Visualizing Molecules

Visualizing Molecules

One of RDKit's most powerful features is its ability to generate high-quality 2D depictions of molecules directly in a Google Colab notebook.

Displaying 2D Molecules

When a molecule object is created with Chem.MolFromSmiles() is the last line in a code cell; the notebook automatically renders its 2D structure. This is the simplest way to visualize a molecule.

Drawing Molecules with Atom Numbering 

For analysis, it's often helpful to see the index number of each atom in the structure. While RDKit doesn't have a single command for this, we can easily add atom numbers by iterating through the atoms and setting a specific property (molAtomMapNumber) before drawing. Let's look at the following examples.

1. Isobutanol with a SMILES "CC(C)CO" (Figure 1).

Code:

# Isobutanol

# Labeling atoms from 1 instead of 0 using RDKit

mol = Chem.MolFromSmiles("CC(C)CO")  

# Label each atom starting from 1

for atom in mol.GetAtoms():

    atom.SetAtomMapNum(atom.GetIdx() + 1)

# Visualize the molecule with atom numbers

Draw.MolToImage(mol, size=(300, 300))

2. Benzene with a SMILES "c1ccccc1" (Figure 2).

Code:

benzene = Chem.MolFromSmiles("c1ccccc1")

# Label each atom starting from 1

for atom in benzene.GetAtoms():

    atom.SetAtomMapNum(atom.GetIdx() + 1)

# Visualize the molecule with atom numbers

Draw.MolToImage(benzene, size=(300, 300))

3. Butane with a SMILES "CCCC" (Figure 3).

Code:

butane = Chem.MolFromSmiles("CCCC")

# Label each atom starting from 1

for atom in butane.GetAtoms():

    atom.SetAtomMapNum(atom.GetIdx() + 1)

# Visualize the molecule with atom numbers

Draw.MolToImage(butane, size=(300, 300))

4. Aspirin with a SMILES "CC(=O)OC1=CC=CC=C1C(=O)O" (Figure 4).

Code:

# Labeling atoms from 1 instead of 0 using RDKit

aspirin = Chem.MolFromSmiles("CC(=O)OC1=CC=CC=C1C(=O)O")

# Label each atom starting from 1

for atom in aspirin.GetAtoms():

    atom.SetAtomMapNum(atom.GetIdx() + 1)

# Visualize the molecule with atom numbers

Draw.MolToImage(aspirin, size=(300, 300))

5. Hexene with a SMILES "C=CCCCC" (Figure 5).

Code:

# Labeling atoms from 1 instead of 0 using RDKit

hexene = Chem.MolFromSmiles("C=CCCCC")

# Label each atom starting from 1

for atom in hexene.GetAtoms():

    atom.SetAtomMapNum(atom.GetIdx() + 1)

# Visualize the molecule with atom numbers

Draw.MolToImage(hexene, size=(300, 300))