Tools

Small tools included in the VPLG release:

rpg -- Random protein graph generator

This is a Perl script which can be used to generate random protein graphs in the VPLG graph file format. These graphs can then be drawn with the [PLCC] software. You can use the following command to access the built-in help:

./rpg.pl -h

Depending on the version, you will see something like this:

[RPG] rpg.pl -- Random Protein Graph -- generate random protein graphs in the plg format of plcc
[RPG] This program is part of plcc, written by Tim Schaefer.
[RPG]   USAGE   : rpg.pl [options]
[RPG]    Valid options are:
[RPG]     -h                    : Print this help message and exit.
[RPG]     -v <num_vertices>     : Number of vertices the graph should have (positive integer). Default=100.
[RPG]     -p <edge_probability> : Probability that an edge is created between a pair of vertices (positive float between 0 and 1). Default=0.1.
[RPG]     -o <outfile>          : Path where to write the output file. Default='random_graph.dpg'.
[RPG]   EXAMPLE : rpg.pl -v 100 -p 0.1 -o random_graph_100_01.plg

We suggest you read the documentation provided with the release or use the built-in help of your version for up-to-date information.