Safe Haskell	None
Language	Haskell2010

Bio.PDB.Type

Contents

Read PDB specification here.

Synopsis

data PDB = PDB {
- title :: Text
- models :: Vector Model
- remarks :: Map RemarkCode RemarkData
- otherFields :: Map FieldType FieldData
}
type RemarkCode = Maybe Int
type RemarkData = Vector Text
type FieldData = Vector Text
data FieldType
- = HEADER
- | OBSLTE
- | SPLT
- | CAVEAT
- | COMPND
- | SOURCE
- | KEYWDS
- | EXPDTA
- | NUMMDL
- | MDLTYP
- | AUTHOR
- | REVDAT
- | SPRSDE
- | JRNL
- | DBREF
- | DBREF1
- | DBREF2
- | SEQADV
- | SEQRES
- | MODRES
- | HET
- | FORMUL
- | HETNAM
- | HETSYN
- | HELIX
- | SHEET
- | SSBOND
- | LINK
- | CISPEP
- | SITE
- | CRYST1
- | MTRIXn
- | ORIGXn
- | SCALEn
- | MASTER
type Model = Vector Chain
type Chain = Vector Atom
data Atom = Atom {
- atomSerial :: Int
- atomName :: Text
- atomAltLoc :: Char
- atomResName :: Text
- atomChainID :: Char
- atomResSeq :: Int
- atomICode :: Char
- atomX :: Float
- atomY :: Float
- atomZ :: Float
- atomOccupancy :: Float
- atomTempFactor :: Float
- atomElement :: Text
- atomCharge :: Text
}

Read PDB specification here.

data PDB Source #

Constructors

PDB
Fields title :: Text models :: Vector Model remarks :: Map RemarkCode RemarkData otherFields :: Map FieldType FieldData

Instances

Eq PDB Source #
Instance details Defined in Bio.PDB.Type Methods (==) :: PDB -> PDB -> Bool # (/=) :: PDB -> PDB -> Bool #
Show PDB Source #
Instance details Defined in Bio.PDB.Type Methods showsPrec :: Int -> PDB -> ShowS # show :: PDB -> String # showList :: [PDB] -> ShowS #
Generic PDB Source #
Instance details Defined in Bio.PDB.Type Associated Types type Rep PDB :: Type -> Type # Methods from :: PDB -> Rep PDB x # to :: Rep PDB x -> PDB #
NFData PDB Source #
Instance details Defined in Bio.PDB.Type Methods rnf :: PDB -> () #
StructureModels PDB Source #
Instance details Defined in Bio.PDB Methods modelsOf :: PDB -> Vector Model Source #
type Rep PDB Source #
Instance details Defined in Bio.PDB.Type type Rep PDB = D1 (MetaData "PDB" "Bio.PDB.Type" "cobot-io-0.1.2.3-KKMpzSzBNPq5aU3uhTWBjY" False) (C1 (MetaCons "PDB" PrefixI True) ((S1 (MetaSel (Just "title") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Text) :: S1 (MetaSel (Just "models") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 (Vector Model))) :: (S1 (MetaSel (Just "remarks") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 (Map RemarkCode RemarkData)) :*: S1 (MetaSel (Just "otherFields") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 (Map FieldType FieldData)))))

type RemarkCode = Maybe Int Source #

type RemarkData = Vector Text Source #

type FieldData = Vector Text Source #

data FieldType Source #

Instances

Eq FieldType Source #
Instance details Defined in Bio.PDB.Type Methods (==) :: FieldType -> FieldType -> Bool # (/=) :: FieldType -> FieldType -> Bool #
Read FieldType Source #
Instance details Defined in Bio.PDB.Type Methods readsPrec :: Int -> ReadS FieldType # readList :: ReadS [FieldType] # readPrec :: ReadPrec FieldType # readListPrec :: ReadPrec [FieldType] #
Show FieldType Source #
Instance details Defined in Bio.PDB.Type Methods showsPrec :: Int -> FieldType -> ShowS # show :: FieldType -> String # showList :: [FieldType] -> ShowS #
Generic FieldType Source #
Instance details Defined in Bio.PDB.Type Associated Types type Rep FieldType :: Type -> Type # Methods from :: FieldType -> Rep FieldType x # to :: Rep FieldType x -> FieldType #
NFData FieldType Source #
Instance details Defined in Bio.PDB.Type Methods rnf :: FieldType -> () #
type Rep FieldType Source #
Instance details Defined in Bio.PDB.Type type Rep FieldType = D1 (MetaData "FieldType" "Bio.PDB.Type" "cobot-io-0.1.2.3-KKMpzSzBNPq5aU3uhTWBjY" False) (((((C1 (MetaCons "HEADER" PrefixI False) (U1 :: Type -> Type) :+: C1 (MetaCons "OBSLTE" PrefixI False) (U1 :: Type -> Type)) :+: (C1 (MetaCons "SPLT" PrefixI False) (U1 :: Type -> Type) :+: C1 (MetaCons "CAVEAT" PrefixI False) (U1 :: Type -> Type))) :+: ((C1 (MetaCons "COMPND" PrefixI False) (U1 :: Type -> Type) :+: C1 (MetaCons "SOURCE" PrefixI False) (U1 :: Type -> Type)) :+: (C1 (MetaCons "KEYWDS" PrefixI False) (U1 :: Type -> Type) :+: C1 (MetaCons "EXPDTA" PrefixI False) (U1 :: Type -> Type)))) :+: (((C1 (MetaCons "NUMMDL" PrefixI False) (U1 :: Type -> Type) :+: C1 (MetaCons "MDLTYP" PrefixI False) (U1 :: Type -> Type)) :+: (C1 (MetaCons "AUTHOR" PrefixI False) (U1 :: Type -> Type) :+: C1 (MetaCons "REVDAT" PrefixI False) (U1 :: Type -> Type))) :+: ((C1 (MetaCons "SPRSDE" PrefixI False) (U1 :: Type -> Type) :+: C1 (MetaCons "JRNL" PrefixI False) (U1 :: Type -> Type)) :+: (C1 (MetaCons "DBREF" PrefixI False) (U1 :: Type -> Type) :+: (C1 (MetaCons "DBREF1" PrefixI False) (U1 :: Type -> Type) :+: C1 (MetaCons "DBREF2" PrefixI False) (U1 :: Type -> Type)))))) :+: ((((C1 (MetaCons "SEQADV" PrefixI False) (U1 :: Type -> Type) :+: C1 (MetaCons "SEQRES" PrefixI False) (U1 :: Type -> Type)) :+: (C1 (MetaCons "MODRES" PrefixI False) (U1 :: Type -> Type) :+: C1 (MetaCons "HET" PrefixI False) (U1 :: Type -> Type))) :+: ((C1 (MetaCons "FORMUL" PrefixI False) (U1 :: Type -> Type) :+: C1 (MetaCons "HETNAM" PrefixI False) (U1 :: Type -> Type)) :+: (C1 (MetaCons "HETSYN" PrefixI False) (U1 :: Type -> Type) :+: (C1 (MetaCons "HELIX" PrefixI False) (U1 :: Type -> Type) :+: C1 (MetaCons "SHEET" PrefixI False) (U1 :: Type -> Type))))) :+: (((C1 (MetaCons "SSBOND" PrefixI False) (U1 :: Type -> Type) :+: C1 (MetaCons "LINK" PrefixI False) (U1 :: Type -> Type)) :+: (C1 (MetaCons "CISPEP" PrefixI False) (U1 :: Type -> Type) :+: C1 (MetaCons "SITE" PrefixI False) (U1 :: Type -> Type))) :+: ((C1 (MetaCons "CRYST1" PrefixI False) (U1 :: Type -> Type) :+: C1 (MetaCons "MTRIXn" PrefixI False) (U1 :: Type -> Type)) :+: (C1 (MetaCons "ORIGXn" PrefixI False) (U1 :: Type -> Type) :+: (C1 (MetaCons "SCALEn" PrefixI False) (U1 :: Type -> Type) :+: C1 (MetaCons "MASTER" PrefixI False) (U1 :: Type -> Type)))))))

type Model = Vector Chain Source #

type Chain = Vector Atom Source #

data Atom Source #

Constructors

Atom

Fields

atomSerial :: Int
Atom serial number.
atomName :: Text
Atom name.
atomAltLoc :: Char
Alternate location indicator.
atomResName :: Text
Residue name.
atomChainID :: Char
Chain identifier.
atomResSeq :: Int
Residue sequence number.
atomICode :: Char
Code for insertion of residues.
atomX :: Float
Orthogonal coordinates for X in Angstroms.
atomY :: Float
Orthogonal coordinates for Y in Angstroms.
atomZ :: Float
Orthogonal coordinates for Z in Angstroms.
atomOccupancy :: Float
Occupancy.
atomTempFactor :: Float
Temperature factor.
atomElement :: Text
Element symbol, right-justified.
atomCharge :: Text
Charge on the atom.

Instances

Eq Atom Source #
Instance details Defined in Bio.PDB.Type Methods (==) :: Atom -> Atom -> Bool # (/=) :: Atom -> Atom -> Bool #
Show Atom Source #
Instance details Defined in Bio.PDB.Type Methods showsPrec :: Int -> Atom -> ShowS # show :: Atom -> String # showList :: [Atom] -> ShowS #
Generic Atom Source #
Instance details Defined in Bio.PDB.Type Associated Types type Rep Atom :: Type -> Type # Methods from :: Atom -> Rep Atom x # to :: Rep Atom x -> Atom #
NFData Atom Source #
Instance details Defined in Bio.PDB.Type Methods rnf :: Atom -> () #
type Rep Atom Source #
Instance details Defined in Bio.PDB.Type type Rep Atom = D1 (MetaData "Atom" "Bio.PDB.Type" "cobot-io-0.1.2.3-KKMpzSzBNPq5aU3uhTWBjY" False) (C1 (MetaCons "Atom" PrefixI True) (((S1 (MetaSel (Just "atomSerial") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Int) :: (S1 (MetaSel (Just "atomName") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Text) :: S1 (MetaSel (Just "atomAltLoc") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Char))) :: ((S1 (MetaSel (Just "atomResName") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Text) :: S1 (MetaSel (Just "atomChainID") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Char)) :: (S1 (MetaSel (Just "atomResSeq") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Int) :: S1 (MetaSel (Just "atomICode") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Char)))) :: ((S1 (MetaSel (Just "atomX") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Float) :: (S1 (MetaSel (Just "atomY") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Float) :: S1 (MetaSel (Just "atomZ") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Float))) :: ((S1 (MetaSel (Just "atomOccupancy") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Float) :: S1 (MetaSel (Just "atomTempFactor") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Float)) :: (S1 (MetaSel (Just "atomElement") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Text) :*: S1 (MetaSel (Just "atomCharge") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Text))))))

HEADER
OBSLTE
SPLT
CAVEAT
COMPND
SOURCE
KEYWDS
EXPDTA
NUMMDL
MDLTYP
AUTHOR
REVDAT
SPRSDE
JRNL
DBREF
DBREF1
DBREF2
SEQADV
SEQRES
MODRES
HET
FORMUL
HETNAM
HETSYN
HELIX
SHEET
SSBOND
LINK
CISPEP
SITE
CRYST1
MTRIXn
ORIGXn
SCALEn
MASTER