Thanks Greg - it's nice of you to even be willing to support the old drawing
methods in terms of documenting them.
I did have a search for Cairo docs but my quick goog ran aground. I had been
expecting to roll something to process obabel svg output, I thought I'd get
more of the control done from the source conversion of InchI to SVG and that's
still the case - I'll look further into the rdkit code. Could I ask:
1) Which of MolDraw2DSVG and MolDraw2DCairo is best (hopefully not too
contentious a question). My requirement is to ideally:
a. Take InchI string
b. Render as a set of SVGs optimised for current iPhone, iPad and latest
Android screen resolutions
- transparent bg
- all white bonds and atom text in sans bold
- ensure all non-carbon atoms' text identifiers are perfectly positioned in the
mol render (think max-posh latest mobile rendering)
+ this is so that as technology advances, each device equivalent will get a
higher res-still, but as SVG, the nearest image to fit will scale OK (probably
until I end up using iPad-optimised images for iPhones...) with no worries
about antialiasing artefacts, bond lines perfectly meeting each end it was
originally rendered to, as the svg is scaled to fit a new, slightly larger
resolution
+ I've given up the notion of being able to rotate a molecule after rendering
and have the text remain the right way up - unless you know of a way (not
googled this yet)
c. Use a self-rolled post-pro script to edit the svg into the required state
(such as bold text etc) as needed
d. Use python where possible
2) You mention using c++ classes, and although I can programme c++ my knowledge
is 20 years old; I can programme c and python more easily, so are you
suggesting I need to actually write this in c++?
Thanks,
Mark Lewis
> On 18 Oct 2017, at 10:48, Greg Landrum <greg.land...@gmail.com> wrote:
>
> Hi Mark,
>
> I'm afraid that a lot of the fine control that it looks like you want is not
> going to be possible. But I will do what I can.
>
> Your questions are all connected to the old, pure Python, drawing code. We're
> not doing anything further with this and I'm encouraging people to switch
> over to the new C++ drawing code. There are some functions in rdkit.Chem.Draw
> that use this, but if you're interested in having a bit more control over the
> options, you should use the MolDraw2DSVG or MolDraw2DCairo classes for this.
>
> A general point is that all of this stuff is "under documented". There is
> some info on the RDKit blog, but the best way to figure out how to use it is
> generally via searching the mailing list, asking here, or just experimenting
> with the options that are there. I will eventually write docs for this, but
> it's one of those things that can also be done by members of the community.
>
> A couple more detailed answers, in the context of using MolDraw2DSVG since I
> think that's what you're looking to generate, are below.
>
> On Wed, Oct 18, 2017 at 7:21 AM, mark <em...@ej73.com
> <mailto:em...@ej73.com>> wrote:
> This outputs several files for various screen sizes of mobile I'm developing
> for.
>
> 1) How can I make the font weight bold? or italic for that matter. The
> sping/piddle docs list these with the font face and size but these are split
> out in the rdkit docs
>
> At the moment there's no way to do this other than editing the SVG that comes
> out of the rendering code. As long as you want all the text to be the same,
> this is a straightforward string replacement operation. Finer control than
> that is not currently possible.
>
> 2) I found
> http://www.rdkit.org/docs/api/rdkit.Chem.Draw.MolDrawing%27.DrawingOptions-class.html
>
> <http://www.rdkit.org/docs/api/rdkit.Chem.Draw.MolDrawing'.DrawingOptions-class.html>
> having looked at the code for MolDrawing, but there appears to be no
> documentation as regard what each of these options does. Where is this
> documentation?
>
> non-existent, see above
>
> 3) Even with options.defaultColor = (1, 1, 1) non-carbon atoms display
> coloured (O red, N blue etc). But I need a monochrome image. Can anyone
> confirm if monochrome images are possible please and how this is done?
>
> Here's how you draw a molecule in black and white using the new code:
> d = Draw.MolDraw2DSVG(300, 300)
> d.drawOptions().useBWAtomPalette()
> d.DrawMolecule(dm)
> d.FinishDrawing()
>
>
> 4) In the attached image, you will notice that the non-carbon, non-hydrogen
> atoms are slightly out of place, too far down from exactly where they are
> expected to be drawn. How can this be adjusted? It appears not to matter
> what I set the font size to, they are always out of place. I think this
> might be because of the fact the glyphs are aligned to the bottom of their
> containers in the svg.
>
> <PastedGraphic-1.png>
>
>
> Dealing with this stuff in a cross-platform way is a really hard problem. Try
> the new code out. You may find that it's better at this. It should at least
> have different pathologies. :-S
>
> Great kit!
>
> Thanks!
>
> -greg
>
>
> Thanks IA,
>
> Mark Lewis
>
>
>
>
>
>
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