name: hPDB version: 1.1 synopsis: Protein Databank file format library homepage: https://github.com/BioHaskell/hPDB stability: stable package-url: http://hackage.haskell.org/package/hPDB description: Protein Data Bank file format is a most popular format for holding biological macromolecular data. . This is a very fast sequential 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. . In its parallel incarnation it is most probably the fastest parser for PDB format. . 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. . category: Bioinformatics license: BSD3 license-file: LICENSE author: Michal J. Gajda 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==7.0.3, 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 source-repository head type: git location: https://github.com/BioHaskell/hPDB flag have-mmap description: Use mmap to read input faster. default: True flag have-sse2 description: Use -msse2 for faster code. default: True flag have-text-format description: Do not use text-format, since it may require double-conversion and thus linking of libstdc++ which may break compilation due to GHC bug #5289: . 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 if flag(have-sse2) ghc-options: -msse2 if flag(have-mmap) build-depends: mmap cpp-options: -DHAVE_MMAP -- These optimization options change a lot for GHC >= 7.4.1 ghc-options: -fspec-constr-count=4 -O3 if flag(have-text-format) 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 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