hPDB: Protein Databank file format library
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.
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Modules
[Index]
Flags
Automatic Flags
| Name | Description | Default |
|---|---|---|
| have-mmap | Use mmap to read input faster. | Enabled |
| have-sse2 | Use -msse2 for faster code. | Enabled |
| have-text-format | 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: | Enabled |
| old-bytestring | Use bytestring before version 0.10 (introduced in GHC 7.6), and define NFData for Data.ByteString yourself. Disable for GHC 7.6. | Disabled |
| old-zlib | Use zlib before version 0.5.4 (introduced in GHC 7.6). Disable for GHC 7.6.1 | Disabled |
| old-vector | 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. | Disabled |
Use -f <flag> to enable a flag, or -f -<flag> to disable that flag. More info
Downloads
- hPDB-0.999.tar.gz [browse] (Cabal source package)
- Package description (as included in the package)
Maintainer's Corner
For package maintainers and hackage trustees
Candidates
| Versions [RSS] | 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, 1.2.0.10, 1.3.0.0, 1.4.0.0, 1.5.0.0 (info) |
|---|---|
| Dependencies | AC-Vector, base (>=4.0 && <4.7), bytestring (<=0.9.2.1 || >=0.10.0.0), containers, deepseq, directory, ghc-prim, iterable (>=1.0), mmap, mtl, QuickCheck (>=2.5.0.0), template-haskell, text (>=0.11.1.13), text-format (>=0.3.1.0), vector (<0.10 || >=0.10.0.0), zlib (<=0.5.3.3 || >=0.5.4.0) [details] |
| Tested with | ghc ==7.0.3, ghc ==7.2.2, ghc ==7.4.1, ghc ==7.4.2, ghc ==7.6.1, ghc ==7.6.2 |
| License | BSD-3-Clause |
| Copyright | Copyright by Michal J. Gajda '2009-'2013 |
| Author | Michal J. Gajda |
| Maintainer | mjgajda@googlemail.com |
| Category | Bioinformatics |
| Home page | https://github.com/mgajda/hpdb |
| Bug tracker | mailto:mjgajda@googlemail.com |
| Source repo | head: git clone https://github.com/mgajda/hPDB head: git clone git://github.com:mgajda/hpdb.git |
| Uploaded | by MichalGajda at 2013-09-22T12:08:25Z |
| Distributions | |
| Reverse Dependencies | 1 direct, 0 indirect [details] |
| Downloads | 15297 total (7 in the last 30 days) |
| Rating | 2.0 (votes: 1) [estimated by Bayesian average] |
| Your Rating | |
| Status | Docs uploaded by user Build status unknown [no reports yet] |
Readme for hPDB-0.999
[back to package description]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.