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Easy to combine two molecules

Project description

Welcome to CombineMols

CombineMols is a python package for easily combining two molecules.

This intuitively aids in the combining of molecules using dummy atoms.

The easiest way to install the dependencies is to install the Anaconda 3 Python distribution and use conda to set up an environment with RDKit.


rdkit / mendeleev


Step 1 :

Make a new conda environment and install RDKit.

conda create -c rdkit -n my-rdkit-env rdkit

Then activate this new environment.

conda activate my-rdkit-env

Step 2 :

Inside this environment install CombineMols.

Using pip

pip install CombineMols



from rdkit import Chem
from CombineMols.CombineMols import CombineMols

Two molecule classes can be combined.

mol1 = Chem.MolFromSmiles('IOc1c[nH]c2ncc(I)cc12')
mol2 = Chem.MolFromSmiles('Sc1cccc(I)c1I')
CombineMols(mol1, mol2, "I")

Molecules can be entered directly in SMILES form.

mol1 = 'IOc1c[nH]c2ncc(I)cc12'
mol2 = 'Sc1cccc(I)c1I'
CombineMols(mol1, mol2, "I")

Dummy atom can be entered by atomic number.

mol1 = 'IOc1c[nH]c2ncc(I)cc12'
mol2 = 'Sc1cccc(I)c1I'
CombineMols(mol1, mol2, 53)

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