hPDB-examples 1.1.2 → 1.2.0.1

raw patch · 2 files changed

+48/−2 lines, 2 filesdep +IfElsedep +processdep +timedep ~basedep ~hPDBdep ~iterable

Dependencies added: IfElse, process, time

Dependency ranges changed: base, hPDB, iterable, text

Files

• hPDB-examples.cabal +9/−2
• tests/TestParser.hs +39/−0

@@ -1,5 +1,5 @@ name:                hPDB-examples-version:             1.1.2+version:             1.2.0.1 synopsis:            Examples for hPDB library stability:           stable homepage:            https://github.com/BioHaskell/hPDB-examples@@ -27,7 +27,7 @@ Executable PDB2Fasta   main-is:          examples/PDB2Fasta.hs   ghc-options:      -fspec-constr-count=4 -O3 -threaded -rtsopts -with-rtsopts=-N-  build-depends:    base>=4.0, base <4.9, bytestring, ghc-prim, directory, mtl, template-haskell, vector, AC-Vector, containers, deepseq, QuickCheck >= 2.5.0.0, text>=0.11.1.13, hPDB >= 1.1, iterable >=2.0+  build-depends:    base>=4.0, base <4.9, bytestring, ghc-prim, directory, mtl, template-haskell, vector, AC-Vector, containers, deepseq, QuickCheck >= 2.5.0.0, text>=0.11.1.13, hPDB >= 1.2, iterable >=3.0   other-extensions:       ScopedTypeVariables OverloadedStrings BangPatterns NoMonomorphismRestriction EmptyDataDecls MagicHash  Executable ShiftToCenter@@ -83,5 +83,12 @@   main-is:          examples/Viewer.hs   ghc-options:      -fspec-constr-count=4 -O3  -threaded -rtsopts -with-rtsopts=-N   Build-depends:    base>=4.0, base <4.9, 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++test-suite ParserPerformance+  main-is:          tests/TestParser.hs+  type:             exitcode-stdio-1.0+  ghc-options:      -fspec-constr-count=4 -O3  -threaded -rtsopts "-with-rtsopts=-N -t"+  Build-depends:    base>=4.0, base <4.9, ghc-prim, directory, mtl, template-haskell, vector, AC-Vector, containers, deepseq, text>=0.11.1.13, hPDB >= 0.999, bytestring, iterable >=1.0, IfElse >= 0.80, process >= 1.0, time >= 1.2   other-extensions:       ScopedTypeVariables OverloadedStrings BangPatterns NoMonomorphismRestriction EmptyDataDecls MagicHash 

@@ -0,0 +1,39 @@+{-# LANGUAGE OverloadedStrings, FlexibleContexts, NoMonomorphismRestriction #-}+module Main(main) where++import Control.Concurrent(getNumCapabilities)+import Data.Time(diffUTCTime, getCurrentTime)+import System.Process+import Control.Exception(throw)+import System.Environment(getProgName, getArgs)+import System.Exit(exitWith, exitSuccess, ExitCode(ExitSuccess), ExitCode(..))+import System.Directory(doesFileExist)+import qualified Bio.PDB as PDB(parse, numResidues)+import Data.Iterable+import Control.Monad.IfElse(whenM)+import Control.Monad(unless)++cmd cmdLine = do exitCode <- system cmdLine+                 unless (exitCode == ExitSuccess) $ throw exitCode++inputPath="tests/1htq.ent"+gzPath=inputPath ++ ".gz"++assureInputPath = whenM (not `fmap` doesFileExist inputPath) $ do+  cmd $ "wget --quiet http://rcsb.org/pdb/files/1htq.pdb.gz -O " ++ inputPath ++ ".gz"+  cmd $ "gzip --decompress " ++ gzPath++timeIt io = do+  cpus <- getNumCapabilities+  putStrLn $ "Running with " ++ show cpus ++ " threads."+  t1 <- getCurrentTime+  r <- io+  t2 <- getCurrentTime+  print $ t2 `diffUTCTime` t1+  return r++main = do+  assureInputPath+  timeIt $ do+    Just structure <- PDB.parse inputPath+    print $ PDB.numResidues structure