Bio.Structure

Documentation

data SecondaryStructure

Protein secondary structure

Constructors

PiHelix

pi helix

Bend

bend

AlphaHelix

alpha helix

Extended

extended

ThreeTenHelix

3-10 helix

Bridge

brigde

Turn

turn

Coil

coil

Undefined

unknown structure

Instances

Generic SecondaryStructure

Defined in Bio.Structure

Associated Types

type Rep SecondaryStructure :: Type -> Type

Methods

from :: SecondaryStructure -> Rep SecondaryStructure x

to :: Rep SecondaryStructure x -> SecondaryStructure

Show SecondaryStructure

Defined in Bio.Structure

Methods

showsPrec :: Int -> SecondaryStructure -> ShowS

show :: SecondaryStructure -> String

showList :: [SecondaryStructure] -> ShowS

NFData SecondaryStructure

Defined in Bio.Structure

Methods

rnf :: SecondaryStructure -> ()

Eq SecondaryStructure

Defined in Bio.Structure

Methods

(==) :: SecondaryStructure -> SecondaryStructure -> Bool

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

type Rep SecondaryStructure

Defined in Bio.Structure

type Rep SecondaryStructure = D1 ('MetaData "SecondaryStructure" "Bio.Structure" "cobot-io-0.1.5.5-2fgiMxNKBm19YNVvDwIPRV" 'False) (((C1 ('MetaCons "PiHelix" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Bend" 'PrefixI 'False) (U1 :: Type -> Type)) :+: (C1 ('MetaCons "AlphaHelix" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Extended" 'PrefixI 'False) (U1 :: Type -> Type))) :+: ((C1 ('MetaCons "ThreeTenHelix" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Bridge" 'PrefixI 'False) (U1 :: Type -> Type)) :+: (C1 ('MetaCons "Turn" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "Coil" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Undefined" 'PrefixI 'False) (U1 :: Type -> Type)))))

data Atom

Generic atom representation

Constructors

Atom

Fields

• atomId :: GlobalID

  global identifier, 0-based

• atomInputIndex :: Int

  atom index from input file

• atomName :: Text

  IUPAC atom name

• atomElement :: Text

  atom chemical element

• atomCoords :: V3 Float

  3D coordinates of atom

• formalCharge :: Int

  Formal charge of atom

• bFactor :: Float

  B-factor of atom

• occupancy :: Float

  the amount of each conformation that is observed in the crystal

Instances

Generic Atom

Defined in Bio.Structure

Associated Types

type Rep Atom :: Type -> Type

Methods

from :: Atom -> Rep Atom x

to :: Rep Atom x -> Atom

Show Atom

Defined in Bio.Structure

Methods

showsPrec :: Int -> Atom -> ShowS

show :: Atom -> String

showList :: [Atom] -> ShowS

NFData Atom

Defined in Bio.Structure

Methods

rnf :: Atom -> ()

Eq Atom

Defined in Bio.Structure

Methods

(==) :: Atom -> Atom -> Bool

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

Ord Atom

Defined in Bio.Structure

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

type Rep Atom

Defined in Bio.Structure

type Rep Atom = D1 ('MetaData "Atom" "Bio.Structure" "cobot-io-0.1.5.5-2fgiMxNKBm19YNVvDwIPRV" 'False) (C1 ('MetaCons "Atom" 'PrefixI 'True) (((S1 ('MetaSel ('Just "atomId") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 GlobalID) :*: S1 ('MetaSel ('Just "atomInputIndex") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Int)) :*: (S1 ('MetaSel ('Just "atomName") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Text) :*: S1 ('MetaSel ('Just "atomElement") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Text))) :*: ((S1 ('MetaSel ('Just "atomCoords") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (V3 Float)) :*: S1 ('MetaSel ('Just "formalCharge") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Int)) :*: (S1 ('MetaSel ('Just "bFactor") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Float) :*: S1 ('MetaSel ('Just "occupancy") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Float)))))

data Bond m

Generic chemical bond

Constructors

Bond

Fields

• bondStart :: m

  index of first incident atom

• bondEnd :: m

  index of second incident atom

• bondOrder :: Int

  the order of chemical bond

Instances

Functor Bond

Defined in Bio.Structure

Methods

fmap :: (a -> b) -> Bond a -> Bond b

(<$) :: a -> Bond b -> Bond a

Generic (Bond m)

Defined in Bio.Structure

Associated Types

type Rep (Bond m) :: Type -> Type

Methods

from :: Bond m -> Rep (Bond m) x

to :: Rep (Bond m) x -> Bond m

Show m => Show (Bond m)

Defined in Bio.Structure

Methods

showsPrec :: Int -> Bond m -> ShowS

show :: Bond m -> String

showList :: [Bond m] -> ShowS

NFData a => NFData (Bond a)

Defined in Bio.Structure

Methods

rnf :: Bond a -> ()

Eq m => Eq (Bond m)

Defined in Bio.Structure

Methods

(==) :: Bond m -> Bond m -> Bool

(/=) :: Bond m -> Bond m -> Bool

Ord (Bond GlobalID)

Defined in Bio.Structure

Methods

compare :: Bond GlobalID -> Bond GlobalID -> Ordering

(<) :: Bond GlobalID -> Bond GlobalID -> Bool

(<=) :: Bond GlobalID -> Bond GlobalID -> Bool

(>) :: Bond GlobalID -> Bond GlobalID -> Bool

(>=) :: Bond GlobalID -> Bond GlobalID -> Bool

max :: Bond GlobalID -> Bond GlobalID -> Bond GlobalID

min :: Bond GlobalID -> Bond GlobalID -> Bond GlobalID

Ord (Bond LocalID)

Defined in Bio.Structure

Methods

compare :: Bond LocalID -> Bond LocalID -> Ordering

(<) :: Bond LocalID -> Bond LocalID -> Bool

(<=) :: Bond LocalID -> Bond LocalID -> Bool

(>) :: Bond LocalID -> Bond LocalID -> Bool

(>=) :: Bond LocalID -> Bond LocalID -> Bool

max :: Bond LocalID -> Bond LocalID -> Bond LocalID

min :: Bond LocalID -> Bond LocalID -> Bond LocalID

type Rep (Bond m)

Defined in Bio.Structure

type Rep (Bond m) = D1 ('MetaData "Bond" "Bio.Structure" "cobot-io-0.1.5.5-2fgiMxNKBm19YNVvDwIPRV" 'False) (C1 ('MetaCons "Bond" 'PrefixI 'True) (S1 ('MetaSel ('Just "bondStart") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 m) :*: (S1 ('MetaSel ('Just "bondEnd") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 m) :*: S1 ('MetaSel ('Just "bondOrder") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Int))))

data Residue

A set of atoms, organized to a residues

Constructors

Residue

Fields

• resName :: Text

  residue name

• resNumber :: Int

  residue number

• resInsertionCode :: Char

  residue insertion code

• resAtoms :: Vector Atom

  a set of residue atoms

• resBonds :: Vector (Bond LocalID)

  a set of residue bonds with local identifiers (position in resAtoms)

• resSecondary :: SecondaryStructure

  residue secondary structure

• resChemCompType :: Text

  chemical component type

Instances

Generic Residue

Defined in Bio.Structure

Associated Types

type Rep Residue :: Type -> Type

Methods

from :: Residue -> Rep Residue x

to :: Rep Residue x -> Residue

Show Residue

Defined in Bio.Structure

Methods

showsPrec :: Int -> Residue -> ShowS

show :: Residue -> String

showList :: [Residue] -> ShowS

NFData Residue

Defined in Bio.Structure

Methods

rnf :: Residue -> ()

Eq Residue

Defined in Bio.Structure

Methods

(==) :: Residue -> Residue -> Bool

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

type Rep Residue

Defined in Bio.Structure

type Rep Residue = D1 ('MetaData "Residue" "Bio.Structure" "cobot-io-0.1.5.5-2fgiMxNKBm19YNVvDwIPRV" 'False) (C1 ('MetaCons "Residue" 'PrefixI 'True) ((S1 ('MetaSel ('Just "resName") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Text) :*: (S1 ('MetaSel ('Just "resNumber") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Int) :*: S1 ('MetaSel ('Just "resInsertionCode") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Char))) :*: ((S1 ('MetaSel ('Just "resAtoms") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Vector Atom)) :*: S1 ('MetaSel ('Just "resBonds") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Vector (Bond LocalID)))) :*: (S1 ('MetaSel ('Just "resSecondary") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 SecondaryStructure) :*: S1 ('MetaSel ('Just "resChemCompType") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Text)))))

data Chain

Chain organizes linear structure of residues

Constructors

Chain

Fields

• chainName :: Text

  name of a chain

• chainResidues :: Vector Residue

  residues of a chain

Instances

Generic Chain

Defined in Bio.Structure

Associated Types

type Rep Chain :: Type -> Type

Methods

from :: Chain -> Rep Chain x

to :: Rep Chain x -> Chain

Show Chain

Defined in Bio.Structure

Methods

showsPrec :: Int -> Chain -> ShowS

show :: Chain -> String

showList :: [Chain] -> ShowS

NFData Chain

Defined in Bio.Structure

Methods

rnf :: Chain -> ()

Eq Chain

Defined in Bio.Structure

Methods

(==) :: Chain -> Chain -> Bool

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

type Rep Chain

Defined in Bio.Structure

type Rep Chain = D1 ('MetaData "Chain" "Bio.Structure" "cobot-io-0.1.5.5-2fgiMxNKBm19YNVvDwIPRV" 'False) (C1 ('MetaCons "Chain" 'PrefixI 'True) (S1 ('MetaSel ('Just "chainName") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Text) :*: S1 ('MetaSel ('Just "chainResidues") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Vector Residue))))

data Model

Model represents a single experiment of structure determination

Constructors

Model

Fields

• modelChains :: Vector Chain

  chains in the model

• modelBonds :: Vector (Bond GlobalID)

  bonds with global identifiers (field atomId in Atom)

Instances

Generic Model

Defined in Bio.Structure

Associated Types

type Rep Model :: Type -> Type

Methods

from :: Model -> Rep Model x

to :: Rep Model x -> Model

Show Model

Defined in Bio.Structure

Methods

showsPrec :: Int -> Model -> ShowS

show :: Model -> String

showList :: [Model] -> ShowS

NFData Model

Defined in Bio.Structure

Methods

rnf :: Model -> ()

Eq Model

Defined in Bio.Structure

Methods

(==) :: Model -> Model -> Bool

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

type Rep Model

Defined in Bio.Structure

type Rep Model = D1 ('MetaData "Model" "Bio.Structure" "cobot-io-0.1.5.5-2fgiMxNKBm19YNVvDwIPRV" 'False) (C1 ('MetaCons "Model" 'PrefixI 'True) (S1 ('MetaSel ('Just "modelChains") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Vector Chain)) :*: S1 ('MetaSel ('Just "modelBonds") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Vector (Bond GlobalID)))))

class StructureModels a where

Convert any format-specific data to an intermediate representation of structure

Methods

modelsOf :: a -> Vector Model

Get an array of models

Instances

StructureModels Mae

Defined in Bio.MAE

Methods

modelsOf :: Mae -> Vector Model

StructureModels MMTF

Defined in Bio.MMTF

Methods

modelsOf :: MMTF -> Vector Model

StructureModels PDB

Defined in Bio.PDB

Methods

modelsOf :: PDB -> Vector Model

class StructureSerializable a where

Serialize an intermediate representation of sequence to some specific format

Methods

serializeModels :: Vector Model -> a

Serialize an array of models to some format

Instances

StructureSerializable PDB

Defined in Bio.PDB

Methods

serializeModels :: Vector Model -> PDB

newtype LocalID

Constructors

LocalID

Fields

• getLocalID :: Int

Instances

Generic LocalID

Defined in Bio.Structure

Associated Types

type Rep LocalID :: Type -> Type

Methods

from :: LocalID -> Rep LocalID x

to :: Rep LocalID x -> LocalID

Show LocalID

Defined in Bio.Structure

Methods

showsPrec :: Int -> LocalID -> ShowS

show :: LocalID -> String

showList :: [LocalID] -> ShowS

NFData LocalID

Defined in Bio.Structure

Methods

rnf :: LocalID -> ()

Eq LocalID

Defined in Bio.Structure

Methods

(==) :: LocalID -> LocalID -> Bool

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

Ord LocalID

Defined in Bio.Structure

Methods

compare :: LocalID -> LocalID -> Ordering

(<) :: LocalID -> LocalID -> Bool

(<=) :: LocalID -> LocalID -> Bool

(>) :: LocalID -> LocalID -> Bool

(>=) :: LocalID -> LocalID -> Bool

max :: LocalID -> LocalID -> LocalID

min :: LocalID -> LocalID -> LocalID

Ord (Bond LocalID)

Defined in Bio.Structure

Methods

compare :: Bond LocalID -> Bond LocalID -> Ordering

(<) :: Bond LocalID -> Bond LocalID -> Bool

(<=) :: Bond LocalID -> Bond LocalID -> Bool

(>) :: Bond LocalID -> Bond LocalID -> Bool

(>=) :: Bond LocalID -> Bond LocalID -> Bool

max :: Bond LocalID -> Bond LocalID -> Bond LocalID

min :: Bond LocalID -> Bond LocalID -> Bond LocalID

type Rep LocalID

Defined in Bio.Structure

type Rep LocalID = D1 ('MetaData "LocalID" "Bio.Structure" "cobot-io-0.1.5.5-2fgiMxNKBm19YNVvDwIPRV" 'True) (C1 ('MetaCons "LocalID" 'PrefixI 'True) (S1 ('MetaSel ('Just "getLocalID") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Int)))

newtype GlobalID

Constructors

GlobalID

Fields

• getGlobalID :: Int

Instances

Generic GlobalID

Defined in Bio.Structure

Associated Types

type Rep GlobalID :: Type -> Type

Methods

from :: GlobalID -> Rep GlobalID x

to :: Rep GlobalID x -> GlobalID

Show GlobalID

Defined in Bio.Structure

Methods

showsPrec :: Int -> GlobalID -> ShowS

show :: GlobalID -> String

showList :: [GlobalID] -> ShowS

NFData GlobalID

Defined in Bio.Structure

Methods

rnf :: GlobalID -> ()

Eq GlobalID

Defined in Bio.Structure

Methods

(==) :: GlobalID -> GlobalID -> Bool

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

Ord GlobalID

Defined in Bio.Structure

Methods

compare :: GlobalID -> GlobalID -> Ordering

(<) :: GlobalID -> GlobalID -> Bool

(<=) :: GlobalID -> GlobalID -> Bool

(>) :: GlobalID -> GlobalID -> Bool

(>=) :: GlobalID -> GlobalID -> Bool

max :: GlobalID -> GlobalID -> GlobalID

min :: GlobalID -> GlobalID -> GlobalID

Ord (Bond GlobalID)

Defined in Bio.Structure

Methods

compare :: Bond GlobalID -> Bond GlobalID -> Ordering

(<) :: Bond GlobalID -> Bond GlobalID -> Bool

(<=) :: Bond GlobalID -> Bond GlobalID -> Bool

(>) :: Bond GlobalID -> Bond GlobalID -> Bool

(>=) :: Bond GlobalID -> Bond GlobalID -> Bool

max :: Bond GlobalID -> Bond GlobalID -> Bond GlobalID

min :: Bond GlobalID -> Bond GlobalID -> Bond GlobalID

type Rep GlobalID

Defined in Bio.Structure

type Rep GlobalID = D1 ('MetaData "GlobalID" "Bio.Structure" "cobot-io-0.1.5.5-2fgiMxNKBm19YNVvDwIPRV" 'True) (C1 ('MetaCons "GlobalID" 'PrefixI 'True) (S1 ('MetaSel ('Just "getGlobalID") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Int)))

atoms :: Lens' Residue (Vector Atom)

localBonds :: Lens' Residue (Vector (Bond LocalID))

residues :: Lens' Chain (Vector Residue)

chains :: Lens' Model (Vector Chain)

globalBonds :: Lens' Model (Vector (Bond GlobalID))