hPDB: Protein Databank file format library

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Warnings:

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, 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, 1.3.0.0, 1.4.0.0, 1.5.0.0
Change log None available
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 BSD-3-Clause
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 repo head: git clone https://github.com/BioHaskell/hPDB
head: git clone git://github.com:mgajda/hpdb.git
Uploaded by MichalGajda at 2013-12-08T19:07:01Z

Modules

Flags

Automatic Flags
NameDescriptionDefault
have-mmap

Use mmap to read input faster.

Enabled
have-sse2

Use -msse2 for faster code.

Enabled
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

Enabled
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.

Disabled
old-zlib

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

Disabled
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.

Disabled

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

Downloads

Maintainer's Corner

Package maintainers

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:

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.