Safe Haskell | None |
---|---|
Language | Haskell2010 |
Bio.Structure
Synopsis
- data SecondaryStructure
- = PiHelix
- | Bend
- | AlphaHelix
- | Extended
- | ThreeTenHelix
- | Bridge
- | Turn
- | Coil
- | Undefined
- data Atom = Atom {
- atomId :: GlobalID
- atomInputIndex :: Int
- atomName :: Text
- atomElement :: Text
- atomCoords :: V3 Float
- formalCharge :: Int
- bFactor :: Float
- occupancy :: Float
- data Bond m = Bond {}
- data Residue = Residue {}
- data Chain = Chain {}
- data Model = Model {
- modelChains :: Vector Chain
- modelBonds :: Vector (Bond GlobalID)
- class StructureModels a where
- class StructureSerializable a where
- serializeModels :: Vector Model -> a
- newtype LocalID = LocalID {
- getLocalID :: Int
- newtype GlobalID = GlobalID {
- getGlobalID :: 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))
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
Generic atom representation
Constructors
Atom | |
Fields
|
Instances
Generic chemical bond
Constructors
Bond | |
Instances
A set of atoms, organized to a residues
Constructors
Residue | |
Fields
|
Instances
Chain organizes linear structure of residues
Constructors
Chain | |
Fields
|
Instances
Eq Chain Source # | |
Show Chain Source # | |
Generic Chain Source # | |
NFData Chain Source # | |
Defined in Bio.Structure | |
type Rep Chain Source # | |
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)))) |
Model represents a single experiment of structure determination
Constructors
Model | |
Fields
|
Instances
Eq Model Source # | |
Show Model Source # | |
Generic Model Source # | |
NFData Model Source # | |
Defined in Bio.Structure | |
type Rep Model Source # | |
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
Instances
StructureModels Mae Source # | |
StructureModels PDB Source # | |
StructureModels MMTF Source # | |
class StructureSerializable a where Source #
Serialize an intermediate representation of sequence to some specific format
Constructors
LocalID | |
Fields
|
Instances
Eq LocalID Source # | |
Ord LocalID Source # | |
Show LocalID Source # | |
Generic LocalID Source # | |
NFData LocalID Source # | |
Defined in Bio.Structure | |
Ord (Bond LocalID) Source # | |
Defined in Bio.Structure | |
type Rep LocalID Source # | |
Defined in Bio.Structure |
Constructors
GlobalID | |
Fields
|
Instances
Eq GlobalID Source # | |
Ord GlobalID Source # | |
Defined in Bio.Structure | |
Show GlobalID Source # | |
Generic GlobalID Source # | |
NFData GlobalID Source # | |
Defined in Bio.Structure | |
Ord (Bond GlobalID) Source # | |
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 # | |
type Rep GlobalID Source # | |
Defined in Bio.Structure |