Is it possible to get a full list of bonds with rdkitminimallib in julia

Yes, it is possible to get a full list of bonds with rdkitminimallib in Julia. There are multiple ways to achieve this, and in this article, we will explore three different options.

Option 1: Using the RDKit.jl Package

The RDKit.jl package is a Julia wrapper for the RDKit cheminformatics library. It provides a wide range of functionality for working with chemical structures, including the ability to retrieve a full list of bonds.

using RDKit

# Load a molecule from a SMILES string
mol = RDKit.MolFromSmiles("CCO")

# Get the list of bonds
bonds = RDKit.GetBonds(mol)

# Print the bonds
for bond in bonds
    println(bond)
end

This code snippet demonstrates how to use the RDKit.jl package to retrieve a full list of bonds from a molecule. The MolFromSmiles function is used to load a molecule from a SMILES string, and the GetBonds function is used to retrieve the bonds. The resulting list of bonds is then printed.

Option 2: Using the rdkitminimallib Package

The rdkitminimallib package is a lightweight alternative to the RDKit.jl package. It provides a minimal set of functionality for working with chemical structures, including the ability to retrieve a full list of bonds.

using rdkitminimallib

# Load a molecule from a SMILES string
mol = rdkitminimallib.MolFromSmiles("CCO")

# Get the list of bonds
bonds = rdkitminimallib.GetBonds(mol)

# Print the bonds
for bond in bonds
    println(bond)
end

This code snippet demonstrates how to use the rdkitminimallib package to retrieve a full list of bonds from a molecule. The MolFromSmiles function is used to load a molecule from a SMILES string, and the GetBonds function is used to retrieve the bonds. The resulting list of bonds is then printed.

Option 3: Using the PyCall Package

If you prefer to use the Python version of RDKit, you can also use the PyCall package to call the RDKit Python library from Julia. This allows you to leverage the full functionality of RDKit, including the ability to retrieve a full list of bonds.

using PyCall

# Import the RDKit module
rdkit = pyimport("rdkit")

# Load a molecule from a SMILES string
mol = rdkit.Chem.MolFromSmiles("CCO")

# Get the list of bonds
bonds = rdkit.Chem.GetBonds(mol)

# Print the bonds
for bond in bonds
    println(bond)
end

This code snippet demonstrates how to use the PyCall package to call the RDKit Python library from Julia. The MolFromSmiles function is used to load a molecule from a SMILES string, and the GetBonds function is used to retrieve the bonds. The resulting list of bonds is then printed.

Among the three options, Option 1 using the RDKit.jl package is the recommended approach. It provides a native Julia interface to the RDKit library and offers a comprehensive set of functionality for working with chemical structures. Option 2 using the rdkitminimallib package is a lightweight alternative but may have limited functionality compared to the RDKit.jl package. Option 3 using the PyCall package allows you to leverage the full functionality of RDKit but requires calling the Python library from Julia, which may introduce additional overhead.