🆕 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 [ ]:

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)))