Generating Transparent PNG

Problem

You want to depict your molecule in a png image with transparent background for your presentation.

Ingredients

OEChem TK - cheminformatics toolkit
OEDepict TK - molecule depiction toolkit

Difficulty Level

🌶️

Solution

If you are rendering a molecule directly into an image file, all you have to do is to call the OERenderMolecule function with the clearbackground = False parameter. If this parameter is True (by default) then the OEWhite color is used to clear the image before rendering the molecule.

def render_molecule(
    mol: oechem.OEMolBase, opts: oedepict.OE2DMolDisplayOptions, filename: str
) -> None:
    """Render molecule with transparent background."""
    disp = oedepict.OE2DMolDisplay(mol, opts)
    clear_background = False
    oedepict.OERenderMolecule(filename, disp, clear_background)

Discussion

In the case where you are rendering a molecule into an OEImage object, this object has to be constructed with the OETransparentColor color.

def render_molecule_to_image(
    mol: oechem.OEMolBase, opts: oedepict.OE2DMolDisplayOptions, filename: str
) -> None:
    """Render molecule to image with transparent background."""
    image = oedepict.OEImage(
        opts.GetWidth(), opts.GetHeight(), oechem.OETransparentColor
    )

    disp = oedepict.OE2DMolDisplay(mol, opts)
    clear_background = False
    oedepict.OERenderMolecule(image, disp, clear_background)
    oedepict.OEWriteImage(filename, image)

Note

The OEDepict TK supports transparent background for png, svg and pdf image files.