Re: [Rdkit-discuss] rdMolDraw2D drawing code

[Dimitri M. <dm...@bm...>]

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.

> 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.

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