[Rdkit-discuss] svg with all atoms and their numbers

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

Hi all,

is there a way to generate an image with all atoms (incl. hydrogens) and
their indexes drawn?

I tried several variations along the lines of
 rdkit.Chem.Draw.MolToFile( mol, "out.svg" )
and

1. the output either has atom numbers (with includeAtomNumbers = True)
or atom symbols (without includeAtomNumbers), but not both. I tried a
couple of different atomNumberOffset settings in case the number is
written on top of the symbol, but they didn't do anything.

2. I didn't find an option to draw all atoms (all hydrogens, all
backbone carbons, etc.) anywhere. Does that exist?

3. size = (300,300) makes a 300x300 rectangle with a molecule in the
middle. Size = (800,800) seems to make a 800x800 rectangle with the same
size molecule drawing in the middle. Setting fitImage = True doesn't
seem to do anything. Is there a way to have the molecule fill the entire
rectangle?

Thanks in advance,
-- 
Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu