PDBtools: A library for analysis of 3-D protein coordinates

[ bioinformatics, gpl, library ] [ Propose Tags ] [ Report a vulnerability ]

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.

[Skip to Readme]

Modules

[Index]

PDBtools

Flags

Automatic Flags

Name	Description	Default
tests		Disabled

Use -f <flag> to enable a flag, or -f -<flag> to disable that flag. More info

Downloads

PDBtools-0.0.3.tar.gz [browse] (Cabal source package)
Package description (as included in the package)

Maintainer's Corner

Package maintainers

GrantRotskoff

For package maintainers and hackage trustees

edit package information

Candidates

No Candidates

Versions [RSS]	0.0.1, 0.0.2, 0.0.3
Dependencies	base (>3 && <5), bytestring, containers [details]
License	GPL-3.0-only
Author	Grant Rotskoff
Maintainer	gmr1887@gmail.com
Category	Bioinformatics
Home page	http://www.github.com/rotskoff
Source repo	head: git clone git://github.com/rotskoff/Haskell-PDB-Utilities
Uploaded	by GrantRotskoff at 2012-06-03T05:48:24Z
Distributions	NixOS:0.0.3
Reverse Dependencies	1 direct, 0 indirect [details]
Executables	Test
Downloads	3209 total (8 in the last 30 days)
Rating	(no votes yet) [estimated by Bayesian average]
Your Rating	λ λ λ
Status	Docs uploaded by user Build status unknown [no reports yet]

Readme for PDBtools-0.0.3

[back to package description]

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.