SpinpharmaR

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spinpharmaR is an R package which provides functionality to parse and analyse output from spINPHARMA.

Download spinpharmaR from URL: http://www.inpharma-wiki.carlomagno-group.org/downloads/spinpharmar/spinpharmar.tar.gz

To install spinpharmaR (from a Linux terminal):

R CMD INSTALL spinpharmar.tar.gz


Load package:

## Open R
R

## Load spinpharmaR
library(spinpharmaR)

## List functions of the package
ls("package:spinpharmaR")

 [1] "calc.rmsd"   "filter.hits" "join.rmsd"   "plot.noes"   "plot.qual"  
 [6] "print.hits"  "print.noes"  "print.qual"  "read.noes"   "read.qual"


For documentation use (in interactive mode):

?function


i.e.:

R
?read.qual
?filter.hits
?plot.qual

See also Analyzing the results for more information on usage.

Dependencies

The RMSD calculation in spinpharmaR depends on the Bio3D (http://thegrantlab.org/bio3d) R-package:

R: http://www.r-project.org Bio3d: http://thegrantlab.org/bio3d

Installation in Ubuntu

To install R, Bio3D, and spinpharmaR:

## Install R
sudo apt-get install r-base

## Install Bio3D
wget http://thegrantlab.org/bio3d/phocadownload/Bio3D_version2.x/bio3d_2.0-1.tar.gz
R CMD INSTALL bio3d_2.0-1.tar.gz

## Install spinpharmaR 
wget http://www.carlomagno.embl.de/downloads/spinpharmar/spinpharmar.tar.gz
R CMD INSTALL spinpharmar.tar.gz

Voila !