Looks like the same issue. Glad that you are planning to work on it so I don't have to enforce a a narrow range of RDKit versions in my installation specs.
Thanks, Giammy On Fri, 6 May 2022, 16:21 David Cosgrove, <davidacosgrov...@gmail.com> wrote: > 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
