Bio.MMTF

Documentation

data UnitCell

Unit cell data

Constructors

UnitCell

Fields

• ucA :: !Float

  length of side a

• ucB :: !Float

  length of side b

• ucC :: !Float

  length of side c

• ucAlpha :: !Float

  alpha angle in degrees

• ucBeta :: !Float

  beta angle in degrees

• ucGamma :: !Float

  gamma angle in degrees

Instances

Eq UnitCell

Defined in Bio.MMTF.Type

Methods

(==) :: UnitCell -> UnitCell -> Bool

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

Show UnitCell

Defined in Bio.MMTF.Type

Methods

showsPrec :: Int -> UnitCell -> ShowS

show :: UnitCell -> String

showList :: [UnitCell] -> ShowS

data Transform

Transform data

Constructors

Transform

Fields

• chainIndexList :: ![Int32]

  indices into the chainIdList and chainNameList fields

• matrix :: ![Float]

  4x4 transformation matrix

Instances

Eq Transform

Defined in Bio.MMTF.Type

Methods

(==) :: Transform -> Transform -> Bool

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

Show Transform

Defined in Bio.MMTF.Type

Methods

showsPrec :: Int -> Transform -> ShowS

show :: Transform -> String

showList :: [Transform] -> ShowS

data Assembly

Assembly data

Constructors

Assembly

Fields

• transformList :: ![Transform]

  List of transform objects

• assemblyName :: !Text

  Name of the biological assembly

Instances

Eq Assembly

Defined in Bio.MMTF.Type

Methods

(==) :: Assembly -> Assembly -> Bool

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

Show Assembly

Defined in Bio.MMTF.Type

Methods

showsPrec :: Int -> Assembly -> ShowS

show :: Assembly -> String

showList :: [Assembly] -> ShowS

data Entity

Entity data

Constructors

Entity

Fields

• entityChainIndexList :: ![Int32]

  indices into the chainIdList and chainNameList fields

• entityDescription :: !Text

  Description of the entity

• entityType :: !Text

  Name of the entity type

• entitySequence :: !Text

  Sequence of the full construct in one-letter-code

Instances

Eq Entity

Defined in Bio.MMTF.Type

Methods

(==) :: Entity -> Entity -> Bool

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

Show Entity

Defined in Bio.MMTF.Type

Methods

showsPrec :: Int -> Entity -> ShowS

show :: Entity -> String

showList :: [Entity] -> ShowS

data GroupType

Group type data

Constructors

GroupType

Fields

• gtFormalChargeList :: ![Int32]

  List of formal charges

• gtAtomNameList :: ![Text]

  List of atom names

• gtElementList :: ![Text]

  List of elements

• gtBondAtomList :: ![Int32]

  List of bonded atom indices

• gtBondOrderList :: ![Int32]

  List of bond orders

• gtGroupName :: !Text

  The name of the group

• gtSingleLetterCode :: !Char

  The single letter code

• gtChemCompType :: !Text

  The chemical component type

Instances

Eq GroupType

Defined in Bio.MMTF.Type

Methods

(==) :: GroupType -> GroupType -> Bool

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

Show GroupType

Defined in Bio.MMTF.Type

Methods

showsPrec :: Int -> GroupType -> ShowS

show :: GroupType -> String

showList :: [GroupType] -> ShowS

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.MMTF.Type

Methods

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

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

Show SecondaryStructure

Defined in Bio.MMTF.Type

Methods

showsPrec :: Int -> SecondaryStructure -> ShowS

show :: SecondaryStructure -> String

showList :: [SecondaryStructure] -> ShowS

data FormatData

MMTF format data

Constructors

FormatData

Fields

• mmtfVersion :: !Text

  The version number of the specification the file adheres to

• mmtfProducer :: !Text

  The name and version of the software used to produce the file

Instances

Eq FormatData

Defined in Bio.MMTF.Type

Methods

(==) :: FormatData -> FormatData -> Bool

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

Show FormatData

Defined in Bio.MMTF.Type

Methods

showsPrec :: Int -> FormatData -> ShowS

show :: FormatData -> String

showList :: [FormatData] -> ShowS

data StructureData

Structure data

Constructors

StructureData

Fields

• title :: !Text

  A short description of the structural data included in the file

• structureId :: !Text

  An ID for the structure, for example the PDB ID if applicable

• depositionDate :: !Text

  A date that relates to the deposition of the structure in a database

• releaseDate :: !Text

  A date that relates to the release of the structure in a database

• numBonds :: !Int32

  The overall number of bonds

• numAtoms :: !Int32

  The overall number of atoms in the structure

• numGroups :: !Int32

  The overall number of groups in the structure

• numChains :: !Int32

  The overall number of chains in the structure

• numModels :: !Int32

  The overall number of models in the structure

• spaceGroup :: !Text

  The Hermann-Mauguin space-group symbol

• unitCell :: !(Maybe UnitCell)

  Array of six values defining the unit cell

• ncsOperatorList :: ![[Float]]

  List of lists representing 4x4 transformation matrices that are stored linearly in row major order (transformation matrices describe noncrystallographic symmetry operations needed to create all molecules in the unit cell)

• bioAssemblyList :: ![Assembly]

  List of instructions on how to transform coordinates for an array of chains to create (biological) assemblies

• entityList :: ![Entity]

  List of unique molecular entities within the structure

• resolution :: !(Maybe Float)

  The experimental resolution in Angstrom

• rFree :: !(Maybe Float)

  The R-free value

• rWork :: !(Maybe Float)

  The R-work value

• experimentalMethods :: ![Text]

  List of experimental methods employed for structure determination

• bondAtomList :: ![Int32]

  Pairs of values represent indices of covalently bonded atoms [binary (type 4)]

• bondOrderList :: ![Int8]

  List of bond orders for bonds in bondAtomList [binary (type 2)]

Instances

Eq StructureData

Defined in Bio.MMTF.Type

Methods

(==) :: StructureData -> StructureData -> Bool

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

Show StructureData

Defined in Bio.MMTF.Type

Methods

showsPrec :: Int -> StructureData -> ShowS

show :: StructureData -> String

showList :: [StructureData] -> ShowS

data ModelData

Models data

Constructors

ModelData

Fields

• chainsPerModel :: ![Int32]

  List of the number of chains in each model

Instances

Eq ModelData

Defined in Bio.MMTF.Type

Methods

(==) :: ModelData -> ModelData -> Bool

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

Show ModelData

Defined in Bio.MMTF.Type

Methods

showsPrec :: Int -> ModelData -> ShowS

show :: ModelData -> String

showList :: [ModelData] -> ShowS

data ChainData

Chains data

Constructors

ChainData

Fields

• groupsPerChain :: ![Int32]

  List of the number of groups (aka residues) in each chain

• chainIdList :: ![Text]

  List of chain IDs [binary (type 5)]

• chainNameList :: ![Text]

  List of chain names [binary (type 5)]

Instances

Eq ChainData

Defined in Bio.MMTF.Type

Methods

(==) :: ChainData -> ChainData -> Bool

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

Show ChainData

Defined in Bio.MMTF.Type

Methods

showsPrec :: Int -> ChainData -> ShowS

show :: ChainData -> String

showList :: [ChainData] -> ShowS

data GroupData

Groups data

Constructors

GroupData

Fields

• groupList :: ![GroupType]

  List of groupType objects

• groupTypeList :: ![Int32]

  List of pointers to groupType entries in groupList by their keys [binary (type 4)]

• groupIdList :: ![Int32]

  List of group (residue) numbers [binary (type 8)]

• secStructList :: ![SecondaryStructure]

  List of secondary structure assignments [binary (type 2)]

• insCodeList :: ![Char]

  List of insertion codes, one for each group (residue) [binary (type 6)]

• sequenceIndexList :: ![Int32]

  List of indices that point into the sequence property of an entity object in the entityList field that is associated with the chain the group belongs to [binary (type 8)]

Instances

Eq GroupData

Defined in Bio.MMTF.Type

Methods

(==) :: GroupData -> GroupData -> Bool

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

Show GroupData

Defined in Bio.MMTF.Type

Methods

showsPrec :: Int -> GroupData -> ShowS

show :: GroupData -> String

showList :: [GroupData] -> ShowS

data AtomData

Atoms data

Constructors

AtomData

Fields

• atomIdList :: ![Int32]

  List of atom serial numbers [binary (type 8)]

• altLocList :: ![Char]

  List of alternate location labels, one for each atom [binary (type 6)]

• bFactorList :: ![Float]

  List of atom B-factors in in A^2, one for each atom [binary (type 10)]

• xCoordList :: ![Float]

  List of x atom coordinates in A, one for each atom [binary (type 10)]

• yCoordList :: ![Float]

  List of y atom coordinates in A, one for each atom [binary (type 10)]

• zCoordList :: ![Float]

  List of z atom coordinates in A, one for each atom [binary (type 10)]

• occupancyList :: ![Float]

  List of atom occupancies, one for each atom [binary (type 9)]

Instances

Eq AtomData

Defined in Bio.MMTF.Type

Methods

(==) :: AtomData -> AtomData -> Bool

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

Show AtomData

Defined in Bio.MMTF.Type

Methods

showsPrec :: Int -> AtomData -> ShowS

show :: AtomData -> String

showList :: [AtomData] -> ShowS

data MMTF

MMTF datatype

Constructors

MMTF

Fields

• format :: !FormatData

  MMTF format data

• structure :: !StructureData

  Biological structure data

• model :: !ModelData

  Models data

• chain :: !ChainData

  Chains data

• group :: !GroupData

  Groups data

• atom :: !AtomData

  Atoms data

Instances

Eq MMTF

Defined in Bio.MMTF.Type

Methods

(==) :: MMTF -> MMTF -> Bool

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

Show MMTF

Defined in Bio.MMTF.Type

Methods

showsPrec :: Int -> MMTF -> ShowS

show :: MMTF -> String

showList :: [MMTF] -> ShowS

MessagePack MMTF

Defined in Bio.MMTF.MessagePack

Methods

toObject :: MMTF -> Object

fromObject :: (Applicative m, Monad m) => Object -> m MMTF

decode :: Monad m => ByteString -> m MMTF

Decodes a ByteString to MMTF

fetch :: MonadIO m => String -> m MMTF

Fetches MMTF structure from RSCB