hPDB: Parser, print and manipulate structures in PDB file format.

[ bioinformatics, bsd3, library ] [ Propose Tags ]

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.

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 && <4.7), bytestring (<=0.9.2.1 || >=0.10.0.0), bytestring-mmap, containers, deepseq, directory, ghc-prim, mtl, QuickCheck (>=2.5.0.0), template-haskell, text (>=0.11.1.13), text-format (<=0.3.0.8 || >=0.3.0.9), 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-'2012
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 git://github.com:mgajda/hpdb.git
Uploaded by MichalGajda at Sun Jul 7 18:17:23 UTC 2013
Distributions NixOS:1.2.0.10
Downloads 5927 total (27 in the last 30 days)
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Status Docs uploaded by user
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Modules

[Index]

Flags

NameDescriptionDefaultType
have-mmap

Use bytestring-mmap to read input faster.

EnabledAutomatic
have-sse2

Use -msse2 for faster code.

EnabledAutomatic
old-text-format

Use text-format versions before 0.3.0.9 (and define Params instance for 11-tuple to 20-tuple yourself.) Disable for (yet unreleased) versions after 0.3.0.8 when change was merged into upstream.

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

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For package maintainers and hackage trustees