🆕 Depicting Molecule in Jupyter Notebook

Problem

You would like to depict molecules in Jupyter Notebook.

Difficulty level

🌶️

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molecule-depiction.ipynb

Molecule Depiction in Jupiter Notebook¶

In [ ]:

# (C) 2026 Cadence Design Systems, Inc. (Cadence)
# All rights reserved.
# TERMS FOR USE OF SAMPLE CODE The software below ("Sample Code") is
# provided to current licensees or subscribers of OpenEye products or
# SaaS offerings (each a "Customer").
# Customer is hereby permitted to use, copy, and modify the Sample Code,
# subject to these terms. Cadence claims no rights to Customer's
# modifications. Modification of Sample Code is at Customer's sole and
# exclusive risk. Sample Code may require Customer to have a then
# current license or subscription to the applicable OpenEye offering.
# THE SAMPLE CODE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED.  CADENCE DISCLAIMS ALL WARRANTIES, INCLUDING, BUT
# NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
# PARTICULAR PURPOSE AND NONINFRINGEMENT. In no event shall Cadence be
# liable for any damages or liability in connection with the Sample Code
# or its use.

from IPython.display import SVG, Image, display
from openeye import oechem, oedepict

mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, "Cn1cnc2c1c(=O)n(c(=O)n2C)C caffeine")
oedepict.OEPrepareDepiction(mol)

image_width, image_height = 300.0, 300.0

PNG Depiction¶

In [2]:

image = oedepict.OEImage(image_width, image_height)
oedepict.OERenderMolecule(image, mol)
oedepict.OEDrawCurvedBorder(image, oedepict.OELightGreyPen, 20)
display(Image(oedepict.OEWriteImageToBytes("png", image)))

SVG Depiction¶

By default, OEDepict generates an SVG image without specifying a fixed width or height, defining only the image's viewBox. When this SVG image is displayed in a Jupyter notebook, it is automatically scaled to fit the width of the cell.

See Also¶

• ViewBox - A Window Into The Soul Of SVG

In [3]:

display(SVG(oedepict.OEWriteImageToBytes("svg", image)))

SVG Depiction (Resized)¶

The SVG image can be displayed at its original size by using the ResizeSVG class.

In [ ]:

class ResizeSVG:
    """Utility class to add with/height to SVG image."""

    def __init__(self, svg: bytes) -> None:
        """Initialize."""
        svg_str: str = svg.decode("utf-8")
        import re  # noqa: PLC0415

        match = re.search(r'viewBox="(\d+\.?\d*)\s+(\d+\.?\d*)\s+(\d+\.?\d*)\s+(\d+\.?\d*)"', svg_str)
        if match and len(match.groups()) == 4:
            width, height = match.group(3), match.group(4)
            self.svg_content = svg_str.replace(match.group(), f'width="{width}" height="{height}"')
        else:
            # SVG can not be resized
            self.svg_content = svg_str

    def _repr_html_(self) -> str:
        return self.svg_content


display(ResizeSVG(oedepict.OEWriteImageToBytes("svg", image)))