diff --git a/Bio/PDB.hs b/Bio/PDB.hs --- a/Bio/PDB.hs +++ b/Bio/PDB.hs @@ -1,3 +1,5 @@ +-- | Default interface for @Bio.PDB@ package. +-- Ideally should expose all commonly used functions and classes. module Bio.PDB(parse, write, PDBWritable, Structure(..), Model(..), Chain(..), Residue(..), Atom(..), Iterable(..), diff --git a/Bio/PDB/EventParser/PDBEvents.hs b/Bio/PDB/EventParser/PDBEvents.hs --- a/Bio/PDB/EventParser/PDBEvents.hs +++ b/Bio/PDB/EventParser/PDBEvents.hs @@ -39,19 +39,19 @@ hetatm :: !Bool } | SIGATM { no :: !Int, - atomtype :: !String, - restype :: !String, - chain :: !Char, - resid :: !Int, - resins :: !Char, - altloc :: !Char, - coords :: !Vector3, - occupancy :: !Double, - bfactor :: !Double, - segid :: !String, - elt :: !String, - charge :: !String -- why not a number? - } | + atomtype :: !String, + restype :: !String, + chain :: !Char, + resid :: !Int, + resins :: !Char, + altloc :: !Char, + coords :: !Vector3, + occupancy :: !Double, + bfactor :: !Double, + segid :: !String, + elt :: !String, + charge :: !String -- why not a number? + } | ANISOU { no :: !Int, atomtype :: !String, restype :: !String, diff --git a/Bio/PDB/EventParser/PDBParsingAbstractions.hs b/Bio/PDB/EventParser/PDBParsingAbstractions.hs --- a/Bio/PDB/EventParser/PDBParsingAbstractions.hs +++ b/Bio/PDB/EventParser/PDBParsingAbstractions.hs @@ -395,14 +395,14 @@ Left (col, BS.concat - [fname, " residue descriptions contains fields: ", - BS.pack $ show [r, c, d, i]]) + [fname, " residue descriptions contains fields: ", + BS.pack $ show [r, c, d, i]]) | otherwise = Right Nothing where obligatoryFields = if delible then [c, i] else [c, d, i] - IFStr unr = r - IFChar unc = c - IFInt und = d - IFChar uni = i + IFStr unr = r + IFChar unc = c + IFInt und = d + IFChar uni = i {-# INLINE fgAtom #-} -- | Merges a set of values that correspond to a mandatory atom description. @@ -460,14 +460,14 @@ Left (col, BS.concat - [fname, " atom descriptions contains fields: ", - BS.pack $ show [a, r, c, d, i]]) + [fname, " atom descriptions contains fields: ", + BS.pack $ show [a, r, c, d, i]]) | otherwise = Right Nothing where IFStr una = a - IFStr unr = r - IFChar unc = c - IFInt und = d - IFChar uni = i + IFStr unr = r + IFChar unc = c + IFInt und = d + IFChar uni = i -- Stage 3 is generation of events - code is separated for each kind of event. diff --git a/Bio/PDB/EventParser/ParseLINK.hs b/Bio/PDB/EventParser/ParseLINK.hs --- a/Bio/PDB/EventParser/ParseLINK.hs +++ b/Bio/PDB/EventParser/ParseLINK.hs @@ -35,26 +35,26 @@ {-# INLINE linkFields #-} linkFields = [(6, mKeyword "record header" "LINK " ), - (12, mSpc 6 ), - (16, mStr "atom name" ), - (17, mChr "alternate location indicator 1" ), - (20, mStr "residue name 1" ), - (21, mSpc 1 ), - (22, mChr "chain id 1" ), - (26, mInt "residue sequence number 1" ), - (27, mChr "insertion code 1" ), - (42, mSpc 15 ), - (46, mStr "atom name 1" ), - (47, mChr "alternate location indicator 2" ), - (50, mStr "residue name 2" ), - (51, mSpc 1 ), - (52, mChr "chain id 2" ), - (56, mInt "residue sequence number 2" ), - (57, mChr "insertion code 2" ), - (59, mSpc 2 ), - (65, mStr "symmetry operator for atom 1" ), - (66, mSpc 1 ), - (72, mStr "symmetry operator for atom 2" ), + (12, mSpc 6 ), + (16, mStr "atom name" ), + (17, mChr "alternate location indicator 1" ), + (20, mStr "residue name 1" ), + (21, mSpc 1 ), + (22, mChr "chain id 1" ), + (26, mInt "residue sequence number 1" ), + (27, mChr "insertion code 1" ), + (42, mSpc 15 ), + (46, mStr "atom name 1" ), + (47, mChr "alternate location indicator 2" ), + (50, mStr "residue name 2" ), + (51, mSpc 1 ), + (52, mChr "chain id 2" ), + (56, mInt "residue sequence number 2" ), + (57, mChr "insertion code 2" ), + (59, mSpc 2 ), + (65, mStr "symmetry operator for atom 1" ), + (66, mSpc 1 ), + (72, mStr "symmetry operator for atom 2" ), (73, mSpc 1 ), (78, pDouble "link distance" )] diff --git a/Bio/PDB/Fasta.hs b/Bio/PDB/Fasta.hs --- a/Bio/PDB/Fasta.hs +++ b/Bio/PDB/Fasta.hs @@ -1,4 +1,6 @@ -{-# LANGUAGE OverloadedStrings, FlexibleContexts #-} +{-# LANGUAGE OverloadedStrings #-} +{-# LANGUAGE FlexibleContexts #-} +{-# LANGUAGE MultiParamTypeClasses #-} -- | Conversion of PDB residue codes to FASTA single-letter sequence codes. module Bio.PDB.Fasta(resname2fastacode, fastacode2resname , defaultResname, defaultFastaCode , diff --git a/Bio/PDB/Structure.hs b/Bio/PDB/Structure.hs --- a/Bio/PDB/Structure.hs +++ b/Bio/PDB/Structure.hs @@ -1,4 +1,6 @@ -{-# LANGUAGE DisambiguateRecordFields, DeriveGeneric #-} +{-# LANGUAGE DisambiguateRecordFields #-} +{-# LANGUAGE DeriveGeneric #-} +-- | Module defines all components of high-level data type description of PDB model. module Bio.PDB.Structure(String, vdot, vnorm, vproj, vperpend, vperpends, vdihedral, (*|), (|*), Structure(..), Model(..), Chain(..), Residue(..), Atom(..)) diff --git a/Bio/PDB/Structure/Elements.hs b/Bio/PDB/Structure/Elements.hs --- a/Bio/PDB/Structure/Elements.hs +++ b/Bio/PDB/Structure/Elements.hs @@ -253,7 +253,10 @@ covalentRadius "ZR" = 1.75 covalentRadius x = defaulting ["Unknown covalent radius for element:", BS.pack $ show x] 0.0 -maxCovalentRadius = covalentRadius "FR" +{-# INLINE maxCovalentRadius #-} +-- | Upper bound of @covalentRadius@. +maxCovalentRadius :: Double +maxCovalentRadius = covalentRadius "FR" {-# INLINE atomicMass #-} -- | Atomic mass of a given element in g/mol @@ -485,7 +488,10 @@ vanDerWaalsRadius "ZR" = 2.00 vanDerWaalsRadius e = defaulting ["Do not know van der Waals radius of", BS.pack $ show e] 0.0 -maxVanDerWaalsRadius = vanDerWaalsRadius "K" +{-# INLINE maxVanDerWaalsRadius #-} +-- | Upper bound of @vanDerWaalsRadius@. +maxVanDerWaalsRadius :: Double +maxVanDerWaalsRadius = vanDerWaalsRadius "K" {-# INLINE assignElement #-} -- | Given a PDB 'Atom' extract or guess its 'Element' name. 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 @@ -1,4 +1,6 @@ -{-# LANGUAGE NoMonomorphismRestriction, FlexibleContexts #-} +{-# LANGUAGE NoMonomorphismRestriction #-} +{-# LANGUAGE FlexibleContexts #-} +{-# LANGUAGE MultiParamTypeClasses #-} -- | Searching for neighbouring atoms in a 3D space using `Octree`. module Bio.PDB.Structure.Neighbours(makeOctree, findInRadius, findNearest, diff --git a/Bio/PDB/StructureBuilder/Internals.hs b/Bio/PDB/StructureBuilder/Internals.hs --- a/Bio/PDB/StructureBuilder/Internals.hs +++ b/Bio/PDB/StructureBuilder/Internals.hs @@ -1,23 +1,31 @@ -{-# LANGUAGE BangPatterns, DisambiguateRecordFields, MultiParamTypeClasses, NamedFieldPuns, FlexibleContexts, OverloadedStrings, RankNTypes #-} -{-# LANGUAGE RecordWildCards #-} -- for convenient debugging +{-# LANGUAGE BangPatterns #-} +{-# LANGUAGE DisambiguateRecordFields #-} +{-# LANGUAGE FlexibleContexts #-} +{-# LANGUAGE MultiParamTypeClasses #-} +{-# LANGUAGE NamedFieldPuns #-} +{-# LANGUAGE OverloadedStrings #-} +{-# LANGUAGE RankNTypes #-} +{-# LANGUAGE RecordWildCards #-} -- for convenient debugging {-# OPTIONS_GHC -fspec-constr-count=2 #-} +-- | This module allows access to internal interface of @StructureBuilder@ in case that user wants to extend it +-- by redefining parts. module Bio.PDB.StructureBuilder.Internals --(parse) where -import Prelude hiding (String) -import qualified Data.ByteString.Char8 as BS hiding (reverse) -import qualified Control.Monad.ST as ST -import Control.Monad.State.Strict as State -import Control.Monad(when) -import Data.STRef as STRef -import Data.Maybe(isNothing, isJust) +import Prelude hiding (String) +import qualified Data.ByteString.Char8 as BS hiding (reverse) +import qualified Control.Monad.ST as ST +import Control.Monad.State.Strict as State +import Control.Monad(when) +import Data.STRef as STRef +import Data.Maybe(isNothing, isJust) -import Bio.PDB.EventParser.PDBEvents(PDBEvent(..), RESID(..)) +import Bio.PDB.EventParser.PDBEvents(PDBEvent(..), RESID(..)) import qualified Bio.PDB.EventParser.PDBEventParser(parsePDBRecords) -import Bio.PDB.Structure -import Bio.PDB.Structure.List as L +import Bio.PDB.Structure +import Bio.PDB.Structure.List as L -- | Shorthand for the State monad in which parsing is done. -- `t` is existential 'phantom' type to keep ST effects from escaping @@ -122,7 +130,6 @@ checkModel :: ParsingMonad t () checkModel = do curModel <- State.gets currentModel when (isNothing curModel) $ openModel defaultModelId --- | Closes construction of a current residue and appends this residue to a current chain. (Monadic action.) --closeResidue :: State.State BState () -- TODO: when createing a dummy model, check that there are no models declared before -- [Otherwise one needs to report an error!] @@ -130,6 +137,7 @@ -- | Default model id, in case none was indicated (for comparison.) defaultModelId = 1 +-- | Closes construction of a current residue and appends this residue to a current chain. (Monadic action.) closeResidue :: ParsingMonad t () closeResidue = do r <- State.gets currentResidue when (isJust r) $ do let Just res = r @@ -194,7 +202,6 @@ -- | Finalizes construction of record holding PDB entry data. -- NOTE: this one is different and should only be used after parsing is complete! - closeStructure :: ParsingMonad t () closeStructure = do closeModel sc <- State.gets structureContents @@ -205,6 +212,7 @@ bstate { currentStructure = aStructure { models = sc }, structureContents = undefined } +-- | Updates line counter. nextLine :: ParsingMonad t () nextLine = do lnref <- State.gets lineNo lift $ STRef.modifySTRef lnref (+1) 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 @@ -1,4 +1,6 @@ {-# LANGUAGE BangPatterns, PatternGuards #-} +-- | This module leverages sequential builder interface in @Bio.PDB.StructureBuilder.Internal@ +-- to run parser and @StructureBuilder@ in parallel with linear speedup. module Bio.PDB.StructureBuilder.Parallel(parseParallel, parseWithNParallel, joinStructure, joinResult) where diff --git a/README.md b/README.md --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ [![Build Status](https://api.travis-ci.org/BioHaskell/hPDB.svg?branch=master)](https://travis-ci.org/BioHaskell/hPDB) [![Hackage](https://budueba.com/hackage/hPDB)](https://hackage.haskell.org/package/hPDB) - +[![Hackage Dependencies](https://img.shields.io/hackage-deps/v/hPDB.svg?style=flat)](http://packdeps.haskellers.com/feed?needle=hPDB) Protein Data Bank file format is a most popular format for holding biomolecule data. diff --git a/changelog b/changelog --- a/changelog +++ b/changelog @@ -1,4 +1,9 @@ -*-Changelog-*- +1.2.0.4 Jun 2015 + * Cleaned, added some documentation. + +1.2.0.3 Apr 2015 + * Version bump. 1.2.0.2 Apr 2015 * Update for zlib version 0.6.1.0. diff --git a/hPDB.cabal b/hPDB.cabal --- a/hPDB.cabal +++ b/hPDB.cabal @@ -1,5 +1,5 @@ name: hPDB -version: 1.2.0.3 +version: 1.2.0.4 synopsis: Protein Databank file format library homepage: https://github.com/BioHaskell/hPDB stability: stable @@ -26,13 +26,13 @@ license-file: LICENSE author: Michal J. Gajda -copyright: Copyright by Michal J. Gajda '2009-'2013 +copyright: Copyright by Michal J. Gajda '2009-'2015 maintainer: mjgajda@googlemail.com bug-reports: mailto:mjgajda@googlemail.com build-type: Simple cabal-version: >=1.8 -tested-with: GHC==7.6.3, GHC==7.8.3 +tested-with: GHC==7.6.3, GHC==7.8.4, GHC==7.10.1 extra-source-files: README.md INSTALL AUTHORS changelog source-repository head