rdkit.Chem.Draw.rdMolDraw2D.MolDraw2DSVG

Cheminformatics Tutorials - Herong's Tutorial Examples

∟rdkit.Chem.Draw - Handle Molecule Images

∟rdkit.Chem.Draw.rdMolDraw2D.MolDraw2DSVG - Molecule SVG Image

This section provides a quick introduction on the rdkit.Chem.Draw.rdMolDraw2D.MolDraw2DSVG class, which creates 2D molecule drawings in SVG format.

What Is rdkit.Chem.Draw.rdMolDraw2D.MolDraw2DSVG? - rdkit.Chem.Draw.rdMolDraw2D.MolDraw2DSVG class, together with its base class rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D, provides functionalities to draw molecules in SVG vector image format.

Before playing with the rdkit.Chem.Draw.rdMolDraw2D.MolDraw2DSVG class, let's take a look at how to display SVG images on the screen.

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

IPython.display.SVG A class to create a SVG image object with given image data from a binary string, file, or URL.

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

IPython.display.display(o) can also be used to display SVG images as described in the last tutorial.

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

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

from rdkit.Chem.Draw import rdMolDraw2D
d = rdMolDraw2D.MolDraw2DSVG(300, 300)
d.DrawMolecule(mol)
d.FinishDrawing()
p = d.GetDrawingText()

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

rdkit.Chem.Draw.rdMolDraw2D.MolDraw2DSVG Class

If you want to get a copy of the SVG string, you can call the print(p) method, as shown below:

>>> from rdkit import Chem
>>> mol = Chem.MolFromSmiles('Cc1ccccc1')
>>> from rdkit.Chem.Draw import rdMolDraw2D
>>> d = rdMolDraw2D.MolDraw2DSVG(300, 300)
>>> d.DrawMolecule(mol)
>>> d.FinishDrawing()
>>> p = d.GetDrawingText()

>>> print(p)
"<?xml version='1.0' encoding='iso-8859-1'?>
<svg version='1.1' baseProfile='full'
    xmlns='http://www.w3.org/2000/svg'
            xmlns:rdkit='http://www.rdkit.org/xml'
            xmlns:xlink='http://www.w3.org/1999/xlink'
        xml:space='preserve'
width='300px' height='300px' viewBox='0 0 300 300'>
<!-- END OF HEADER -->
<rect style='opacity:1.0;fill:#FFFFFF;stroke:none' width='300' height=...
<path class='bond-0 atom-0 atom-1' d='M 286.364,150 L 195.455,150' sty...
<path class='bond-1 atom-1 atom-2' d='M 195.455,150 L 150,228.73' styl...
<path class='bond-1 atom-1 atom-2' d='M 172.89,152.719 L 141.072,207.8...
<path class='bond-6 atom-6 atom-1' d='M 150,71.2704 L 195.455,150' sty...
<path class='bond-2 atom-2 atom-3' d='M 150,228.73 L 59.0909,228.73' s...
<path class='bond-3 atom-3 atom-4' d='M 59.0909,228.73 L 13.6364,150' ...
<path class='bond-3 atom-3 atom-4' d='M 68.0186,207.829 L 36.2005,152....
<path class='bond-4 atom-4 atom-5' d='M 13.6364,150 L 59.0909,71.2704'...
<path class='bond-5 atom-5 atom-6' d='M 59.0909,71.2704 L 150,71.2704'...
<path class='bond-5 atom-5 atom-6' d='M 72.7273,89.4522 L 136.364,89.4...
</svg>"