Plotting Behaviour

This section demonstrates how to manipulate the reaction profile plotting beyond aesthetics: controlling x-axis positions, skipping points, starting later, finishing earlier, or placing individual points between indices.

1. Point repeated for spacing

Sometimes you want a point placed between two x-indices. This can be done by repeating the same energy value in consecutive positions.

Example:

from plotprofile import ReactionProfilePlotter

energy_sets = {
    "Pathway A": [0.0, 5.0, 5.0, 2.0],  # repeated 5.0 creates midpoint
    "Pathway B": [0.0, 3.0, 1.0, 4.0],
}

plotter = ReactionProfilePlotter()
plotter.plot(energy_sets, filename="images/behaviour1")

2. Skipping an index

You can skip an index by inserting None in the energy list. The line will connect non-None values automatically.

Example:

energy_sets = {
    "Pathway A": [0.0, 5.0, 2.0, 3.0],
    "Pathway B": [1.0, None, 4.0, 6.0],
}

plotter = ReactionProfilePlotter()
plotter.plot(energy_sets, filename="images/behaviour2")

3. Starting later

A secondary curve can start after the first point. Place None in all preceding positions.

Example:

energy_sets = {
    "Pathway A": [0.0, -2.0, 5.0, 4.0],
    "Pathway B": [None, None, 3.0, 6.0],
}

plotter = ReactionProfilePlotter()
plotter.plot(energy_sets, filename="images/behaviour3")

4. Finishing earlier

If you want a curve to finish before the last index, just end the list before the other series.

Example:

energy_sets = {
    "Pathway A": [0.0, -2.0, 5.0, 4.0],
    "Pathway B": [0.0, 2.0, 3.0],  # ends earlier
}

plotter = ReactionProfilePlotter()
plotter.plot(energy_sets, filename="images/behaviour4")

5. Single isolated points

Individual points can be placed by providing a list with only one energy value or surrounding None.

Example:

energy_sets = {
    "Pathway A": [0.0, 5.0, -2.0, 4.0],
    "TS1": [None, 7.0],
}

plotter = ReactionProfilePlotter()
plotter.plot(energy_sets, filename="images/behaviour5")