The hPDB package

[ Tags: bioinformatics, bsd3, library ] [ Propose Tags ]

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, 1.2.0.10 (info)
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
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
head: git clone git://github.com:mgajda/hpdb.git
Uploaded Sun Dec 8 19:07:38 UTC 2013 by MichalGajda
Distributions LTSHaskell:1.2.0.10, NixOS:1.2.0.10, Tumbleweed:1.2.0.9
Downloads 4009 total (591 in the last 30 days)
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Status Docs available [build log]
Successful builds reported [all 1 reports]
Hackage Matrix CI

Modules

[Index]

Flags

NameDescriptionDefaultType
have-mmap

Use mmap to read input faster.

EnabledAutomatic
have-sse2

Use -msse2 for faster code.

EnabledAutomatic
have-text-format

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

EnabledAutomatic
old-bytestring

Use bytestring before version 0.10 (introduced in GHC 7.6), and define NFData for Data.ByteString yourself. Disable for GHC 7.6.

DisabledAutomatic
old-zlib

Use zlib before version 0.5.4 (introduced in GHC 7.6). Disable for GHC 7.6.1

DisabledAutomatic
old-vector

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.

DisabledAutomatic

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-1.1

[back to package description]

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.