cobot-io-0.1.3.4: Biological data file formats and IO

Safe HaskellNone
LanguageHaskell2010

Bio.Structure

Synopsis

Documentation

data SecondaryStructure Source #

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 Source # 
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Defined in Bio.Structure

Show SecondaryStructure Source # 
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Generic SecondaryStructure Source # 
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Associated Types

type Rep SecondaryStructure :: Type -> Type #

NFData SecondaryStructure Source # 
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Methods

rnf :: SecondaryStructure -> () #

type Rep SecondaryStructure Source # 
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Defined in Bio.Structure

type Rep SecondaryStructure = D1 (MetaData "SecondaryStructure" "Bio.Structure" "cobot-io-0.1.3.4-CElExkvFmWX1GjkIMR62w3" 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 Source #

Generic atom representation

Constructors

Atom 

Fields

Instances
Eq Atom Source # 
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Defined in Bio.Structure

Methods

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

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

Ord Atom Source # 
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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 # 
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Defined in Bio.Structure

Methods

showsPrec :: Int -> Atom -> ShowS #

show :: Atom -> String #

showList :: [Atom] -> ShowS #

Generic Atom Source # 
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Associated Types

type Rep Atom :: Type -> Type #

Methods

from :: Atom -> Rep Atom x #

to :: Rep Atom x -> Atom #

NFData Atom Source # 
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Defined in Bio.Structure

Methods

rnf :: Atom -> () #

type Rep Atom Source # 
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data Bond m Source #

Generic chemical bond

Constructors

Bond 

Fields

Instances
Functor Bond Source # 
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Defined in Bio.Structure

Methods

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

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

Eq m => Eq (Bond m) Source # 
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Defined in Bio.Structure

Methods

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

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

Ord (Bond LocalID) Source # 
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Defined in Bio.Structure

Ord (Bond GlobalID) Source # 
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Show m => Show (Bond m) Source # 
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Methods

showsPrec :: Int -> Bond m -> ShowS #

show :: Bond m -> String #

showList :: [Bond m] -> ShowS #

Generic (Bond m) Source # 
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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 #

NFData a => NFData (Bond a) Source # 
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Methods

rnf :: Bond a -> () #

type Rep (Bond m) Source # 
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Defined in Bio.Structure

type Rep (Bond m) = D1 (MetaData "Bond" "Bio.Structure" "cobot-io-0.1.3.4-CElExkvFmWX1GjkIMR62w3" 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 Source #

A set of atoms, organized to a residues

Constructors

Residue 

Fields

Instances
Eq Residue Source # 
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Defined in Bio.Structure

Methods

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

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

Show Residue Source # 
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Generic Residue Source # 
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type Rep Residue :: Type -> Type #

Methods

from :: Residue -> Rep Residue x #

to :: Rep Residue x -> Residue #

NFData Residue Source # 
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Methods

rnf :: Residue -> () #

type Rep Residue Source # 
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data Chain Source #

Chain organizes linear structure of residues

Constructors

Chain 

Fields

Instances
Eq Chain Source # 
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Methods

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

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

Show Chain Source # 
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Methods

showsPrec :: Int -> Chain -> ShowS #

show :: Chain -> String #

showList :: [Chain] -> ShowS #

Generic Chain Source # 
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Defined in Bio.Structure

Associated Types

type Rep Chain :: Type -> Type #

Methods

from :: Chain -> Rep Chain x #

to :: Rep Chain x -> Chain #

NFData Chain Source # 
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Defined in Bio.Structure

Methods

rnf :: Chain -> () #

type Rep Chain Source # 
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Defined in Bio.Structure

type Rep Chain = D1 (MetaData "Chain" "Bio.Structure" "cobot-io-0.1.3.4-CElExkvFmWX1GjkIMR62w3" 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 Source #

Model represents a single experiment of structure determination

Constructors

Model 

Fields

Instances
Eq Model Source # 
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Defined in Bio.Structure

Methods

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

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

Show Model Source # 
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Defined in Bio.Structure

Methods

showsPrec :: Int -> Model -> ShowS #

show :: Model -> String #

showList :: [Model] -> ShowS #

Generic Model Source # 
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Associated Types

type Rep Model :: Type -> Type #

Methods

from :: Model -> Rep Model x #

to :: Rep Model x -> Model #

NFData Model Source # 
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Methods

rnf :: Model -> () #

type Rep Model Source # 
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Defined in Bio.Structure

type Rep Model = D1 (MetaData "Model" "Bio.Structure" "cobot-io-0.1.3.4-CElExkvFmWX1GjkIMR62w3" 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 Source #

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

Methods

modelsOf :: a -> Vector Model Source #

Get an array of models

Instances
StructureModels Mae Source # 
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Defined in Bio.MAE

StructureModels PDB Source # 
Instance details

Defined in Bio.PDB

StructureModels MMTF Source # 
Instance details

Defined in Bio.MMTF

class StructureSerializable a where Source #

Serialize an intermediate representation of sequence to some specific format

Methods

serializeModels :: Vector Model -> a Source #

Serialize an array of models to some format

newtype LocalID Source #

Constructors

LocalID 

Fields

Instances
Eq LocalID Source # 
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Methods

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

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

Ord LocalID Source # 
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Show LocalID Source # 
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Generic LocalID Source # 
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Associated Types

type Rep LocalID :: Type -> Type #

Methods

from :: LocalID -> Rep LocalID x #

to :: Rep LocalID x -> LocalID #

NFData LocalID Source # 
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Methods

rnf :: LocalID -> () #

Ord (Bond LocalID) Source # 
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type Rep LocalID Source # 
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Defined in Bio.Structure

type Rep LocalID = D1 (MetaData "LocalID" "Bio.Structure" "cobot-io-0.1.3.4-CElExkvFmWX1GjkIMR62w3" True) (C1 (MetaCons "LocalID" PrefixI True) (S1 (MetaSel (Just "getLocalID") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Int)))

newtype GlobalID Source #

Constructors

GlobalID 

Fields

Instances
Eq GlobalID Source # 
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Defined in Bio.Structure

Ord GlobalID Source # 
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Show GlobalID Source # 
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Generic GlobalID Source # 
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Defined in Bio.Structure

Associated Types

type Rep GlobalID :: Type -> Type #

Methods

from :: GlobalID -> Rep GlobalID x #

to :: Rep GlobalID x -> GlobalID #

NFData GlobalID Source # 
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Defined in Bio.Structure

Methods

rnf :: GlobalID -> () #

Ord (Bond GlobalID) Source # 
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Defined in Bio.Structure

type Rep GlobalID Source # 
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Defined in Bio.Structure

type Rep GlobalID = D1 (MetaData "GlobalID" "Bio.Structure" "cobot-io-0.1.3.4-CElExkvFmWX1GjkIMR62w3" True) (C1 (MetaCons "GlobalID" PrefixI True) (S1 (MetaSel (Just "getGlobalID") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Int)))