hPDB: Protein Databank file format library

This is a package candidate release! Here you can preview how this package release will appear once published to the main package index (which can be accomplished via the 'maintain' link below). Please note that once a package has been published to the main package index it cannot be undone! Please consult the package uploading documentation for more information.

[maintain] [Publish]

Warnings:

Exposed modules use unallocated top-level names: Bio

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

This is a very fast sequential 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.

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.

[Skip to Readme]

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

Bio
- Bio.PDB
  - EventParser
    - Bio.PDB.EventParser.ExperimentalMethods
    - Bio.PDB.EventParser.HelixTypes
    - Bio.PDB.EventParser.PDBEventParser
    - Bio.PDB.EventParser.PDBEventPrinter
    - Bio.PDB.EventParser.PDBEvents
    - Bio.PDB.EventParser.StrandSense
  - Bio.PDB.Fasta
  - Bio.PDB.IO
    - Bio.PDB.IO.OpenAnyFile
  - Bio.PDB.Iterable
  - Bio.PDB.Structure
    - Bio.PDB.Structure.Elements
    - Bio.PDB.Structure.List
    - Bio.PDB.Structure.Neighbours
    - Bio.PDB.Structure.Vector
  - Bio.PDB.StructureBuilder
  - Bio.PDB.StructurePrinter

Flags

Automatic Flags

Name	Description	Default
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

hPDB-1.1.tar.gz [browse] (Cabal source package)
Package description (as included in the package)

Maintainer's Corner

Package maintainers

MichalGajda

For package maintainers and hackage trustees

edit package information

Readme for hPDB-1.1

[back to package description]

hPDB

Haskell PDB file format parser.

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.