Safe Haskell	Safe
Language	Haskell98

Bio.PDB.EventParser.PDBEvents

Description

This module contains datatype declaration for PDB parsing events generated by PDBEventParser module.

Synopsis

Documentation

type String = ByteString Source #

We use only strict ByteString as strings in PDB parser.

data Vector3 :: * #

Constructors

Vector3
Fields v3x :: ~Scalar v3y :: ~Scalar v3z :: ~Scalar

Instances

Eq Vector3
Methods (==) :: Vector3 -> Vector3 -> Bool # (/=) :: Vector3 -> Vector3 -> Bool #
Fractional Vector3
Methods (/) :: Vector3 -> Vector3 -> Vector3 # recip :: Vector3 -> Vector3 # fromRational :: Rational -> Vector3 #
Num Vector3
Methods (+) :: Vector3 -> Vector3 -> Vector3 # (-) :: Vector3 -> Vector3 -> Vector3 # (*) :: Vector3 -> Vector3 -> Vector3 # negate :: Vector3 -> Vector3 # abs :: Vector3 -> Vector3 # signum :: Vector3 -> Vector3 # fromInteger :: Integer -> Vector3 #
Show Vector3
Methods showsPrec :: Int -> Vector3 -> ShowS # show :: Vector3 -> String # showList :: [Vector3] -> ShowS #
Vector Vector3

BasicVector Vector3
Methods vmap :: (Scalar -> Scalar) -> Vector3 -> Vector3 vzip :: (Scalar -> Scalar -> Scalar) -> Vector3 -> Vector3 -> Vector3 vfold :: (Scalar -> Scalar -> Scalar) -> Vector3 -> Scalar vpack :: [Scalar] -> Maybe Vector3 vunpack :: Vector3 -> [Scalar] vpromote :: Scalar -> Vector3

newtype ATID Source #

Atom id: atom name, residue name, chain, residue id, residue insertion code

Constructors

ATID (String, String, Char, Int, Char)

Instances

Eq ATID Source #
Methods (==) :: ATID -> ATID -> Bool # (/=) :: ATID -> ATID -> Bool #
Ord ATID Source #
Methods compare :: ATID -> ATID -> Ordering # (<) :: ATID -> ATID -> Bool # (<=) :: ATID -> ATID -> Bool # (>) :: ATID -> ATID -> Bool # (>=) :: ATID -> ATID -> Bool # max :: ATID -> ATID -> ATID # min :: ATID -> ATID -> ATID #
Show ATID Source #
Methods showsPrec :: Int -> ATID -> ShowS # show :: ATID -> String # showList :: [ATID] -> ShowS #

newtype RESID Source #

Residue id: residue name, chain, residue id, residue insertion code

Constructors

RESID (String, Char, Int, Char)

Instances

Eq RESID Source #
Methods (==) :: RESID -> RESID -> Bool # (/=) :: RESID -> RESID -> Bool #
Ord RESID Source #
Methods compare :: RESID -> RESID -> Ordering # (<) :: RESID -> RESID -> Bool # (<=) :: RESID -> RESID -> Bool # (>) :: RESID -> RESID -> Bool # (>=) :: RESID -> RESID -> Bool # max :: RESID -> RESID -> RESID # min :: RESID -> RESID -> RESID #
Show RESID Source #
Methods showsPrec :: Int -> RESID -> ShowS # show :: RESID -> String # showList :: [RESID] -> ShowS #

data PDBEvent Source #

Datatype for event-based PDB parser

Constructors

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

Instances

Eq PDBEvent Source #
Methods (==) :: PDBEvent -> PDBEvent -> Bool # (/=) :: PDBEvent -> PDBEvent -> Bool #
Show PDBEvent Source #
Methods showsPrec :: Int -> PDBEvent -> ShowS # show :: PDBEvent -> String # showList :: [PDBEvent] -> ShowS #

data StrandSenseT Source #

Enumeration of beta-strand sense.

Constructors

Parallel
Antiparallel

Instances

Eq StrandSenseT Source #
Methods (==) :: StrandSenseT -> StrandSenseT -> Bool # (/=) :: StrandSenseT -> StrandSenseT -> Bool #
Ord StrandSenseT Source #
Methods compare :: StrandSenseT -> StrandSenseT -> Ordering # (<) :: StrandSenseT -> StrandSenseT -> Bool # (<=) :: StrandSenseT -> StrandSenseT -> Bool # (>) :: StrandSenseT -> StrandSenseT -> Bool # (>=) :: StrandSenseT -> StrandSenseT -> Bool # max :: StrandSenseT -> StrandSenseT -> StrandSenseT # min :: StrandSenseT -> StrandSenseT -> StrandSenseT #
Read StrandSenseT Source #
Methods readsPrec :: Int -> ReadS StrandSenseT # readList :: ReadS [StrandSenseT] # readPrec :: ReadPrec StrandSenseT # readListPrec :: ReadPrec [StrandSenseT] #
Show StrandSenseT Source #
Methods showsPrec :: Int -> StrandSenseT -> ShowS # show :: StrandSenseT -> String # showList :: [StrandSenseT] -> ShowS #

data HelixT Source #

Enumeration of helix types

PDB Class number in columns 39-40 for each type of helix in HELIX record:

Right-handed alpha (default, most common)
Right-handed omega
Right-handed pi
Right-handed gamma
Right-handed 3 - 10
Left-handed alpha
Left-handed omega
Left-handed gamma
2 - 7 ribbon/helix
Polyproline

Instances

Eq HelixT Source #
Methods (==) :: HelixT -> HelixT -> Bool # (/=) :: HelixT -> HelixT -> Bool #
Ord HelixT Source #
Methods compare :: HelixT -> HelixT -> Ordering # (<) :: HelixT -> HelixT -> Bool # (<=) :: HelixT -> HelixT -> Bool # (>) :: HelixT -> HelixT -> Bool # (>=) :: HelixT -> HelixT -> Bool # max :: HelixT -> HelixT -> HelixT # min :: HelixT -> HelixT -> HelixT #
Read HelixT Source #
Methods readsPrec :: Int -> ReadS HelixT # readList :: ReadS [HelixT] # readPrec :: ReadPrec HelixT # readListPrec :: ReadPrec [HelixT] #
Show HelixT Source #
Methods showsPrec :: Int -> HelixT -> ShowS # show :: HelixT -> String # showList :: [HelixT] -> ShowS #

data ExpMethod Source #

Enumeration of experimental methods occuring in the PDB archive.

Constructors

XRayDiffraction
FiberDiffraction
NeutronDiffraction
ElectronCrystallography
ElectronMicroscopy
SolidStateNMR
SolutionNMR
SolutionScattering
OtherExpMethod !ByteString

Instances

Eq ExpMethod Source #
Methods (==) :: ExpMethod -> ExpMethod -> Bool # (/=) :: ExpMethod -> ExpMethod -> Bool #
Ord ExpMethod Source #
Methods compare :: ExpMethod -> ExpMethod -> Ordering # (<) :: ExpMethod -> ExpMethod -> Bool # (<=) :: ExpMethod -> ExpMethod -> Bool # (>) :: ExpMethod -> ExpMethod -> Bool # (>=) :: ExpMethod -> ExpMethod -> Bool # max :: ExpMethod -> ExpMethod -> ExpMethod # min :: ExpMethod -> ExpMethod -> ExpMethod #
Read ExpMethod Source #
Methods readsPrec :: Int -> ReadS ExpMethod # readList :: ReadS [ExpMethod] # readPrec :: ReadPrec ExpMethod # readListPrec :: ReadPrec [ExpMethod] #
Show ExpMethod Source #
Methods showsPrec :: Int -> ExpMethod -> ShowS # show :: ExpMethod -> String # showList :: [ExpMethod] -> ShowS #