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
- | SPLIT
- | 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
- | MTRIX1
- | MTRIX2
- | MTRIX3
- | ORIGX1
- | ORIGX2
- | ORIGX3
- | SCALE1
- | SCALE2
- | SCALE3
- | 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

Instances details

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 -> () #
StructureSerializable PDB Source #
Instance details Defined in Bio.PDB Methods serializeModels :: Vector Model -> PDB Source #
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-0.1.3.20-HPhNL0gUcHREQ55zp5Rm8s" '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

Instances details

Eq FieldType Source #
Instance details Defined in Bio.PDB.Type Methods (==) :: FieldType -> FieldType -> Bool # (/=) :: FieldType -> FieldType -> Bool #
Ord FieldType Source #
Instance details Defined in Bio.PDB.Type Methods compare :: FieldType -> FieldType -> Ordering # (<) :: FieldType -> FieldType -> Bool # (<=) :: FieldType -> FieldType -> Bool # (>) :: FieldType -> FieldType -> Bool # (>=) :: FieldType -> FieldType -> Bool # max :: FieldType -> FieldType -> FieldType # min :: FieldType -> FieldType -> FieldType #
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-0.1.3.20-HPhNL0gUcHREQ55zp5Rm8s" 'False) (((((C1 ('MetaCons "HEADER" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "OBSLTE" 'PrefixI 'False) (U1 :: Type -> Type)) :+: (C1 ('MetaCons "SPLIT" '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 "MTRIX1" 'PrefixI 'False) (U1 :: Type -> Type)) :+: (C1 ('MetaCons "MTRIX2" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "MTRIX3" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "ORIGX1" 'PrefixI 'False) (U1 :: Type -> Type)))) :+: ((C1 ('MetaCons "ORIGX2" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "ORIGX3" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "SCALE1" 'PrefixI 'False) (U1 :: Type -> Type))) :+: (C1 ('MetaCons "SCALE2" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "SCALE3" '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

Instances details

Eq Atom Source #
Instance details Defined in Bio.PDB.Type Methods (==) :: Atom -> Atom -> Bool # (/=) :: Atom -> Atom -> Bool #
Ord Atom Source #	We cannot use only atomSerial as key because there \| can be two atoms with the same atomSerial in different chains
Instance details Defined in Bio.PDB.Type Methods compare :: Atom -> Atom -> Ordering # (<) :: Atom -> Atom -> Bool # (<=) :: Atom -> Atom -> Bool # (>) :: Atom -> Atom -> Bool # (>=) :: Atom -> Atom -> Bool # max :: Atom -> Atom -> Atom # min :: Atom -> Atom -> Atom #
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-0.1.3.20-HPhNL0gUcHREQ55zp5Rm8s" '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
SPLIT
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
MTRIX1
MTRIX2
MTRIX3
ORIGX1
ORIGX2
ORIGX3
SCALE1
SCALE2
SCALE3
MASTER