The PDBtools package

[Tags: gpl, library]

This is a collection of modules for the analysis of protein coordinates. The suite allows efficient computation on a large data set of RCSB protein data bank files. Parsing returns both protein and ligand coordinates. All of the information in ATOM and HETATM records of a PDB file is preserved.


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Properties

Versions0.0.1, 0.0.2, 0.0.3
Change logNone available
Dependenciesbase (>3 && <5), bytestring, containers [details]
LicenseGPL-3
AuthorGrant Rotskoff
Maintainergmr1887@gmail.com
StabilityExperiemental
CategoryBioinformatics
Home pagehttp://www.github.com/rotskoff
Source repositoryhead: git clone git://github.com/rotskoff/Haskell-PDB-Utilities
ExecutablesTest
UploadedWed Apr 4 23:24:39 UTC 2012 by GrantRotskoff
DistributionsNixOS:0.0.3
Downloads673 total (34 in last 30 days)
Votes
0 []
StatusDocs not available [build log]
All reported builds failed as of 2015-05-22 [all 2 reports]

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For package maintainers and hackage trustees

Readme for PDBtools-0.0.2

These modules provide an algebraic data type for atoms and proteins.
The data is expected to come from Protein Data Bank .pdb files. 
The parser will interpret ATOM and HETATM record types.

When implementing the parser over a large number of files:

1. Compile your code. 
2. Use mapM_ in your main loop to ensure computations are done sequentially, otherwise you'll likely see a stack overflow.
   There are certainly other solutions to memory management, depending on the sorts of computations that you're hoping to do.
   If mapM_ doesn't suit your goals, you may want to explore seq and deepSeq.


At the moment, all vector operations are conducted by Vectors.hs. Be warned that
this is an unsafe module (it makes no effort to check vector lengths, etc. In our case everything is three dimensional, so this isn't a problem. Vectors.hs is a module that could benefit from a great deal of expansion. Matrix operations are hopefully coming soon.