[Rdkit-discuss] Annotations get trimmed on molecule renderings

[Gianmarco Ghiandoni]

Hi all,

I am using rdkit_pypi==2021.9.4 to generate visualisation of compounds with
their atomic hydrogen bond strengths. In particular, I am using this
function to produce an SVG string:

d2d = rdMolDraw2D.MolDraw2DSVG(fig_size[0], fig_size[1])
    d2d.drawOptions().annotationFontScale = 0.7
    d2d.DrawMolecule(
        rwmol,
        highlightAtoms=atoms_to_highlight,
        highlightAtomColors=idx2rgb,
        highlightBonds=None,
    )
    d2d.FinishDrawing()
    return d2d.GetDrawingText()

Note that I am increasing the font scale to from 0.5 to 0.7 and for certain
molecules that produces renderings where annotations are cut out:

[image: image.png]

Any suggestions on how to fix this?

Thanks,

Giammy
-- 
*Gianmarco*


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