PyEnergyDiagrams

PyEnergyDiagrams allows the plotting of energy profile diagrams using Python and Matplotlib.

Installation

If you are new to Python, the easiest way to get started is to use a distribution like Anaconda. Then you can use the terminal to install the module using pip:

pip install git+https://github.com/giacomomarchioro/PyEnergyDiagrams

The only requirement is matplotlib, which is installed by default using Anaconda.

How to use it?

import matplotlib.pyplot as plt
from energydiagram import ED
diagram = ED()
diagram.add_level(0,'Separated Reactants')
diagram.add_level(-5.4,'mlC1')
diagram.add_level(-15.6,'mlC2','last',) #Using 'last'  or 'l' it will be together with the previous level
diagram.add_level(28.5,'mTS1',color='g')
diagram.add_level(-9.7,'mCARB1')
diagram.add_level(-19.8,'mCARB2','l')
diagram.add_level(20,'mCARBX','last')

Show the IDs (red numbers) to understand how to link the levels:

diagram.plot(show_IDs=True)

Add the links using diagram.add_link(starting_level_ID,ending_level_ID):

diagram.add_link(0,1)
diagram.add_link(0,2)
diagram.add_link(2,3)
diagram.add_link(1,3)
diagram.add_link(3,4)
diagram.add_link(3,5)
diagram.add_link(0,6)

For plotting the final result:

diagram.plot(ylabel="Energy / $kcal$ $mol^{-1}$") # this is the default ylabel

To show it:

import matplotlib.pyplot as plt
plt.show()

The results are displayed above.

Electron boxes

Also electron boxes can be added, the electron spin is automatically changed following the aufbau principle.

import matplotlib.pyplot as plt
from energydiagram import ED
a = ED()
a.add_level(0,'2pxy',top_text='')
a.add_level(10,'$\sigma*$',top_text='')
a.add_level(5,'$\pi*$','last',top_text='')
a.add_level(-5,'$\pi$','last',color='g',top_text='')
a.add_level(-10,'$\sigma$',top_text='',position='l')
a.add_level(0,'2pxy',top_text='')
for i in range(1,5):
    a.add_link(0,i,color='g')
    a.add_link(i,5,color='b')
a.add_electronbox(level_id=0, boxes=1, electrons=2, side=1.5, spacing_f=2.5)
a.add_electronbox(1,2,0,1.5,3)
a.add_electronbox(2,5,10,1.5,3)
a.add_electronbox(3,3,4,1.5,3)
a.add_electronbox(4,3,2,1.5,3)
a.add_electronbox(5,3,5,1.5,3)
a.offset *= 1.5
a.plot(show_IDs=True)
plt.show()

Troubleshooting and fine-tuning

Most of the time, there could be a problem with text padding. Some parameters can be changed in this way.

diagram.offset = 10

To make the change effective, you must use the command diagram.plot() again. Remember that once you have made a first attempt at plotting. You can adjust the plot as every matplotlib plot. For convenience you can access ax and fig from the instance of the class.

# we adjust some parameters
diagram.ax.set_ylabel('My label')
diagram.fig.set_figwidth(10)
# don't want tikcs on the y label
diagram.ax.set_yticks([])
# I want to show on the x axis instead
diagram.ax.axes.get_xaxis().set_visible(True)
diagram.ax.spines['bottom'].set_visible(True)
diagram.ax.set_xlabel("My x label")
# we replot the figure (sometimes we have to resize with the mouse the figure so we force to refresh)
diagram.fig.show()

If you use the command diagram.plot() now all the changes will be overwritten, so these minor adjustment must be done after.

Contributors

Thanks to Kalyan Jyoti Kalita for the arrow functionality and O2-AC, agrass15268 for bug fixing.