rdkit.Chem.Draw.rdMolDraw2D.MolDraw2DCairo

Cheminformatics Tutorials - Herong's Tutorial Examples

∟rdkit.Chem.Draw - Handle Molecule Images

∟rdkit.Chem.Draw.rdMolDraw2D.MolDraw2DCairo - Molecule PNG Image

This section provides a quick introduction on the rdkit.Chem.Draw.rdMolDraw2D.MolDraw2DCairo class, which creates 2D molecule drawings in PNG format.

What Is rdkit.Chem.Draw.rdMolDraw2D.MolDraw2DCairo? - rdkit.Chem.Draw.rdMolDraw2D.MolDraw2DCairo class, together with its base class rdkirdkit.Chem.Draw.rdMolDraw2D.MolDraw2D, provides functionalities to draw molecules in PNG raster image format.

Before playing with the rdkit.Chem.Draw.rdMolDraw2D.MolDraw2DCairo class, let's take a look at how to display PNG images on the screen.

The best way to display PNG image with Python is to use Jupyter Notebook, which uses the IPython kernel and related image display libraries as shown below.

IPython.display.Image A class to create a PNG/JPEG/GIF image object with given image data from a binary string, file, or URL.

i = IPython.display.Image(d) - Creates a PNG/JPEG/GIF image object with given image data from a binary string.
i = IPython.display.Image(data=d) - Same as IPython.display.Image(d).
i = IPython.display.Image(filename=f) - Creates a PNG/JPEG/GIF image object with given image data from an external file.
i = IPython.display.Image(url=u) - Creates a PNG/JPEG/GIF image object with given image data from a URL.

IPython.display.display(o) - A powerful method that allows you to display IPython image objects and almost any other objects in Notebook. You can use it instead of the Python system print() method to display any object.

The display(o) method is also very special that:

It is automatically imported in Jupyter and IPython environments. So you can use it anywhere.
It is the implicit object method in Jupyter and IPython environments. So you can just type o, instead of display(o).

Now, if we combine the power of RDKit and IPython, we can create and display a molecule PNG image very easily in Jupyter Notebook:

from rdkit import Chem
mol = Chem.MolFromSmiles('Cc1ccccc1')

from rdkit.Chem.Draw import rdMolDraw2D
d = rdMolDraw2D.MolDraw2DCairo(300, 300)
d.DrawMolecule(mol)
d.FinishDrawing()
p = d.GetDrawingText()

import IPython.display
i = IPython.display.Image(p)
display(i)

rdkit.Chem.Draw.rdMolDraw2D.MolDraw2DCairo Class

If you want to save the image to a PNG file, you can call the WriteDrawingText(f) method, as shown below:

from rdkit import Chem
mol = Chem.MolFromSmiles('Cc1ccccc1')

from rdkit.Chem.Draw import rdMolDraw2D
d = rdMolDraw2D.MolDraw2DCairo(300, 300)
d.DrawMolecule(mol)
d.FinishDrawing()
d.WriteDrawingText("molecule.png")