Hi Giammy, You're right, the new pictures look pretty rubbish. I assume it's related to https://github.com/rdkit/rdkit/discussions/5195. I'll fix it over the weekend, and hopefully it'll show up in the next patch release. Dave
On Fri, May 6, 2022 at 1:07 PM Gianmarco Ghiandoni <ghiandon...@gmail.com> wrote: > Hi Dave, > > Thanks for your reply. The reason why my library sticks to 2021.09 is > because I get even more trouble with later versions of RDKit. These are two > examples of rendering with 2021 and 2022: > > [image: image.png][image: image.png] > > The good news is that your padding suggestion works, so I set > d2d.drawOptions().padding = 0.15 and voilá: > > [image: image.png] > > Amazing. Thanks! > Giammy > > On Thu, 5 May 2022 at 10:32, David Cosgrove <davidacosgrov...@gmail.com> > wrote: > >> 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 >> >> > > -- > *Gianmarco* > -- David Cosgrove Freelance computational chemistry and chemoinformatics developer http://cozchemix.co.uk
_______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
