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:

.. code-block:: python

    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")

.. image:: ../images/behaviour1.png
   :height: 300
   :alt: Behaviour Example 1

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:

.. code-block:: python

    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")

.. image:: ../images/behaviour2.png
   :height: 300
   :alt: Behaviour Example 2

3. Starting later
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


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

Example:

.. code-block:: python

    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")

.. image:: ../images/behaviour3.png
   :height: 300
   :alt: Behaviour Example 3

4. Finishing earlier
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


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

Example:

.. code-block:: python

    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")

.. image:: ../images/behaviour4.png
   :height: 300
   :alt: Behaviour Example 4

5. Single isolated points
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


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

Example:

.. code-block:: python

    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")

.. image:: ../images/behaviour5.png
   :height: 300
   :alt: Behaviour Example 5