diff --git a/Bio/PDB.hs b/Bio/PDB.hs --- a/Bio/PDB.hs +++ b/Bio/PDB.hs @@ -1,4 +1,4 @@ -module Bio.PDB(parse, write, +module Bio.PDB(parse, write, PDBWritable, Structure(..), Model(..), Chain(..), Residue(..), Atom(..), Iterable(..), numAtoms, numResidues, numChains, numModels, @@ -10,7 +10,7 @@ atomicNumber, atomicMass, covalentRadius, vanDerWaalsRadius ) where -import Bio.PDB.IO(parse, write) +import Bio.PDB.IO(parse, write, PDBWritable) import Bio.PDB.Structure import Bio.PDB.Iterable import Bio.PDB.Fasta diff --git a/Bio/PDB/IO.hs b/Bio/PDB/IO.hs --- a/Bio/PDB/IO.hs +++ b/Bio/PDB/IO.hs @@ -1,6 +1,6 @@ {-# LANGUAGE OverloadedStrings #-} -- | Simple input/output wrappers taking filenames, and handling compression. -module Bio.PDB.IO(parse, write) where +module Bio.PDB.IO(parse, write, PDBWritable()) where import qualified Control.Exception(catch) import Control.Exception.Base(SomeException) @@ -9,6 +9,7 @@ import Bio.PDB.EventParser.PDBParsingAbstractions import Bio.PDB.Structure.List as L import qualified Bio.PDB.StructurePrinter as PDBSP +import Bio.PDB.StructurePrinter(PDBWritable()) import Control.Monad(when) import Bio.PDB.EventParser.PDBEvents(PDBEvent(PDBParseError, PDBIgnoredLine)) @@ -51,6 +52,6 @@ printError [BS.pack filename, ": IGNORED ", line] -- | Write structure to a .pdb file. -write :: Bio.PDB.Structure.Structure -> FilePath -> IO () +write :: PDBWritable a => a -> FilePath -> IO () write structure fname = writeFile fname $ \h -> PDBSP.write h structure diff --git a/Bio/PDB/Structure/Neighbours.hs b/Bio/PDB/Structure/Neighbours.hs --- a/Bio/PDB/Structure/Neighbours.hs +++ b/Bio/PDB/Structure/Neighbours.hs @@ -1,6 +1,8 @@ {-# LANGUAGE NoMonomorphismRestriction, FlexibleContexts #-} -- | Searching for neighbouring atoms in a 3D space using `Octree`. -module Bio.PDB.Structure.Neighbours(makeOctree, findInRadius, findNearest) +module Bio.PDB.Structure.Neighbours(makeOctree, + findInRadius, findNearest, + AtomOctree(..)) where import qualified Data.Octree as Oct diff --git a/Bio/PDB/StructureBuilder/Parallel.hs b/Bio/PDB/StructureBuilder/Parallel.hs --- a/Bio/PDB/StructureBuilder/Parallel.hs +++ b/Bio/PDB/StructureBuilder/Parallel.hs @@ -8,6 +8,7 @@ import Bio.PDB.EventParser.PDBEvents(PDBEvent(PDBParseError)) import GHC.Conc(numCapabilities) import Control.Parallel.Strategies +import Bio.PDB.Util.ParFold(parFold1) import Control.Arrow((&&&)) import qualified Bio.PDB.Structure.List as L import qualified Data.ByteString.Char8 as BS @@ -101,7 +102,8 @@ chunks = chunkString chunkLen input pList = map (partialParse fname) chunks partialResults = pList `using` parList (evalTuple3 rdeepseq r0 r0) - (struct, errs, ln) = foldl joinResult (head partialResults) (tail partialResults) + (struct, errs, ln) = parFold1 joinResult partialResults + --(struct, errs, ln) = foldl joinResult (head partialResults) (tail partialResults) -- TODO: correct line numbers! partial parse should return Structure + line number -- | Splits a ByteString into chunks of given size, and ending at end of line. diff --git a/Bio/PDB/StructurePrinter.hs b/Bio/PDB/StructurePrinter.hs --- a/Bio/PDB/StructurePrinter.hs +++ b/Bio/PDB/StructurePrinter.hs @@ -1,22 +1,66 @@ -{-# LANGUAGE NamedFieldPuns, DisambiguateRecordFields #-} +{-# LANGUAGE NamedFieldPuns, DisambiguateRecordFields, OverloadedStrings #-} -- | High-level output routines for 'Structure'. -module Bio.PDB.StructurePrinter(write) where +module Bio.PDB.StructurePrinter(write, PDBWritable()) where import Prelude hiding(print) +import Control.Monad(mapM_) +import System.IO(Handle) import Data.ByteString.Char8 as BS + import Bio.PDB.Structure import Bio.PDB.Iterable import Bio.PDB.Structure.List as L import Bio.PDB.EventParser.PDBEventPrinter as PR -import Control.Monad(mapM_) import Bio.PDB.EventParser.PDBEvents -- | ShowS like type for a list of `PDBEvent`s. type PDBEventS = [PDBEvent] -> [PDBEvent] --- | Writes a structure in a PDB format to a filehandle. -write handle structure = mapM_ (PR.print handle) (structureEvents structure) - +-- * Class-based interface for generating PDB events from structure fragments. +-- | Writes a structure or its part in a PDB format to a filehandle. +write :: PDBWritable a => Handle -> a -> IO () +write handle structure = mapM_ (PR.print handle) (pdbEvents structure) + +-- | Class generating events for PDB structure fragments. +class PDBWritable a where + pdbEvents :: a -> [PDBEvent] + pdbEvents = flip pdbEventS [] + pdbEventS :: a -> PDBEventS + +instance PDBWritable Structure + where + pdbEvents = structureEvents + pdbEventS = error "Structure is closed by definition cannot have continuation!" + +instance PDBWritable Model + where + pdbEventS = modelEvents + +instance PDBWritable Chain + where + pdbEventS = chainEvents + +instance PDBWritable Residue + where + pdbEventS = residueEvents blankChain + +instance PDBWritable Atom + where + pdbEventS = atomEvents blankChain blankResidue + +-- | Helper: blank chain in case we don't know which chain residue belongs to. +blankChain :: Chain +blankChain = Chain { chainId = ' ' + , residues = L.empty } + +-- | Helper blank residue in case we don't know which residue the atom belongs to. +blankResidue :: Residue +blankResidue = Residue { resName = "UNK" + , resSeq = 0 + , insCode = ' ' + , atoms = L.empty } + +-- * Routines for writing event list for fragments of the structure. -- | Generates list of `PDBEvent`s from a given Structure. structureEvents :: Structure -> [PDBEvent] structureEvents s = itfoldr modelEvents [END] s @@ -79,3 +123,4 @@ charge = ch, hetatm = isHet } : c + diff --git a/Bio/PDB/Util/ParFold.hs b/Bio/PDB/Util/ParFold.hs new file mode 100644 --- /dev/null +++ b/Bio/PDB/Util/ParFold.hs @@ -0,0 +1,29 @@ +{-# LANGUAGE TemplateHaskell #-} +-- | Basic parallel folding utility. +module Bio.PDB.Util.ParFold(parFold1) where + +import Data.Tree +import Data.List +import Test.QuickCheck.All(quickCheckAll) +import Test.QuickCheck.Arbitrary +import Control.Parallel.Strategies(parList, rseq, using) + +-- | Parallel folding like fold1, but assuming associativity and using O(n*lg) +parFold1 f [ ] = error "parFold of empty list!" +parFold1 f [a] = a +parFold1 f l = parFold1 f . (`using` parList rseq) $ aList + where + aList = foldLevel l + -- | reduction by one level + foldLevel [ ] = [ ] + foldLevel [a] = [a] + foldLevel (a:b:l) = (a `f` b):foldLevel l + + +-- NOTE: join function must be associative +-- | Checks parFold1 with a given associative function +--check_join f l = foldBin f l == foldl1 f l + +--prop_join_plus l = check_join (+) l + +--main = $quickCheckAll diff --git a/README.md b/README.md --- a/README.md +++ b/README.md @@ -15,3 +15,5 @@ It is aimed to not only deliver event-based interface, but also a high-level data structure for manipulating data in spirit of BioPython's PDB parser. Details on official releases are on [Hackage](http://hackage.haskell.org/package/hPDB). + +This package is also a part of [Stackage](http://daniel-diaz.github.io/stackagelist/) - a stable subset of Hackage. diff --git a/changelog b/changelog new file mode 100644 --- /dev/null +++ b/changelog @@ -0,0 +1,19 @@ +-*-Changelog-*- + +1.1.1 Jan 2014 + * Exposed PDBWritable class for all objects that can be written to PDB + file. + +1.1 Jan 2014 + * Octree building with Bio.PDB.Structure.Neighbours. + +0.9999.1 Sep 2013 + * Removed most compilation options and replaced them with conditionals + on library versions. + +0.9999 Sep 2013 + * Parallel parsing. + * Change of Iterable interface from imap -> itmap etc. + +0.99 Sep 2013 + * First public release. diff --git a/hPDB.cabal b/hPDB.cabal --- a/hPDB.cabal +++ b/hPDB.cabal @@ -1,5 +1,5 @@ name: hPDB -version: 1.1 +version: 1.1.1 synopsis: Protein Databank file format library homepage: https://github.com/BioHaskell/hPDB stability: stable @@ -32,12 +32,12 @@ build-type: Simple cabal-version: >=1.8 -tested-with: GHC==7.0.3, GHC==7.2.2, GHC==7.4.1, GHC==7.4.2, GHC==7.6.1, GHC==7.6.2 -extra-source-files: README.md INSTALL AUTHORS +tested-with: GHC==7.0.3, GHC==7.2.2, GHC==7.4.1, GHC==7.4.2, GHC==7.6.1, GHC==7.6.2, GHC==7.6.3 +extra-source-files: README.md INSTALL AUTHORS changelog source-repository head type: git - location: https://github.com/BioHaskell/hPDB + location: https://github.com/BioHaskell/hPDB.git flag have-mmap description: Use mmap to read input faster. @@ -55,26 +55,6 @@ http://ghc.haskell.org/trac/ghc/ticket/5289 default: True --- TODO: Remove these old flags... -flag old-bytestring - description: Use bytestring before version 0.10 (introduced in GHC 7.6), and define NFData for Data.ByteString yourself. - Disable for GHC 7.6. - default: False - -flag old-zlib - description: Use zlib before version 0.5.4 (introduced in GHC 7.6). - Disable for GHC 7.6.1 - default: False - -flag old-vector - description: Use old vector library before version 0.10 (introduced along with GHC 7.6). - Disable for GHC 7.6.1 and latest 7.4.2. - default: False - -source-repository head - type: git - location: git://github.com:mgajda/hpdb.git - Library ghc-options: -fspec-constr-count=4 -O3 build-depends: base>=4.0, base <4.8, ghc-prim, directory, mtl, template-haskell, vector, AC-Vector, containers, deepseq, QuickCheck >= 2.5.0.0, text>=0.11.1.13, iterable >= 2.0, parallel >= 3.0.0.0, bytestring, zlib, Octree>= 0.5 @@ -89,7 +69,7 @@ cpp-options: -DHAVE_TEXT_FORMAT build-depends: text-format >= 0.3.1.0 other-extensions: ScopedTypeVariables OverloadedStrings BangPatterns NoMonomorphismRestriction EmptyDataDecls MagicHash CPP PatternGuards NamedFieldPuns DisambiguateRecordFields TemplateHaskell MultiParamTypeClasses FlexibleInstances FlexibleContexts - other-modules: Bio.PDB.EventParser.ParseATOM, Bio.PDB.EventParser.ParseCAVEAT, Bio.PDB.EventParser.ParseCISPEP, Bio.PDB.EventParser.ParseCONECT, Bio.PDB.EventParser.ParseCRYST1, Bio.PDB.EventParser.ParseDBREF, Bio.PDB.EventParser.ParseFORMUL, Bio.PDB.EventParser.ParseHEADER, Bio.PDB.EventParser.ParseHELIX, Bio.PDB.EventParser.ParseHET, Bio.PDB.EventParser.ParseHETNAM, Bio.PDB.EventParser.ParseHYDBND, Bio.PDB.EventParser.ParseIntRecord, Bio.PDB.EventParser.ParseJRNL, Bio.PDB.EventParser.ParseLINK, Bio.PDB.EventParser.ParseListRecord, Bio.PDB.EventParser.ParseMASTER, Bio.PDB.EventParser.ParseMatrixRecord, Bio.PDB.EventParser.ParseMODRES, Bio.PDB.EventParser.ParseObsoleting, Bio.PDB.EventParser.ParseREMARK, Bio.PDB.EventParser.ParseREVDAT, Bio.PDB.EventParser.ParseSEQADV, Bio.PDB.EventParser.ParseSEQRES, Bio.PDB.EventParser.ParseSHEET, Bio.PDB.EventParser.ParseSITE, Bio.PDB.EventParser.ParseSLTBRG, Bio.PDB.EventParser.ParseSpecListRecord, Bio.PDB.EventParser.ParseSPLIT, Bio.PDB.EventParser.ParseSSBOND, Bio.PDB.EventParser.ParseTER, Bio.PDB.EventParser.ParseTITLE, Bio.PDB.EventParser.ParseTVECT, Bio.PDB.EventParser.PDBParsingAbstractions, Bio.PDB.EventParser.FastParse, Bio.PDB.Util.MissingInstances, Bio.PDB.Common, Bio.PDB.Iterable.Utils, Bio.PDB.Iterable.Instances, Bio.PDB.StructureBuilder.Internals, Bio.PDB.StructureBuilder.Parallel + other-modules: Bio.PDB.EventParser.ParseATOM, Bio.PDB.EventParser.ParseCAVEAT, Bio.PDB.EventParser.ParseCISPEP, Bio.PDB.EventParser.ParseCONECT, Bio.PDB.EventParser.ParseCRYST1, Bio.PDB.EventParser.ParseDBREF, Bio.PDB.EventParser.ParseFORMUL, Bio.PDB.EventParser.ParseHEADER, Bio.PDB.EventParser.ParseHELIX, Bio.PDB.EventParser.ParseHET, Bio.PDB.EventParser.ParseHETNAM, Bio.PDB.EventParser.ParseHYDBND, Bio.PDB.EventParser.ParseIntRecord, Bio.PDB.EventParser.ParseJRNL, Bio.PDB.EventParser.ParseLINK, Bio.PDB.EventParser.ParseListRecord, Bio.PDB.EventParser.ParseMASTER, Bio.PDB.EventParser.ParseMatrixRecord, Bio.PDB.EventParser.ParseMODRES, Bio.PDB.EventParser.ParseObsoleting, Bio.PDB.EventParser.ParseREMARK, Bio.PDB.EventParser.ParseREVDAT, Bio.PDB.EventParser.ParseSEQADV, Bio.PDB.EventParser.ParseSEQRES, Bio.PDB.EventParser.ParseSHEET, Bio.PDB.EventParser.ParseSITE, Bio.PDB.EventParser.ParseSLTBRG, Bio.PDB.EventParser.ParseSpecListRecord, Bio.PDB.EventParser.ParseSPLIT, Bio.PDB.EventParser.ParseSSBOND, Bio.PDB.EventParser.ParseTER, Bio.PDB.EventParser.ParseTITLE, Bio.PDB.EventParser.ParseTVECT, Bio.PDB.EventParser.PDBParsingAbstractions, Bio.PDB.EventParser.FastParse, Bio.PDB.Util.MissingInstances, Bio.PDB.Common, Bio.PDB.Iterable.Utils, Bio.PDB.Iterable.Instances, Bio.PDB.StructureBuilder.Internals, Bio.PDB.StructureBuilder.Parallel, Bio.PDB.Util.ParFold exposed-modules: Bio.PDB.EventParser.PDBEvents, Bio.PDB.EventParser.PDBEventParser, Bio.PDB.EventParser.ExperimentalMethods, Bio.PDB.EventParser.HelixTypes, Bio.PDB.EventParser.StrandSense, Bio.PDB.Structure, Bio.PDB.StructureBuilder, Bio.PDB.Iterable, Bio.PDB.IO, Bio.PDB.Fasta, Bio.PDB, Bio.PDB.Structure.Vector, Bio.PDB.Structure.Elements, Bio.PDB.Structure.List, Bio.PDB.StructurePrinter, Bio.PDB.EventParser.PDBEventPrinter, Bio.PDB.IO.OpenAnyFile, Bio.PDB.Structure.Neighbours exposed: True