Hi Greg,
that’s what I have been thinking, unlucky. Essentially, I want to color the
molecule in web-browser with various annotations and make it interactive. For
that part I’m converting it internally to the d3.js internal representation
(https://d3js.org/) and connecting it to its
Hi Lukas,
There's not currently a way to do this at the moment. The closest you can
get is by calling AddMoleculeMetadata():
In [6]: d = Draw.MolDraw2DSVG(200,200)
In [8]: d.DrawMolecule(nm)
In [10]: d.AddMoleculeMetadata(nm)
In [11]: d.FinishDrawing()
In [12]: svg = d.GetDrawingText()
In
I've done some in-memory translation of molecules to ROMols, and have used
#2 without major problems. I do remember needing to make sure that the
stereoatoms are in the correct order - that is, that the first stereoatom
is bonded to the beginAtom of the bond. In Python, this is something like:
Hi Kovas,
For your use-case #2 should suffice, "set STEREOCIS/STEREOTRANS tags +
manually set stereo atoms". This is what the EnumerateStereoisomers code
does:
https://github.com/rdkit/rdkit/blob/master/rdkit/Chem/EnumerateStereoisomers.py#L38
As to what is the 'ground truth', that is a more
Ok cool! I did actually just run into an issue while doing some tests:
https://github.com/rdkit/rdkit/issues/2183. This issue brings up a question
for me about where the smiles writer actually looks for stereochem info when it
decides what to write.
Also, I ran into the same snag earlier too
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