Re: [Rdkit-discuss] rdMolDraw2D drawing code

[Greg L. <gre...@gm...>]

On Tue, Sep 6, 2016 at 10:00 PM, Dimitri Maziuk <dm...@bm...>
wrote:

> On 09/05/2016 03:47 AM, Greg Landrum wrote:
> > Dave's right about the font size: it's expressed in whatever coordinates
> > the molecule is being drawn in.
>
> I'd put Dave's explanation in the doc++ (?) comment on FontSize
> get/setter in MolDraw2D:
> http://www.rdkit.org/Python_Docs/rdkit.Chem.Draw.
> rdMolDraw2D.MolDraw2D-class.html
>
> Right now they just say "float". If you're dealing with SVG output, font
> sizes are px, em, and points, and you need a couple of tries to figure
> them out. It's a minor thing.
>
>
Pull requests with documentation tweaks/corrections are always welcome.


> > I suspect the other part of Dmitri's question is about the way bonds are
> > shortened so that they don't draw all the way through the atom labels.
>
> Yes, I think. It looks like there's more padding on the top and the
> right, and less padding on the left and bottom. E.g. H39 in the attached
> "all" version is the worst, but it is consistent in all 3.
>
> The other one on the "all" picture is that the bond to O21 isn't
> shortened enough and there isn't much room left between 021 and O24.
>
> OTOH all three labels: H38, O21, H39 could be drawn without even
> shortening the bonds if we could just move them up a little. (Well, H39
> could be just drawn without shortening the bond at all.)
>
> Last but not least, my starting point is a 3D MOL file and I call
> rdkit.Chem.AllChem.Compute2DCoords( mh ) -- last thing before
> DrawMolecule(). Attached CID112084.svg is the one generated without
> AddHs(), notice how layout is very different on that one.
>

Yes, the layout will always be different when you are using different
atoms. ;-)

2D depictions of non-trivial molecules that include H atoms have a tendency
to be pretty crowded. This makes them a challenge for the coordinate
generation algorithm. This is an example of that. I'm not sure that there's
a good general solution, or if it's worth investing the time in trying to
find one given that this is something of a special case.


>
> I've a suspicion that that layout might look better with all the Hs and
> numbers added, than the one I get (the other 3 pictures).
>
> --
> Dimitri Maziuk
> Programmer/sysadmin
> BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
>
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