Well since someone suggested hacking B factors and using Pymol... not using
RDKit but
CCCOCC |$_AV:;;;3.14$|
AV=Atom Value, round tripped through MOLfile and ChemAxon extended SMILES.
[image: image.png]
Live Depiction:
https://www.simolecule.com/cdkdepict/depict/bow/svg?smi=CCCOCC%20%7C%24_AV%3
The joy of aromaticity models. Via Noel if you're running the (dev/master)
version of OpenBabel you can specify *-aa* to take the aromaticity from the
input. For example
>obabel -:o11 -omol2 -aa
> @MOLECULE
> *
> 5 5 0 0 0
> SMALL
> GASTEIGER
> @ATOM
> 1 O 0.0.
InChI is an identifier and not a representation, you should not read
InChIs... but we are beyond hope there so...
The InChI string is correct and is the same if you roundtrip your preferred
one with charge separated bonds and the 5 valent one.
All toolkits will use the InChI library to read/write
>
> Is there something that the compute2DCoords() is doing that makes it a
> dependency for WedgeMolBonds()
Yes, calculating 2D coordinates. Look at these two molecules, they are the
same but the atoms have been positioned differently in 2D and hence the
wedging needs to be different. Therefore y
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