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

Eq SecondaryStructure

Defined in Bio.Structure

Methods

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

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

Show SecondaryStructure

Defined in Bio.Structure

Methods

showsPrec :: Int -> SecondaryStructure -> ShowS

show :: SecondaryStructure -> String

showList :: [SecondaryStructure] -> ShowS

Generic SecondaryStructure

Defined in Bio.Structure

Associated Types

type Rep SecondaryStructure :: Type -> Type

Methods

from :: SecondaryStructure -> Rep SecondaryStructure x

to :: Rep SecondaryStructure x -> SecondaryStructure

NFData SecondaryStructure

Defined in Bio.Structure

Methods

rnf :: SecondaryStructure -> ()

type Rep SecondaryStructure

Defined in Bio.Structure

type Rep SecondaryStructure = D1 (MetaData "SecondaryStructure" "Bio.Structure" "cobot-io-0.1.2.0-Edw5pXm2rhDLW8sGnHkG2U" 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

• 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

Eq Atom

Defined in Bio.Structure

Methods

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

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

Show Atom

Defined in Bio.Structure

Methods

showsPrec :: Int -> Atom -> ShowS

show :: Atom -> String

showList :: [Atom] -> ShowS

Generic Atom

Defined in Bio.Structure

Associated Types

type Rep Atom :: Type -> Type

Methods

from :: Atom -> Rep Atom x

to :: Rep Atom x -> Atom

NFData Atom

Defined in Bio.Structure

Methods

rnf :: Atom -> ()

type Rep Atom

Defined in Bio.Structure

type Rep Atom = D1 (MetaData "Atom" "Bio.Structure" "cobot-io-0.1.2.0-Edw5pXm2rhDLW8sGnHkG2U" False) (C1 (MetaCons "Atom" PrefixI True) ((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

Generic chemical bond

Constructors

Bond

Fields

• bondStart :: Int

  index of first incident atom

• bondEnd :: Int

  index of second incident atom

• bondOrder :: Int

  the order of chemical bond

Instances

Eq Bond

Defined in Bio.Structure

Methods

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

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

Show Bond

Defined in Bio.Structure

Methods

showsPrec :: Int -> Bond -> ShowS

show :: Bond -> String

showList :: [Bond] -> ShowS

Generic Bond

Defined in Bio.Structure

Associated Types

type Rep Bond :: Type -> Type

Methods

from :: Bond -> Rep Bond x

to :: Rep Bond x -> Bond

NFData Bond

Defined in Bio.Structure

Methods

rnf :: Bond -> ()

type Rep Bond

Defined in Bio.Structure

type Rep Bond = D1 (MetaData "Bond" "Bio.Structure" "cobot-io-0.1.2.0-Edw5pXm2rhDLW8sGnHkG2U" False) (C1 (MetaCons "Bond" PrefixI True) (S1 (MetaSel (Just "bondStart") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Int) :*: (S1 (MetaSel (Just "bondEnd") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Int) :*: 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

• resAtoms :: Array Int Atom

  a set of residue atoms

• resBonds :: Array Int Bond

  a set of residue bonds

• resSecondary :: SecondaryStructure

  residue secondary structure

• resChemCompType :: Text

  chemical component type

Instances

Eq Residue

Defined in Bio.Structure

Methods

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

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

Show Residue

Defined in Bio.Structure

Methods

showsPrec :: Int -> Residue -> ShowS

show :: Residue -> String

showList :: [Residue] -> ShowS

Generic Residue

Defined in Bio.Structure

Associated Types

type Rep Residue :: Type -> Type

Methods

from :: Residue -> Rep Residue x

to :: Rep Residue x -> Residue

NFData Residue

Defined in Bio.Structure

Methods

rnf :: Residue -> ()

type Rep Residue

Defined in Bio.Structure

type Rep Residue = D1 (MetaData "Residue" "Bio.Structure" "cobot-io-0.1.2.0-Edw5pXm2rhDLW8sGnHkG2U" False) (C1 (MetaCons "Residue" PrefixI True) ((S1 (MetaSel (Just "resName") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Text) :*: S1 (MetaSel (Just "resAtoms") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 (Array Int Atom))) :*: (S1 (MetaSel (Just "resBonds") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 (Array Int Bond)) :*: (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 :: Array Int Residue

  residues of a chain

Instances

Eq Chain

Defined in Bio.Structure

Methods

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

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

Show Chain

Defined in Bio.Structure

Methods

showsPrec :: Int -> Chain -> ShowS

show :: Chain -> String

showList :: [Chain] -> ShowS

Generic Chain

Defined in Bio.Structure

Associated Types

type Rep Chain :: Type -> Type

Methods

from :: Chain -> Rep Chain x

to :: Rep Chain x -> Chain

NFData Chain

Defined in Bio.Structure

Methods

rnf :: Chain -> ()

type Rep Chain

Defined in Bio.Structure

type Rep Chain = D1 (MetaData "Chain" "Bio.Structure" "cobot-io-0.1.2.0-Edw5pXm2rhDLW8sGnHkG2U" False) (C1 (MetaCons "Chain" PrefixI True) (S1 (MetaSel (Just "chainName") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Text) :*: S1 (MetaSel (Just "chainResidues") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 (Array Int Residue))))

newtype Model

Model represents a single experiment of structure determination

Constructors

Model

Fields

• modelChains :: Array Int Chain

Instances

Eq Model

Defined in Bio.Structure

Methods

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

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

Show Model

Defined in Bio.Structure

Methods

showsPrec :: Int -> Model -> ShowS

show :: Model -> String

showList :: [Model] -> ShowS

Generic Model

Defined in Bio.Structure

Associated Types

type Rep Model :: Type -> Type

Methods

from :: Model -> Rep Model x

to :: Rep Model x -> Model

NFData Model

Defined in Bio.Structure

Methods

rnf :: Model -> ()

type Rep Model

Defined in Bio.Structure

type Rep Model = D1 (MetaData "Model" "Bio.Structure" "cobot-io-0.1.2.0-Edw5pXm2rhDLW8sGnHkG2U" True) (C1 (MetaCons "Model" PrefixI True) (S1 (MetaSel (Just "modelChains") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 (Array Int Chain))))

class StructureModels a where

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

Methods

modelsOf :: a -> Array Int Model

Get an array of models

Instances

StructureModels MMTF

Defined in Bio.MMTF

Methods

modelsOf :: MMTF -> Array Int Model

class StructureSerializable a where

Serialize an intermediate representation of sequence to some specific format

Methods

serializeModels :: Array Int Model -> a

Serialize an array of models to some format