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6.3 KROME with Graphviz

Warning: now superseded by DOCMAKE

Among other features KROME generates a file network.dot. This file is generated in the Graphviz format (more here) and then the users can visualise their network as a graph.

To generate a plot from the "network.dot" file first you need to install Graphviz on your machine and then you can run one of the following command on the shell:

dot -Tps input.dot > output.eps
dot -Tpng input.dot > output.png

The representation of a network as a graph is very useful to have structural information about the network and know which are the most important species (hubs).

Additional information about Graphviz can be found here.
Note that KROME has a Python tool to produce subgraph (see 6.3.2 below).

##6.3.1 Install graphviz

On Linux machines use

sudo apt-get install graphviz

##6.3.2 Chemical network graph python tool (pathway)

Warning: now superseded by DOCMAKE

KROME also provides a pre-built python tool which allows users to plot sub-networks based on a given hub species pathway.py. This is placed in krome/tools.

Run the script as

python pathway.py INPUT OUTPUT BASE

where INPUT is a chemical network file, OUTPUT is the name of the eps image (e.g. test.eps), and BASE is the reference atom, i.e. the atom shared by the species you want to include in the graph.
For example if your species are H, OH, H2O, CH, using O as reference atom will include only OH and H2O, while using C only CH.