ClickReaction 0.3.1

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

Click

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.

Requirements

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

Installation

To install Click, run

pip install ClickReaction

Usage

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