Hi Giammy, On reflection overnight, you might try d2d.drawOptions().padding = 0.2 or something. That should increase the amount of empty space around the molecule (the default is 0.05, and it's the fraction of the width/height of the image) such that there's enough room to show the whole annotation. It's a bit of a kludge, but it might work.
Dave On Wed, May 4, 2022 at 4:20 PM Gianmarco Ghiandoni <ghiandon...@gmail.com> wrote: > 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* > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > -- David Cosgrove Freelance computational chemistry and chemoinformatics developer http://cozchemix.co.uk
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