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
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
lensto 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.