hPDB: Protein Databank file format library

[ bioinformatics-, bsd3, library ] [ Propose Tags ]
This version is deprecated.

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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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

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Package maintainers

For package maintainers and hackage trustees

Candidates

Versions [RSS] 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, 1.3.0.0, 1.4.0.0, 1.5.0.0 (info)
Dependencies AC-Vector, base (>=4.0 && <4.7), bytestring (<=0.9.2.1 || >=0.10.0.0), 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 (<0.10 || >=0.10.0.0), zlib (<=0.5.3.3 || >=0.5.4.0) [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/mgajda/hpdb
Bug tracker mailto:mjgajda@googlemail.com
Source repo head: git clone https://github.com/mgajda/hPDB
head: git clone git://github.com:mgajda/hpdb.git
Uploaded by MichalGajda at 2013-09-25T00:51:29Z
Distributions
Reverse Dependencies 1 direct, 0 indirect [details]
Downloads 14786 total (53 in the last 30 days)
Rating 2.0 (votes: 1) [estimated by Bayesian average]
Your Rating
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Status Docs uploaded by user
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Readme for hPDB-0.9999

[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.