If the issue is a 2D coordinate issue (rather than a drawing layout one), is there a way to do post-coordgen "bond rotation" in 2D coordinate space? (That is, flip the cis/trans choice for certain bonds).
I could imagine an algorithm which samples the "2D rotatable" bonds on Tim's structure, then figures out that by flipping the N-phenyl bond (and potentially others) it makes the molecule suitably long and thin. On Fri, Feb 11, 2022 at 9:24 AM Tim Dudgeon <tdudgeon...@gmail.com> wrote: > Greg, > Thanks for the clarification. > > On Fri, Feb 11, 2022 at 3:19 PM Greg Landrum <greg.land...@gmail.com> > wrote: > >> Oh, you want the layout itself changed, not just the orientation. >> >> No, there's nothing in place to do that and adding such a thing would be >> extremely non-trivial. >> >> -greg >> >> >> On Fri, Feb 11, 2022 at 3:49 PM Tim Dudgeon <tdudgeon...@gmail.com> >> wrote: >> >>> Hi Greg, >>> yes, but my situation is that the X dimension is much larger than the Y >>> and most of the time things are aligned nicely. But not always. Here is an >>> example. >>> OC(C(=O)NC=1C=CC=CC1NS(=O)(=O)C=2C=CC(F)=CC2)C=3C=CC=NC3 >>> [image: image.png] >>> Clearly there is potential to lay this out using more of the X dimension >>> and less of the Y. >>> >>> Tim >>> >>> On Fri, Feb 11, 2022 at 1:57 PM Greg Landrum <greg.land...@gmail.com> >>> wrote: >>> >>>> Hi Tim, >>>> >>>> That's a nice one. >>>> >>>> For people not familiar with the problem: >>>> The RDKit coordinate generation prefers aligning molecules with the X >>>> axis; this can lead to "sub-optimal" drawings if your drawing canvas is >>>> taller than it is wide. >>>> >>>> One easy solution is to just generate coordinates as usual and then >>>> rotate them to favor the Y axis if your canvas is larger along Y. >>>> Here's a gist showing how to do that: >>>> https://gist.github.com/greglandrum/12b793b240d27e3c0899c9c6c62d4f30 >>>> >>>> -greg >>>> >>>> >>>> On Fri, Feb 11, 2022 at 10:20 AM Tim Dudgeon <tdudgeon...@gmail.com> >>>> wrote: >>>> >>>>> At Dave Cosgrove's suggestion I raise this as a new topic, though it >>>>> was touched on briefly recently. >>>>> >>>>> I'd like to know if it's possible to depict a molecule in a way that >>>>> takes into account the dimensions of the box it will appear in. In my case >>>>> I have a rectangle that is short and wide (aspect ratio of 1:3) and the >>>>> molecules are typically compressed because of the lack of available >>>>> height. >>>>> So is it possible to make the layout engine aware of the bounds it has >>>>> available (e.g. in my example short and wide)? >>>>> >>>>> Thanks >>>>> Tim >>>>> _______________________________________________ >>>>> Rdkit-discuss mailing list >>>>> Rdkit-discuss@lists.sourceforge.net >>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >>>>> >>>> _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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