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:
- Migrate out of
text-format, since it gives portability trouble, and slows things down when printing.
- Migrate from
AC-Vectorto another vector library:
lensto 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.
126.96.36.199 Jun 2016
* Use hashmap for element properties.
Great thanks to Ben Gamari:
188.8.131.52 Jun 2016
* Updated bounds again.
184.108.40.206 Jun 2016
* Updated bounds for GHC 8.0.
220.127.116.11 Jun 2015
* Cleaned, added some documentation.
18.104.22.168 Apr 2015
* Version bump.
22.214.171.124 Apr 2015
* Update for zlib version 0.6.1.0.
126.96.36.199 Dec 2014
* Relaxed upper bounds
1.2.0 May 2014
* Iterable 3.0
1.1.1 Jan 2014
* Exposed PDBWritable class for all objects that can be written to PDB
1.1 Jan 2014
* Octree building with Bio.PDB.Structure.Neighbours.
0.9999.1 Sep 2013
* Removed most compilation options and replaced them with conditionals
on library versions.
0.9999 Sep 2013
* Parallel parsing.
* Change of Iterable interface from imap -> itmap etc.
0.99 Sep 2013
* First public release.