thermo

Thermodynamic plot module. Given the energies of the compounds and the transition states, this module creates a graph summarizing the thermodynamic/kinetic behavior of the system. The background of the nodes and the fill color of the edges is set depending on their energies, while the width of the edges is based on their computed kinetic constants.

rnets.plotter.thermo.build_dotgraph(nw: Network, graph_cfg: GraphCfg = GraphCfg(), chem_cfg: ChemCfg = ChemCfg(), colorbar_cfg: ColorbarCfg | None = None) → Graph[source]

Build a dotgraph from a reaction network.

Parameters:

nw (Network) -- Network object to be converted into dot graph.
graph_cfg (GraphCfg, optional) -- Graphviz configuration. Defaults to ChemCfg
chem_cfg (ChemCfg, optional) -- Chemical parameters fo the system. Defaults to ChemCfg
colorbar_cfg (ColorbarCfg or None, optional) -- Colorbar parameters of the system. Defaults to None.

Returns:

Dot Graph with the colors and shapes of the netwkork.

rnets.plotter.thermo.get_colorbar(nw: Network, graph_cfg: GraphCfg, chem_cfg: ChemCfg, colorbar_cfg: ColorbarCfg, colorspace: ColorSpace = 'lab') → tuple[Node, Edge | tuple[()]][source]

Build a colorbar for the thermodynamic plot.

Parameters:

graph_cfg (GraphCfg, optional) -- Graphviz configuration. Defaults to ChemCfg.
chem_cfg (ChemCfg, optional) -- Chemical parameters fo the system. Defaults to ChemCfg.
colorbar_cfg (ColorbarCfg or None, optional) -- Colorbar parameters of the system. Defaults to None.
colorspace (ColorSpace, optional) -- Colorspace of the colorbar. Defaults to "lab".

Returns:

Node representing the color bar and the second value being an invisible edge that anchors the colorbar to another node.

Return type:

tuple of two values, the first one being a obj