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All Projects → BioHaskell → hPDB

BioHaskell / hPDB

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PDB parser in Haskell

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Labels

pdbprotein-data-bankprotein-structurefile-formathackagepdb-parser

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hPDB

Haskell PDB file format parser.

Build Status Hackage Hackage Dependencies Join the chat at https://gitter.im/BioHaskell/hPDB

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:

  • Implement basic spatial operations of RMS superposition (with SVD), affine transform on a substructure.
  • 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.)
  • Migrate out of text-format, since it gives portability trouble, and slows things down when printing.
  • 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.
  • Class-based wrappers showing Structure-Model-Chain-Residue-Atom interface with possible wrapping of Repa/Accelerate arrays for fast computation.

Please ask me any questions on Gitter.

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