Safe Haskell	Safe-Inferred
Language	Haskell2010

Bio.MMTF.Type

Synopsis

data M44 = M44 Float Float Float Float Float Float Float Float Float Float Float Float Float Float Float Float
data UnitCell = UnitCell {
- ucA :: !Float
- ucB :: !Float
- ucC :: !Float
- ucAlpha :: !Float
- ucBeta :: !Float
- ucGamma :: !Float
}
data Transform = Transform {
- chainIndexList :: !(Vector Int32)
- matrix :: !M44
}
data Assembly = Assembly {
- transformList :: !(Vector Transform)
- assemblyName :: !Text
}
data Entity = Entity {
- entityChainIndexList :: !(Vector Int32)
- entityDescription :: !Text
- entityType :: !Text
- entitySequence :: !Text
}
data GroupType = GroupType {
- gtFormalChargeList :: !(Vector Int32)
- gtAtomNameList :: !(Vector Text)
- gtElementList :: !(Vector Text)
- gtBondAtomList :: !(Vector (Int32, Int32))
- gtBondOrderList :: !(Vector Int32)
- gtGroupName :: !Text
- gtSingleLetterCode :: !Char
- gtChemCompType :: !Text
}
data FormatData = FormatData {
- mmtfVersion :: !Text
- mmtfProducer :: !Text
}
data StructureData = StructureData {
- title :: !Text
- structureId :: !Text
- depositionDate :: !Text
- releaseDate :: !Text
- numBonds :: !Int32
- numAtoms :: !Int32
- numGroups :: !Int32
- numChains :: !Int32
- numModels :: !Int32
- spaceGroup :: !Text
- unitCell :: !(Maybe UnitCell)
- ncsOperatorList :: !(Vector M44)
- bioAssemblyList :: !(Vector Assembly)
- entityList :: !(Vector Entity)
- resolution :: !(Maybe Float)
- rFree :: !(Maybe Float)
- rWork :: !(Maybe Float)
- experimentalMethods :: !(Vector Text)
- bondAtomList :: !(Vector (Int32, Int32))
- bondOrderList :: !(Vector Int8)
}
data ModelData = ModelData {
- chainsPerModel :: !(Vector Int32)
}
data ChainData = ChainData {
- groupsPerChain :: !(Vector Int32)
- chainIdList :: !(Vector Text)
- chainNameList :: !(Vector Text)
}
data GroupData = GroupData {
- groupList :: !(Vector GroupType)
- groupTypeList :: !(Vector Int32)
- groupIdList :: !(Vector Int32)
- secStructList :: !(Vector SecondaryStructure)
- insCodeList :: !(Vector Text)
- sequenceIndexList :: !(Vector Int32)
}
data AtomData = AtomData {
- atomIdList :: !(Vector Int32)
- altLocList :: !(Vector Text)
- bFactorList :: !(Vector Float)
- xCoordList :: !(Vector Float)
- yCoordList :: !(Vector Float)
- zCoordList :: !(Vector Float)
- occupancyList :: !(Vector Float)
}
data MMTF = MMTF {
- format :: !FormatData
- structure :: !StructureData
- model :: !ModelData
- chain :: !ChainData
- group :: !GroupData
- atom :: !AtomData
}

Documentation

data M44 Source #

Transformation matrix

Constructors

M44 Float Float Float Float Float Float Float Float Float Float Float Float Float Float Float Float

Instances

Instances details

Generic M44 Source #
Instance details Defined in Bio.MMTF.Type Associated Types type Rep M44 :: Type -> Type # Methods from :: M44 -> Rep M44 x # to :: Rep M44 x -> M44 #
Show M44 Source #
Instance details Defined in Bio.MMTF.Type Methods showsPrec :: Int -> M44 -> ShowS # show :: M44 -> String # showList :: [M44] -> ShowS #
NFData M44 Source #
Instance details Defined in Bio.MMTF.Type Methods rnf :: M44 -> () #
Eq M44 Source #
Instance details Defined in Bio.MMTF.Type Methods (==) :: M44 -> M44 -> Bool # (/=) :: M44 -> M44 -> Bool #
type Rep M44 Source #
Instance details Defined in Bio.MMTF.Type type Rep M44 = D1 ('MetaData "M44" "Bio.MMTF.Type" "cobot-io-0.1.5.5-2fgiMxNKBm19YNVvDwIPRV" 'False) (C1 ('MetaCons "M44" 'PrefixI 'False) ((((S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Float) :: S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Float)) :: (S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Float) :: S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Float))) :: ((S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Float) :: S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Float)) :: (S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Float) :: S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Float)))) :: (((S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Float) :: S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Float)) :: (S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Float) :: S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Float))) :: ((S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Float) :: S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Float)) :: (S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Float) :*: S1 ('MetaSel ('Nothing :: Maybe Symbol) 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Float))))))

data UnitCell Source #

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

Instances details

Generic UnitCell Source #
Instance details Defined in Bio.MMTF.Type Associated Types type Rep UnitCell :: Type -> Type # Methods from :: UnitCell -> Rep UnitCell x # to :: Rep UnitCell x -> UnitCell #
Show UnitCell Source #
Instance details Defined in Bio.MMTF.Type Methods showsPrec :: Int -> UnitCell -> ShowS # show :: UnitCell -> String # showList :: [UnitCell] -> ShowS #
NFData UnitCell Source #
Instance details Defined in Bio.MMTF.Type Methods rnf :: UnitCell -> () #
Eq UnitCell Source #
Instance details Defined in Bio.MMTF.Type Methods (==) :: UnitCell -> UnitCell -> Bool # (/=) :: UnitCell -> UnitCell -> Bool #
type Rep UnitCell Source #
Instance details Defined in Bio.MMTF.Type type Rep UnitCell = D1 ('MetaData "UnitCell" "Bio.MMTF.Type" "cobot-io-0.1.5.5-2fgiMxNKBm19YNVvDwIPRV" 'False) (C1 ('MetaCons "UnitCell" 'PrefixI 'True) ((S1 ('MetaSel ('Just "ucA") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Float) :: (S1 ('MetaSel ('Just "ucB") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Float) :: S1 ('MetaSel ('Just "ucC") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Float))) :: (S1 ('MetaSel ('Just "ucAlpha") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Float) :: (S1 ('MetaSel ('Just "ucBeta") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Float) :*: S1 ('MetaSel ('Just "ucGamma") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Float)))))

data Transform Source #

Transform data

Constructors

Transform
Fields chainIndexList :: !(Vector Int32) indices into the `chainIdList` and `chainNameList` fields matrix :: !M44 4x4 transformation matrix

Instances

Instances details

Generic Transform Source #
Instance details Defined in Bio.MMTF.Type Associated Types type Rep Transform :: Type -> Type # Methods from :: Transform -> Rep Transform x # to :: Rep Transform x -> Transform #
Show Transform Source #
Instance details Defined in Bio.MMTF.Type Methods showsPrec :: Int -> Transform -> ShowS # show :: Transform -> String # showList :: [Transform] -> ShowS #
NFData Transform Source #
Instance details Defined in Bio.MMTF.Type Methods rnf :: Transform -> () #
Eq Transform Source #
Instance details Defined in Bio.MMTF.Type Methods (==) :: Transform -> Transform -> Bool # (/=) :: Transform -> Transform -> Bool #
type Rep Transform Source #
Instance details Defined in Bio.MMTF.Type type Rep Transform = D1 ('MetaData "Transform" "Bio.MMTF.Type" "cobot-io-0.1.5.5-2fgiMxNKBm19YNVvDwIPRV" 'False) (C1 ('MetaCons "Transform" 'PrefixI 'True) (S1 ('MetaSel ('Just "chainIndexList") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (Vector Int32)) :*: S1 ('MetaSel ('Just "matrix") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 M44)))

data Assembly Source #

Assembly data

Constructors

Assembly
Fields transformList :: !(Vector Transform) List of transform objects assemblyName :: !Text Name of the biological assembly

Instances

Instances details

Generic Assembly Source #
Instance details Defined in Bio.MMTF.Type Associated Types type Rep Assembly :: Type -> Type # Methods from :: Assembly -> Rep Assembly x # to :: Rep Assembly x -> Assembly #
Show Assembly Source #
Instance details Defined in Bio.MMTF.Type Methods showsPrec :: Int -> Assembly -> ShowS # show :: Assembly -> String # showList :: [Assembly] -> ShowS #
NFData Assembly Source #
Instance details Defined in Bio.MMTF.Type Methods rnf :: Assembly -> () #
Eq Assembly Source #
Instance details Defined in Bio.MMTF.Type Methods (==) :: Assembly -> Assembly -> Bool # (/=) :: Assembly -> Assembly -> Bool #
type Rep Assembly Source #
Instance details Defined in Bio.MMTF.Type type Rep Assembly = D1 ('MetaData "Assembly" "Bio.MMTF.Type" "cobot-io-0.1.5.5-2fgiMxNKBm19YNVvDwIPRV" 'False) (C1 ('MetaCons "Assembly" 'PrefixI 'True) (S1 ('MetaSel ('Just "transformList") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (Vector Transform)) :*: S1 ('MetaSel ('Just "assemblyName") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Text)))

data Entity Source #

Entity data

Constructors

Entity
Fields entityChainIndexList :: !(Vector 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

Instances details

Generic Entity Source #
Instance details Defined in Bio.MMTF.Type Associated Types type Rep Entity :: Type -> Type # Methods from :: Entity -> Rep Entity x # to :: Rep Entity x -> Entity #
Show Entity Source #
Instance details Defined in Bio.MMTF.Type Methods showsPrec :: Int -> Entity -> ShowS # show :: Entity -> String # showList :: [Entity] -> ShowS #
NFData Entity Source #
Instance details Defined in Bio.MMTF.Type Methods rnf :: Entity -> () #
Eq Entity Source #
Instance details Defined in Bio.MMTF.Type Methods (==) :: Entity -> Entity -> Bool # (/=) :: Entity -> Entity -> Bool #
type Rep Entity Source #
Instance details Defined in Bio.MMTF.Type type Rep Entity = D1 ('MetaData "Entity" "Bio.MMTF.Type" "cobot-io-0.1.5.5-2fgiMxNKBm19YNVvDwIPRV" 'False) (C1 ('MetaCons "Entity" 'PrefixI 'True) ((S1 ('MetaSel ('Just "entityChainIndexList") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (Vector Int32)) :: S1 ('MetaSel ('Just "entityDescription") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Text)) :: (S1 ('MetaSel ('Just "entityType") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Text) :*: S1 ('MetaSel ('Just "entitySequence") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Text))))

data GroupType Source #

Group type data

Constructors

GroupType

Fields

gtFormalChargeList :: !(Vector Int32)
List of formal charges
gtAtomNameList :: !(Vector Text)
List of atom names
gtElementList :: !(Vector Text)
List of elements
gtBondAtomList :: !(Vector (Int32, Int32))
List of bonded atom indices
gtBondOrderList :: !(Vector 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

Instances details

Generic GroupType Source #
Instance details Defined in Bio.MMTF.Type Associated Types type Rep GroupType :: Type -> Type # Methods from :: GroupType -> Rep GroupType x # to :: Rep GroupType x -> GroupType #
Show GroupType Source #
Instance details Defined in Bio.MMTF.Type Methods showsPrec :: Int -> GroupType -> ShowS # show :: GroupType -> String # showList :: [GroupType] -> ShowS #
NFData GroupType Source #
Instance details Defined in Bio.MMTF.Type Methods rnf :: GroupType -> () #
Eq GroupType Source #
Instance details Defined in Bio.MMTF.Type Methods (==) :: GroupType -> GroupType -> Bool # (/=) :: GroupType -> GroupType -> Bool #
type Rep GroupType Source #
Instance details Defined in Bio.MMTF.Type type Rep GroupType = D1 ('MetaData "GroupType" "Bio.MMTF.Type" "cobot-io-0.1.5.5-2fgiMxNKBm19YNVvDwIPRV" 'False) (C1 ('MetaCons "GroupType" 'PrefixI 'True) (((S1 ('MetaSel ('Just "gtFormalChargeList") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (Vector Int32)) :: S1 ('MetaSel ('Just "gtAtomNameList") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (Vector Text))) :: (S1 ('MetaSel ('Just "gtElementList") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (Vector Text)) :: S1 ('MetaSel ('Just "gtBondAtomList") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (Vector (Int32, Int32))))) :: ((S1 ('MetaSel ('Just "gtBondOrderList") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (Vector Int32)) :: S1 ('MetaSel ('Just "gtGroupName") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Text)) :: (S1 ('MetaSel ('Just "gtSingleLetterCode") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Char) :*: S1 ('MetaSel ('Just "gtChemCompType") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Text)))))

data FormatData Source #

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

Instances details

Generic FormatData Source #
Instance details Defined in Bio.MMTF.Type Associated Types type Rep FormatData :: Type -> Type # Methods from :: FormatData -> Rep FormatData x # to :: Rep FormatData x -> FormatData #
Show FormatData Source #
Instance details Defined in Bio.MMTF.Type Methods showsPrec :: Int -> FormatData -> ShowS # show :: FormatData -> String # showList :: [FormatData] -> ShowS #
NFData FormatData Source #
Instance details Defined in Bio.MMTF.Type Methods rnf :: FormatData -> () #
Eq FormatData Source #
Instance details Defined in Bio.MMTF.Type Methods (==) :: FormatData -> FormatData -> Bool # (/=) :: FormatData -> FormatData -> Bool #
type Rep FormatData Source #
Instance details Defined in Bio.MMTF.Type type Rep FormatData = D1 ('MetaData "FormatData" "Bio.MMTF.Type" "cobot-io-0.1.5.5-2fgiMxNKBm19YNVvDwIPRV" 'False) (C1 ('MetaCons "FormatData" 'PrefixI 'True) (S1 ('MetaSel ('Just "mmtfVersion") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Text) :*: S1 ('MetaSel ('Just "mmtfProducer") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Text)))

data StructureData Source #

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 :: !(Vector M44)
List of 4x4 transformation matrices (transformation matrices describe noncrystallographic symmetry operations needed to create all molecules in the unit cell)
bioAssemblyList :: !(Vector Assembly)
List of instructions on how to transform coordinates for an array of chains to create (biological) assemblies
entityList :: !(Vector 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 :: !(Vector Text)
List of experimental methods employed for structure determination
bondAtomList :: !(Vector (Int32, Int32))
Pairs of values represent indices of covalently bonded atoms [binary (type 4)]
bondOrderList :: !(Vector Int8)
List of bond orders for bonds in bondAtomList [binary (type 2)]

Instances

Instances details

Generic StructureData Source #
Instance details Defined in Bio.MMTF.Type Associated Types type Rep StructureData :: Type -> Type # Methods from :: StructureData -> Rep StructureData x # to :: Rep StructureData x -> StructureData #
Show StructureData Source #
Instance details Defined in Bio.MMTF.Type Methods showsPrec :: Int -> StructureData -> ShowS # show :: StructureData -> String # showList :: [StructureData] -> ShowS #
NFData StructureData Source #
Instance details Defined in Bio.MMTF.Type Methods rnf :: StructureData -> () #
Eq StructureData Source #
Instance details Defined in Bio.MMTF.Type Methods (==) :: StructureData -> StructureData -> Bool # (/=) :: StructureData -> StructureData -> Bool #
type Rep StructureData Source #
Instance details Defined in Bio.MMTF.Type type Rep StructureData = D1 ('MetaData "StructureData" "Bio.MMTF.Type" "cobot-io-0.1.5.5-2fgiMxNKBm19YNVvDwIPRV" 'False) (C1 ('MetaCons "StructureData" 'PrefixI 'True) ((((S1 ('MetaSel ('Just "title") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Text) :: S1 ('MetaSel ('Just "structureId") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Text)) :: (S1 ('MetaSel ('Just "depositionDate") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Text) :: (S1 ('MetaSel ('Just "releaseDate") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Text) :: S1 ('MetaSel ('Just "numBonds") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Int32)))) :: ((S1 ('MetaSel ('Just "numAtoms") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Int32) :: S1 ('MetaSel ('Just "numGroups") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Int32)) :: (S1 ('MetaSel ('Just "numChains") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Int32) :: (S1 ('MetaSel ('Just "numModels") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Int32) :: S1 ('MetaSel ('Just "spaceGroup") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 Text))))) :: (((S1 ('MetaSel ('Just "unitCell") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (Maybe UnitCell)) :: S1 ('MetaSel ('Just "ncsOperatorList") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (Vector M44))) :: (S1 ('MetaSel ('Just "bioAssemblyList") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (Vector Assembly)) :: (S1 ('MetaSel ('Just "entityList") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (Vector Entity)) :: S1 ('MetaSel ('Just "resolution") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (Maybe Float))))) :: ((S1 ('MetaSel ('Just "rFree") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (Maybe Float)) :: S1 ('MetaSel ('Just "rWork") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (Maybe Float))) :: (S1 ('MetaSel ('Just "experimentalMethods") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (Vector Text)) :: (S1 ('MetaSel ('Just "bondAtomList") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (Vector (Int32, Int32))) :*: S1 ('MetaSel ('Just "bondOrderList") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (Vector Int8))))))))

data ModelData Source #

Models data

Constructors

ModelData
Fields chainsPerModel :: !(Vector Int32) List of the number of chains in each model

Instances

Instances details

Generic ModelData Source #
Instance details Defined in Bio.MMTF.Type Associated Types type Rep ModelData :: Type -> Type # Methods from :: ModelData -> Rep ModelData x # to :: Rep ModelData x -> ModelData #
Show ModelData Source #
Instance details Defined in Bio.MMTF.Type Methods showsPrec :: Int -> ModelData -> ShowS # show :: ModelData -> String # showList :: [ModelData] -> ShowS #
NFData ModelData Source #
Instance details Defined in Bio.MMTF.Type Methods rnf :: ModelData -> () #
Eq ModelData Source #
Instance details Defined in Bio.MMTF.Type Methods (==) :: ModelData -> ModelData -> Bool # (/=) :: ModelData -> ModelData -> Bool #
type Rep ModelData Source #
Instance details Defined in Bio.MMTF.Type type Rep ModelData = D1 ('MetaData "ModelData" "Bio.MMTF.Type" "cobot-io-0.1.5.5-2fgiMxNKBm19YNVvDwIPRV" 'False) (C1 ('MetaCons "ModelData" 'PrefixI 'True) (S1 ('MetaSel ('Just "chainsPerModel") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (Vector Int32))))

data ChainData Source #

Chains data

Constructors

ChainData
Fields groupsPerChain :: !(Vector Int32) List of the number of groups (aka residues) in each chain chainIdList :: !(Vector Text) List of chain IDs [binary (type 5)] chainNameList :: !(Vector Text) List of chain names [binary (type 5)]

Instances

Instances details

Generic ChainData Source #
Instance details Defined in Bio.MMTF.Type Associated Types type Rep ChainData :: Type -> Type # Methods from :: ChainData -> Rep ChainData x # to :: Rep ChainData x -> ChainData #
Show ChainData Source #
Instance details Defined in Bio.MMTF.Type Methods showsPrec :: Int -> ChainData -> ShowS # show :: ChainData -> String # showList :: [ChainData] -> ShowS #
NFData ChainData Source #
Instance details Defined in Bio.MMTF.Type Methods rnf :: ChainData -> () #
Eq ChainData Source #
Instance details Defined in Bio.MMTF.Type Methods (==) :: ChainData -> ChainData -> Bool # (/=) :: ChainData -> ChainData -> Bool #
type Rep ChainData Source #
Instance details Defined in Bio.MMTF.Type type Rep ChainData = D1 ('MetaData "ChainData" "Bio.MMTF.Type" "cobot-io-0.1.5.5-2fgiMxNKBm19YNVvDwIPRV" 'False) (C1 ('MetaCons "ChainData" 'PrefixI 'True) (S1 ('MetaSel ('Just "groupsPerChain") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (Vector Int32)) :: (S1 ('MetaSel ('Just "chainIdList") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (Vector Text)) :: S1 ('MetaSel ('Just "chainNameList") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (Vector Text)))))

data GroupData Source #

Groups data

Constructors

GroupData

Fields

groupList :: !(Vector GroupType)
List of groupType objects
groupTypeList :: !(Vector Int32)
List of pointers to groupType entries in groupList by their keys [binary (type 4)]
groupIdList :: !(Vector Int32)
List of group (residue) numbers [binary (type 8)]
secStructList :: !(Vector SecondaryStructure)
List of secondary structure assignments [binary (type 2)]
insCodeList :: !(Vector Text)
List of insertion codes, one for each group (residue) [binary (type 6)]
sequenceIndexList :: !(Vector 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

Instances details

Generic GroupData Source #
Instance details Defined in Bio.MMTF.Type Associated Types type Rep GroupData :: Type -> Type # Methods from :: GroupData -> Rep GroupData x # to :: Rep GroupData x -> GroupData #
Show GroupData Source #
Instance details Defined in Bio.MMTF.Type Methods showsPrec :: Int -> GroupData -> ShowS # show :: GroupData -> String # showList :: [GroupData] -> ShowS #
NFData GroupData Source #
Instance details Defined in Bio.MMTF.Type Methods rnf :: GroupData -> () #
Eq GroupData Source #
Instance details Defined in Bio.MMTF.Type Methods (==) :: GroupData -> GroupData -> Bool # (/=) :: GroupData -> GroupData -> Bool #
type Rep GroupData Source #
Instance details Defined in Bio.MMTF.Type type Rep GroupData = D1 ('MetaData "GroupData" "Bio.MMTF.Type" "cobot-io-0.1.5.5-2fgiMxNKBm19YNVvDwIPRV" 'False) (C1 ('MetaCons "GroupData" 'PrefixI 'True) ((S1 ('MetaSel ('Just "groupList") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (Vector GroupType)) :: (S1 ('MetaSel ('Just "groupTypeList") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (Vector Int32)) :: S1 ('MetaSel ('Just "groupIdList") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (Vector Int32)))) :: (S1 ('MetaSel ('Just "secStructList") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (Vector SecondaryStructure)) :: (S1 ('MetaSel ('Just "insCodeList") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (Vector Text)) :*: S1 ('MetaSel ('Just "sequenceIndexList") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (Vector Int32))))))

data AtomData Source #

Atoms data

Constructors

AtomData

Fields

atomIdList :: !(Vector Int32)
List of atom serial numbers [binary (type 8)]
altLocList :: !(Vector Text)
List of alternate location labels, one for each atom [binary (type 6)]
bFactorList :: !(Vector Float)
List of atom B-factors in in A^2, one for each atom [binary (type 10)]
xCoordList :: !(Vector Float)
List of x atom coordinates in A, one for each atom [binary (type 10)]
yCoordList :: !(Vector Float)
List of y atom coordinates in A, one for each atom [binary (type 10)]
zCoordList :: !(Vector Float)
List of z atom coordinates in A, one for each atom [binary (type 10)]
occupancyList :: !(Vector Float)
List of atom occupancies, one for each atom [binary (type 9)]

Instances

Instances details

Generic AtomData Source #
Instance details Defined in Bio.MMTF.Type Associated Types type Rep AtomData :: Type -> Type # Methods from :: AtomData -> Rep AtomData x # to :: Rep AtomData x -> AtomData #
Show AtomData Source #
Instance details Defined in Bio.MMTF.Type Methods showsPrec :: Int -> AtomData -> ShowS # show :: AtomData -> String # showList :: [AtomData] -> ShowS #
NFData AtomData Source #
Instance details Defined in Bio.MMTF.Type Methods rnf :: AtomData -> () #
Eq AtomData Source #
Instance details Defined in Bio.MMTF.Type Methods (==) :: AtomData -> AtomData -> Bool # (/=) :: AtomData -> AtomData -> Bool #
type Rep AtomData Source #
Instance details Defined in Bio.MMTF.Type type Rep AtomData = D1 ('MetaData "AtomData" "Bio.MMTF.Type" "cobot-io-0.1.5.5-2fgiMxNKBm19YNVvDwIPRV" 'False) (C1 ('MetaCons "AtomData" 'PrefixI 'True) ((S1 ('MetaSel ('Just "atomIdList") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (Vector Int32)) :: (S1 ('MetaSel ('Just "altLocList") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (Vector Text)) :: S1 ('MetaSel ('Just "bFactorList") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (Vector Float)))) :: ((S1 ('MetaSel ('Just "xCoordList") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (Vector Float)) :: S1 ('MetaSel ('Just "yCoordList") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (Vector Float))) :: (S1 ('MetaSel ('Just "zCoordList") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (Vector Float)) :: S1 ('MetaSel ('Just "occupancyList") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (Vector Float))))))

data MMTF Source #

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

Instances details

Generic MMTF Source #
Instance details Defined in Bio.MMTF.Type Associated Types type Rep MMTF :: Type -> Type # Methods from :: MMTF -> Rep MMTF x # to :: Rep MMTF x -> MMTF #
Show MMTF Source #
Instance details Defined in Bio.MMTF.Type Methods showsPrec :: Int -> MMTF -> ShowS # show :: MMTF -> String # showList :: [MMTF] -> ShowS #
StructureModels MMTF Source #
Instance details Defined in Bio.MMTF Methods modelsOf :: MMTF -> Vector Model Source #
MessagePack MMTF Source #
Instance details Defined in Bio.MMTF.MessagePack Methods toObject :: MMTF -> Object # fromObject :: (Applicative m, Monad m, MonadFail m) => Object -> m MMTF #
NFData MMTF Source #
Instance details Defined in Bio.MMTF.Type Methods rnf :: MMTF -> () #
Eq MMTF Source #
Instance details Defined in Bio.MMTF.Type Methods (==) :: MMTF -> MMTF -> Bool # (/=) :: MMTF -> MMTF -> Bool #
type Rep MMTF Source #
Instance details Defined in Bio.MMTF.Type type Rep MMTF = D1 ('MetaData "MMTF" "Bio.MMTF.Type" "cobot-io-0.1.5.5-2fgiMxNKBm19YNVvDwIPRV" 'False) (C1 ('MetaCons "MMTF" 'PrefixI 'True) ((S1 ('MetaSel ('Just "format") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 FormatData) :: (S1 ('MetaSel ('Just "structure") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 StructureData) :: S1 ('MetaSel ('Just "model") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 ModelData))) :: (S1 ('MetaSel ('Just "chain") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 ChainData) :: (S1 ('MetaSel ('Just "group") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 GroupData) :*: S1 ('MetaSel ('Just "atom") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 AtomData)))))