The hPDB package

[Tags: bsd3, library]

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.


Properties

Versions0.99, 0.999, 0.9999, 0.9999.1, 1.0, 1.1, 1.1.1, 1.1.2, 1.2.0
DependenciesAC-Vector, base (>=4.0 && <4.7), bytestring (<=0.9.2.1), containers, deepseq, directory, ghc-prim, mtl, QuickCheck (>=2.5.0.0), template-haskell, text (>=0.11.1.13), text-format (<=0.3.0.8), vector (<0.10), zlib (<=0.5.3.3) or
AC-Vector, base (>=4.0 && <4.7), bytestring (<=0.9.2.1), containers, deepseq, directory, ghc-prim, mtl, QuickCheck (>=2.5.0.0), template-haskell, text (>=0.11.1.13), text-format (<=0.3.0.8), vector (<0.10), zlib (>=0.5.4.0) or
AC-Vector, base (>=4.0 && <4.7), bytestring (<=0.9.2.1), containers, deepseq, directory, ghc-prim, mtl, QuickCheck (>=2.5.0.0), template-haskell, text (>=0.11.1.13), text-format (<=0.3.0.8), vector (>=0.10.0.0), zlib (<=0.5.3.3) or
AC-Vector, base (>=4.0 && <4.7), bytestring (<=0.9.2.1), containers, deepseq, directory, ghc-prim, mtl, QuickCheck (>=2.5.0.0), template-haskell, text (>=0.11.1.13), text-format (<=0.3.0.8), vector (>=0.10.0.0), zlib (>=0.5.4.0) or
AC-Vector, base (>=4.0 && <4.7), bytestring (<=0.9.2.1), containers, deepseq, directory, ghc-prim, mtl, QuickCheck (>=2.5.0.0), template-haskell, text (>=0.11.1.13), text-format (>=0.3.0.9), vector (<0.10), zlib (<=0.5.3.3) or
AC-Vector, base (>=4.0 && <4.7), bytestring (<=0.9.2.1), containers, deepseq, directory, ghc-prim, mtl, QuickCheck (>=2.5.0.0), template-haskell, text (>=0.11.1.13), text-format (>=0.3.0.9), vector (<0.10), zlib (>=0.5.4.0) or
AC-Vector, base (>=4.0 && <4.7), bytestring (<=0.9.2.1), containers, deepseq, directory, ghc-prim, mtl, QuickCheck (>=2.5.0.0), template-haskell, text (>=0.11.1.13), text-format (>=0.3.0.9), vector (>=0.10.0.0), zlib (<=0.5.3.3) or
AC-Vector, base (>=4.0 && <4.7), bytestring (<=0.9.2.1), containers, deepseq, directory, ghc-prim, mtl, QuickCheck (>=2.5.0.0), template-haskell, text (>=0.11.1.13), text-format (>=0.3.0.9), vector (>=0.10.0.0), zlib (>=0.5.4.0) or
AC-Vector, base (>=4.0 && <4.7), bytestring (>=0.10.0.0), containers, deepseq, directory, ghc-prim, mtl, QuickCheck (>=2.5.0.0), template-haskell, text (>=0.11.1.13), text-format (<=0.3.0.8), vector (<0.10), zlib (<=0.5.3.3) or
AC-Vector, base (>=4.0 && <4.7), bytestring (>=0.10.0.0), containers, deepseq, directory, ghc-prim, mtl, QuickCheck (>=2.5.0.0), template-haskell, text (>=0.11.1.13), text-format (<=0.3.0.8), vector (<0.10), zlib (>=0.5.4.0) or
AC-Vector, base (>=4.0 && <4.7), bytestring (>=0.10.0.0), containers, deepseq, directory, ghc-prim, mtl, QuickCheck (>=2.5.0.0), template-haskell, text (>=0.11.1.13), text-format (<=0.3.0.8), vector (>=0.10.0.0), zlib (<=0.5.3.3) or
AC-Vector, base (>=4.0 && <4.7), bytestring (>=0.10.0.0), containers, deepseq, directory, ghc-prim, mtl, QuickCheck (>=2.5.0.0), template-haskell, text (>=0.11.1.13), text-format (<=0.3.0.8), vector (>=0.10.0.0), zlib (>=0.5.4.0) or
AC-Vector, base (>=4.0 && <4.7), bytestring (>=0.10.0.0), containers, deepseq, directory, ghc-prim, mtl, QuickCheck (>=2.5.0.0), template-haskell, text (>=0.11.1.13), text-format (>=0.3.0.9), vector (<0.10), zlib (<=0.5.3.3) or
AC-Vector, base (>=4.0 && <4.7), bytestring (>=0.10.0.0), containers, deepseq, directory, ghc-prim, mtl, QuickCheck (>=2.5.0.0), template-haskell, text (>=0.11.1.13), text-format (>=0.3.0.9), vector (<0.10), zlib (>=0.5.4.0) or
AC-Vector, base (>=4.0 && <4.7), bytestring (>=0.10.0.0), containers, deepseq, directory, ghc-prim, mtl, QuickCheck (>=2.5.0.0), template-haskell, text (>=0.11.1.13), text-format (>=0.3.0.9), vector (>=0.10.0.0), zlib (<=0.5.3.3) or
AC-Vector, base (>=4.0 && <4.7), bytestring (>=0.10.0.0), containers, deepseq, directory, ghc-prim, mtl, QuickCheck (>=2.5.0.0), template-haskell, text (>=0.11.1.13), text-format (>=0.3.0.9), vector (>=0.10.0.0), zlib (>=0.5.4.0)
LicenseBSD3
CopyrightCopyright by Michal J. Gajda '2009-'2012
AuthorMichal J. Gajda
Maintainermjgajda@googlemail.com
Stabilitybeta
CategoryBioinformatics
Home pagehttps://github.com/mgajda/hpdb
Bug trackermailto:mjgajda@googlemail.com
Source repositoryhead: git clone git://github.com:mgajda/hpdb.git
Upload dateSun Jul 7 18:17:23 UTC 2013
Uploaded byMichalGajda
DistributionsStackage:1.2.0
Downloads908 total (85 in last 30 days)

Modules

[Index]

Flags

NameDescriptionDefault
have-mmapUse bytestring-mmap to read input faster.Enabled
have-sse2Use -msse2 for faster code.Enabled
old-text-formatUse text-format versions before 0.3.0.9 (and define Params instance for 11-tuple to 20-tuple yourself.) Disable for (yet unreleased) versions after 0.3.0.8 when change was merged into upstream.Enabled
old-bytestringUse bytestring before version 0.10 (introduced in GHC 7.6), and define NFData for Data.ByteString yourself. Disable for GHC 7.6.Disabled
old-zlibUse zlib before version 0.5.4 (introduced in GHC 7.6). Disable for GHC 7.6.1Disabled
old-vectorUse old vector library before version 0.10 (introduced along with GHC 7.6). Disable for GHC 7.6.1 and latest 7.4.2.Disabled

Use -f <flag> to enable a flag, or -f -<flag> to disable that flag. More info

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