Hi Greg,
Thanks for the prompt response, I’ve already patched it in this way and
although it is just a one I look forward to the patched release to have it
cleaner.
Cheers,
Lukas
From: Greg Landrum <greg.land...@gmail.com>
Date: Tuesday, 30 October 2018 at 17:16
To: Lukas Pravda <lpra...@ebi.ac.uk>
Cc: RDKIT mailing list <rdkit-discuss@lists.sourceforge.net>
Subject: Re: [Rdkit-discuss] How to set bond width with use of MolDraw2DSVG
Hi Lukas,
It looks like I forgot to expose the method to change line width to the Python
wrapper, so you can't currently change it using the new drawing code.
Until that's fixed (and I think we can describe the missing wrapper method as a
bug and get it in the next patch release, but I will have to confirm that), I'm
afraid that you'll need to edit the SVG. Let know if you want tips on how to do
that.
For the next release, the drawing options object should certainly support a
bondWidth.
-greg
On Tue, Oct 30, 2018 at 4:37 PM Lukas Pravda <lpra...@ebi.ac.uk> wrote:
Hi all,
First of all, my configuration is following:
macOS: 10.14
conda: 4.5.11
python: 3.6.6
rdkit: 2018.09.01
I just tried to set bond width for 2D SVG images and I run into situation I
don’t understand much (nothing surprising ☺). I’m aware of 2 ways how to
generate SVG images
A simple one
from rdkit import Chem
from rdkit.Chem import Draw
width=100
mol = Chem.MolFromSmiles('c1cc(CCCO)ccc1')
Draw.DrawingOptions.bondLineWidth = 10
Draw.MolToFile(mol, 'img.svg', size=(width, width))
Here I can set bondLineWidth, it works like a charm, but if I use the other
approach I know, which allows a bit more configuration,
from rdkit import Chem
from rdkit.Chem import Draw
mol = Chem.MolFromSmiles('c1cc(CCCO)ccc1')
drawer = Draw.MolDraw2DSVG(width, width)
options = drawer.drawOptions()
options.bondLineWidth = 10 # does not work
Draw.DrawingOptions.bondLineWidth = 10 # does not work either
mol = Draw.PrepareMolForDrawing(mol)
drawer.DrawMolecule(mol)
drawer.FinishDrawing()
with open(f'img.svg', 'w') as f:
f.write(drawer.GetDrawingText())
the bondLineWidth property is not part of the object returned by drawOptions().
And setting it in a similar fashion as with the previous case does not work.
So, I am bit puzzled at this point, If I do something wrong, or if it is
possible to set it at all in the other approach.
At best, I’d like to set the other approach as it allows a bit more
configuration and I would like to avoid manipulating the svg text directly. I
appreciate all your help.
Thank you!
Lukas
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