Bio.PDB.EventParser.PDBEvents

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

Documentation

type String = ByteString

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

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

Vector Vector3

newtype ATID

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

Constructors

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

Instances

Eq ATID

Methods

(==) :: ATID -> ATID -> Bool

(/=) :: ATID -> ATID -> Bool

Ord ATID

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

Methods

showsPrec :: Int -> ATID -> ShowS

show :: ATID -> String

showList :: [ATID] -> ShowS

newtype RESID

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

Constructors

RESID (String, Char, Int, Char)

Instances

Eq RESID

Methods

(==) :: RESID -> RESID -> Bool

(/=) :: RESID -> RESID -> Bool

Ord RESID

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

Methods

showsPrec :: Int -> RESID -> ShowS

show :: RESID -> String

showList :: [RESID] -> ShowS

data PDBEvent

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

Methods

(==) :: PDBEvent -> PDBEvent -> Bool

(/=) :: PDBEvent -> PDBEvent -> Bool

Show PDBEvent

Methods

showsPrec :: Int -> PDBEvent -> ShowS

show :: PDBEvent -> String

showList :: [PDBEvent] -> ShowS

data StrandSenseT

Enumeration of beta-strand sense.

Constructors

Parallel

Antiparallel

Instances

Eq StrandSenseT

Methods

(==) :: StrandSenseT -> StrandSenseT -> Bool

(/=) :: StrandSenseT -> StrandSenseT -> Bool

Ord StrandSenseT

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

Methods

readsPrec :: Int -> ReadS StrandSenseT

readList :: ReadS [StrandSenseT]

readPrec :: ReadPrec StrandSenseT

readListPrec :: ReadPrec [StrandSenseT]

Show StrandSenseT

Methods

showsPrec :: Int -> StrandSenseT -> ShowS

show :: StrandSenseT -> String

showList :: [StrandSenseT] -> ShowS

data HelixT

Enumeration of helix types

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

1. Right-handed alpha (default, most common)
2. Right-handed omega
3. Right-handed pi
4. Right-handed gamma
5. Right-handed 3 - 10
6. Left-handed alpha
7. Left-handed omega
8. Left-handed gamma
9. 2 - 7 ribbon/helix
10. Polyproline

Instances

Eq HelixT

Methods

(==) :: HelixT -> HelixT -> Bool

(/=) :: HelixT -> HelixT -> Bool

Ord HelixT

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

Methods

readsPrec :: Int -> ReadS HelixT

readList :: ReadS [HelixT]

readPrec :: ReadPrec HelixT

readListPrec :: ReadPrec [HelixT]

Show HelixT

Methods

showsPrec :: Int -> HelixT -> ShowS

show :: HelixT -> String

showList :: [HelixT] -> ShowS

data ExpMethod

Enumeration of experimental methods occuring in the PDB archive.

Constructors

XRayDiffraction

FiberDiffraction

NeutronDiffraction

ElectronCrystallography

ElectronMicroscopy

SolidStateNMR

SolutionNMR

SolutionScattering

OtherExpMethod !ByteString

Instances

Eq ExpMethod

Methods

(==) :: ExpMethod -> ExpMethod -> Bool

(/=) :: ExpMethod -> ExpMethod -> Bool

Ord ExpMethod

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

Methods

readsPrec :: Int -> ReadS ExpMethod

readList :: ReadS [ExpMethod]

readPrec :: ReadPrec ExpMethod

readListPrec :: ReadPrec [ExpMethod]

Show ExpMethod

Methods

showsPrec :: Int -> ExpMethod -> ShowS

show :: ExpMethod -> String

showList :: [ExpMethod] -> ShowS