2D Reaction Schematics from PLAMS Molecules

Technical Visualization Reaction equations

Generate compact 2D depictions of reactants and products directly from PLAMS molecule objects for reports and notebooks.

Downloads: Notebook | Script ?

Requires: AMS2026 or later

Related examples
Related tutorials
Related documentation
../_images/plot_reaction_2d_1_0_4e5c3266.svg

Creating 2D images of molecules

from IPython.display import SVG
from scm.plams import ReactionEquation
from scm.plams import from_smiles, to_image, get_reaction_image

img_size=(150, 150)
aspirin = from_smiles("CC(=O)OC1=CC=CC=C1C(=O)O")
text = to_image(aspirin, size=img_size)
SVG(text)
image generated from notebook

It is also possible to write the image to file in a range of different formats (SVG, PNG, EPS, PDF, JPEG)

text = to_image(aspirin, filename="aspirin.svg")
text = to_image(aspirin, filename="aspiring.png")

Creating 2D images of reactions

We can have aspirin react with water to form acetic acid and salicylic acid

acetic_acid = from_smiles("CC(O)=O")
text = to_image(acetic_acid, size=img_size)
SVG(text)
image generated from notebook
salicylic_acid = from_smiles("O=C(O)c1ccccc1O")
text = to_image(salicylic_acid, size=img_size)
SVG(text)
image generated from notebook

We can create a 2D image of the reaction as well, and optionally store it to file

reactants = [aspirin, from_smiles("O")]
products = [acetic_acid, salicylic_acid]
text = get_reaction_image(reactants, products, filename="reaction.svg")
SVG(text)
image generated from notebook

See also

Python Script

#!/usr/bin/env python
# coding: utf-8

# ## Creating 2D images of molecules

from IPython.display import SVG
from scm.plams import ReactionEquation
from scm.plams import from_smiles, to_image, get_reaction_image

img_size = (150, 150)
aspirin = from_smiles("CC(=O)OC1=CC=CC=C1C(=O)O")
text = to_image(aspirin, size=img_size)
SVG(text)


# It is also possible to write the image to file in a range of different formats (SVG, PNG, EPS, PDF, JPEG)

text = to_image(aspirin, filename="aspirin.svg")
text = to_image(aspirin, filename="aspiring.png")


# ## Creating 2D images of reactions

# We can have aspirin react with water to form acetic acid and salicylic acid

acetic_acid = from_smiles("CC(O)=O")
text = to_image(acetic_acid, size=img_size)
SVG(text)


salicylic_acid = from_smiles("O=C(O)c1ccccc1O")
text = to_image(salicylic_acid, size=img_size)
SVG(text)


# We can create a 2D image of the reaction as well, and optionally store it to file

reactants = [aspirin, from_smiles("O")]
products = [acetic_acid, salicylic_acid]
text = get_reaction_image(reactants, products, filename="reaction.svg")
SVG(text)