diff --git a/AUTHORS b/AUTHORS new file mode 100644 --- /dev/null +++ b/AUTHORS @@ -0,0 +1,3 @@ +This parser and associated example programs were created by: +Michal J. Gajda 2010-2013 +In his free time, unencumbered by work duties. diff --git a/INSTALL b/INSTALL new file mode 100644 --- /dev/null +++ b/INSTALL @@ -0,0 +1,7 @@ +With a modern Cabal one can install dependencies with: +`cabal install`. + +Some dependencies may require GL/GLUT library headers. + +On Ubuntu one can install them using: +apt-get install freeglut3-dev libgl1-mesa-dev diff --git a/README.md b/README.md new file mode 100644 --- /dev/null +++ b/README.md @@ -0,0 +1,7 @@ +hPDB - examples +=============== +Haskell PDB file format parser - example scripts. + +[![Build Status](https://api.travis-ci.org/mgajda/hPDB-examples.png?branch=master)](https://www.travis-ci.org/mgajda/hPDB-examples) + +Details on official releases are on [Hackage](http://hackage.haskell.org/package/hPDB-examples). diff --git a/Setup.hs b/Setup.hs --- a/Setup.hs +++ b/Setup.hs @@ -1,4 +1,18 @@ #! /usr/bin/env runhaskell +module Main(main) where + import Distribution.Simple -main = defaultMain +import System.Environment +import Control.Monad(when) +import Data.List(isPrefixOf) + +-- Defaults to installing in --user package database. +isPkgDbOpts arg = ("--package-db" `isPrefixOf` arg ) || (arg `elem` ["--user", "--global"]) +haveNotPkgDbOpts = not . any isPkgDbOpts + +main = do args <- getArgs + defaultMainArgs $ if (length args > 0 && (head args `elem` ["configure", "install"]) && haveNotPkgDbOpts args) + then (head args:"--user":tail args) + else args + diff --git a/examples/CanonicalAxes.hs b/examples/CanonicalAxes.hs --- a/examples/CanonicalAxes.hs +++ b/examples/CanonicalAxes.hs @@ -1,5 +1,4 @@ {-# LANGUAGE OverloadedStrings, BangPatterns, FlexibleInstances,UndecidableInstances #-} - module Main where import Control.Monad(when) @@ -14,18 +13,19 @@ import Data.List import Text.Printf +--ifoldrPairs :: (Iterable Structure b, Iterable Structure b1) =>(t -> c -> c) -> (b -> b1 -> t) -> c -> Structure -> c ifoldrPairs fred fpair e s = pairs where pairs' a cont = It.ifoldr (\at r -> (at `fpair` a) `fred` r) cont (s :: Structure) - pairs = It.ifoldr (\at r -> pairs' at r) e (s :: Structure) + pairs = It.ifoldr pairs' e (s :: Structure) +--ifoldPairs :: (Iterable Structure b, Iterable Structure c) =>(c -> c -> c) -> (b -> c -> c) -> c -> Structure -> c ifoldPairs fred fpair e s = pairs where pairs' a cont = It.ifoldl' (\r at -> (at `fpair` a) `fred` r) cont (s :: Structure) - pairs = It.ifoldl' (\r at -> pairs' at r) e (s :: Structure) + pairs = It.ifoldl' pairs' e (s :: Structure) -- | findAxes finds all three principal axes so that dimensions are ordered. --- TODO: find a way to loop v1, v2, v3 assignment findAxes structure = let v1 = findLongestOrthogonalVector [ ] structure axis1 = vnormalise v1 dim1 = vnorm v1 @@ -37,27 +37,18 @@ dim3 = vnorm v3 in dim1 `seq` dim2 `seq` dim3 `seq` ([dim1, dim2, dim3], [axis1, axis2, axis3]) where - findLongestOrthogonalVector axes = ifoldPairs pickMaxDist (atDistPerpend axes) nullVector + findLongestOrthogonalVector axes = undefined --ifoldPairs pickMaxDist (atDistPerpend axes) nullVector nullVector = fromInteger 0 - atDistPerpend axes !a1 !a2 = vperpends ((coord a1) - (coord a2)) axes + atDistPerpend :: [Vector3] -> Atom -> Vector3 -> Vector3 + atDistPerpend axes !a1 !a2 = vperpends (coord a1 - a2) axes + pickMaxDist :: Vector3 -> Vector3 -> Vector3 pickMaxDist !v1 !v2 = if vnorm v1 > vnorm v2 then v1 else v2 - -{-center :: Structure -> (Double, Double, Double) -center s = (realToFrac sx, realToFrac sy, realToFrac sz) - where - - result = It.ifoldr - maxFst (a, b) (c, d) = if a >= c then (a, b) else (c, d) - coords = [It.ifoldr (\at r -> coord (at :: PDBS.Atom) : r) [] (s :: Structure)] --} - - main = do args <- getArgs when (length args /= 2) $ do hPutStrLn stderr "USAGE: CanonicalAxes " exitFailure let [inpfname, outfname] = args - Just structure <- PDBIO.parse $ BS.pack inpfname + Just structure <- PDBIO.parse inpfname let ([d1, d2, d3], axes@[yaxis, xaxis, zaxis]) = findAxes structure printf "Dimensions: %.2f %.2f %.2f\n" d1 d2 d3 putStr "Axis 1 (Y): " diff --git a/examples/CleanPDB.hs b/examples/CleanPDB.hs --- a/examples/CleanPDB.hs +++ b/examples/CleanPDB.hs @@ -18,7 +18,7 @@ return r runCounterM :: CounterM a -> a -runCounterM = fst . (flip runState) 1 +runCounterM = fst . flip runState 1 renumberResidues :: (Iterable s Chain) => s -> s renumberResidues = imap (\ch -> runCounterM . @@ -40,8 +40,8 @@ return $ at { atSerial = v } main = do [inpfname, outfname] <- getArgs - Just structure <- PDB.parse $ BS.pack inpfname + Just structure <- PDB.parse inpfname putStrLn $ show (PDB.numAtoms structure) ++ " atoms." - let s1 = renumberResidues $ renumberAtoms $ structure - PDB.write s1 $ BS.pack outfname + let s1 = renumberResidues $ renumberAtoms structure + PDB.write s1 outfname diff --git a/examples/PDB2Fasta.hs b/examples/PDB2Fasta.hs --- a/examples/PDB2Fasta.hs +++ b/examples/PDB2Fasta.hs @@ -2,14 +2,14 @@ module Main(main) where import System.Environment(getProgName, getArgs) -import System.Exit(exitWith, ExitCode(ExitSuccess), ExitCode(..)) +import System.Exit(exitWith, exitSuccess, ExitCode(ExitSuccess), ExitCode(..)) import System.Console.GetOpt import Bio.PDB as PDB -import Bio.PDB.Fasta(fastaRecord) import qualified Data.ByteString.Char8 as BS import qualified Data.Map as Map import Bio.PDB.Fasta import Control.Monad(when) +import Data.Foldable(forM_) data Options = Options { gapped :: Bool, allModels :: Bool @@ -47,12 +47,12 @@ args <- getArgs let (actions, filenames, opts) = getOpt RequireOrder options args opts <- foldl (>>=) (return defaultOptions) actions - when (length filenames == 0) $ exitAfter showHelp (ExitFailure 3) undefined + when (null filenames) $ exitAfter showHelp (ExitFailure 3) undefined mapM_ (processFile opts) filenames - exitWith ExitSuccess -- TODO: only if no errors! + exitSuccess -- TODO: only if no errors! -- | This program loads a PDB file and outputs FASTA sequences of all chains within -printFastaRecords :: Options -> [Char] -> Structure -> IO () +printFastaRecords :: Options -> FilePath -> Structure -> IO () printFastaRecords opts fname s = if allModels opts then process s @@ -68,8 +68,6 @@ --printFastaRecords fname s = PDB.ifoldM (\() ch -> Prelude.putStrLn $ fastaRecord fname ch) () s -processFile opts fname = do maybePDB <- PDB.parse $ BS.pack fname - case maybePDB of - Nothing -> return () - Just structure -> printFastaRecords opts fname structure +processFile opts fname = do maybePDB <- PDB.parse fname + forM_ maybePDB $ printFastaRecords opts fname diff --git a/examples/Rg.hs b/examples/Rg.hs --- a/examples/Rg.hs +++ b/examples/Rg.hs @@ -1,4 +1,4 @@ -{-# LANGUAGE ScopedTypeVariables, OverloadedStrings, BangPatterns, FlexibleContexts, OverloadedStrings #-} +{-# LANGUAGE ScopedTypeVariables, OverloadedStrings, BangPatterns, FlexibleContexts #-} module Main(main) where import Bio.PDB as PDB @@ -14,8 +14,8 @@ import Bio.PDB.Structure.Elements(atomicMass, assignElement) main = do args <- getArgs - mapM (readAndComputeRg . BS.pack) args - exitWith ExitSuccess + mapM_ readAndComputeRg args + exitSuccess readAndComputeRg filename = do Just structure <- PDB.parse filename @@ -25,7 +25,7 @@ hFlush stdout rnf structure `seq` BS.putStrLn " atoms!" rg <- return $! radiusOfGyration structure - printf "%s: %.2f\n" (BS.unpack filename) rg + printf "%s: %.2f\n" filename rg return rg -- TODO: consider mass of an atom @@ -35,8 +35,8 @@ radiusOfGyration structure = avgDistDev where -- (c -> b -> c) -> c -> a -> c - avgDistDev = sqrt ((ifoldl' addDistDev 0.0 structure)/totalMass) - addDistDev !total at = total + (vnorm $ coord at - center)**2 * atMass at + avgDistDev = sqrt (ifoldl' addDistDev 0.0 structure/totalMass) + addDistDev !total at = total + vnorm (coord at - center)**2 * atMass at atMass :: Atom -> Double atMass at = atomicMass $ case assignElement at of "" -> "C" diff --git a/examples/ShiftToCenter.hs b/examples/ShiftToCenter.hs --- a/examples/ShiftToCenter.hs +++ b/examples/ShiftToCenter.hs @@ -22,9 +22,9 @@ subCoord (at@Atom { coord = c }) = at { coord = c - v } main = do [inpfname, outfname] <- getArgs - Just structure <- PDB.parse $ BS.pack inpfname + Just structure <- PDB.parse inpfname let c@(Vector3 x y z) = center structure printf "Center %.2f %.2f %.2f\n" x y z putStrLn $ show (PDB.numAtoms structure) ++ " atoms." let s1 = shift c structure - PDB.write s1 $ BS.pack outfname + PDB.write s1 outfname diff --git a/examples/SplitModels.hs b/examples/SplitModels.hs --- a/examples/SplitModels.hs +++ b/examples/SplitModels.hs @@ -19,16 +19,16 @@ splitModels aStructure = map mkStructure . V.toList . models $ aStructure where mkStructure aModel = aStructure{ models = V.singleton aModel } -usage = do hPutStrLn stderr $ concat [ "Usage: SplitModels " - , "Splitting of PDB files with multiple MODEL entries." ] +usage = do hPutStrLn stderr $ "Usage: SplitModels " ++ + "Splitting of PDB files with multiple MODEL entries." exitFailure main = do lenArgs <- length `fmap` getArgs when (lenArgs /= 2) usage [inpfname, outfname] <- getArgs - Just structure <- PDB.parse $ BS.pack inpfname + Just structure <- PDB.parse inpfname let splitted = zip [1..] $ splitModels structure forM splitted $ \(num, aStructure) -> do let fname = outfname ++ show num ++ ".pdb" putStrLn $ "Writing " ++ show fname ++ " with " ++ show (numAtoms aStructure) ++ " atoms." - PDB.write aStructure $ BS.pack fname + PDB.write aStructure fname diff --git a/examples/StericClashCheck.hs b/examples/StericClashCheck.hs --- a/examples/StericClashCheck.hs +++ b/examples/StericClashCheck.hs @@ -37,8 +37,8 @@ size ot = length . Oct.toList $ ot main = do [input1, input2] <- Env.getArgs - Just structure1 <- PDB.parse $ BS.pack input1 - Just structure2 <- PDB.parse $ BS.pack input2 + Just structure1 <- PDB.parse input1 + Just structure2 <- PDB.parse input2 print $ clashCheck structure1 structure2 print "Depths:" print . Oct.depth . makeOctree $ structure1 diff --git a/examples/Viewer.hs b/examples/Viewer.hs --- a/examples/Viewer.hs +++ b/examples/Viewer.hs @@ -15,6 +15,7 @@ import Bio.PDB.Iterable as PDBI import Data.ByteString.Char8 as BS import Bio.PDB.Structure.Vector +import Data.Vector.V3 data UIState = UIState { manipulationCenter :: Maybe GL.Position , pressedButton :: Maybe GL.MouseButton @@ -24,7 +25,7 @@ } initialUIState = do GL.loadIdentity - initialViewMatrix :: GL.GLmatrix GL.GLdouble <- GL.get $ GL.matrix $ Nothing + initialViewMatrix :: GL.GLmatrix GL.GLdouble <- GL.get $ GL.matrix Nothing --m <- GL.getMatrixComponents GL.ColumnMajor initialViewMatrix return $ cleanUIState initialViewMatrix @@ -42,14 +43,14 @@ main = do (progname, [filename]) <- GL.getArgsAndInitialize -- First read structure - Just structure <- PDBIO.parse $ BS.pack filename + Just structure <- PDBIO.parse filename -- Initialize OpenGL --displayMode $= [With DisplayDepth, With DisplayRGB] -- is it glutInitDisplayModel (GLUT_SINGLE | GLUT_RGB | GLUT_DEPTH) setup progname -- setup OpenGL scene model -- Initialize camera initUIState <- initialUIState uiState <- newIORef initUIState - translateViewMatrix uiState $ vec3DToVector3 $ (-(center structure)) + translateViewMatrix uiState $ vector3ToGLVector3 (-(center structure)) translateViewMatrix uiState $ GL.Vector3 0 0 (-frustumMiddle) -- Now set callbacks GL.displayCallback $= display uiState structure @@ -105,7 +106,7 @@ zaxis = GL.Vector3 0 0 1 :: GL.Vector3 GL.GLdouble negateVector3 :: (Num a) => GL.Vector3 a -> GL.Vector3 a -negateVector3 = fmap (\a -> (-a)) +negateVector3 = fmap negate handleKeys :: IORef UIState -> GL.Key -> GL.KeyState -> GL.Modifiers -> GL.Position -> IO () handleKeys uiState (GL.Char 'q') GL.Down _modifiers _position = rotateViewMatrix uiState 10.0 yaxis @@ -186,8 +187,8 @@ (GL.Position w h ) = (angle, GL.Vector3 dy dx 0.0) where [xf, yf, wf, hf] = Prelude.map fromIntegral [curX - initX, curY - initY, w, h] - dx = xf / (min hf wf) - dy = yf / (min hf wf) + dx = xf / min hf wf + dy = yf / min hf wf angle = 180.0 * sqrt (dx*dx + dy*dy) getPosChange :: GL.Position -> GL.Position -> GL.Position -> (GL.GLdouble, GL.GLdouble) @@ -210,11 +211,11 @@ GL.depthFunc $= Just GL.Less -- Assessing dimensions for initial focus -center :: PDBS.Structure -> Vec3D +center :: PDBS.Structure -> Vector3 center structure = average where (!average, _count) = PDBI.ifoldl' step (fromIntegral 0, 0) structure - step :: (Vec3D, Double) -> PDBS.Atom -> (Vec3D, Double) + step :: (Vector3, Double) -> PDBS.Atom -> (Vector3, Double) step (!r, !i) at = let i' = i + 1 in (coord at |* (1/i') + r |* (i/i'), i') @@ -225,21 +226,21 @@ vzip max maxv c)) (cs, cs) structure !cs = center structure -vec3DToVector3 :: Vec3D -> GL.Vector3 GL.GLdouble -vec3DToVector3 v = GL.Vector3 x' y' z' +vector3ToGLVector3 :: Vector3 -> GL.Vector3 GL.GLdouble +vector3ToGLVector3 v = GL.Vector3 x' y' z' where - (x, y, z) = unpackVec3D v + Vector3 x y z = v [x', y', z'] :: [GL.GLdouble] = Prelude.map realToFrac [x, y, z] renderStructure :: IORef UIState -> PDBS.Structure -> IO () -renderStructure uiState structure = PDBI.ifoldM (\_ -> renderAtom) () structure +renderStructure uiState = PDBI.ifoldM (const renderAtom) () where renderAtom (at :: Atom) = GL.preservingMatrix $ do GL.matrixMode $= GL.Modelview 0 uiSt <- readIORef uiState --m :: GL.GLmatrix GL.GLdouble <- GL.newMatrix GL.ColumnMajor $ currentViewMatrix uiSt GL.matrix Nothing $= currentViewMatrix uiSt --cm <- GL.getMatrixComponents GL.ColumnMajor $ currentViewMatrix uiSt --print cm - GL.translate $ vec3DToVector3 $ PDBS.coord at + GL.translate $ vector3ToGLVector3 $ PDBS.coord at GL.renderObject GL.Solid $ GL.Sphere' (realToFrac radius) 40 32 -- much smoother looks! where radius = realToFrac $ PDBE.vanDerWaalsRadius $ PDBS.element at @@ -250,11 +251,12 @@ renderStructure uiState structure GL.swapBuffers +{-# ANN myOrtho "HLint: ignore Redundant bracket" #-} myOrtho w h = let hw = fromIntegral h/fromIntegral w wh = fromIntegral w/fromIntegral h in if w <= h - then GL.ortho (-1.5) (1.5) (-1.5*hw) (1.5*hw) (-10) (10) - else GL.ortho (-1.5*wh) (1.5*wh) (-1.5) (1.5) (-10) (10) + then GL.ortho (-1.5 ) (1.5 ) (-1.5*hw) (1.5*hw) (-10) (10) + else GL.ortho (-1.5*wh) (1.5*wh) (-1.5 ) (1.5 ) (-10) (10) frustumFront = 5.0 frustumBack = 1000.0 diff --git a/hPDB-examples.cabal b/hPDB-examples.cabal --- a/hPDB-examples.cabal +++ b/hPDB-examples.cabal @@ -1,87 +1,88 @@ name: hPDB-examples -version: 0.99 +version: 0.999 +synopsis: Examples for hPDB library stability: beta -homepage: https://github.com/mgajda/hpdb +homepage: https://github.com/mgajda/hpdb-examples package-url: http://hackage.haskell.org/package/hPDB -synopsis: Parser, print and manipulate structures in PDB file format. -description: Protein Data Bank file format is a most popular format for holding biomolecule data. This is a very fast parser (below 7s for the largest entry in PDB - 1HTQ which is over 70MB - as compared with 11s of RASMOL 2.7.5, or 2m15s of BioPython with Python 2.6 interpreter.) 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. +description: Examples for handling Protein Data Bank file format. category: Bioinformatics license: BSD3 license-file: LICENSE author: Michal J. Gajda -copyright: Copyright by Michal J. Gajda '2009-'2012 +copyright: Copyright by Michal J. Gajda '2009-'2013 maintainer: mjgajda@googlemail.com bug-reports: mailto:mjgajda@googlemail.com build-type: Simple cabal-version: >=1.8 -tested-with: GHC==7.4.1, GHC==7.0.3, GHC==7.4.2 +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 --Need to re-test: GHC==6.12.1, GHC==7.0.4, GHC==7.1.20101026 --data-files: 1CRN.pdb, 1HTQ.pdb, 3JYV.pdb +extra-source-files: README.md INSTALL AUTHORS source-repository head type: git - location: git://github.com:mgajda/hpdb-examples.git + location: https://github.com/mgajda/hPDB-examples Executable PDB2Fasta main-is: examples/PDB2Fasta.hs ghc-options: -fspec-constr-count=4 -O3 - build-depends: base>=4.0, base <4.7, bytestring, ghc-prim, directory, mtl, template-haskell, vector, AC-Vector, containers, deepseq, QuickCheck >= 2.5.0.0, text>=0.11.1.13, hPDB >= 0.99 + build-depends: base>=4.0, base <4.7, bytestring, ghc-prim, directory, mtl, template-haskell, vector, AC-Vector, containers, deepseq, QuickCheck >= 2.5.0.0, text>=0.11.1.13, hPDB >= 0.999, iterable >=1.0 other-extensions: ScopedTypeVariables OverloadedStrings BangPatterns NoMonomorphismRestriction EmptyDataDecls MagicHash Executable ShiftToCenter main-is: examples/ShiftToCenter.hs ghc-options: -fspec-constr-count=4 -O3 - build-depends: base>=4.0, base <4.7, ghc-prim, directory, mtl, template-haskell, vector, AC-Vector, containers, deepseq,QuickCheck >= 2.5.0.0, text>=0.11.1.13, hPDB >= 0.99, bytestring + build-depends: base>=4.0, base <4.7, ghc-prim, directory, mtl, template-haskell, vector, AC-Vector, containers, deepseq,QuickCheck >= 2.5.0.0, text>=0.11.1.13, hPDB >= 0.999, bytestring, iterable >=1.0 other-extensions: ScopedTypeVariables OverloadedStrings BangPatterns NoMonomorphismRestriction EmptyDataDecls MagicHash Executable CleanPDB main-is: examples/CleanPDB.hs ghc-options: -fspec-constr-count=4 -O3 - build-depends: base>=4.0, base <4.7, bytestring, ghc-prim, directory, mtl, template-haskell, vector, AC-Vector, containers, deepseq,QuickCheck >= 2.5.0.0, text>=0.11.1.13, hPDB >= 0.99 + build-depends: base>=4.0, base <4.7, bytestring, ghc-prim, directory, mtl, template-haskell, vector, AC-Vector, containers, deepseq,QuickCheck >= 2.5.0.0, text>=0.11.1.13, hPDB >= 0.999, iterable >=1.0 other-extensions: ScopedTypeVariables OverloadedStrings BangPatterns NoMonomorphismRestriction EmptyDataDecls MagicHash Executable SplitModels main-is: examples/SplitModels.hs ghc-options: -fspec-constr-count=4 -O3 - build-depends: base>=4.0, base <4.7, ghc-prim, directory, mtl, template-haskell, vector, AC-Vector, containers, deepseq,QuickCheck >= 2.5.0.0, text>=0.11.1.13, hPDB >= 0.99, bytestring + build-depends: base>=4.0, base <4.7, ghc-prim, directory, mtl, template-haskell, vector, AC-Vector, containers, deepseq,QuickCheck >= 2.5.0.0, text>=0.11.1.13, hPDB >= 0.999, bytestring, iterable >=1.0 other-extensions: ScopedTypeVariables OverloadedStrings BangPatterns NoMonomorphismRestriction EmptyDataDecls MagicHash Executable CanonicalAxes main-is: examples/CanonicalAxes.hs ghc-options: -fspec-constr-count=4 -O3 - Build-depends: base>=4.0, base <4.7, bytestring, ghc-prim, directory, mtl, template-haskell, vector, AC-Vector, containers, deepseq,QuickCheck >= 2.5.0.0, text>=0.11.1.13, hPDB >= 0.99 + Build-depends: base>=4.0, base <4.7, bytestring, ghc-prim, directory, mtl, template-haskell, vector, AC-Vector, containers, deepseq,QuickCheck >= 2.5.0.0, text>=0.11.1.13, hPDB >= 0.999, iterable >=1.0 other-extensions: ScopedTypeVariables OverloadedStrings BangPatterns NoMonomorphismRestriction EmptyDataDecls MagicHash Executable PrintEvents Main-is: tests/PrintEvents.hs ghc-options: -fspec-constr-count=4 -O3 - Build-depends: base>=4.0, base <4.7, bytestring, ghc-prim, directory, mtl, template-haskell, vector, AC-Vector, containers, deepseq, QuickCheck >= 2.5.0.0, text>=0.11.1.13, hPDB >= 0.99 + Build-depends: base>=4.0, base <4.7, bytestring, ghc-prim, directory, mtl, template-haskell, vector, AC-Vector, containers, deepseq, QuickCheck >= 2.5.0.0, text>=0.11.1.13, hPDB >= 0.999, iterable >=1.0 other-extensions: ScopedTypeVariables OverloadedStrings BangPatterns NoMonomorphismRestriction EmptyDataDecls Executable PrintStructureObject ghc-options: -fspec-constr-count=4 -O3 - Build-depends: base>=4.0, base <4.7, bytestring, ghc-prim, directory, mtl, template-haskell, vector, AC-Vector, containers, deepseq,QuickCheck >= 2.5.0.0, text>=0.11.1.13, hPDB >= 0.99 + Build-depends: base>=4.0, base <4.7, bytestring, ghc-prim, directory, mtl, template-haskell, vector, AC-Vector, containers, deepseq,QuickCheck >= 2.5.0.0, text>=0.11.1.13, hPDB >= 0.999, iterable >=1.0 Main-is: tests/PrintStructureObject.hs other-extensions: ScopedTypeVariables OverloadedStrings BangPatterns NoMonomorphismRestriction EmptyDataDecls Executable Rg main-is: examples/Rg.hs ghc-options: -fspec-constr-count=4 -O3 - Build-depends: base>=4.0, base <4.7, ghc-prim, bytestring, directory, mtl, template-haskell, vector, AC-Vector, containers, deepseq,QuickCheck >= 2.5.0.0, text>=0.11.1.13, hPDB >= 0.99 + Build-depends: base>=4.0, base <4.7, ghc-prim, bytestring, directory, mtl, template-haskell, vector, AC-Vector, containers, deepseq,QuickCheck >= 2.5.0.0, text>=0.11.1.13, hPDB >= 0.999, iterable >=1.0 other-extensions: ScopedTypeVariables OverloadedStrings BangPatterns NoMonomorphismRestriction EmptyDataDecls Executable StericClashCheck main-is: examples/StericClashCheck.hs ghc-options: -fspec-constr-count=4 -O3 - Build-Depends: base>=4.0, base<4.7, bytestring, ghc-prim, directory, mtl, template-haskell, vector, AC-Vector, containers, deepseq, Octree >= 0.5, QuickCheck, text, text-format, hPDB >= 0.4 + Build-Depends: base>=4.0, base<4.7, bytestring, ghc-prim, directory, mtl, template-haskell, vector, AC-Vector, containers, deepseq, Octree >= 0.5, QuickCheck, text, text-format, hPDB >= 0.999, iterable >=1.0 other-extensions: ScopedTypeVariables OverloadedStrings BangPatterns NoMonomorphismRestriction EmptyDataDecls -- if flag(haveOpenGL) -- why can't we make it conditionally available? Executable Viewer main-is: examples/Viewer.hs ghc-options: -fspec-constr-count=4 -O3 - Build-depends: base>=4.0, base <4.7, ghc-prim, directory, mtl, template-haskell, vector, AC-Vector, containers, deepseq,QuickCheck >= 2.5.0.0, text>=0.11.1.13, OpenGL, GLUT, hPDB >= 0.4, bytestring + Build-depends: base>=4.0, base <4.7, ghc-prim, directory, mtl, template-haskell, vector, AC-Vector, containers, deepseq,QuickCheck >= 2.5.0.0, text>=0.11.1.13, OpenGL, GLUT, hPDB >= 0.999, bytestring, iterable >=1.0 other-extensions: ScopedTypeVariables OverloadedStrings BangPatterns NoMonomorphismRestriction EmptyDataDecls MagicHash diff --git a/tests/PrintStructureObject.hs b/tests/PrintStructureObject.hs --- a/tests/PrintStructureObject.hs +++ b/tests/PrintStructureObject.hs @@ -7,5 +7,5 @@ import Data.ByteString.Char8 as BS main = do [inpfname, outfname] <- getArgs - Just structure <- PDBIO.parse $ BS.pack inpfname - PDBIO.write structure $ BS.pack outfname + Just structure <- PDBIO.parse inpfname + PDBIO.write structure outfname