The results of the centrality analysis can be stored into a text file. It contains the network name, a list of the selected nodes, the name of the saved centrality parameter and a list of nodes along with their respective centrality values. The nodes are sorted alphabetically. A small example is presented below.
pdb1abc.sif Selected nodes: A, B, C Shortest Path Betweenness A:42:_:GLU 0.2 A:86:_:SER 0.0 A:57:_:PRO 0.3 A:88:_:ARG 1.0
If the user saves all measures in one file, then the network name and the list of selected nodes are included only at the beginning of the file. The files with such format have the extension centstats.
The node set file has a simple structure. A header line defines the file type. The file can contain more than one set separated by new lines. Each set is defined by a line consisting of the set name and the name of the network, to which the nodes in the set belong. These are separated by a tabular and followed by a list of node names/identifiers. The extension for node set files is nodeset. An example for a node set file is shown below:
# RINalyzer node sets Set1 pdb1abc.sif A:42:_:GLU A:57:_:PRO Set2 pdb1abc.sif A:86:_:SER A:88:_:ARG
The default visual properties values provided by RINalyzer use the Java Properties format. They include the secondary structure node colors, the edge type colors, the node and label size, the line width of backbone edges and all other edges, and the width of the space between parallel edges. Here, the default properties file, the rinalyzer.props, can be seen:
## RINalyzer visual properties #Sat Jul 11 21:15:49 CEST 2009 bbedgewidth=4 edgewidth=3 edgespace=4 nodesize=40 labelsize=14 color.Background=255,255,255 color.default=255,146,148 color.Helix=255,0,0 color.Sheet=0,0,255 color.Loop=153,153,153 color.backbone=0,0,0 color.combi\:all_all=0,0,0 color.cnt\:mc_mc=0,0,255 color.cnt\:mc_sc=0,153,255 color.cnt\:sc_sc=153,204,255 color.cnt\:mc_lig=0,153,51 color.cnt\:sc_lig=102,255,0 color.hbond\:mc_mc=153,0,51 color.hbond\:mc_sc=255,0,0 color.hbond\:sc_sc=255,204,204 color.hbond\:sc_lig=255,255,0 color.hbond\:mc_lig=153,153,0 color.ovl\:mc_mc=51,51,51 color.ovl\:mc_sc=153,153,153 color.ovl\:sc_sc=204,204,204 color.pp=0,0,0