mmtf 0.1.0.0 → 0.1.0.1

raw patch · 4 files changed

+110/−79 lines, 4 filesPVP: minor bump suggested

API additions: PVP suggests at least a minor version bump

API changes (from Hackage documentation)

Files

• README.md +17/−0
• mmtf.cabal +1/−1
• src/Bio/MMTF.hs +2/−2
• src/Bio/MMTF/Type.hs +90/−76

@@ -0,0 +1,17 @@+MMTF Haskell Library+====================++[![Travis](https://img.shields.io/travis/zmactep/mmtf.svg)](https://travis-ci.org/zmactep/mmtf)+[![hackage](https://img.shields.io/hackage/v/mmtf.svg)](https://hackage.haskell.org/package/mmtf)+[![hackage-deps](https://img.shields.io/hackage-deps/v/mmtf.svg)](https://hackage.haskell.org/package/mmtf)++Haskell implementation of MMTF biological structure format.++Documentation+-------------++To build Haddock documentation run:+```+$ stack haddock+```+

@@ -1,5 +1,5 @@ name:                mmtf-version:             0.1.0.0+version:             0.1.0.1 synopsis:            Macromolecular Transmission Format implementation description:         Haskell implementation of MMTF biological structure format. homepage:            https://github.com/zmactep/mmtf#readme

@@ -1,10 +1,10 @@ module Bio.MMTF-  ( module T+  ( module Bio.MMTF.Type   , decode   ) where  import           Bio.MMTF.MessagePack ()-import           Bio.MMTF.Type        as T+import           Bio.MMTF.Type  import           Data.ByteString.Lazy (ByteString) import           Data.MessagePack     (unpack)

@@ -3,115 +3,129 @@ import           Data.Int  (Int32, Int8) import           Data.Text (Text) -data UnitCell = UnitCell { ucA     :: !Float-                         , ucB     :: !Float-                         , ucC     :: !Float-                         , ucAlpha :: !Float-                         , ucBeta  :: !Float-                         , ucGamma :: !Float+-- |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) -data Transform = Transform { chainIndexList :: ![Int32]-                           , matrix         :: ![Float]+-- |Transform data+data Transform = Transform { chainIndexList :: ![Int32] -- ^indices into the 'chainIdList' and 'chainNameList' fields+                           , matrix         :: ![Float] -- ^4x4 transformation matrix                            }   deriving (Show, Eq) -data Assembly = Assembly { transformList :: ![Transform]-                         , assemblyName  :: !Text+-- |Assembly data+data Assembly = Assembly { transformList :: ![Transform] -- ^List of transform objects+                         , assemblyName  :: !Text        -- ^Name of the biological assembly                          }   deriving (Show, Eq) -data Entity = Entity { entityChainIndexList :: ![Int32]-                     , entityDescription    :: !Text-                     , entityType           :: !Text-                     , entitySequence       :: !Text+-- |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) -data GroupType = GroupType { gtFormalChargeList :: ![Int32]-                           , gtAtomNameList     :: ![Text]-                           , gtElementList      :: ![Text]-                           , gtBondAtomList     :: ![Int32]-                           , gtBondOrderList    :: ![Int32]-                           , gtGroupName        :: !Text-                           , gtSingleLetterCode :: !Char-                           , gtChemCompType     :: !Text+-- |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) -data SecondaryStructure = PiHelix       -- 0-                        | Bend          -- 1-                        | AlphaHelix    -- 2-                        | Extended      -- 3-                        | ThreeTenHelix -- 4-                        | Bridge        -- 5-                        | Turn          -- 6-                        | Coil          -- 7-                        | Undefined     -- -1+-- |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) -data FormatData = FormatData { mmtfVersion  :: !Text-                             , mmtfProducer :: !Text+-- |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) -data StructureData = StructureData { title               :: !(Maybe Text)-                                   , structureId         :: !(Maybe Text)-                                   , depositionDate      :: !(Maybe Text)-                                   , releaseDate         :: !(Maybe Text)-                                   , numBonds            :: !Int32-                                   , numAtoms            :: !Int32-                                   , numGroups           :: !Int32-                                   , numChains           :: !Int32-                                   , numModels           :: !Int32-                                   , spaceGroup          :: !(Maybe Text)-                                   , unitCell            :: !(Maybe UnitCell)-                                   , ncsOperatorList     :: !(Maybe [[Float]])-                                   , bioAssemblyList     :: !(Maybe [Assembly])-                                   , entityList          :: !(Maybe [Entity])-                                   , resolution          :: !(Maybe Float)-                                   , rFree               :: !(Maybe Float)-                                   , rWork               :: !(Maybe Float)-                                   , experimentalMethods :: !(Maybe [Text])-                                   , bondAtomList        :: !(Maybe [Int32]) -- binary (type 4)-                                   , bondOrderList       :: !(Maybe [Int8])  -- 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) -data ModelData = ModelData { chainsPerModel :: ![Int32] }+-- |Models data+data ModelData = ModelData { chainsPerModel :: ![Int32] -- ^List of the number of chains in each model+                           }   deriving (Show, Eq) -data ChainData = ChainData { groupsPerChain :: ![Int32]-                           , chainIdList    :: ![Text] -- binary (type 5, length 4)-                           , chainNameList  :: !(Maybe [Text]) -- binary (type 5, length 4)+-- |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) -data GroupData = GroupData { groupList         :: ![GroupType]-                           , groupTypeList     :: ![Int32] -- binary (type 4)-                           , groupIdList       :: ![Int32] -- binary (type 8)-                           , secStructList     :: !(Maybe [SecondaryStructure]) -- binary (type 2)-                           , insCodeList       :: !(Maybe [Char]) -- binary (type 6)-                           , sequenceIndexList :: !(Maybe [Int32]) -- 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) -data AtomData = AtomData { atomIdList    :: !(Maybe [Int32]) -- binary (type 8)-                         , altLocList    :: !(Maybe [Char]) -- binary (type 6)-                         , bFactorList   :: !(Maybe [Float]) -- binary (type 10)-                         , xCoordList    :: ![Float] -- binary (type 10)-                         , yCoordList    :: ![Float] -- binary (type 10)-                         , zCoordList    :: ![Float] -- binary (type 10)-                         , occupancyList :: !(Maybe [Float]) -- 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) -data MMTF = MMTF { format    :: !FormatData-                 , structure :: !StructureData-                 , model     :: !ModelData-                 , chain     :: !ChainData-                 , group     :: !GroupData-                 , atom      :: !AtomData+-- |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)