?]
finalize :: MonadTrans t => TempList s a -> t (ST s) (Vector a)

-- | Length of mutable vector.
tempLength :: MonadTrans t1 => TempList s t -> t1 (ST s) Int

-- | Empty vector.
empty :: Vector a

-- | <a>last</a> on immutable vectors.
last :: Vector a -> a

-- | Vector with a single element
singleton :: a -> Vector a

-- | <a>map</a> on immutable vectors.
map :: (a -> b) -> Vector a -> Vector b

-- | <a>mapM</a> on immutable vectors.
mapM :: Monad m => (a -> m b) -> Vector a -> m (Vector b)

-- | <a>foldl</a> on immutable vectors.
foldl :: (a -> b -> a) -> a -> Vector b -> a

-- | <a>foldl'</a> on immutable vectors.
foldl' :: (a -> b -> a) -> a -> Vector b -> a

-- | <a>foldr</a> on immutable vectors.
foldr :: (a -> b -> b) -> b -> Vector a -> b

-- | <a>foldM</a> on immutable vectors.
foldM :: Monad m => (a -> b -> m a) -> a -> Vector b -> m a

-- | <a>filter</a> on immutable vectors.
filter :: (a -> Bool) -> Vector a -> Vector a

-- | <a>length</a> on immutable vectors.
length :: Vector a -> Int

-- | Default initial size of a mutable vector for structure contents.
defaultSize :: Num a => a

-- | Default initial size of a mutable vector for residue contents.
residueVectorSize :: Num a => a

-- | Default initial size of a mutable vector for chain contents.
chainVectorSize :: Num a => a

-- | Conversion of an immutable vector to list.
toList :: Vector a -> [a]

-- | <a>map</a> on immutable vectors.
vimap :: (Int -> a -> b) -> Vector a -> Vector b

-- | Indexing of an immutable vector.
(!) :: Vector a -> Int -> a

-- | Concatenation of two immutable
(++) :: Vector a -> Vector a -> Vector a

-- | Concatenation of a list of immutable vectors.
concat :: [Vector a] -> Vector a

-- | Remove last element of immutable vectors.
init :: Vector a -> Vector a

-- | Remove first element of immutable vector.
tail :: Vector a -> Vector a

-- | First element of immutable vector.
head :: Vector a -> a
instance NFData (TempList m a)


-- | Module with enumeration of beta-strand senses.
module Bio.PDB.EventParser.StrandSense

-- | Enumeration of beta-strand sense.
data StrandSenseT
Parallel :: StrandSenseT
Antiparallel :: StrandSenseT
instance Eq StrandSenseT
instance Ord StrandSenseT
instance Show StrandSenseT
instance Read StrandSenseT


-- | Module contains enumeration of helix types, and auxiliary functions
--   for converting these into PDB CLASS codes.
module Bio.PDB.EventParser.HelixTypes

-- | Enumeration of helix types
--   
--   PDB Class number in columns 39-40 for each type of helix in HELIX
--   record:
--   
--   <ol>
--   <li>Right-handed alpha (default, most common)</li>
--   <li>Right-handed omega</li>
--   <li>Right-handed pi</li>
--   <li>Right-handed gamma</li>
--   <li>Right-handed 3 - 10</li>
--   <li>Left-handed alpha</li>
--   <li>Left-handed omega</li>
--   <li>Left-handed gamma</li>
--   <li>2 - 7 ribbon/helix</li>
--   <li>Polyproline</li>
--   </ol>
data HelixT

-- | helix2code converts a <a>HelixT</a> enumeration into an PDB CLASS
--   code.
helix2code :: Num a => HelixT -> a

-- | helix2code converts an PDB CLASS code into a <a>HelixT</a>
--   enumeration.
code2helix :: (Eq a, Num a) => a -> HelixT
instance Eq HelixT
instance Ord HelixT
instance Show HelixT
instance Read HelixT


-- | This module contains an enumeration of experimental methods.
module Bio.PDB.EventParser.ExperimentalMethods

-- | Enumeration of experimental methods occuring in the PDB archive.
data ExpMethod
XRayDiffraction :: ExpMethod
FiberDiffraction :: ExpMethod
NeutronDiffraction :: ExpMethod
ElectronCrystallography :: ExpMethod
ElectronMicroscopy :: ExpMethod
SolidStateNMR :: ExpMethod
SolutionNMR :: ExpMethod
SolutionScattering :: ExpMethod
OtherExpMethod :: !ByteString -> ExpMethod

-- | Generates an <a>ExpMethod</a> from words in PDB
mkExpMethod :: [ByteString] -> ExpMethod

-- | Converts an <a>ExpMethod</a> back into text
showExpMethod :: ExpMethod -> ByteString
instance Show ExpMethod
instance Read ExpMethod
instance Eq ExpMethod
instance Ord ExpMethod


-- | This module contains datatype declaration for PDB parsing events
--   generated by <tt>PDBEventParser</tt> module.
module Bio.PDB.EventParser.PDBEvents

-- | We use only strict <tt>ByteString</tt> as strings in PDB parser.
type String = ByteString
data Vector3 :: *
Vector3 :: !Scalar -> !Scalar -> !Scalar -> Vector3
v3x :: Vector3 -> !Scalar
v3y :: Vector3 -> !Scalar
v3z :: Vector3 -> !Scalar

-- | Atom id: atom name, residue name, chain, residue id, residue insertion
--   code
newtype ATID
ATID :: (String, String, Char, Int, Char) -> ATID

-- | Residue id: residue name, chain, residue id, residue insertion code
newtype RESID
RESID :: (String, Char, Int, Char) -> RESID

-- | Datatype for event-based PDB parser
data PDBEvent
ATOM :: !Int -> !String -> !String -> !Char -> !Int -> !Char -> !Char -> !Vector3 -> !Double -> !Double -> !String -> !String -> !String -> !Bool -> PDBEvent
no :: PDBEvent -> !Int
atomtype :: PDBEvent -> !String
restype :: PDBEvent -> !String
chain :: PDBEvent -> !Char
resid :: PDBEvent -> !Int
resins :: PDBEvent -> !Char
altloc :: PDBEvent -> !Char
coords :: PDBEvent -> !Vector3
occupancy :: PDBEvent -> !Double
bfactor :: PDBEvent -> !Double
segid :: PDBEvent -> !String
elt :: PDBEvent -> !String
charge :: PDBEvent -> !String
hetatm :: PDBEvent -> !Bool
SIGATM :: !Int -> !String -> !String -> !Char -> !Int -> !Char -> !Char -> !Vector3 -> !Double -> !Double -> !String -> !String -> !String -> PDBEvent
no :: PDBEvent -> !Int
atomtype :: PDBEvent -> !String
restype :: PDBEvent -> !String
chain :: PDBEvent -> !Char
resid :: PDBEvent -> !Int
resins :: PDBEvent -> !Char
altloc :: PDBEvent -> !Char
coords :: PDBEvent -> !Vector3
occupancy :: PDBEvent -> !Double
bfactor :: PDBEvent -> !Double
segid :: PDBEvent -> !String
elt :: PDBEvent -> !String
charge :: PDBEvent -> !String
ANISOU :: !Int -> !String -> !String -> !Char -> !Int -> !Char -> !Char -> !Int -> !Int -> !Int -> !Int -> !Int -> !Int -> !String -> !String -> !String -> PDBEvent
no :: PDBEvent -> !Int
atomtype :: PDBEvent -> !String
restype :: PDBEvent -> !String
chain :: PDBEvent -> !Char
resid :: PDBEvent -> !Int
resins :: PDBEvent -> !Char
altloc :: PDBEvent -> !Char
u_1_1 :: PDBEvent -> !Int
u_2_2 :: PDBEvent -> !Int
u_3_3 :: PDBEvent -> !Int
u_1_2 :: PDBEvent -> !Int
u_1_3 :: PDBEvent -> !Int
u_2_3 :: PDBEvent -> !Int
segid :: PDBEvent -> !String
elt :: PDBEvent -> !String
charge :: PDBEvent -> !String
SIGUIJ :: !Int -> !String -> !String -> !Char -> !Int -> !Char -> !Char -> !Int -> !Int -> !Int -> !Int -> !Int -> !Int -> !String -> !String -> !String -> PDBEvent
no :: PDBEvent -> !Int
atomtype :: PDBEvent -> !String
restype :: PDBEvent -> !String
chain :: PDBEvent -> !Char
resid :: PDBEvent -> !Int
resins :: PDBEvent -> !Char
altloc :: PDBEvent -> !Char
u_1_1 :: PDBEvent -> !Int
u_2_2 :: PDBEvent -> !Int
u_3_3 :: PDBEvent -> !Int
u_1_2 :: PDBEvent -> !Int
u_1_3 :: PDBEvent -> !Int
u_2_3 :: PDBEvent -> !Int
segid :: PDBEvent -> !String
elt :: PDBEvent -> !String
charge :: PDBEvent -> !String
SEQRES :: !Int -> !Char -> !Int -> ![String] -> PDBEvent
serial :: PDBEvent -> !Int
chain :: PDBEvent -> !Char
num :: PDBEvent -> !Int
resList :: PDBEvent -> ![String]
HEADER :: !String -> !String -> !String -> PDBEvent
classification :: PDBEvent -> !String
depDate :: PDBEvent -> !String
idCode :: PDBEvent -> !String
TITLE :: !Int -> !String -> PDBEvent
continuation :: PDBEvent -> !Int
title :: PDBEvent -> !String
KEYWDS :: !Int -> ![String] -> PDBEvent
continuation :: PDBEvent -> !Int
aList :: PDBEvent -> ![String]
AUTHOR :: !Int -> ![String] -> PDBEvent
continuation :: PDBEvent -> !Int
aList :: PDBEvent -> ![String]
REMARK :: !Int -> ![String] -> PDBEvent
num :: PDBEvent -> !Int
text :: PDBEvent -> ![String]
EXPDTA :: !Int -> ![ExpMethod] -> PDBEvent
continuation :: PDBEvent -> !Int
expMethods :: PDBEvent -> ![ExpMethod]
MDLTYP :: !Int -> ![String] -> PDBEvent
continuation :: PDBEvent -> !Int
aList :: PDBEvent -> ![String]
NUMMDL :: !Int -> PDBEvent
num :: PDBEvent -> !Int
MODEL :: !Int -> PDBEvent
num :: PDBEvent -> !Int
CONECT :: ![Int] -> PDBEvent
atoms :: PDBEvent -> ![Int]
CAVEAT :: !Int -> !String -> !String -> PDBEvent
cont :: PDBEvent -> !Int
pdbid :: PDBEvent -> !String
comment :: PDBEvent -> !String
DBREF :: !String -> !Char -> !Int -> !Char -> !Int -> !Char -> !String -> !String -> !String -> !Int -> !Char -> !Int -> !Char -> PDBEvent
idCode :: PDBEvent -> !String
chain :: PDBEvent -> !Char
iniSeqNumPDB :: PDBEvent -> !Int
iniInsCodePDB :: PDBEvent -> !Char
endSeqNumPDB :: PDBEvent -> !Int
endInsCodePDB :: PDBEvent -> !Char
seqDbName :: PDBEvent -> !String
seqDbAccCode :: PDBEvent -> !String
seqDbIdCode :: PDBEvent -> !String
iniSeqNumInDb :: PDBEvent -> !Int
iniInsCodeInPDBRef :: PDBEvent -> !Char
endSeqNumInDb :: PDBEvent -> !Int
endInsCodeInPDBRef :: PDBEvent -> !Char
REVDAT :: !Int -> !Int -> !String -> !String -> !Int -> ![String] -> PDBEvent
modNum :: PDBEvent -> !Int
cont :: PDBEvent -> !Int
modDat :: PDBEvent -> !String
modId :: PDBEvent -> !String
modTyp :: PDBEvent -> !Int
details :: PDBEvent -> ![String]
HETNAM :: !Int -> !String -> !String -> !Bool -> PDBEvent
cont :: PDBEvent -> !Int
hetId :: PDBEvent -> !String
name :: PDBEvent -> !String
notSynonym :: PDBEvent -> !Bool
HET :: !String -> !Char -> !Int -> !Char -> !Int -> !String -> PDBEvent
hetId :: PDBEvent -> !String
chain :: PDBEvent -> !Char
seqNum :: PDBEvent -> !Int
insCode :: PDBEvent -> !Char
atmNum :: PDBEvent -> !Int
description :: PDBEvent -> !String
FORMUL :: !Int -> !String -> !Int -> !Bool -> ![String] -> PDBEvent
compNum :: PDBEvent -> !Int
hetId :: PDBEvent -> !String
cont :: PDBEvent -> !Int
isWater :: PDBEvent -> !Bool
formula :: PDBEvent -> ![String]
CISPEP :: !Int -> !RESID -> !RESID -> !Int -> Maybe Double -> PDBEvent
serial :: PDBEvent -> !Int
res1 :: PDBEvent -> !RESID
res2 :: PDBEvent -> !RESID
modNum :: PDBEvent -> !Int
angle :: PDBEvent -> Maybe Double
HELIX :: Int -> RESID -> RESID -> HelixT -> String -> Int -> PDBEvent
serial :: PDBEvent -> Int
iniRes :: PDBEvent -> RESID
endRes :: PDBEvent -> RESID
helixClass :: PDBEvent -> HelixT
comment :: PDBEvent -> String
len :: PDBEvent -> Int
SHEET :: Int -> String -> Int -> Maybe StrandSenseT -> RESID -> RESID -> Maybe ATID -> Maybe ATID -> PDBEvent
strandId :: PDBEvent -> Int
sheetId :: PDBEvent -> String
numStrands :: PDBEvent -> Int
sense :: PDBEvent -> Maybe StrandSenseT
iniRes :: PDBEvent -> RESID
endRes :: PDBEvent -> RESID
curAt :: PDBEvent -> Maybe ATID
prevAt :: PDBEvent -> Maybe ATID
ORIGXn :: Int -> [Vector3] -> [Double] -> PDBEvent
n :: PDBEvent -> Int
o :: PDBEvent -> [Vector3]
t :: PDBEvent -> [Double]
SCALEn :: Int -> [Vector3] -> [Double] -> PDBEvent
n :: PDBEvent -> Int
o :: PDBEvent -> [Vector3]
t :: PDBEvent -> [Double]
MTRIXn :: !Int -> !Bool -> !Int -> ![Vector3] -> ![Double] -> PDBEvent
serial :: PDBEvent -> !Int
relMol :: PDBEvent -> !Bool
n :: PDBEvent -> !Int
o :: PDBEvent -> ![Vector3]
t :: PDBEvent -> ![Double]
CRYST1 :: !Double -> !Double -> !Double -> !Double -> !Double -> !Double -> !String -> !Int -> PDBEvent
a :: PDBEvent -> !Double
b :: PDBEvent -> !Double
c :: PDBEvent -> !Double
alpha :: PDBEvent -> !Double
beta :: PDBEvent -> !Double
gamma :: PDBEvent -> !Double
spcGrp :: PDBEvent -> !String
zValue :: PDBEvent -> !Int
COMPND :: !Int -> ![(String, String)] -> PDBEvent
cont :: PDBEvent -> !Int
tokens :: PDBEvent -> ![(String, String)]
SOURCE :: !Int -> ![(String, String)] -> PDBEvent
cont :: PDBEvent -> !Int
tokens :: PDBEvent -> ![(String, String)]
TER :: !Int -> !String -> !Char -> !Int -> !Char -> PDBEvent
num :: PDBEvent -> !Int
resname :: PDBEvent -> !String
chain :: PDBEvent -> !Char
resid :: PDBEvent -> !Int
insCode :: PDBEvent -> !Char
MASTER :: !Int -> !Int -> !Int -> !Int -> !Int -> !Int -> !Int -> !Int -> !Int -> !Int -> !Int -> PDBEvent
numRemark :: PDBEvent -> !Int
numHet :: PDBEvent -> !Int
numHelix :: PDBEvent -> !Int
numSheet :: PDBEvent -> !Int
numTurn :: PDBEvent -> !Int
numSite :: PDBEvent -> !Int
numXform :: PDBEvent -> !Int
numAts :: PDBEvent -> !Int
numMaster :: PDBEvent -> !Int
numConect :: PDBEvent -> !Int
numSeqres :: PDBEvent -> !Int
END :: PDBEvent
ENDMDL :: PDBEvent
SITE :: !Int -> !String -> !Int -> ![RESID] -> PDBEvent
serial :: PDBEvent -> !Int
siteid :: PDBEvent -> !String
numres :: PDBEvent -> !Int
residues :: PDBEvent -> ![RESID]
OBSLTE :: !Int -> !String -> !String -> ![String] -> PDBEvent
cont :: PDBEvent -> !Int
date :: PDBEvent -> !String
this :: PDBEvent -> !String
entries :: PDBEvent -> ![String]
SPRSDE :: !Int -> !String -> !String -> ![String] -> PDBEvent
cont :: PDBEvent -> !Int
date :: PDBEvent -> !String
this :: PDBEvent -> !String
entries :: PDBEvent -> ![String]
SPLIT :: !Int -> ![String] -> PDBEvent
cont :: PDBEvent -> !Int
codes :: PDBEvent -> ![String]
SSBOND :: !Int -> RESID -> RESID -> !String -> !String -> !Double -> PDBEvent
serial :: PDBEvent -> !Int
res1 :: PDBEvent -> RESID
res2 :: PDBEvent -> RESID
symOp1 :: PDBEvent -> !String
symOp2 :: PDBEvent -> !String
bondLen :: PDBEvent -> !Double
LINK :: !ATID -> !Char -> !ATID -> !Char -> !String -> !String -> Maybe Double -> PDBEvent
at1 :: PDBEvent -> !ATID
altloc1 :: PDBEvent -> !Char
at2 :: PDBEvent -> !ATID
altloc2 :: PDBEvent -> !Char
symop1 :: PDBEvent -> !String
symop2 :: PDBEvent -> !String
linkdist :: PDBEvent -> Maybe Double
SLTBRG :: !ATID -> !Char -> !ATID -> !Char -> !String -> !String -> PDBEvent
at1 :: PDBEvent -> !ATID
altloc1 :: PDBEvent -> !Char
at2 :: PDBEvent -> !ATID
altloc2 :: PDBEvent -> !Char
symOp1 :: PDBEvent -> !String
symOp2 :: PDBEvent -> !String
HYDBND :: !ATID -> !Char -> !ATID -> !Char -> !ATID -> !Char -> !String -> !String -> PDBEvent
at1 :: PDBEvent -> !ATID
altloc1 :: PDBEvent -> !Char
atH :: PDBEvent -> !ATID
altlocH :: PDBEvent -> !Char
at2 :: PDBEvent -> !ATID
altloc2 :: PDBEvent -> !Char
symOp1 :: PDBEvent -> !String
symOp2 :: PDBEvent -> !String
TVECT :: !Int -> Vector3 -> PDBEvent
serial :: PDBEvent -> !Int
vec :: PDBEvent -> Vector3
JRNL :: !Int -> ![(String, String)] -> !Bool -> PDBEvent
cont :: PDBEvent -> !Int
content :: PDBEvent -> ![(String, String)]
isFirst :: PDBEvent -> !Bool
MODRES :: !String -> !RESID -> !String -> !String -> PDBEvent
pdbCode :: PDBEvent -> !String
residue :: PDBEvent -> !RESID
stdRes :: PDBEvent -> !String
comment :: PDBEvent -> !String
SEQADV :: !String -> Maybe RESID -> !String -> !String -> !String -> Maybe Int -> !String -> PDBEvent
pdbId :: PDBEvent -> !String
advResidue :: PDBEvent -> Maybe RESID
database :: PDBEvent -> !String
accessionCode :: PDBEvent -> !String
dbResname :: PDBEvent -> !String
dbSeqNum :: PDBEvent -> Maybe Int
comment :: PDBEvent -> !String
PDBParseError :: !Int -> !Int -> !String -> PDBEvent
PDBIgnoredLine :: ByteString -> PDBEvent

-- | Enumeration of beta-strand sense.
data StrandSenseT
Parallel :: StrandSenseT
Antiparallel :: StrandSenseT

-- | Enumeration of helix types
--   
--   PDB Class number in columns 39-40 for each type of helix in HELIX
--   record:
--   
--   <ol>
--   <li>Right-handed alpha (default, most common)</li>
--   <li>Right-handed omega</li>
--   <li>Right-handed pi</li>
--   <li>Right-handed gamma</li>
--   <li>Right-handed 3 - 10</li>
--   <li>Left-handed alpha</li>
--   <li>Left-handed omega</li>
--   <li>Left-handed gamma</li>
--   <li>2 - 7 ribbon/helix</li>
--   <li>Polyproline</li>
--   </ol>
data HelixT

-- | Enumeration of experimental methods occuring in the PDB archive.
data ExpMethod
XRayDiffraction :: ExpMethod
FiberDiffraction :: ExpMethod
NeutronDiffraction :: ExpMethod
ElectronCrystallography :: ExpMethod
ElectronMicroscopy :: ExpMethod
SolidStateNMR :: ExpMethod
SolutionNMR :: ExpMethod
SolutionScattering :: ExpMethod
OtherExpMethod :: !ByteString -> ExpMethod
instance Show ATID
instance Ord ATID
instance Eq ATID
instance Show RESID
instance Ord RESID
instance Eq RESID
instance Show PDBEvent
instance Eq PDBEvent


-- | Low-level event-based parser interface.
module Bio.PDB.EventParser.PDBEventParser

-- | Parses a strict ByteString <tt>contents</tt> named <tt>fname</tt> and
--   performs <tt>action</tt> on events given by parsing chunks, returning
--   accumulated results. Accumulator is primed by <tt>acc</tt>.
parsePDBRecords :: Monad m => t -> ByteString -> (b -> PDBEvent -> m b) -> b -> m b

module Bio.PDB.Structure

-- | We use only strict <tt>ByteString</tt> as strings in PDB parser.
type String = ByteString

-- | Computes a dot product of two 3D vectors.
vdot :: Vector3 -> Vector3 -> Double

-- | 2-norm of a vector (also called a magnitude or length.)
vnorm :: Vector3 -> Double

-- | Finds a vector component of the first vector that is a projection onto
--   direction of second vector.
vproj :: Vector3 -> Vector3 -> Vector3

-- | Returns a component of the vector v that is perpendicular to w.
vperpend :: Vector3 -> Vector3 -> Vector3

-- | Finds a component of the vector v that is perpendicular to all vectors
--   in a list.
vperpends :: Vector3 -> [Vector3] -> Vector3

-- | Compute dihedral between three bond vectors using spherical angle
--   formula.
vdihedral :: Vector3 -> Vector3 -> Vector3 -> Double

-- | Scalar product. (asterisk - <a>*</a> - indicates side on which one can
--   put a scalar.)
(*|) :: Double -> Vector3 -> Vector3

-- | Scalar product. (asterisk - <a>*</a> - indicates side on which one can
--   put a scalar.)
(|*) :: Vector3 -> Double -> Vector3

-- | Structure holds all data parsed from a single PDB entry
data Structure
Structure :: List Model -> Structure
models :: Structure -> List Model

-- | PDB entry may contain multiple models, with slight differences in
--   coordinates etc.
data Model
Model :: !Int -> List Chain -> Model
modelId :: Model -> !Int
chains :: Model -> List Chain

-- | Single linear polymer chain of protein, or nucleic acids
data Chain
Chain :: !Char -> List Residue -> Chain
chainId :: Chain -> !Char
residues :: Chain -> List Residue

-- | Residue groups all atoms assigned to the same aminoacid or nucleic
--   acid base within a polymer chain.
data Residue
Residue :: !String -> !Int -> List Atom -> !Char -> Residue
resName :: Residue -> !String
resSeq :: Residue -> !Int
atoms :: Residue -> List Atom
insCode :: Residue -> !Char

-- | Single atom position | NOTE: disordered atoms are now reported as
--   multiplicates
data Atom
Atom :: !String -> !Int -> !Vector3 -> !Double -> !Double -> !String -> !String -> !String -> !Bool -> Atom
atName :: Atom -> !String
atSerial :: Atom -> !Int
coord :: Atom -> !Vector3
bFactor :: Atom -> !Double
occupancy :: Atom -> !Double
element :: Atom -> !String
segid :: Atom -> !String
charge :: Atom -> !String
hetatm :: Atom -> !Bool
instance Eq Atom
instance Show Atom
instance Eq Residue
instance Show Residue
instance Eq Chain
instance Show Chain
instance Eq Model
instance Show Model
instance Eq Structure
instance Show Structure
instance NFData Atom
instance NFData Residue
instance NFData Chain
instance NFData Model
instance NFData Structure


-- | Iterable instances and convenience functions.
module Bio.PDB.Iterable

-- | Class for iterating all nested components <tt>b</tt> of type
--   <tt>a</tt>.
class Iterable a b
itmapM :: (Iterable a b, Monad m) => (b -> m b) -> a -> m a
itmap :: Iterable a b => (b -> b) -> a -> a
itfoldM :: (Iterable a b, Monad m) => (c -> b -> m c) -> c -> a -> m c
itfoldr :: Iterable a b => (b -> c -> c) -> c -> a -> c
itfoldl :: Iterable a b => (c -> b -> c) -> c -> a -> c
itfoldl' :: Iterable a b => (c -> b -> c) -> c -> a -> c
itlength :: Iterable a b => Proxy * b -> a -> Int

-- | Takes a first model.
firstModel :: Iterable a Model => a -> Maybe Model

-- | Number of all atoms within the structure.
numAtoms :: Iterable a Atom => a -> Int

-- | Number of all residues within the structure.
numResidues :: Iterable a Residue => a -> Int

-- | Number of all chains within the structure.
numChains :: Iterable a Chain => a -> Int

-- | Number of all models within the structure.
numModels :: Iterable a Model => a -> Int


-- | Conversion of PDB residue codes to FASTA single-letter sequence codes.
module Bio.PDB.Fasta

-- | Dictionary mapping three-letter PDB residue code to a single-letter
--   FASTA code.
resname2fastacode :: String -> Char

-- | Dictionary mapping single-letter FASTA standard aminoacid code to a
--   PDB residue name
fastacode2resname :: Char -> String

-- | Three-letter PDB code for an unknown type of residue.
defaultResname :: String

-- | One-letter aminoacid code for an unknown type of residue.
defaultFastaCode :: Char

-- | Converts an <a>Iterable</a> yielding <a>Residue</a>s into a list of
--   aminoacid one-character codes.
fastaSequence :: Iterable a Residue => a -> [Char]

-- | Converts an <a>Iterable</a> yielding <a>Residue</a>s into a list of
--   aminoacid one-character codes.
fastaGappedSequence :: Iterable a Residue => a -> [Char]

-- | Returns <a>String</a> with ungapped sequence of a given PDB
--   <a>Chain</a>.
fastaRecord :: [Char] -> Chain -> [Char]

-- | Returns <a>String</a> with gapped sequence of a given PDB
--   <a>Chain</a>. Gaps are placed to assure consistent numbering of
--   residues and indices in the output <a>String</a>.
fastaGappedRecord :: [Char] -> Chain -> [Char]


-- | Basic properties of chemical <a>Element</a>s as suggested by Cambridge
--   Structural Database.
module Bio.PDB.Structure.Elements

-- | Type alias for <a>Element</a> names.
type Element = ByteString

-- | Given a PDB <a>Atom</a> extract or guess its <a>Element</a> name.
assignElement :: Atom -> Element

-- | Guessing an <a>Element</a> name from PDB <a>Atom</a> name. Returns
--   empty string, if <a>Element</a> can't be guessed.
guessElement :: ByteString -> Element

-- | Atomic number of a given element
atomicNumber :: Element -> Int

-- | Atomic mass of a given element in g/mol
atomicMass :: Element -> Double

-- | Covalent radius of an element with a given name.
covalentRadius :: (Eq a1, Fractional a, Show a1, IsString a1) => a1 -> a
maxCovalentRadius :: Double

-- | Van der Waals radius of the given element
vanDerWaalsRadius :: Element -> Double
maxVanDerWaalsRadius :: Double


-- | Searching for neighbouring atoms in a 3D space using <tt>Octree</tt>.
module Bio.PDB.Structure.Neighbours

-- | Make an Octree of <a>Atom</a>s
makeOctree :: Iterable a Atom => a -> AtomOctree

-- | Find all <a>Atom</a>s within a given radius from a point.
findInRadius :: AtomOctree -> Double -> Vector3 -> [(Vector3, Atom)]

-- | Find an <a>Atom</a>s closest to a point.
findNearest :: AtomOctree -> Vector3 -> Maybe (Vector3, Atom)

-- | Octree of <a>Atom</a>s.
type AtomOctree = Octree Atom


-- | Front-end module presenting minimal interface for serial and parallel
--   parsing.
module Bio.PDB.StructureBuilder

-- | Default parser - uses parallel capabilities, if available.
parse :: FilePath -> String -> (Structure, List PDBEvent)

-- | Given filename, and contents, parses a whole PDB file, returning a
--   monadic action | with a tuple of (Structure, [PDBEvent]), where the
--   list of events contains all | parsing or construction errors.
parseSerial :: FilePath -> String -> (Structure, List PDBEvent)

-- | Parse file in parallel with as many threads as we have capabilities.
parseParallel :: [Char] -> ByteString -> (Structure, List PDBEvent)

-- | Parse input file with N parallel threads.
parseWithNParallel :: Integral a => a -> [Char] -> ByteString -> (Structure, List PDBEvent)


-- | Low-level output routines: printing any <a>PDBEvent</a>.
module Bio.PDB.EventParser.PDBEventPrinter

-- | Prints a PDBEvent to a filehandle.
print :: Handle -> PDBEvent -> IO ()

-- | Reports whether a given PDB record is already printable [temporary
--   method, they all should be.] Including errors.
isPrintable :: PDBEvent -> Bool


-- | High-level output routines for <a>Structure</a>.
module Bio.PDB.StructurePrinter

-- | Writes a structure or its part in a PDB format to a filehandle.
write :: PDBWritable a => Handle -> a -> IO ()

-- | Class generating events for PDB structure fragments.
class PDBWritable a where pdbEvents = flip pdbEventS []
instance PDBWritable Atom
instance PDBWritable Residue
instance PDBWritable Chain
instance PDBWritable Model
instance PDBWritable Structure


-- | Simple input/output wrappers taking filenames, and handling
--   compression.
module Bio.PDB.IO

-- | Parse a .pdb file and return <a>Structure</a>.
parse :: FilePath -> IO (Maybe Structure)

-- | Write structure to a .pdb file.
write :: PDBWritable a => a -> FilePath -> IO ()

-- | Class generating events for PDB structure fragments.
class PDBWritable a where pdbEvents = flip pdbEventS []

module Bio.PDB

-- | Parse a .pdb file and return <a>Structure</a>.
parse :: FilePath -> IO (Maybe Structure)

-- | Write structure to a .pdb file.
write :: PDBWritable a => a -> FilePath -> IO ()

-- | Class generating events for PDB structure fragments.
class PDBWritable a where pdbEvents = flip pdbEventS []

-- | Structure holds all data parsed from a single PDB entry
data Structure
Structure :: List Model -> Structure
models :: Structure -> List Model

-- | PDB entry may contain multiple models, with slight differences in
--   coordinates etc.
data Model
Model :: !Int -> List Chain -> Model
modelId :: Model -> !Int
chains :: Model -> List Chain

-- | Single linear polymer chain of protein, or nucleic acids
data Chain
Chain :: !Char -> List Residue -> Chain
chainId :: Chain -> !Char
residues :: Chain -> List Residue

-- | Residue groups all atoms assigned to the same aminoacid or nucleic
--   acid base within a polymer chain.
data Residue
Residue :: !String -> !Int -> List Atom -> !Char -> Residue
resName :: Residue -> !String
resSeq :: Residue -> !Int
atoms :: Residue -> List Atom
insCode :: Residue -> !Char

-- | Single atom position | NOTE: disordered atoms are now reported as
--   multiplicates
data Atom
Atom :: !String -> !Int -> !Vector3 -> !Double -> !Double -> !String -> !String -> !String -> !Bool -> Atom
atName :: Atom -> !String
atSerial :: Atom -> !Int
coord :: Atom -> !Vector3
bFactor :: Atom -> !Double
occupancy :: Atom -> !Double
element :: Atom -> !String
segid :: Atom -> !String
charge :: Atom -> !String
hetatm :: Atom -> !Bool

-- | Class for iterating all nested components <tt>b</tt> of type
--   <tt>a</tt>.
class Iterable a b
itmapM :: (Iterable a b, Monad m) => (b -> m b) -> a -> m a
itmap :: Iterable a b => (b -> b) -> a -> a
itfoldM :: (Iterable a b, Monad m) => (c -> b -> m c) -> c -> a -> m c
itfoldr :: Iterable a b => (b -> c -> c) -> c -> a -> c
itfoldl :: Iterable a b => (c -> b -> c) -> c -> a -> c
itfoldl' :: Iterable a b => (c -> b -> c) -> c -> a -> c
itlength :: Iterable a b => Proxy * b -> a -> Int

-- | Number of all atoms within the structure.
numAtoms :: Iterable a Atom => a -> Int

-- | Number of all residues within the structure.
numResidues :: Iterable a Residue => a -> Int

-- | Number of all chains within the structure.
numChains :: Iterable a Chain => a -> Int

-- | Number of all models within the structure.
numModels :: Iterable a Model => a -> Int

-- | Takes a first model.
firstModel :: Iterable a Model => a -> Maybe Model

-- | Dictionary mapping three-letter PDB residue code to a single-letter
--   FASTA code.
resname2fastacode :: String -> Char

-- | Dictionary mapping single-letter FASTA standard aminoacid code to a
--   PDB residue name
fastacode2resname :: Char -> String

-- | Scalar product. (asterisk - <a>*</a> - indicates side on which one can
--   put a scalar.)
(*|) :: Double -> Vector3 -> Vector3

-- | Scalar product. (asterisk - <a>*</a> - indicates side on which one can
--   put a scalar.)
(|*) :: Vector3 -> Double -> Vector3

-- | 2-norm of a vector (also called a magnitude or length.)
vnorm :: Vector3 -> Double

-- | Type alias for <a>Element</a> names.
type Element = ByteString

-- | Given a PDB <a>Atom</a> extract or guess its <a>Element</a> name.
assignElement :: Atom -> Element

-- | Atomic number of a given element
atomicNumber :: Element -> Int

-- | Atomic mass of a given element in g/mol
atomicMass :: Element -> Double

-- | Covalent radius of an element with a given name.
covalentRadius :: (Eq a1, Fractional a, Show a1, IsString a1) => a1 -> a

-- | Van der Waals radius of the given element
vanDerWaalsRadius :: Element -> Double