Yep, I’m aware .. but it wouldn’t take too much work to at least ignore
“<“ and “>” in the Open Babel parser.
In the meantime, my Python scripts will strip them from the SMILES strings
before passing them to Open Babel.
-Geoff
On Aug 14, 2022 at 4:42:25 AM, David Cosgrove
wrote:
> Hi
Hi Geoff,
You should bear in mind that the dative bond syntax is an RDKIt extension
to SMILES so is not guaranteed to be parsed correctly by other
cheminformatics toolkits.
Dave
On Sun, 14 Aug 2022 at 00:42, Geoffrey Hutchison
wrote:
> mol =
> mol = Chem.MolFromSmiles("C12=CC=CC=[N]1->[*]<-[N]3=C2C=CC=C3")
Hmm. I forgot the SMILES syntax of dative bonds. That's a nice idea.
I actually decided to use the noFreeType=True option, add a highlight as the
"metal" and remove the * from the depiction.
The initial set is at:
Hi Geoff,
you can indeed use DrawWavyLine() coupled to some basic 2D geometry as in
the example below:
from rdkit import Chem
from rdkit.Geometry import Point3D, Point2D
from rdkit.Chem.Draw import rdDepictor, rdMolDraw2D
from IPython.display import SVG
mol =
Hi Geoff,
The drawer has the GetDrawCoords() method. There are 2 overloads, one
takes a Point2D, the other an atom index, and both return the coordinates
in the drawers reference frame. Assuming you're working in Python. In
C++, they're getDrawCoords().
I've been using RDKit for depicting sets of ligands from SMILES, which has been
great.
I'd like to add some bidentate and tridentate ligands. Let's stick to
bipyridine at first (see image)
I have the appropriate SMILES, leaving * as part of a 5 atom ring involving the
nitrogen atoms (and
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