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.


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Properties

Versions0.99, 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
Change logNone available
DependenciesAC-Vector, base (>=4.0 && <4.7), bytestring, containers, deepseq, directory, ghc-prim, iterable (>=2.0), mmap, mtl, parallel (>=3.0.0.0), QuickCheck (>=2.5.0.0), template-haskell, text (>=0.11.1.13), text-format (>=0.3.1.0), vector, zlib [details]
LicenseBSD3
CopyrightCopyright by Michal J. Gajda '2009-'2013
AuthorMichal J. Gajda
Maintainermjgajda@googlemail.com
Stabilitybeta
CategoryBioinformatics
Home pagehttps://github.com/mgajda/hpdb
Bug trackermailto:mjgajda@googlemail.com
Source repositoryhead: git clone https://github.com/mgajda/hPDB
head: git clone git://github.com:mgajda/hpdb.git
UploadedMon Nov 11 13:34:57 UTC 2013 by MichalGajda
DistributionsLTSHaskell:1.2.0.4, NixOS:1.2.0.4, Stackage:1.2.0.4
Downloads1784 total (98 in last 30 days)
Votes
0 []
StatusDocs available [build log]
Successful builds reported [all 1 reports]

Modules

[Index]

Flags

NameDescriptionDefault
have-mmapUse mmap to read input faster.Enabled
have-sse2Use -msse2 for faster code.Enabled
have-text-formatDo 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/5289Enabled
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

Downloads

Maintainers' corner

For package maintainers and hackage trustees

Readme for hPDB-0.9999.1

hPDB

Haskell PDB file format parser.

Build Status

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.

Details on official releases are on Hackage.