@hackage hPDB1.0

Protein Databank file format library

  • Installation

  • Dependencies (17)

  • Dependents (2)

    @hackage/acme-everything, @hackage/hPDB-examples

    • Package Flags

      have-mmap
       (on by default)

      Use mmap to read input faster.

      have-sse2
       (on by default)

      Use -msse2 for faster code.

      have-text-format
       (on by default)

      Do 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/5289

      old-bytestring
       (off by default)

      Use bytestring before version 0.10 (introduced in GHC 7.6), and define NFData for Data.ByteString yourself. Disable for GHC 7.6.

      old-zlib
       (off by default)

      Use zlib before version 0.5.4 (introduced in GHC 7.6). Disable for GHC 7.6.1

      old-vector
       (off by default)

      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.

hPDB

Haskell PDB file format parser.

Build Status

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.