mmtf 0.1.0.1 → 0.1.1.0

raw patch · 7 files changed

+191/−139 lines, 7 filesdep +http-conduitdep ~QuickCheckdep ~binarydep ~containersPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

Dependencies added: http-conduit

Dependency ranges changed: QuickCheck, binary, containers, hspec

API changes (from Hackage documentation)

Files

• mmtf.cabal +4/−3
• src/Bio/MMTF.hs +15/−3
• src/Bio/MMTF/Decode.hs +25/−15
• src/Bio/MMTF/Decode/Codec.hs +38/−22
• src/Bio/MMTF/Decode/MessagePack.hs +5/−5
• src/Bio/MMTF/Type.hs +102/−89
• test/Spec.hs +2/−2

@@ -1,5 +1,5 @@ name:                mmtf-version:             0.1.0.1+version:             0.1.1.0 synopsis:            Macromolecular Transmission Format implementation description:         Haskell implementation of MMTF biological structure format. homepage:            https://github.com/zmactep/mmtf#readme@@ -25,8 +25,9 @@                      , data-msgpack >= 0.0.9 && < 0.1                      , text >= 1.2.2.1 && < 1.3                      , bytestring >= 0.10.8.1 && < 0.11-                     , binary >= 0.8.3.0 && < 0.9-                     , containers >= 0.5.7.1 && < 0.6+                     , binary >= 0.8.3.0 && < 1.0+                     , containers >= 0.5.7.1 && < 0.7+                     , http-conduit >= 2.3 && < 2.4   default-language:    Haskell2010   ghc-options:         -Wall 

@@ -1,14 +1,26 @@ module Bio.MMTF   ( module Bio.MMTF.Type   , decode+  , fetch   ) where  import           Bio.MMTF.MessagePack () import           Bio.MMTF.Type -import           Data.ByteString.Lazy (ByteString)-import           Data.MessagePack     (unpack)+import           Data.ByteString.Lazy   (ByteString)+import           Data.MessagePack       (unpack)+import           Data.Monoid            ((<>))+import           Data.String            (IsString (..))+import           Control.Monad.IO.Class (MonadIO)+import           Network.HTTP.Simple    (httpLBS, getResponseBody) --- |Decodes a 'ByteString' to 'MMTF'+-- | Decodes a 'ByteString' to 'MMTF'+-- decode :: Monad m => ByteString -> m MMTF decode = unpack++-- | Fetches MMTF structure from RSCB+fetch :: MonadIO m => String -> m MMTF+fetch pdbid = do let url = fromString $ "https://mmtf.rcsb.org/v1.0/full/" <> pdbid+                 resp <- httpLBS url+                 decode (getResponseBody resp) 

@@ -11,24 +11,28 @@ import           Data.MessagePack            (Object) import           Data.Text                   (Text) --- |Parses format data from ObjectMap+-- | Parses format data from ObjectMap+-- formatData :: Monad m => Map Text Object -> m FormatData formatData mp = do v <- atP mp "mmtfVersion" asStr                    p <- atP mp "mmtfProducer" asStr                    pure $ FormatData v p --- |Parses model data from ObjectMap+-- | Parses model data from ObjectMap+-- modelData :: Monad m => Map Text Object -> m ModelData-modelData mp = atP mp "chainsPerModel" asIntList >>= return . ModelData+modelData mp = ModelData <$> atP mp "chainsPerModel" asIntList --- |Parses chain data from ObjectMap+-- | Parses chain data from ObjectMap+-- chainData :: Monad m => Map Text Object -> m ChainData chainData mp = do gpc <- atP mp "groupsPerChain" asIntList                   cil <- codec5 . parseBinary <$> atP mp "chainIdList" asBinary                   cnl <- (codec5 . parseBinary <$>) <$> atPM mp "chainNameList" asBinary                   pure $ ChainData gpc cil cnl --- |Parses atom data from ObjectMap+-- | Parses atom data from ObjectMap+-- atomData :: Monad m => Map Text Object -> m AtomData atomData mp = do ail' <- (codec8 . parseBinary <$>) <$> atPM mp "atomIdList" asBinary                  all' <- (codec6 . parseBinary <$>) <$> atPM mp "altLocList" asBinary@@ -39,9 +43,10 @@                  ol' <-  (codec9 . parseBinary <$>) <$> atPM mp "occupancyList" asBinary                  pure $ AtomData ail' all' bfl' xcl' ycl' zcl' ol' --- |Parses group data from ObjectMap+-- | Parses group data from ObjectMap+-- groupData :: Monad m => Map Text Object -> m GroupData-groupData mp = do gl' <- atP mp "groupList" asObjectList >>= sequence . map (transformObjectMap >=> groupType)+groupData mp = do gl' <- atP mp "groupList" asObjectList >>= traverse (transformObjectMap >=> groupType)                   gtl' <- codec4 . parseBinary <$> atP mp "groupTypeList" asBinary                   gil' <- codec8 . parseBinary <$> atP mp "groupIdList" asBinary                   ssl' <- (map ssDec . codec2 . parseBinary <$>) <$> atPM mp "secStructList" asBinary@@ -49,7 +54,8 @@                   sil' <- (codec8 . parseBinary <$>) <$> atPM mp "sequenceIndexList" asBinary                   pure $ GroupData gl' gtl' gil' ssl' icl' sil' --- |Parses group type from ObjectMap+-- | Parses group type from ObjectMap+-- groupType :: Monad m => Map Text Object -> m GroupType groupType mp = do fcl' <- atP mp "formalChargeList" asIntList                   anl' <- atP mp "atomNameList" asStrList@@ -61,7 +67,8 @@                   cct' <- atP mp "chemCompType" asStr                   pure $ GroupType fcl' anl' el' bal' bol' gn' slc' cct' --- |Parses structure data from ObjectMap+-- | Parses structure data from ObjectMap+-- structureData :: Monad m => Map Text Object -> m StructureData structureData mp = do ttl' <- atPM mp "title" asStr                       sid' <- atPM mp "structureId" asStr@@ -75,8 +82,8 @@                       sg'  <- atPM mp "spaceGroup" asStr                       uc'  <- (>>= ucDec) <$> atPM mp "unitCell" asFloatList                       nol' <- ((>>= asFloatList) <$>) <$> atPM mp "ncsOperatorList" asObjectList-                      bal' <- (>>= sequence . map (transformObjectMap >=> bioAssembly)) <$> atPM mp "bioAssemblyList" asObjectList-                      el'  <- (>>= sequence . map (transformObjectMap >=> entity)) <$> atPM mp "entityList" asObjectList+                      bal' <- (>>= traverse (transformObjectMap >=> bioAssembly)) <$> atPM mp "bioAssemblyList" asObjectList+                      el'  <- (>>= traverse (transformObjectMap >=> entity)) <$> atPM mp "entityList" asObjectList                       res' <- atPM mp "resolution" asFloat                       rf'  <- atPM mp "rFree" asFloat                       rw'  <- atPM mp "rWork" asFloat@@ -86,19 +93,22 @@                       pure $ StructureData ttl' sid' dd' rd' nb' na' ng' nc' nm' sg' uc' nol'                                            bal' el' res' rf' rw' em' btl' bol' --- |Parses bio assembly data from ObjectMap+-- | Parses bio assembly data from ObjectMap+-- bioAssembly :: Monad m => Map Text Object -> m Assembly bioAssembly mp = do nme' <- atP mp "name" asStr-                    tlt' <- atP mp "transformList" asObjectList >>= sequence . map (transformObjectMap >=> transform)+                    tlt' <- atP mp "transformList" asObjectList >>= traverse (transformObjectMap >=> transform)                     pure $ Assembly tlt' nme' --- |Parses transform data from ObjectMap+-- | Parses transform data from ObjectMap+-- transform :: Monad m => Map Text Object -> m Transform transform mp = do cil' <- atP mp "chainIndexList" asIntList                   mtx' <- atP mp "matrix" asFloatList                   pure $ Transform cil' mtx' --- |Parses entity data from ObjectMap+-- | Parses entity data from ObjectMap+-- entity :: Monad m => Map Text Object -> m Entity entity mp = do cil' <- atP mp "chainIndexList" asIntList                dsc' <- atP mp "description" asStr

@@ -18,95 +18,111 @@                                            in f start : codecCommon f th rest   where ith = fromIntegral th -data BinaryData = BD { binaryCodec  :: Int32-                     , binaryLength :: Int32-                     , binaryParam  :: Int32-                     , binaryData   :: ByteString+data BinaryData = BD { binaryCodec  :: !Int32+                     , binaryLength :: !Int32+                     , binaryParam  :: !Int32+                     , binaryData   :: !ByteString                      } --- |Parse useless header for binary data+-- | Parse useless header for binary data+-- parseBinary :: ByteString -> BinaryData parseBinary bs = let (cdc, rest1) = B.splitAt 4 bs                      (lnh, rest2) = B.splitAt 4 rest1                      (prm, rest)  = B.splitAt 4 rest2                  in  BD (decode cdc) (decode lnh) (decode prm) rest --- |Interpret bytes as array of 32-bit floating-point numbers.+-- | Interpret bytes as array of 32-bit floating-point numbers.+-- codec1 :: BinaryData -> [Float] codec1 = codecCommon decode 4 . binaryData --- |Interpret bytes as array of 8-bit signed integers.+-- | Interpret bytes as array of 8-bit signed integers.+-- codec2 :: BinaryData -> [Int8] codec2 = codecCommon decode 1 . binaryData --- |Interpret bytes as array of 16-bit signed integers.+-- | Interpret bytes as array of 16-bit signed integers.+-- codec3 :: BinaryData -> [Int16] codec3 = codecCommon decode 2 . binaryData --- |Interpret bytes as array of 32-bit signed integers.+-- | Interpret bytes as array of 32-bit signed integers.+-- codec4 :: BinaryData -> [Int32] codec4 = codecCommon decode 4 . binaryData --- |Interpret bytes as array of 8-bit unsigned integers, then iteratively+-- | Interpret bytes as array of 8-bit unsigned integers, then iteratively -- consume length many bytes to form a string array.+-- codec5 :: BinaryData -> [Text] codec5 bd = codecCommon decodeBytes (fromIntegral $ binaryParam bd) (binaryData bd)   where decodeBytes :: ByteString -> Text         decodeBytes bs = T.pack $ chr <$> filter (/=0) (fromIntegral <$> B.unpack bs) --- |Interpret bytes as array of 32-bit signed integers, then run-length+-- | Interpret bytes as array of 32-bit signed integers, then run-length -- decode into array of characters.+-- codec6 :: BinaryData -> [Char] codec6 = map (chr . fromIntegral) . codec7 --- |Interpret bytes as array of 32-bit signed integers, then run-length+-- | Interpret bytes as array of 32-bit signed integers, then run-length -- decode into array of 32-bit signed integers.+-- codec7 :: BinaryData -> [Int32] codec7 = runLengthDec . codec4 --- |Interpret bytes as array of 32-bit signed integers, then run-length+-- | Interpret bytes as array of 32-bit signed integers, then run-length -- decode into array of 32-bit signed integers, then delta decode into -- array of 32-bit signed integers.+-- codec8 :: BinaryData -> [Int32] codec8 = deltaDec . codec7 --- |Interpret bytes as array of 32-bit signed integers, then run-length+-- | Interpret bytes as array of 32-bit signed integers, then run-length -- decode into array of 32-bit signed integers, then integer decode into -- array of 32-bit floating-point numbers using the divisor parameter.+-- codec9 :: BinaryData -> [Float] codec9 bd = integerDec (binaryParam bd) $ codec7 bd --- |Interpret bytes as array of 16-bit signed integers, then unpack into+-- | Interpret bytes as array of 16-bit signed integers, then unpack into -- array of 32-bit integers, then delta decode into array of 32-bit -- integers, then integer decode into array of 32-bit floating-point -- numbers using the divisor parameter.+-- codec10 :: BinaryData -> [Float] codec10 bd = integerDec (binaryParam bd) $ map fromIntegral $ deltaDec $ codec3 bd --- |Interpret bytes as array of 16-bit signed integers, then integer+-- | Interpret bytes as array of 16-bit signed integers, then integer -- decode into array of 32-bit floating-point numbers using the divisor parameter.+-- codec11 :: BinaryData -> [Float] codec11 bd = integerDec (binaryParam bd) $ map fromIntegral $ codec3 bd --- |Interpret bytes as array of 16-bit signed integers, then unpack into+-- | Interpret bytes as array of 16-bit signed integers, then unpack into -- array of 32-bit signed integers, then integer decode into array -- of 32-bit floating-point numbers using the divisor parameter.+-- codec12 :: BinaryData -> [Float] codec12 bd = integerDec (binaryParam bd) $ recIndexDec $ codec3 bd --- |Interpret array of bytes as array of 8-bit signed integers, then+-- | Interpret array of bytes as array of 8-bit signed integers, then -- unpack into array of 32-bit signed integers, then integer decode into -- array of 32-bit floating-point numbers using the divisor parameter.+-- codec13 :: BinaryData -> [Float] codec13 bd = integerDec (binaryParam bd) $ recIndexDec $ codec2 bd --- |Interpret bytes as array of 16-bit signed integers, then unpack+-- | Interpret bytes as array of 16-bit signed integers, then unpack -- into array of 32-bit signed integers.+-- codec14 :: BinaryData -> [Int32] codec14 bd = recIndexDec $ codec3 bd --- |Interpret bytes as array of 8-bit signed integers, then unpack+-- | Interpret bytes as array of 8-bit signed integers, then unpack -- into array of 32-bit signed integers.+-- codec15 :: BinaryData -> [Int32] codec15 bd = recIndexDec $ codec2 bd @@ -115,7 +131,7 @@ runLengthDec :: Integral a => [a] -> [a] runLengthDec [] = [] runLengthDec [_] = error "List must have even length for run-length encoding"-runLengthDec (x:l:xs) = (replicate (fromIntegral l) x) ++ runLengthDec xs+runLengthDec (x:l:xs) = replicate (fromIntegral l) x ++ runLengthDec xs  deltaDec :: Num a => [a] -> [a] deltaDec = snd . mapAccumL (\x y -> (x+y,x+y)) 0@@ -145,4 +161,4 @@  ucDec :: Monad m => [Float] -> m UnitCell ucDec [a,b,c,d,e,f] = pure $ UnitCell a b c d e f-ucDec _  = fail "Wrong list format for unit cell"+ucDec _             = fail "Wrong list format for unit cell"

@@ -9,9 +9,9 @@  transformObjectMap :: Monad m => Object -> m (Map Text Object) transformObjectMap (ObjectMap kv) = let mkPair :: Monad m => (Object, Object) -> m (Text, Object)-                                        mkPair ((ObjectStr txt), v) = pure (txt, v)+                                        mkPair (ObjectStr txt, v) = pure (txt, v)                                         mkPair _ = fail "Non-string key"-                                    in  fromList <$> sequence (map mkPair kv)+                                    in  fromList <$> traverse mkPair kv transformObjectMap _ = fail "Wrong MessagePack MMTF format"  atP :: Monad m => Map Text Object -> Text -> (Object -> m a) -> m a@@ -41,15 +41,15 @@ asFloat _               = fail "Not a float data"  asIntList :: (Monad m, Integral a) => Object -> m [a]-asIntList (ObjectArray l) = sequence $ map asInt l+asIntList (ObjectArray l) = traverse asInt l asIntList _               = fail "Not an array of ints data"  asStrList :: Monad m => Object -> m [Text]-asStrList (ObjectArray l) = sequence $ map asStr l+asStrList (ObjectArray l) = traverse asStr l asStrList _               = fail "Not an array of string data"  asFloatList :: Monad m => Object -> m [Float]-asFloatList (ObjectArray l) = sequence $ map asFloat l+asFloatList (ObjectArray l) = traverse asFloat l asFloatList _               = fail "Not an array of float data"  asObjectList :: Monad m => Object -> m [Object]

@@ -3,129 +3,142 @@ import           Data.Int  (Int32, Int8) import           Data.Text (Text) --- |Unit cell data-data UnitCell = UnitCell { 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+-- | Unit cell data+--+data UnitCell = UnitCell { 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                          }   deriving (Show, Eq) --- |Transform data-data Transform = Transform { chainIndexList :: ![Int32] -- ^indices into the 'chainIdList' and 'chainNameList' fields-                           , matrix         :: ![Float] -- ^4x4 transformation matrix+-- | Transform data+--+data Transform = Transform { chainIndexList :: ![Int32] -- ^ indices into the 'chainIdList' and 'chainNameList' fields+                           , matrix         :: ![Float] -- ^ 4x4 transformation matrix                            }   deriving (Show, Eq) --- |Assembly data-data Assembly = Assembly { transformList :: ![Transform] -- ^List of transform objects-                         , assemblyName  :: !Text        -- ^Name of the biological assembly+-- | Assembly data+--+data Assembly = Assembly { transformList :: ![Transform] -- ^ List of transform objects+                         , assemblyName  :: !Text        -- ^ Name of the biological assembly                          }   deriving (Show, Eq) --- |Entity data-data Entity = Entity { 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+-- | Entity data+--+data Entity = Entity { 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                      }   deriving (Show, Eq) --- |Group type data-data GroupType = GroupType { 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+-- | Group type data+--+data GroupType = GroupType { 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                            }   deriving (Show, Eq) --- |Protein secondary structure-data SecondaryStructure = PiHelix       -- ^pi helix-                        | Bend          -- ^bend-                        | AlphaHelix    -- ^alpha helix-                        | Extended      -- ^extended-                        | ThreeTenHelix -- ^3-10 helix-                        | Bridge        -- ^brigde-                        | Turn          -- ^turn-                        | Coil          -- ^coil-                        | Undefined     -- ^unknown structure+-- | Protein secondary structure+--+data SecondaryStructure = PiHelix       -- ^ pi helix+                        | Bend          -- ^ bend+                        | AlphaHelix    -- ^ alpha helix+                        | Extended      -- ^ extended+                        | ThreeTenHelix -- ^ 3-10 helix+                        | Bridge        -- ^ brigde+                        | Turn          -- ^ turn+                        | Coil          -- ^ coil+                        | Undefined     -- ^ unknown structure   deriving (Show, Eq) --- |MMTF format data-data FormatData = FormatData { 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+-- | MMTF format data+--+data FormatData = FormatData { 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                              }   deriving (Show, Eq) --- |Structure data-data StructureData = StructureData { title               :: !(Maybe Text)       -- ^A short description of the structural data included in the file-                                   , structureId         :: !(Maybe Text)       -- ^An ID for the structure, for example the PDB ID if applicable-                                   , depositionDate      :: !(Maybe Text)       -- ^A date that relates to the deposition of the structure in a database-                                   , releaseDate         :: !(Maybe 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          :: !(Maybe Text)       -- ^The Hermann-Mauguin space-group symbol-                                   , unitCell            :: !(Maybe UnitCell)   -- ^Array of six values defining the unit cell-                                   , ncsOperatorList     :: !(Maybe [[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     :: !(Maybe [Assembly]) -- ^List of instructions on how to transform coordinates for an array of chains to create (biological) assemblies-                                   , entityList          :: !(Maybe [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 :: !(Maybe [Text])     -- ^List of experimental methods employed for structure determination-                                   , bondAtomList        :: !(Maybe [Int32])    -- ^Pairs of values represent indices of covalently bonded atoms [binary (type 4)]-                                   , bondOrderList       :: !(Maybe [Int8])     -- ^List of bond orders for bonds in 'bondAtomList' [binary (type 2)]+-- | Structure data+--+data StructureData = StructureData { title               :: !(Maybe Text)       -- ^ A short description of the structural data included in the file+                                   , structureId         :: !(Maybe Text)       -- ^ An ID for the structure, for example the PDB ID if applicable+                                   , depositionDate      :: !(Maybe Text)       -- ^ A date that relates to the deposition of the structure in a database+                                   , releaseDate         :: !(Maybe 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          :: !(Maybe Text)       -- ^ The Hermann-Mauguin space-group symbol+                                   , unitCell            :: !(Maybe UnitCell)   -- ^ Array of six values defining the unit cell+                                   , ncsOperatorList     :: !(Maybe [[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     :: !(Maybe [Assembly]) -- ^ List of instructions on how to transform coordinates for an array of chains to create (biological) assemblies+                                   , entityList          :: !(Maybe [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 :: !(Maybe [Text])     -- ^ List of experimental methods employed for structure determination+                                   , bondAtomList        :: !(Maybe [Int32])    -- ^ Pairs of values represent indices of covalently bonded atoms [binary (type 4)]+                                   , bondOrderList       :: !(Maybe [Int8])     -- ^ List of bond orders for bonds in 'bondAtomList' [binary (type 2)]                                    }   deriving (Show, Eq) --- |Models data-data ModelData = ModelData { chainsPerModel :: ![Int32] -- ^List of the number of chains in each model+-- | Models data+--+data ModelData = ModelData { chainsPerModel :: ![Int32] -- ^ List of the number of chains in each model                            }   deriving (Show, Eq) --- |Chains data-data ChainData = ChainData { groupsPerChain :: ![Int32]        -- ^List of the number of groups (aka residues) in each chain-                           , chainIdList    :: ![Text]         -- ^List of chain IDs [binary (type 5)]-                           , chainNameList  :: !(Maybe [Text]) -- ^List of chain names [binary (type 5)]+-- | Chains data+--+data ChainData = ChainData { groupsPerChain :: ![Int32]        -- ^ List of the number of groups (aka residues) in each chain+                           , chainIdList    :: ![Text]         -- ^ List of chain IDs [binary (type 5)]+                           , chainNameList  :: !(Maybe [Text]) -- ^ List of chain names [binary (type 5)]                            }   deriving (Show, Eq) --- |Groups data-data GroupData = GroupData { 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     :: !(Maybe [SecondaryStructure]) -- ^List of secondary structure assignments [binary (type 2)]-                           , insCodeList       :: !(Maybe [Char])               -- ^List of insertion codes, one for each group (residue) [binary (type 6)]-                           , sequenceIndexList :: !(Maybe [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)]+-- | Groups data+--+data GroupData = GroupData { 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     :: !(Maybe [SecondaryStructure]) -- ^ List of secondary structure assignments [binary (type 2)]+                           , insCodeList       :: !(Maybe [Char])               -- ^ List of insertion codes, one for each group (residue) [binary (type 6)]+                           , sequenceIndexList :: !(Maybe [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)]                            }   deriving (Show, Eq) --- |Atoms data-data AtomData = AtomData { atomIdList    :: !(Maybe [Int32]) -- ^List of atom serial numbers [binary (type 8)]-                         , altLocList    :: !(Maybe [Char])  -- ^List of alternate location labels, one for each atom [binary (type 6)]-                         , bFactorList   :: !(Maybe [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 :: !(Maybe [Float]) -- ^List of atom occupancies, one for each atom [binary (type 9)]+-- | Atoms data+--+data AtomData = AtomData { atomIdList    :: !(Maybe [Int32]) -- ^ List of atom serial numbers [binary (type 8)]+                         , altLocList    :: !(Maybe [Char])  -- ^ List of alternate location labels, one for each atom [binary (type 6)]+                         , bFactorList   :: !(Maybe [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 :: !(Maybe [Float]) -- ^ List of atom occupancies, one for each atom [binary (type 9)]                          }   deriving (Show, Eq) --- |MMTF datatype-data MMTF = MMTF { 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+-- | MMTF datatype+--+data MMTF = MMTF { 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                  }   deriving (Show, Eq)

@@ -10,5 +10,5 @@     it "should parse 1FSD" $ do       contents <- B.readFile "resource/1FSD.mmtf"       m <- decode contents-      let sid = (structureId . structure) m-      sid `shouldBe` Just "1FSD"+      (structureId . structure) m `shouldBe` Just "1FSD"+      (numModels . structure) m `shouldBe` 41