RDKit can plot molecules, thought the structures are surrounded by an ugly frame with ticks. How can I turn that off and plot the molecules without that frame?
Note, the %pylab inline portion of this code is from the Jupyter environment.
%pylab inline
from rdkit import Chem
from rdkit.Chem import Draw
smiles = 'CCC'
m = Chem.MolFromSmiles(smiles)
fig = Draw.MolToMPL(m)
title('Test')
It looks like rdkit and rdkit's Chem just use the matplotlib. So, if you import matplotlib you can edit your figure like any other matplotlib figure.
I produced this from the command line, so it may work differently in the Jupyter environment.
It looks like Chem doesn't properly scale the drawing based on how large the chemical is, so I added plt.xlim and plt.ylim to make the molecule larger in the frame.
from rdkit import Chem
from rdkit.Chem import Draw
import matplotlib.pyplot as plt
smiles = 'CCC'
m = Chem.MolFromSmiles(smiles)
fig = Draw.MolToMPL(m)
plt.title('Test')
plt.axis('off')
coord_min = 0.35
coord_max = 0.65
plt.xlim((coord_min, coord_max))
plt.ylim((coord_min, coord_max))
fig.savefig('mol.jpeg', bbox_inches='tight')
