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A collection of chemical reaction formulations for use with rdkit. Requires rdkit.

Project description


Click is a collection of pre-made and tested reaction patterns to use with RDKit molecules. The reactions can be used to sequentially modify a molecule, or to create combinatorial libraries. Click is only doing the reaction as you've specified and does not check if the reaction would work.


  • RDKit (version >= 2019.03)
  • Python (version >= 3.6)


To install Click, run

pip install ClickReaction


Many examples can be found in the tests folder.

Boc removal

from rdkit import Chem
from ClickReaction import BocRemoval

boc_protected_amine = Chem.MolFromSmiles("CNC(OC(C)(C)C)=O")

reaction = BocRemoval(bocamine=boc_protected_amine)
product = reaction.get_product()

assert "CN" == Chem.MolToSmiles(product)

Click Reaction

from rdkit import Chem
from ClickReaction import CuAAC

alkyne = Chem.MolFromSmiles("c1ccccc1C#C")
azide = Chem.MolFromSmiles("C-[N-]-[N+]#N")

reaction = CuAAC(alkyne=alkyne, azide=azide)
product = reaction.get_product()

assert "Cn1cc(-c2ccccc2)nn1" == Chem.MolToSmiles(product)

Supported reactions

Simple transformations

  • Boc removal
  • Fmoc removal
  • Alkaline ester hydrolysis

Bimolecular reactions

  • Amide coupling (with or without anilines)
  • CuAAC
  • Sulfon amide formation from amines and sulfonyl chlorides
  • Suzuki-Miyaura cross coupling

Project details

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