The hPDB package

[Tags:bsd3, library]

Protein Data Bank file format is a most popular format for holding biological macromolecular data.

This is a very fast sequential parser:

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.

hPDB - Haskell library for processing atomic biomolecular structures in Protein Data Bank format - Michal Jan Gajda. BMC Research Notes 2013, 6:483.


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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)
Change log changelog
Dependencies AC-Vector, base (>=4.0 && <4.8), bytestring, containers, deepseq, directory, ghc-prim, iterable (>=2.0), mmap, mtl, Octree (>=0.5), 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]
License BSD3
Copyright Copyright by Michal J. Gajda '2009-'2013
Author Michal J. Gajda
Maintainer mjgajda@googlemail.com
Stability stable
Category Bioinformatics
Home page https://github.com/BioHaskell/hPDB
Bug tracker mailto:mjgajda@googlemail.com
Source repository head: git clone https://github.com/BioHaskell/hPDB.git
Uploaded Tue Apr 8 13:03:53 UTC 2014 by MichalGajda
Distributions LTSHaskell:1.2.0.9, NixOS:1.2.0.9, Stackage:1.2.0.9
Downloads 2513 total (77 in the last 30 days)
Votes
0 []
Status Docs available [build log]
Successful builds reported [all 1 reports]

Modules

[Index]

Flags

NameDescriptionDefaultType
have-mmapUse mmap to read input faster.EnabledAutomatic
have-sse2Use -msse2 for faster code.EnabledAutomatic
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/5289EnabledAutomatic

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

Downloads

Maintainer's Corner

For package maintainers and hackage trustees

Readme for hPDB

Readme for hPDB-1.1.2

hPDB

Haskell PDB file format parser.

Build Status Hackage

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

This package is also a part of Stackage - a stable subset of Hackage.