Safe Haskell	Safe-Inferred

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
Fractional Vector3
Num Vector3
Show Vector3
BasicVector Vector3
Vector Vector3
Arbitrary 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
Ord ATID
Show ATID

newtype RESID Source

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

Constructors

RESID (String, Char, Int, Char)

Instances

Eq RESID
Ord RESID
Show RESID

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
Show PDBEvent

data StrandSenseT Source

Enumeration of beta-strand sense.

Constructors

Parallel
Antiparallel

Instances

Eq StrandSenseT
Ord StrandSenseT
Read StrandSenseT
Show StrandSenseT

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
Ord HelixT
Read HelixT
Show HelixT

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
Ord ExpMethod
Read ExpMethod
Show ExpMethod