Reaction Class

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Introduction

The Reaction class handles chemical reactions involving multiple Molecule objects. It simplifies tasks like reaction visualization, transformation from strings, and applying reaction templates to specific reactants.

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Loading Reactions

The easiest way to load a reaction is from a SMILES or SMARTS string using the from_smiles method.

from simmate.toolkit import Reaction

# Standard reactant > reagent > product SMILES
smiles = "CC(=O)O.OCC>S(=O)(=O)(O)O>CC(=O)OCC.O"
reaction = Reaction.from_smiles(smiles)

# You can also use SMARTS for general reaction templates
template = "[C:1](=[O:2])-[OD1].[O:3]-[C:4]>>[C:1](=[O:2])-[O:3]-[C:4]"
reaction = Reaction.from_smarts(template)

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Visualization

Simmate can generate high-quality images for reactions, making them easy to view in an interactive environment or export for a publication.

# Returns an image for interactive display
img = reaction.image

# Export as a PNG file
reaction.to_png_file("my_reaction.png")

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Reaction Templates

Simmate supports reaction templates that can be applied to specific reactants to predict products.

# Create a general reaction template
template = Reaction.from_smarts("[C:1](=[O:2])-[OD1].[O:3]-[C:4]>>[C:1](=[O:2])-[O:3]-[C:4]")

# Apply the template to specific molecules
from simmate.toolkit import Molecule
reactants = [
    Molecule.from_smiles("CC(=O)O"), 
    Molecule.from_smiles("CO")
]
products = template.apply_template(reactants)

# View the results
for product in products:
    print(product.to_smiles())

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