The hPDB package

[Tags:bsd3, library]

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 (info)
Change log changelog
Dependencies AC-Vector, base (>=4.0 && <4.10), bytestring, containers, deepseq, directory, ghc-prim, iterable (>=3.0), mmap, mtl, Octree (>=0.5), parallel (>=3.0.0.0), QuickCheck (>=2.5.0.0), tagged (>=0.7), template-haskell, text (>=0.11.1.13), text-format (>=0.3.1.0), unordered-containers (>=0.2.5.0), vector, zlib [details]
License BSD3
Copyright Copyright by Michal J. Gajda '2009-'2015
Author Michal J. Gajda
Maintainer mjgajda@googlemail.com
Stability stable
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.git
Uploaded Sun Jun 5 10:07:58 UTC 2016 by MichalGajda
Distributions LTSHaskell:1.2.0.9, NixOS:1.2.0.9, Stackage:1.2.0.9, Tumbleweed:1.2.0.9
Downloads 2586 total (72 in the last 30 days)
Votes
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Status Docs uploaded by user
Build status unknown [no reports yet]

Modules

[Index]

Flags

NameDescriptionDefaultType
have-mmapUse mmap to read input faster.EnabledAutomatic
have-sse2Use -msse2 for faster code.EnabledAutomatic
have-text-formatDo 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/5289DisabledAutomatic

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

Readme for hPDB-1.2.0.9

hPDB

Haskell PDB file format parser.

Build Status Hackage Hackage Dependencies

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

This package is also a part of Stackage - a stable subset of Hackage.

Projects for the future:

Please let me know if you would be willing to push the project further.

In particular one may considering these features:

  • Migrate out of text-format, since it gives portability trouble, and slows things down when printing.
  • Migrate from AC-Vector to another vector library:
    • vector-space
    • or linear
  • Use lens to facilitate access to the data structures.
    • torsion angles within protein/RNA chain.
  • Add Octree to the default data structure (with automatic update.)
  • Write a combinator library for generic fast parsing.
  • Checking whether GHC 7.8 improved efficiency of fixed point arithmetic, since PDB coordinates have dynamic range of just ~2^20 bits, with smallest step of 0.001.
  • Implement basic spatial operations of RMS superposition (with SVD), affine transform on a substructure.
  • Class-based wrappers showing Structure-Model-Chain-Residue-Atom interface with possible wrapping of Repa/Accelerate arrays for fast computation.