Drawing Diagrams with MolDraw2DCairo and MolDraw2DSVG

Cheminformatics Tutorials - Herong's Tutorial Examples

∟rdkit.Chem.Draw - Handle Molecule Images

∟Drawing Diagrams with MolDraw2DCairo and MolDraw2DSVG

This section provides a tutorial example on how to use MolDraw2DCairo and MolDraw2DSVG classes to add custom diagram elements to molecule 2-D images.

Both rdkit.Chem.Draw.rdMolDraw2D.MolDraw2DCairo and rdkit.Chem.Draw.rdMolDraw2D.MolDraw2DSVG classes can be used to draw custom diagrams using drawing methods like DrawLine(), DrawRect(), DrawString(), etc.. Molecule 2-D structures can also be added.

Here is an example of drawing diagram with rdkit.Chem.Draw.rdMolDraw2D.MolDraw2DCairo class in a Jupyter Notebook:

from rdkit.Chem.Draw import rdMolDraw2D
from rdkit import Chem
from rdkit.Geometry.rdGeometry import Point2D
mol = Chem.MolFromSmiles('Cc1ccccc1')
d = rdMolDraw2D.MolDraw2DCairo(300, 300)
d.drawOptions().clearBackground = False;

d.SetColour((0.8, 0.8, 0.8))
d.DrawRect(Point2D(120, 100), Point2D(220, 200))
d.SetColour((1, 0, 0))
d.DrawLine(Point2D(200, 160), Point2D(220, 240))

d.DrawMolecule(mol)
d.FinishDrawing()
p = d.GetDrawingText()

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

Note that:

"d.drawOptions().clearBackground = False;" is used to stop each d.Draw*() call erasing existing drawings.
"IPython.display.Image(p)" is equivalent to "i = IPython.display.Image(p); display(i)".
The above code can be easily changed to use the MolDraw2DSVG class.