Creating Free Energy Diagrams

ccu features a GUI utility, FancyPlots, for creating free energy diagrams for mechanistic studies.

Using the GUI

FancyPlots can be launched from the command line via the ccu fed subcommand:

ccu fed

or by the ccu.fancyplots subpackage:

import tkinter as tk
from ccu.fancyplots import FancyPlotsGUI
root = tk.Tk()
app = FancyPlotsGUI(master=root)
app.master.mainloop()

With FancyPlots, you can design reaction mechanisms, define their reaction energies, modify plotting parameters, and save the free energy diagram.

FancyPlots produces a cache file (extension .fancy) that can be used to initialize FancyPlots with the values from a previous session. To seed FancyPlots with data from a previous session run:

ccu fed --cache=CACHE_FILE

from the command line or

import tkinter as tk
from ccu.fancyplots. import FancyPlotsGUI
root = tk.Tk()
app = FancyPlotsGUI(cache_file=Path("CACHE_FILE"), master=root)
app.master.mainloop()

within Python.

Tip

The cache file contains the information required to re-populate all the FancyPlots data. (For more details about this information, see the ccu.fancyplots.data.FEDData class.) Sometimes, however, you may only have mechanistic data that you would like to use to initialize FancyPlots with. In this case, you can use the --data CLI option:

ccu fed --data=DATA_FILE

Creating Free Energy Diagrams Programatically

You can create free energy diagram without ever launching the GUI. Assuming that you have the free energy diagram data saved in a file named feddata.json, you can create an FED like so:

import json
from pathlib import Path

from ccu.fancyplots import DEFAULT_PARAMETERS, generate_figure

with Path("feddata.json").open(mode="r", encoding="utf-8") as file:
        data = json.load(file)

parameters = DEFAULT_PARAMETERS
parameters["savename"] = "saved_fed.svg"

ax1, ax2, fig = generate_figure(
        diagram_data=data,
        parameters=parameters,
        visual=False,
)