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

Versions 0.99, 0.999, 0.9999, 0.9999.1, 1.0, 1.1, 1.1.1, 1.1.2, 1.2.0, 1.2.0.1, 1.2.0.2, 1.2.0.3, 1.2.0.4, 1.2.0.5, 1.2.0.6, 1.2.0.7, 1.2.0.8, 1.2.0.9 (info)
Dependencies AC-Vector, base (>=4.0 && <4.7), bytestring (<=0.9.2.1 || >=0.10.0.0), bytestring-mmap, containers, deepseq, directory, ghc-prim, mtl, QuickCheck (>=2.5.0.0), template-haskell, text (>=0.11.1.13), text-format (<=0.3.0.8 || >=0.3.0.9), vector (<0.10 || >=0.10.0.0), zlib (<=0.5.3.3 || >=0.5.4.0) [details]
License BSD3
Copyright Copyright by Michal J. Gajda '2009-'2012
Author Michal J. Gajda
Maintainer mjgajda@googlemail.com
Stability beta
Category Bioinformatics
Home page https://github.com/mgajda/hpdb
Bug tracker mailto:mjgajda@googlemail.com
Source repository head: git clone git://github.com:mgajda/hpdb.git
Uploaded Sun Jul 7 18:17:23 UTC 2013 by MichalGajda
Distributions LTSHaskell:1.2.0.9, NixOS:1.2.0.9, Stackage:1.2.0.9, Tumbleweed:1.2.0.9
Downloads 2655 total (42 in the last 30 days)
Votes
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Status Docs uploaded by user
Build status unknown [no reports yet]

Modules

[Index]

Flags

NameDescriptionDefaultType
have-mmapUse bytestring-mmap to read input faster.EnabledAutomatic
have-sse2Use -msse2 for faster code.EnabledAutomatic
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.EnabledAutomatic
old-bytestringUse bytestring before version 0.10 (introduced in GHC 7.6), and define NFData for Data.ByteString yourself. Disable for GHC 7.6.DisabledAutomatic
old-zlibUse zlib before version 0.5.4 (introduced in GHC 7.6). Disable for GHC 7.6.1DisabledAutomatic
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.DisabledAutomatic

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

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