Command-line help

rNets was designed mainly with its command-line utility in mind. By enabling the flag --help or -h the following information will be displayed:

rNets, create a dotfile.

usage: rnets [-h] [-cf COMP_FILE] [-rf REAC_FILE] [-o OUT_FILE] [-cfg CONFIG]
             [-T CHEM.T] [-u {eV,kj/mol,kcal/mol}] [-kb CHEM.KB] [-A CHEM.A]
             [-k GRAPH.KIND]
             [-c {viridis,plasma,magma,inferno,cividis,viridis_r,plasma_r,magma_r,inferno_r,cividis_r}]
             [-off GRAPH.COLOR_OFFSET GRAPH.COLOR_OFFSET]
             [-go GRAPH.OPTS [GRAPH.OPTS ...]] [-w GRAPH.EDGE.WIDTH]
             [-mw GRAPH.EDGE.MAX_WIDTH]
             [-eo GRAPH.EDGE.OPTS [GRAPH.EDGE.OPTS ...]]
             [-f GRAPH.NODE.FONT_COLOR] [-a GRAPH.NODE.FONT_COLOR_ALT]
             [-l GRAPH.NODE.FONT_LUM_THRESHOLD]
             [-no GRAPH.NODE.OPTS [GRAPH.NODE.OPTS ...]]

Named Arguments

-cf, --compfile: Compounds file
-rf, --reacfile: Reactions file
-o, --outfile: Output file name
-cfg, --config: Configuration file name

Chemistry

-T, --temperature

Temperature value in K

-u, --units

Possible choices: eV, kj/mol, kcal/mol

Energy units. Used to select kb and A if not provided

-kb, --boltzmann

Boltzmann constant. Overrides the default

-A, --preexp

Eyring equation pre-exponetial factor. Overrides the default

Graph configuration

-k, --kind

Kind of dotgraph

-c, --colorscheme

Possible choices: viridis, plasma, magma, inferno, cividis, viridis_r, plasma_r, magma_r, inferno_r, cividis_r

Color scheme

-off, --offset

Colorscheme offset

-go, --graph_opts

Graphviz options for graph in dictionary format

Edge configuration

-w, --width: Edge constant/minimum width
-mw, --maxwidth: Edge maximum width
-eo, --edge-opts: Graphviz options for edges in dictionary format

Node configuration

-f, --fontcolor: Font color of the nodes
-a, --fontcoloralt: Alternate font color of the nodes
-l, --lumthreshold: Luminance threshold for the nodes
-no, --node-opts: Graphviz options for nodes in dictionary format