PyEnergyDiagrams

This is a simple module to plot 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 requirments is matplotlib which is installed by defult using Anaconda.

How to use it?

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) for understanding 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 is displayed above.

Electron boxes

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

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()

Trouble shooting and fine tuning

Most of the times there could be a problem of test padding. There are some parameters that can be changed in this way.

diagram.offset = 10

To make the change effective you have to use the command diagram.plot() again. Remember that once you have done a first attempt for 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.

rlaplaza / PyEnergyDiagrams