PLCC_Graph_Exporters

The PLCC application allows you to export the computed graphs in a number of standard graph file formats including GML, TGF and DOT Language. These files can be opened in standard graph software (Gephi, GraphViz, Cytoscape, ...) or parsed by your own application.

You can control the output formats of PLCC by using the -O or --outputformats command line parameter.

Here are some screenshots showing exported protein graphs computed by PLCC, opened in other applications:

• The albelig graph (with backbone) of 7TIM, chain A opened in Gephi
• The albelig graph (with backbone) of 7TIM, chain A opened in GraphViz
• The albelig graph (with backbone) of 7TIM, chain A opened in Cytoscape

Graph formats

For information on the formats use your favorite internet search engine or read:

• GML info at Wikipedia or the article by M Himsolt
• TGF info at Wikipedia
• DOT language (.gv) info at Wikipedia

The (Kavosh) Edge List format is very simple. It's ASCII and line-based, the first line holds the number of vertices in the graph and all other lines represent an edge between two vertices. No annotations. Here is a small example graph, consisting of 3 vertices and 4 directed edges:

3
1 2
1 3
2 1
3 1